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@article{DBLP:journals/almob/AbedAllahY20,
  author    = {Loai AbedAllah and
               Malik Yousef},
  title     = {GrpClassifierEC: a novel classification approach based on the ensemble
               clustering space},
  journal   = {Algorithms Mol. Biol.},
  volume    = {15},
  number    = {1},
  pages     = {3},
  year      = {2020},
  url       = {https://doi.org/10.1186/s13015-020-0162-7},
  doi       = {10.1186/s13015-020-0162-7},
  timestamp = {Sat, 30 May 2020 01:00:00 +0200},
  biburl    = {https://dblp.org/rec/journals/almob/AbedAllahY20.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/AlankoBCPS20,
  author    = {Jarno Alanko and
               Hideo Bannai and
               Bastien Cazaux and
               Pierre Peterlongo and
               Jens Stoye},
  title     = {Finding all maximal perfect haplotype blocks in linear time},
  journal   = {Algorithms Mol. Biol.},
  volume    = {15},
  number    = {1},
  pages     = {2},
  year      = {2020},
  url       = {https://doi.org/10.1186/s13015-020-0163-6},
  doi       = {10.1186/s13015-020-0163-6},
  timestamp = {Sat, 30 May 2020 01:00:00 +0200},
  biburl    = {https://dblp.org/rec/journals/almob/AlankoBCPS20.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/Bansal20,
  author    = {Mukul S. Bansal},
  title     = {Linear-time algorithms for phylogenetic tree completion under Robinson-Foulds
               distance},
  journal   = {Algorithms Mol. Biol.},
  volume    = {15},
  number    = {1},
  pages     = {6},
  year      = {2020},
  url       = {https://doi.org/10.1186/s13015-020-00166-1},
  doi       = {10.1186/s13015-020-00166-1},
  timestamp = {Sat, 30 May 2020 01:00:00 +0200},
  biburl    = {https://dblp.org/rec/journals/almob/Bansal20.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/ChristensenMVYW20,
  author    = {Sarah Christensen and
               Erin K. Molloy and
               Pranjal Vachaspati and
               Ananya Yammanuru and
               Tandy J. Warnow},
  title     = {Non-parametric correction of estimated gene trees using {TRACTION}},
  journal   = {Algorithms Mol. Biol.},
  volume    = {15},
  number    = {1},
  pages     = {1},
  year      = {2020},
  url       = {https://doi.org/10.1186/s13015-019-0161-8},
  doi       = {10.1186/s13015-019-0161-8},
  timestamp = {Sat, 30 May 2020 01:00:00 +0200},
  biburl    = {https://dblp.org/rec/journals/almob/ChristensenMVYW20.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/ManeLFC20,
  author    = {Aniket C. Mane and
               Manuel Lafond and
               Pedro Cipriano Feij{\~{a}}o and
               C{\'{e}}dric Chauve},
  title     = {The distance and median problems in the single-cut-or-join model with
               single-gene duplications},
  journal   = {Algorithms Mol. Biol.},
  volume    = {15},
  number    = {1},
  pages     = {8},
  year      = {2020},
  url       = {https://doi.org/10.1186/s13015-020-00169-y},
  doi       = {10.1186/s13015-020-00169-y},
  timestamp = {Sat, 30 May 2020 01:00:00 +0200},
  biburl    = {https://dblp.org/rec/journals/almob/ManeLFC20.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/StadlerGSLLVHH20,
  author    = {Peter F. Stadler and
               Manuela Gei{\ss} and
               David T. Schaller and
               Alitzel L{\'{o}}pez and
               Marcos Gonz{\'{a}}lez Laffitte and
               Dulce I. Valdivia and
               Marc Hellmuth and
               Maribel Hernandez{-}Rosales},
  title     = {From pairs of most similar sequences to phylogenetic best matches},
  journal   = {Algorithms Mol. Biol.},
  volume    = {15},
  number    = {1},
  pages     = {5},
  year      = {2020},
  url       = {https://doi.org/10.1186/s13015-020-00165-2},
  doi       = {10.1186/s13015-020-00165-2},
  timestamp = {Sat, 05 Sep 2020 01:00:00 +0200},
  biburl    = {https://dblp.org/rec/journals/almob/StadlerGSLLVHH20.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/WangSHL20,
  author    = {Wei Wang and
               Jack Smith and
               Hussein A. Hejase and
               Kevin J. Liu},
  title     = {Non-parametric and semi-parametric support estimation using SEquential
               RESampling random walks on biomolecular sequences},
  journal   = {Algorithms Mol. Biol.},
  volume    = {15},
  number    = {1},
  pages     = {7},
  year      = {2020},
  url       = {https://doi.org/10.1186/s13015-020-00167-0},
  doi       = {10.1186/s13015-020-00167-0},
  timestamp = {Sat, 30 May 2020 01:00:00 +0200},
  biburl    = {https://dblp.org/rec/journals/almob/WangSHL20.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/Wittler20,
  author    = {Roland Wittler},
  title     = {Alignment- and reference-free phylogenomics with colored de Bruijn
               graphs},
  journal   = {Algorithms Mol. Biol.},
  volume    = {15},
  number    = {1},
  pages     = {4},
  year      = {2020},
  url       = {https://doi.org/10.1186/s13015-020-00164-3},
  doi       = {10.1186/s13015-020-00164-3},
  timestamp = {Sat, 30 May 2020 01:00:00 +0200},
  biburl    = {https://dblp.org/rec/journals/almob/Wittler20.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/AllmanBR19,
  author    = {Elizabeth S. Allman and
               Hector Ba{\~{n}}os and
               John A. Rhodes},
  title     = {{NANUQ:} a method for inferring species networks from gene trees under
               the coalescent model},
  journal   = {Algorithms Mol. Biol.},
  volume    = {14},
  number    = {1},
  pages     = {24},
  year      = {2019},
  url       = {https://doi.org/10.1186/s13015-019-0159-2},
  doi       = {10.1186/s13015-019-0159-2},
  timestamp = {Sat, 30 May 2020 01:00:00 +0200},
  biburl    = {https://dblp.org/rec/journals/almob/AllmanBR19.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/AmbroiseDNRV19,
  author    = {Christophe Ambroise and
               Alia Dehman and
               Pierre Neuvial and
               Guillem Rigaill and
               Nathalie Villa{-}Vialaneix},
  title     = {Adjacency-constrained hierarchical clustering of a band similarity
               matrix with application to genomics},
  journal   = {Algorithms Mol. Biol.},
  volume    = {14},
  number    = {1},
  pages     = {22:1--22:14},
  year      = {2019},
  url       = {https://doi.org/10.1186/s13015-019-0157-4},
  doi       = {10.1186/s13015-019-0157-4},
  timestamp = {Sat, 30 May 2020 01:00:00 +0200},
  biburl    = {https://dblp.org/rec/journals/almob/AmbroiseDNRV19.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/BoucherGKLMM19,
  author    = {Christina Boucher and
               Travis Gagie and
               Alan Kuhnle and
               Ben Langmead and
               Giovanni Manzini and
               Taher Mun},
  title     = {Prefix-free parsing for building big BWTs},
  journal   = {Algorithms Mol. Biol.},
  volume    = {14},
  number    = {1},
  pages     = {13:1--13:15},
  year      = {2019},
  url       = {https://doi.org/10.1186/s13015-019-0148-5},
  doi       = {10.1186/s13015-019-0148-5},
  timestamp = {Fri, 27 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/BoucherGKLMM19.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/ChindelevitchLM19,
  author    = {Leonid Chindelevitch and
               Sean La and
               Joao Meidanis},
  title     = {A cubic algorithm for the generalized rank median of three genomes},
  journal   = {Algorithms Mol. Biol.},
  volume    = {14},
  number    = {1},
  pages     = {16:1--16:16},
  year      = {2019},
  url       = {https://doi.org/10.1186/s13015-019-0150-y},
  doi       = {10.1186/s13015-019-0150-y},
  timestamp = {Sat, 30 May 2020 01:00:00 +0200},
  biburl    = {https://dblp.org/rec/journals/almob/ChindelevitchLM19.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/DondiLS19,
  author    = {Riccardo Dondi and
               Manuel Lafond and
               C{\'{e}}line Scornavacca},
  title     = {Reconciling multiple genes trees via segmental duplications and losses},
  journal   = {Algorithms Mol. Biol.},
  volume    = {14},
  number    = {1},
  pages     = {7:1--7:19},
  year      = {2019},
  url       = {https://doi.org/10.1186/s13015-019-0139-6},
  doi       = {10.1186/s13015-019-0139-6},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/DondiLS19.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/EgidiLMT19,
  author    = {Lavinia Egidi and
               Felipe A. Louza and
               Giovanni Manzini and
               Guilherme P. Telles},
  title     = {External memory {BWT} and {LCP} computation for sequence collections
               with applications},
  journal   = {Algorithms Mol. Biol.},
  volume    = {14},
  number    = {1},
  pages     = {6:1--6:15},
  year      = {2019},
  url       = {https://doi.org/10.1186/s13015-019-0140-0},
  doi       = {10.1186/s13015-019-0140-0},
  timestamp = {Fri, 10 Jul 2020 01:00:00 +0200},
  biburl    = {https://dblp.org/rec/journals/almob/EgidiLMT19.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/EnglerCVGMK19,
  author    = {Martin S. Engler and
               Bertrand Caron and
               Lourens Veen and
               Daan P. Geerke and
               Alan E. Mark and
               Gunnar W. Klau},
  title     = {Automated partial atomic charge assignment for drug-like molecules:
               a fast knapsack approach},
  journal   = {Algorithms Mol. Biol.},
  volume    = {14},
  number    = {1},
  pages     = {1:1--1:10},
  year      = {2019},
  url       = {https://doi.org/10.1186/s13015-019-0138-7},
  doi       = {10.1186/s13015-019-0138-7},
  timestamp = {Fri, 27 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/EnglerCVGMK19.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/HajkarimUV19,
  author    = {Morteza Chalabi Hajkarim and
               Eli Upfal and
               Fabio Vandin},
  title     = {Differentially mutated subnetworks discovery},
  journal   = {Algorithms Mol. Biol.},
  volume    = {14},
  number    = {1},
  pages     = {10:1--10:11},
  year      = {2019},
  url       = {https://doi.org/10.1186/s13015-019-0146-7},
  doi       = {10.1186/s13015-019-0146-7},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/HajkarimUV19.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/KarpovMRS19,
  author    = {Nikolai Karpov and
               Salem Malikic and
               Md. Khaledur Rahman and
               S{\"{u}}leyman Cenk Sahinalp},
  title     = {A multi-labeled tree dissimilarity measure for comparing "clonal trees"
               of tumor progression},
  journal   = {Algorithms Mol. Biol.},
  volume    = {14},
  number    = {1},
  pages     = {17:1--17:18},
  year      = {2019},
  url       = {https://doi.org/10.1186/s13015-019-0152-9},
  doi       = {10.1186/s13015-019-0152-9},
  timestamp = {Sat, 30 May 2020 01:00:00 +0200},
  biburl    = {https://dblp.org/rec/journals/almob/KarpovMRS19.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/KiryuIK19,
  author    = {Hisanori Kiryu and
               Yuto Ichikawa and
               Yasuhiro Kojima},
  title     = {{TMRS:} an algorithm for computing the time to the most recent substitution
               event from a multiple alignment column},
  journal   = {Algorithms Mol. Biol.},
  volume    = {14},
  number    = {1},
  pages     = {23:1--23:14},
  year      = {2019},
  url       = {https://doi.org/10.1186/s13015-019-0158-3},
  doi       = {10.1186/s13015-019-0158-3},
  timestamp = {Sat, 30 May 2020 01:00:00 +0200},
  biburl    = {https://dblp.org/rec/journals/almob/KiryuIK19.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/LemosLM19,
  author    = {Alexandre Lemos and
               In{\^{e}}s Lynce and
               Pedro T. Monteiro},
  title     = {Repairing Boolean logical models from time-series data using Answer
               Set Programming},
  journal   = {Algorithms Mol. Biol.},
  volume    = {14},
  number    = {1},
  pages     = {9:1--9:16},
  year      = {2019},
  url       = {https://doi.org/10.1186/s13015-019-0145-8},
  doi       = {10.1186/s13015-019-0145-8},
  timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
  biburl    = {https://dblp.org/rec/journals/almob/LemosLM19.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/MolloyW19,
  author    = {Erin K. Molloy and
               Tandy J. Warnow},
  title     = {Statistically consistent divide-and-conquer pipelines for phylogeny
               estimation using NJMerge},
  journal   = {Algorithms Mol. Biol.},
  volume    = {14},
  number    = {1},
  pages     = {14:1--14:17},
  year      = {2019},
  url       = {https://doi.org/10.1186/s13015-019-0151-x},
  doi       = {10.1186/s13015-019-0151-x},
  timestamp = {Sat, 30 May 2020 01:00:00 +0200},
  biburl    = {https://dblp.org/rec/journals/almob/MolloyW19.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/MuggliPB19,
  author    = {Martin D. Muggli and
               Simon J. Puglisi and
               Christina Boucher},
  title     = {Kohdista: an efficient method to index and query possible Rmap alignments},
  journal   = {Algorithms Mol. Biol.},
  volume    = {14},
  number    = {1},
  pages     = {25},
  year      = {2019},
  url       = {https://doi.org/10.1186/s13015-019-0160-9},
  doi       = {10.1186/s13015-019-0160-9},
  timestamp = {Sat, 30 May 2020 01:00:00 +0200},
  biburl    = {https://dblp.org/rec/journals/almob/MuggliPB19.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/NorriCKM19,
  author    = {Tuukka Norri and
               Bastien Cazaux and
               Dmitry Kosolobov and
               Veli M{\"{a}}kinen},
  title     = {Linear time minimum segmentation enables scalable founder reconstruction},
  journal   = {Algorithms Mol. Biol.},
  volume    = {14},
  number    = {1},
  pages     = {12:1--12:15},
  year      = {2019},
  url       = {https://doi.org/10.1186/s13015-019-0147-6},
  doi       = {10.1186/s13015-019-0147-6},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/NorriCKM19.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/OliveiraJFDD19,
  author    = {Andre Rodrigues Oliveira and
               G{\'{e}}raldine Jean and
               Guillaume Fertin and
               Ulisses Dias and
               Zanoni Dias},
  title     = {Super short operations on both gene order and intergenic sizes},
  journal   = {Algorithms Mol. Biol.},
  volume    = {14},
  number    = {1},
  pages     = {21:1--21:17},
  year      = {2019},
  url       = {https://doi.org/10.1186/s13015-019-0156-5},
  doi       = {10.1186/s13015-019-0156-5},
  timestamp = {Sat, 30 May 2020 01:00:00 +0200},
  biburl    = {https://dblp.org/rec/journals/almob/OliveiraJFDD19.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/PrezzaPSR19,
  author    = {Nicola Prezza and
               Nadia Pisanti and
               Marinella Sciortino and
               Giovanna Rosone},
  title     = {SNPs detection by eBWT positional clustering},
  journal   = {Algorithms Mol. Biol.},
  volume    = {14},
  number    = {1},
  pages     = {3:1--3:13},
  year      = {2019},
  url       = {https://doi.org/10.1186/s13015-019-0137-8},
  doi       = {10.1186/s13015-019-0137-8},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/PrezzaPSR19.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/RosenP19,
  author    = {Yohei M. Rosen and
               Benedict J. Paten},
  title     = {An average-case sublinear forward algorithm for the haploid Li and
               Stephens model},
  journal   = {Algorithms Mol. Biol.},
  volume    = {14},
  number    = {1},
  pages     = {11:1--11:12},
  year      = {2019},
  url       = {https://doi.org/10.1186/s13015-019-0144-9},
  doi       = {10.1186/s13015-019-0144-9},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/RosenP19.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/SeferK19,
  author    = {Emre Sefer and
               Carl Kingsford},
  title     = {Semi-nonparametric modeling of topological domain formation from epigenetic
               data},
  journal   = {Algorithms Mol. Biol.},
  volume    = {14},
  number    = {1},
  pages     = {4:1--4:11},
  year      = {2019},
  url       = {https://doi.org/10.1186/s13015-019-0142-y},
  doi       = {10.1186/s13015-019-0142-y},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/SeferK19.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/SimonaitisCS19,
  author    = {Pijus Simonaitis and
               Annie Chateau and
               Krister M. Swenson},
  title     = {A general framework for genome rearrangement with biological constraints},
  journal   = {Algorithms Mol. Biol.},
  volume    = {14},
  number    = {1},
  pages     = {15:1--15:14},
  year      = {2019},
  url       = {https://doi.org/10.1186/s13015-019-0149-4},
  doi       = {10.1186/s13015-019-0149-4},
  timestamp = {Sat, 30 May 2020 01:00:00 +0200},
  biburl    = {https://dblp.org/rec/journals/almob/SimonaitisCS19.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/WalveRS19,
  author    = {Riku Walve and
               Pasi Rastas and
               Leena Salmela},
  title     = {Kermit: linkage map guided long read assembly},
  journal   = {Algorithms Mol. Biol.},
  volume    = {14},
  number    = {1},
  pages     = {8:1--8:10},
  year      = {2019},
  url       = {https://doi.org/10.1186/s13015-019-0143-x},
  doi       = {10.1186/s13015-019-0143-x},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/WalveRS19.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/WiedenhoeftCKGS19,
  author    = {John Wiedenhoeft and
               Alex Cagan and
               Rimma Kozhemyakina and
               Rimma Gulevich and
               Alexander Schliep},
  title     = {Bayesian localization of {CNV} candidates in {WGS} data within minutes},
  journal   = {Algorithms Mol. Biol.},
  volume    = {14},
  number    = {1},
  pages     = {20:1--20:16},
  year      = {2019},
  url       = {https://doi.org/10.1186/s13015-019-0154-7},
  doi       = {10.1186/s13015-019-0154-7},
  timestamp = {Sat, 30 May 2020 01:00:00 +0200},
  biburl    = {https://dblp.org/rec/journals/almob/WiedenhoeftCKGS19.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/WuKWY19,
  author    = {Jimmy Wu and
               Alex Khodaverdian and
               Benjamin Weitz and
               Nir Yosef},
  title     = {Connectivity problems on heterogeneous graphs},
  journal   = {Algorithms Mol. Biol.},
  volume    = {14},
  number    = {1},
  pages     = {5:1--5:17},
  year      = {2019},
  url       = {https://doi.org/10.1186/s13015-019-0141-z},
  doi       = {10.1186/s13015-019-0141-z},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/WuKWY19.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/ZhangRW19,
  author    = {Qiuyi (Richard) Zhang and
               Satish Rao and
               Tandy J. Warnow},
  title     = {Constrained incremental tree building: new absolute fast converging
               phylogeny estimation methods with improved scalability and accuracy},
  journal   = {Algorithms Mol. Biol.},
  volume    = {14},
  number    = {1},
  pages     = {2:1--2:12},
  year      = {2019},
  url       = {https://doi.org/10.1186/s13015-019-0136-9},
  doi       = {10.1186/s13015-019-0136-9},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/ZhangRW19.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/ZhangZS19,
  author    = {Yue Zhang and
               Chunfang Zheng and
               David Sankoff},
  title     = {A branching process for homology distribution-based inference of polyploidy,
               speciation and loss},
  journal   = {Algorithms Mol. Biol.},
  volume    = {14},
  number    = {1},
  pages     = {18:1--18:13},
  year      = {2019},
  url       = {https://doi.org/10.1186/s13015-019-0153-8},
  doi       = {10.1186/s13015-019-0153-8},
  timestamp = {Sat, 30 May 2020 01:00:00 +0200},
  biburl    = {https://dblp.org/rec/journals/almob/ZhangZS19.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/AcostaMT18,
  author    = {Nidia Obscura Acosta and
               Veli M{\"{a}}kinen and
               Alexandru I. Tomescu},
  title     = {A safe and complete algorithm for metagenomic assembly},
  journal   = {Algorithms Mol. Biol.},
  volume    = {13},
  number    = {1},
  pages     = {3:1--3:12},
  year      = {2018},
  url       = {https://doi.org/10.1186/s13015-018-0122-7},
  doi       = {10.1186/s13015-018-0122-7},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/AcostaMT18.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/BayzidW18,
  author    = {Md. Shamsuzzoha Bayzid and
               Tandy J. Warnow},
  title     = {Gene tree parsimony for incomplete gene trees: addressing true biological
               loss},
  journal   = {Algorithms Mol. Biol.},
  volume    = {13},
  number    = {1},
  pages     = {1:1--1:12},
  year      = {2018},
  url       = {https://doi.org/10.1186/s13015-017-0120-1},
  doi       = {10.1186/s13015-017-0120-1},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/BayzidW18.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/CarricoCFPRV18,
  author    = {Jo{\~{a}}o A. Carri{\c{c}}o and
               Maxime Crochemore and
               Alexandre P. Francisco and
               Solon P. Pissis and
               Bruno Ribeiro{-}Gon{\c{c}}alves and
               C{\'{a}}tia Vaz},
  title     = {Fast phylogenetic inference from typing data},
  journal   = {Algorithms Mol. Biol.},
  volume    = {13},
  number    = {1},
  pages     = {4:1--4:14},
  year      = {2018},
  url       = {https://doi.org/10.1186/s13015-017-0119-7},
  doi       = {10.1186/s13015-017-0119-7},
  timestamp = {Fri, 27 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/CarricoCFPRV18.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/ChristensenMVW18,
  author    = {Sarah Christensen and
               Erin K. Molloy and
               Pranjal Vachaspati and
               Tandy J. Warnow},
  title     = {{OCTAL:} Optimal Completion of gene trees in polynomial time},
  journal   = {Algorithms Mol. Biol.},
  volume    = {13},
  number    = {1},
  pages     = {6:1--6:18},
  year      = {2018},
  url       = {https://doi.org/10.1186/s13015-018-0124-5},
  doi       = {10.1186/s13015-018-0124-5},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/ChristensenMVW18.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/CiachMG18,
  author    = {Michal Aleksander Ciach and
               Anna Muszewska and
               Pawel G{\'{o}}recki},
  title     = {Locus-aware decomposition of gene trees with respect to polytomous
               species trees},
  journal   = {Algorithms Mol. Biol.},
  volume    = {13},
  number    = {1},
  pages     = {11:1--11:18},
  year      = {2018},
  url       = {https://doi.org/10.1186/s13015-018-0128-1},
  doi       = {10.1186/s13015-018-0128-1},
  timestamp = {Fri, 17 Jul 2020 01:00:00 +0200},
  biburl    = {https://dblp.org/rec/journals/almob/CiachMG18.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/DonathS18,
  author    = {Alexander Donath and
               Peter F. Stadler},
  title     = {Split-inducing indels in phylogenomic analysis},
  journal   = {Algorithms Mol. Biol.},
  volume    = {13},
  number    = {1},
  pages     = {12:1--12:12},
  year      = {2018},
  url       = {https://doi.org/10.1186/s13015-018-0130-7},
  doi       = {10.1186/s13015-018-0130-7},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/DonathS18.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/FrankHTV18,
  author    = {Yves Frank and
               Tomas Hruz and
               Thomas Tschager and
               Valentin Venzin},
  title     = {Improved de novo peptide sequencing using {LC} retention time information},
  journal   = {Algorithms Mol. Biol.},
  volume    = {13},
  number    = {1},
  pages     = {14:1--14:16},
  year      = {2018},
  url       = {https://doi.org/10.1186/s13015-018-0132-5},
  doi       = {10.1186/s13015-018-0132-5},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/FrankHTV18.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/GartnerMS18,
  author    = {Fabian G{\"{a}}rtner and
               Lydia M{\"{u}}ller and
               Peter F. Stadler},
  title     = {Superbubbles revisited},
  journal   = {Algorithms Mol. Biol.},
  volume    = {13},
  number    = {1},
  pages     = {16:1--16:17},
  year      = {2018},
  url       = {https://doi.org/10.1186/s13015-018-0134-3},
  doi       = {10.1186/s13015-018-0134-3},
  timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
  biburl    = {https://dblp.org/rec/journals/almob/GartnerMS18.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/GartnerSMS18,
  author    = {Fabian G{\"{a}}rtner and
               Christian H{\"{o}}ner zu Siederdissen and
               Lydia M{\"{u}}ller and
               Peter F. Stadler},
  title     = {Coordinate systems for supergenomes},
  journal   = {Algorithms Mol. Biol.},
  volume    = {13},
  number    = {1},
  pages     = {15:1--15:19},
  year      = {2018},
  url       = {https://doi.org/10.1186/s13015-018-0133-4},
  doi       = {10.1186/s13015-018-0133-4},
  timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
  biburl    = {https://dblp.org/rec/journals/almob/GartnerSMS18.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/GirottoCP18,
  author    = {Samuele Girotto and
               Matteo Comin and
               Cinzia Pizzi},
  title     = {{FSH:} fast spaced seed hashing exploiting adjacent hashes},
  journal   = {Algorithms Mol. Biol.},
  volume    = {13},
  number    = {1},
  pages     = {8:1--8:11},
  year      = {2018},
  url       = {https://doi.org/10.1186/s13015-018-0125-4},
  doi       = {10.1186/s13015-018-0125-4},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/GirottoCP18.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/NielsenTMHP18,
  author    = {Morten Muhlig Nielsen and
               Paula Tataru and
               Tobias Madsen and
               Asger Hobolth and
               Jakob Skou Pedersen},
  title     = {Regmex: a statistical tool for exploring motifs in ranked sequence
               lists from genomics experiments},
  journal   = {Algorithms Mol. Biol.},
  volume    = {13},
  number    = {1},
  pages     = {17:1--17:11},
  year      = {2018},
  url       = {https://doi.org/10.1186/s13015-018-0135-2},
  doi       = {10.1186/s13015-018-0135-2},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/NielsenTMHP18.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/NojgaardGMSWH18,
  author    = {Nikolai N{\o}jgaard and
               Manuela Gei{\ss} and
               Daniel Merkle and
               Peter F. Stadler and
               Nicolas Wieseke and
               Marc Hellmuth},
  title     = {Time-consistent reconciliation maps and forbidden time travel},
  journal   = {Algorithms Mol. Biol.},
  volume    = {13},
  number    = {1},
  pages     = {2:1--2:17},
  year      = {2018},
  url       = {https://doi.org/10.1186/s13015-018-0121-8},
  doi       = {10.1186/s13015-018-0121-8},
  timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
  biburl    = {https://dblp.org/rec/journals/almob/NojgaardGMSWH18.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/OliveiraFDD18,
  author    = {Andre Rodrigues Oliveira and
               Guillaume Fertin and
               Ulisses Dias and
               Zanoni Dias},
  title     = {Sorting signed circular permutations by super short operations},
  journal   = {Algorithms Mol. Biol.},
  volume    = {13},
  number    = {1},
  pages     = {13:1--13:16},
  year      = {2018},
  url       = {https://doi.org/10.1186/s13015-018-0131-6},
  doi       = {10.1186/s13015-018-0131-6},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/OliveiraFDD18.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/ShahAP18,
  author    = {Nidhi Shah and
               Stephen F. Altschul and
               Mihai Pop},
  title     = {Outlier detection in {BLAST} hits},
  journal   = {Algorithms Mol. Biol.},
  volume    = {13},
  number    = {1},
  pages     = {7:1--7:9},
  year      = {2018},
  url       = {https://doi.org/10.1186/s13015-018-0126-3},
  doi       = {10.1186/s13015-018-0126-3},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/ShahAP18.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/SimonaitisS18,
  author    = {Pijus Simonaitis and
               Krister M. Swenson},
  title     = {Finding local genome rearrangements},
  journal   = {Algorithms Mol. Biol.},
  volume    = {13},
  number    = {1},
  pages     = {9:1--9:14},
  year      = {2018},
  url       = {https://doi.org/10.1186/s13015-018-0127-2},
  doi       = {10.1186/s13015-018-0127-2},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/SimonaitisS18.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/WuZ18,
  author    = {Jingli Wu and
               Qian Zhang},
  title     = {A fast and accurate enumeration-based algorithm for haplotyping a
               triploid individual},
  journal   = {Algorithms Mol. Biol.},
  volume    = {13},
  number    = {1},
  pages     = {10:1--10:10},
  year      = {2018},
  url       = {https://doi.org/10.1186/s13015-018-0129-0},
  doi       = {10.1186/s13015-018-0129-0},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/WuZ18.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/Yamada18,
  author    = {Kazunori D. Yamada},
  title     = {Derivative-free neural network for optimizing the scoring functions
               associated with dynamic programming of pairwise-profile alignment},
  journal   = {Algorithms Mol. Biol.},
  volume    = {13},
  number    = {1},
  pages     = {5:1--5:8},
  year      = {2018},
  url       = {https://doi.org/10.1186/s13015-018-0123-6},
  doi       = {10.1186/s13015-018-0123-6},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/Yamada18.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/AbdallahFRM17,
  author    = {Emna Ben Abdallah and
               Maxime Folschette and
               Olivier F. Roux and
               Morgan Magnin},
  title     = {ASP-based method for the enumeration of attractors in non-deterministic
               synchronous and asynchronous multi-valued networks},
  journal   = {Algorithms Mol. Biol.},
  volume    = {12},
  number    = {1},
  pages     = {20:1--20:23},
  year      = {2017},
  url       = {https://doi.org/10.1186/s13015-017-0111-2},
  doi       = {10.1186/s13015-017-0111-2},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/AbdallahFRM17.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/AlmirantisCGIMP17,
  author    = {Yannis Almirantis and
               Panagiotis Charalampopoulos and
               Jia Gao and
               Costas S. Iliopoulos and
               Manal Mohamed and
               Solon P. Pissis and
               Dimitris Polychronopoulos},
  title     = {On avoided words, absent words, and their application to biological
               sequence analysis},
  journal   = {Algorithms Mol. Biol.},
  volume    = {12},
  number    = {1},
  pages     = {5:1--5:12},
  year      = {2017},
  url       = {https://doi.org/10.1186/s13015-017-0094-z},
  doi       = {10.1186/s13015-017-0094-z},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/AlmirantisCGIMP17.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/ArabBSTS17,
  author    = {Marwa Al Arab and
               Matthias Bernt and
               Christian H{\"{o}}ner zu Siederdissen and
               Kifah Tout and
               Peter F. Stadler},
  title     = {Partially local three-way alignments and the sequence signatures of
               mitochondrial genome rearrangements},
  journal   = {Algorithms Mol. Biol.},
  volume    = {12},
  number    = {1},
  pages     = {22:1--22:11},
  year      = {2017},
  url       = {https://doi.org/10.1186/s13015-017-0113-0},
  doi       = {10.1186/s13015-017-0113-0},
  timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
  biburl    = {https://dblp.org/rec/journals/almob/ArabBSTS17.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/BorkCWSL17,
  author    = {Daniel Bork and
               Ricson Cheng and
               Jincheng Wang and
               Jean Sung and
               Ran Libeskind{-}Hadas},
  title     = {On the computational complexity of the maximum parsimony reconciliation
               problem in the duplication-loss-coalescence model},
  journal   = {Algorithms Mol. Biol.},
  volume    = {12},
  number    = {1},
  pages     = {6:1--6:12},
  year      = {2017},
  url       = {https://doi.org/10.1186/s13015-017-0098-8},
  doi       = {10.1186/s13015-017-0098-8},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/BorkCWSL17.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/BrejovaGPSV17,
  author    = {Brona Brejov{\'{a}} and
               Askar Gafurov and
               Dana Pardubsk{\'{a}} and
               Michal Sabo and
               Tom{\'{a}}s Vinar},
  title     = {Isometric gene tree reconciliation revisited},
  journal   = {Algorithms Mol. Biol.},
  volume    = {12},
  number    = {1},
  pages     = {17:1--17:16},
  year      = {2017},
  url       = {https://doi.org/10.1186/s13015-017-0108-x},
  doi       = {10.1186/s13015-017-0108-x},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/BrejovaGPSV17.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/DeBlasioK17,
  author    = {Dan F. DeBlasio and
               John D. Kececioglu},
  title     = {Core column prediction for protein multiple sequence alignments},
  journal   = {Algorithms Mol. Biol.},
  volume    = {12},
  number    = {1},
  pages     = {11:1--11:16},
  year      = {2017},
  url       = {https://doi.org/10.1186/s13015-017-0102-3},
  doi       = {10.1186/s13015-017-0102-3},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/DeBlasioK17.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/DengF17,
  author    = {Yun Deng and
               David Fern{\'{a}}ndez{-}Baca},
  title     = {An efficient algorithm for testing the compatibility of phylogenies
               with nested taxa},
  journal   = {Algorithms Mol. Biol.},
  volume    = {12},
  number    = {1},
  pages     = {7:1--7:12},
  year      = {2017},
  url       = {https://doi.org/10.1186/s13015-017-0099-7},
  doi       = {10.1186/s13015-017-0099-7},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/DengF17.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/DoerrBFC17,
  author    = {Daniel Doerr and
               Metin Balaban and
               Pedro Feij{\~{a}}o and
               C{\'{e}}dric Chauve},
  title     = {The gene family-free median of three},
  journal   = {Algorithms Mol. Biol.},
  volume    = {12},
  number    = {1},
  pages     = {14:1--14:14},
  year      = {2017},
  url       = {https://doi.org/10.1186/s13015-017-0106-z},
  doi       = {10.1186/s13015-017-0106-z},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/DoerrBFC17.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/DondiLE17,
  author    = {Riccardo Dondi and
               Manuel Lafond and
               Nadia El{-}Mabrouk},
  title     = {Approximating the correction of weighted and unweighted orthology
               and paralogy relations},
  journal   = {Algorithms Mol. Biol.},
  volume    = {12},
  number    = {1},
  pages     = {4:1--4:15},
  year      = {2017},
  url       = {https://doi.org/10.1186/s13015-017-0096-x},
  doi       = {10.1186/s13015-017-0096-x},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/DondiLE17.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/El-KebirRSSZZZ17,
  author    = {Mohammed El{-}Kebir and
               Benjamin J. Raphael and
               Ron Shamir and
               Roded Sharan and
               Simone Zaccaria and
               Meirav Zehavi and
               Ron Zeira},
  title     = {Complexity and algorithms for copy-number evolution problems},
  journal   = {Algorithms Mol. Biol.},
  volume    = {12},
  number    = {1},
  pages     = {13:1--13:11},
  year      = {2017},
  url       = {https://doi.org/10.1186/s13015-017-0103-2},
  doi       = {10.1186/s13015-017-0103-2},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/El-KebirRSSZZZ17.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/ErbertRM17,
  author    = {Marius Erbert and
               Steffen Rechner and
               Matthias M{\"{u}}ller{-}Hannemann},
  title     = {Gerbil: a fast and memory-efficient k-mer counter with GPU-support},
  journal   = {Algorithms Mol. Biol.},
  volume    = {12},
  number    = {1},
  pages     = {9:1--9:12},
  year      = {2017},
  url       = {https://doi.org/10.1186/s13015-017-0097-9},
  doi       = {10.1186/s13015-017-0097-9},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/ErbertRM17.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/FertinJT17,
  author    = {Guillaume Fertin and
               G{\'{e}}raldine Jean and
               Eric Tannier},
  title     = {Algorithms for computing the double cut and join distance on both
               gene order and intergenic sizes},
  journal   = {Algorithms Mol. Biol.},
  volume    = {12},
  number    = {1},
  pages     = {16:1--16:11},
  year      = {2017},
  url       = {https://doi.org/10.1186/s13015-017-0107-y},
  doi       = {10.1186/s13015-017-0107-y},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/FertinJT17.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/FitimeRGP17,
  author    = {Louis Fippo Fitime and
               Olivier F. Roux and
               Carito Guziolowski and
               Lo{\"{\i}}c Paulev{\'{e}}},
  title     = {Identification of bifurcation transitions in biological regulatory
               networks using Answer-Set Programming},
  journal   = {Algorithms Mol. Biol.},
  volume    = {12},
  number    = {1},
  pages     = {19:1--19:14},
  year      = {2017},
  url       = {https://doi.org/10.1186/s13015-017-0110-3},
  doi       = {10.1186/s13015-017-0110-3},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/FitimeRGP17.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/Hellmuth17,
  author    = {Marc Hellmuth},
  title     = {Biologically feasible gene trees, reconciliation maps and informative
               triples},
  journal   = {Algorithms Mol. Biol.},
  volume    = {12},
  number    = {1},
  pages     = {23:1--23:16},
  year      = {2017},
  url       = {https://doi.org/10.1186/s13015-017-0114-z},
  doi       = {10.1186/s13015-017-0114-z},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/Hellmuth17.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/JagerSBBSH17,
  author    = {Sven Jager and
               Benjamin Schiller and
               Philipp Babel and
               Malte Blumenroth and
               Thorsten Strufe and
               Kay Hamacher},
  title     = {StreAM-T\({}_{\mbox{g}}\): algorithms for analyzing coarse grained
               {RNA} dynamics based on Markov models of connectivity-graphs},
  journal   = {Algorithms Mol. Biol.},
  volume    = {12},
  number    = {1},
  pages     = {15:1--15:16},
  year      = {2017},
  url       = {https://doi.org/10.1186/s13015-017-0105-0},
  doi       = {10.1186/s13015-017-0105-0},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/JagerSBBSH17.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/JammaliKRBSO17,
  author    = {Safa Jammali and
               Esaie Kuitche and
               Ayoub Rachati and
               Fran{\c{c}}ois B{\'{e}}langer and
               Michelle S. Scott and
               A{\"{\i}}da Ouangraoua},
  title     = {Aligning coding sequences with frameshift extension penalties},
  journal   = {Algorithms Mol. Biol.},
  volume    = {12},
  number    = {1},
  pages     = {10:1--10:18},
  year      = {2017},
  url       = {https://doi.org/10.1186/s13015-017-0101-4},
  doi       = {10.1186/s13015-017-0101-4},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/JammaliKRBSO17.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/LimaSSLMMSL17,
  author    = {Leandro Lima and
               Blerina Sinaimeri and
               Gustavo Sacomoto and
               H{\'{e}}l{\`{e}}ne Lopez{-}Maestre and
               Camille Marchet and
               Vincent Miele and
               Marie{-}France Sagot and
               Vincent Lacroix},
  title     = {Playing hide and seek with repeats in local and global de novo transcriptome
               assembly of short RNA-seq reads},
  journal   = {Algorithms Mol. Biol.},
  volume    = {12},
  number    = {1},
  pages     = {2:1--2:19},
  year      = {2017},
  url       = {https://doi.org/10.1186/s13015-017-0091-2},
  doi       = {10.1186/s13015-017-0091-2},
  timestamp = {Sat, 05 Sep 2020 01:00:00 +0200},
  biburl    = {https://dblp.org/rec/journals/almob/LimaSSLMMSL17.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/LouzaTHC17,
  author    = {Felipe A. Louza and
               Guilherme P. Telles and
               Steve Hoffmann and
               Cristina Dutra de Aguiar Ciferri},
  title     = {Generalized enhanced suffix array construction in external memory},
  journal   = {Algorithms Mol. Biol.},
  volume    = {12},
  number    = {1},
  pages     = {26:1--26:16},
  year      = {2017},
  url       = {https://doi.org/10.1186/s13015-017-0117-9},
  doi       = {10.1186/s13015-017-0117-9},
  timestamp = {Fri, 10 Jul 2020 01:00:00 +0200},
  biburl    = {https://dblp.org/rec/journals/almob/LouzaTHC17.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/MorgensternSL17,
  author    = {Burkhard Morgenstern and
               Svenja Sch{\"{o}}bel and
               Chris{-}Andr{\'{e}} Leimeister},
  title     = {Phylogeny reconstruction based on the length distribution of k-mismatch
               common substrings},
  journal   = {Algorithms Mol. Biol.},
  volume    = {12},
  number    = {1},
  pages     = {27:1--27:12},
  year      = {2017},
  url       = {https://doi.org/10.1186/s13015-017-0118-8},
  doi       = {10.1186/s13015-017-0118-8},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/MorgensternSL17.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/Noe17,
  author    = {Laurent No{\'{e}}},
  title     = {Best hits of 11110110111: model-free selection and parameter-free
               sensitivity calculation of spaced seeds},
  journal   = {Algorithms Mol. Biol.},
  volume    = {12},
  number    = {1},
  pages     = {1:1--1:16},
  year      = {2017},
  url       = {https://doi.org/10.1186/s13015-017-0092-1},
  doi       = {10.1186/s13015-017-0092-1},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/Noe17.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/NovakGP17,
  author    = {Adam M. Novak and
               Erik Garrison and
               Benedict Paten},
  title     = {A graph extension of the positional Burrows-Wheeler transform and
               its applications},
  journal   = {Algorithms Mol. Biol.},
  volume    = {12},
  number    = {1},
  pages     = {18:1--18:12},
  year      = {2017},
  url       = {https://doi.org/10.1186/s13015-017-0109-9},
  doi       = {10.1186/s13015-017-0109-9},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/NovakGP17.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/RubertFBSM17,
  author    = {Diego P. Rubert and
               Pedro Feij{\~{a}}o and
               Mar{\'{\i}}lia Dias Vieira Braga and
               Jens Stoye and
               F{\'{a}}bio Viduani Martinez},
  title     = {Approximating the {DCJ} distance of balanced genomes in linear time},
  journal   = {Algorithms Mol. Biol.},
  volume    = {12},
  number    = {1},
  pages     = {3:1--3:13},
  year      = {2017},
  url       = {https://doi.org/10.1186/s13015-017-0095-y},
  doi       = {10.1186/s13015-017-0095-y},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/RubertFBSM17.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/SchroderR17,
  author    = {Christopher Schr{\"{o}}der and
               Sven Rahmann},
  title     = {A hybrid parameter estimation algorithm for beta mixtures and applications
               to methylation state classification},
  journal   = {Algorithms Mol. Biol.},
  volume    = {12},
  number    = {1},
  pages     = {21:1--21:12},
  year      = {2017},
  url       = {https://doi.org/10.1186/s13015-017-0112-1},
  doi       = {10.1186/s13015-017-0112-1},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/SchroderR17.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/Taylor17,
  author    = {William R. Taylor},
  title     = {Algorithms for matching partially labelled sequence graphs},
  journal   = {Algorithms Mol. Biol.},
  volume    = {12},
  number    = {1},
  pages     = {24:1--24:22},
  year      = {2017},
  url       = {https://doi.org/10.1186/s13015-017-0115-y},
  doi       = {10.1186/s13015-017-0115-y},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/Taylor17.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/ThiagarajanAPBB17,
  author    = {Raghuram Thiagarajan and
               Amir Alavi and
               Jagdeep T. Podichetty and
               Jason N. Bazil and
               Daniel A. Beard},
  title     = {The feasibility of genome-scale biological network inference using
               Graphics Processing Units},
  journal   = {Algorithms Mol. Biol.},
  volume    = {12},
  number    = {1},
  pages     = {8:1--8:13},
  year      = {2017},
  url       = {https://doi.org/10.1186/s13015-017-0100-5},
  doi       = {10.1186/s13015-017-0100-5},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/ThiagarajanAPBB17.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/TschagerRGW17,
  author    = {Thomas Tschager and
               Simon R{\"{o}}sch and
               Ludovic Gillet and
               Peter Widmayer},
  title     = {A better scoring model for de novo peptide sequencing: the symmetric
               difference between explained and measured masses},
  journal   = {Algorithms Mol. Biol.},
  volume    = {12},
  number    = {1},
  pages     = {12:1--12:13},
  year      = {2017},
  url       = {https://doi.org/10.1186/s13015-017-0104-1},
  doi       = {10.1186/s13015-017-0104-1},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/TschagerRGW17.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/WanZ17,
  author    = {Shixiang Wan and
               Quan Zou},
  title     = {HAlign-II: efficient ultra-large multiple sequence alignment and phylogenetic
               tree reconstruction with distributed and parallel computing},
  journal   = {Algorithms Mol. Biol.},
  volume    = {12},
  number    = {1},
  pages     = {25:1--25:10},
  year      = {2017},
  url       = {https://doi.org/10.1186/s13015-017-0116-x},
  doi       = {10.1186/s13015-017-0116-x},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/WanZ17.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/AmbroiseBNRDG16,
  author    = {J{\'{e}}r{\^{o}}me Ambroise and
               Jamal Badir and
               Louise Nienhaus and
               Annie Robert and
               Anne{-}France Dekairelle and
               Jean{-}Luc Gala},
  title     = {Using a constraint-based regression method for relative quantification
               of somatic mutations in pyrosequencing signals: a case for {NRAS}
               analysis},
  journal   = {Algorithms Mol. Biol.},
  volume    = {11},
  pages     = {24},
  year      = {2016},
  url       = {https://doi.org/10.1186/s13015-016-0086-4},
  doi       = {10.1186/s13015-016-0086-4},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/AmbroiseBNRDG16.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/AndradeWKAMMSS16,
  author    = {Ricardo Andrade and
               Martin Wannagat and
               Cecilia Coimbra Klein and
               Vicente Acu{\~{n}}a and
               Alberto Marchetti{-}Spaccamela and
               Paulo Vieira Milreu and
               Leen Stougie and
               Marie{-}France Sagot},
  title     = {Enumeration of minimal stoichiometric precursor sets in metabolic
               networks},
  journal   = {Algorithms Mol. Biol.},
  volume    = {11},
  pages     = {25},
  year      = {2016},
  url       = {https://doi.org/10.1186/s13015-016-0087-3},
  doi       = {10.1186/s13015-016-0087-3},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/AndradeWKAMMSS16.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/BellerO16,
  author    = {Timo Beller and
               Enno Ohlebusch},
  title     = {A representation of a compressed de Bruijn graph for pan-genome analysis
               that enables search},
  journal   = {Algorithms Mol. Biol.},
  volume    = {11},
  pages     = {20},
  year      = {2016},
  url       = {https://doi.org/10.1186/s13015-016-0083-7},
  doi       = {10.1186/s13015-016-0083-7},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/BellerO16.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/BellerO16a,
  author    = {Timo Beller and
               Enno Ohlebusch},
  title     = {Erratum to: {A} representation of a compressed de Bruijn graph for
               pan-genome analysis that enables search},
  journal   = {Algorithms Mol. Biol.},
  volume    = {11},
  pages     = {28:1--28:2},
  year      = {2016},
  url       = {https://doi.org/10.1186/s13015-016-0090-8},
  doi       = {10.1186/s13015-016-0090-8},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/BellerO16a.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/DrinkwaterC16,
  author    = {Benjamin Drinkwater and
               Michael A. Charleston},
  title     = {Towards sub-quadratic time and space complexity solutions for the
               dated tree reconciliation problem},
  journal   = {Algorithms Mol. Biol.},
  volume    = {11},
  pages     = {15},
  year      = {2016},
  url       = {https://doi.org/10.1186/s13015-016-0077-5},
  doi       = {10.1186/s13015-016-0077-5},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/DrinkwaterC16.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/FridG16,
  author    = {Yelena Frid and
               Dan Gusfield},
  title     = {An improved Four-Russians method and sparsified Four-Russians algorithm
               for {RNA} folding},
  journal   = {Algorithms Mol. Biol.},
  volume    = {11},
  pages     = {22},
  year      = {2016},
  url       = {https://doi.org/10.1186/s13015-016-0081-9},
  doi       = {10.1186/s13015-016-0081-9},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/FridG16.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/GrossiIMPPRV16,
  author    = {Roberto Grossi and
               Costas S. Iliopoulos and
               Robert Mercas and
               Nadia Pisanti and
               Solon P. Pissis and
               Ahmad Retha and
               Fatima Vayani},
  title     = {Circular sequence comparison: algorithms and applications},
  journal   = {Algorithms Mol. Biol.},
  volume    = {11},
  pages     = {12},
  year      = {2016},
  url       = {https://doi.org/10.1186/s13015-016-0076-6},
  doi       = {10.1186/s13015-016-0076-6},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/GrossiIMPPRV16.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/GrossiIMPPRV16a,
  author    = {Roberto Grossi and
               Costas S. Iliopoulos and
               Robert Mercas and
               Nadia Pisanti and
               Solon P. Pissis and
               Ahmad Retha and
               Fatima Vayani},
  title     = {Erratum to: Circular sequence comparison: algorithms and applications},
  journal   = {Algorithms Mol. Biol.},
  volume    = {11},
  pages     = {21},
  year      = {2016},
  url       = {https://doi.org/10.1186/s13015-016-0084-6},
  doi       = {10.1186/s13015-016-0084-6},
  timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
  biburl    = {https://dblp.org/rec/journals/almob/GrossiIMPPRV16a.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/HenriquesM16,
  author    = {Rui Henriques and
               Sara C. Madeira},
  title     = {BicNET: Flexible module discovery in large-scale biological networks
               using biclustering},
  journal   = {Algorithms Mol. Biol.},
  volume    = {11},
  pages     = {14},
  year      = {2016},
  url       = {https://doi.org/10.1186/s13015-016-0074-8},
  doi       = {10.1186/s13015-016-0074-8},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/HenriquesM16.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/HenriquesM16a,
  author    = {Rui Henriques and
               Sara C. Madeira},
  title     = {BiC2PAM: constraint-guided biclustering for biological data analysis
               with domain knowledge},
  journal   = {Algorithms Mol. Biol.},
  volume    = {11},
  pages     = {23},
  year      = {2016},
  url       = {https://doi.org/10.1186/s13015-016-0085-5},
  doi       = {10.1186/s13015-016-0085-5},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/HenriquesM16a.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/HobbsPOE16,
  author    = {Elizabeth T. Hobbs and
               Talmo Pereira and
               Patrick K. O'Neill and
               Ivan Erill},
  title     = {A Bayesian inference method for the analysis of transcriptional regulatory
               networks in metagenomic data},
  journal   = {Algorithms Mol. Biol.},
  volume    = {11},
  pages     = {19},
  year      = {2016},
  url       = {https://doi.org/10.1186/s13015-016-0082-8},
  doi       = {10.1186/s13015-016-0082-8},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/HobbsPOE16.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/HolleyWS16,
  author    = {Guillaume Holley and
               Roland Wittler and
               Jens Stoye},
  title     = {Bloom Filter Trie: an alignment-free and reference-free data structure
               for pan-genome storage},
  journal   = {Algorithms Mol. Biol.},
  volume    = {11},
  pages     = {3},
  year      = {2016},
  url       = {https://doi.org/10.1186/s13015-016-0066-8},
  doi       = {10.1186/s13015-016-0066-8},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/HolleyWS16.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/IndrischekWSP16,
  author    = {Henrike Indrischek and
               Nicolas Wieseke and
               Peter F. Stadler and
               Sonja J. Prohaska},
  title     = {The paralog-to-contig assignment problem: high quality gene models
               from fragmented assemblies},
  journal   = {Algorithms Mol. Biol.},
  volume    = {11},
  pages     = {1},
  year      = {2016},
  url       = {https://doi.org/10.1186/s13015-016-0063-y},
  doi       = {10.1186/s13015-016-0063-y},
  timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
  biburl    = {https://dblp.org/rec/journals/almob/IndrischekWSP16.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/LafondDE16,
  author    = {Manuel Lafond and
               Riccardo Dondi and
               Nadia El{-}Mabrouk},
  title     = {The link between orthology relations and gene trees: a correction
               perspective},
  journal   = {Algorithms Mol. Biol.},
  volume    = {11},
  pages     = {4},
  year      = {2016},
  url       = {https://doi.org/10.1186/s13015-016-0067-7},
  doi       = {10.1186/s13015-016-0067-7},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/LafondDE16.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/LorenzHS16,
  author    = {Ronny Lorenz and
               Ivo L. Hofacker and
               Peter F. Stadler},
  title     = {{RNA} folding with hard and soft constraints},
  journal   = {Algorithms Mol. Biol.},
  volume    = {11},
  pages     = {8},
  year      = {2016},
  url       = {https://doi.org/10.1186/s13015-016-0070-z},
  doi       = {10.1186/s13015-016-0070-z},
  timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
  biburl    = {https://dblp.org/rec/journals/almob/LorenzHS16.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/LuMYL16,
  author    = {Songjian Lu and
               Gunasheil Mandava and
               Gaibo Yan and
               Xinghua Lu},
  title     = {An exact algorithm for finding cancer driver somatic genome alterations:
               the weighted mutually exclusive maximum set cover problem},
  journal   = {Algorithms Mol. Biol.},
  volume    = {11},
  pages     = {11},
  year      = {2016},
  url       = {https://doi.org/10.1186/s13015-016-0073-9},
  doi       = {10.1186/s13015-016-0073-9},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/LuMYL16.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/LuXZL16,
  author    = {Jianbo Lu and
               Guoliang Xu and
               Shihua Zhang and
               Benzhuo Lu},
  title     = {An effective sequence-alignment-free superpositioning of pairwise
               or multiple structures with missing data},
  journal   = {Algorithms Mol. Biol.},
  volume    = {11},
  pages     = {18},
  year      = {2016},
  url       = {https://doi.org/10.1186/s13015-016-0079-3},
  doi       = {10.1186/s13015-016-0079-3},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/LuXZL16.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/MeherSRW16,
  author    = {Prabina Kumar Meher and
               Tanmaya Kumar Sahu and
               Atmakuri Rao and
               Sant Wahi},
  title     = {Identification of donor splice sites using support vector machine:
               a computational approach based on positional, compositional and dependency
               features},
  journal   = {Algorithms Mol. Biol.},
  volume    = {11},
  pages     = {16},
  year      = {2016},
  url       = {https://doi.org/10.1186/s13015-016-0078-4},
  doi       = {10.1186/s13015-016-0078-4},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/MeherSRW16.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/MiclotteHDRPAF16,
  author    = {Giles Miclotte and
               Mahdi Heydari and
               Piet Demeester and
               Stephane Rombauts and
               Yves Van de Peer and
               Pieter Audenaert and
               Jan Fostier},
  title     = {Jabba: hybrid error correction for long sequencing reads},
  journal   = {Algorithms Mol. Biol.},
  volume    = {11},
  pages     = {10},
  year      = {2016},
  url       = {https://doi.org/10.1186/s13015-016-0075-7},
  doi       = {10.1186/s13015-016-0075-7},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/MiclotteHDRPAF16.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/Pizzi16,
  author    = {Cinzia Pizzi},
  title     = {MissMax: alignment-free sequence comparison with mismatches through
               filtering and heuristics},
  journal   = {Algorithms Mol. Biol.},
  volume    = {11},
  pages     = {6},
  year      = {2016},
  url       = {https://doi.org/10.1186/s13015-016-0072-x},
  doi       = {10.1186/s13015-016-0072-x},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/Pizzi16.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/SrivastavaLMACR16,
  author    = {S. Srivastava and
               Shashi Bhushan Lal and
               Dwijesh C. Mishra and
               U. B. Angadi and
               K. K. Chaturvedi and
               Shesh N. Rai and
               Anil Rai},
  title     = {An efficient algorithm for protein structure comparison using elastic
               shape analysis},
  journal   = {Algorithms Mol. Biol.},
  volume    = {11},
  pages     = {27},
  year      = {2016},
  url       = {https://doi.org/10.1186/s13015-016-0089-1},
  doi       = {10.1186/s13015-016-0089-1},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/SrivastavaLMACR16.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/SwensonSB16,
  author    = {Krister M. Swenson and
               Pijus Simonaitis and
               Mathieu Blanchette},
  title     = {Models and algorithms for genome rearrangement with positional constraints},
  journal   = {Algorithms Mol. Biol.},
  volume    = {11},
  pages     = {13},
  year      = {2016},
  url       = {https://doi.org/10.1186/s13015-016-0065-9},
  doi       = {10.1186/s13015-016-0065-9},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/SwensonSB16.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/Taylor16,
  author    = {William R. Taylor},
  title     = {An algorithm to parse segment packing in predicted protein contact
               maps},
  journal   = {Algorithms Mol. Biol.},
  volume    = {11},
  pages     = {17},
  year      = {2016},
  url       = {https://doi.org/10.1186/s13015-016-0080-x},
  doi       = {10.1186/s13015-016-0080-x},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/Taylor16.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/WillJ16,
  author    = {Sebastian Will and
               Hosna Jabbari},
  title     = {Sparse {RNA} folding revisited: space-efficient minimum free energy
               structure prediction},
  journal   = {Algorithms Mol. Biol.},
  volume    = {11},
  pages     = {7},
  year      = {2016},
  url       = {https://doi.org/10.1186/s13015-016-0071-y},
  doi       = {10.1186/s13015-016-0071-y},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/WillJ16.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/Wu16,
  author    = {Thomas D. Wu},
  title     = {Bitpacking techniques for indexing genomes: I. Hash tables},
  journal   = {Algorithms Mol. Biol.},
  volume    = {11},
  pages     = {5},
  year      = {2016},
  url       = {https://doi.org/10.1186/s13015-016-0069-5},
  doi       = {10.1186/s13015-016-0069-5},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/Wu16.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/Wu16a,
  author    = {Thomas D. Wu},
  title     = {Bitpacking techniques for indexing genomes: {II.} Enhanced suffix
               arrays},
  journal   = {Algorithms Mol. Biol.},
  volume    = {11},
  pages     = {9},
  year      = {2016},
  url       = {https://doi.org/10.1186/s13015-016-0068-6},
  doi       = {10.1186/s13015-016-0068-6},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/Wu16a.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/ZhouLRHFT16,
  author    = {Jun Zhou and
               Yu Lin and
               Vaibhav Rajan and
               William Hoskins and
               Bing Feng and
               Jijun Tang},
  title     = {Analysis of gene copy number changes in tumor phylogenetics},
  journal   = {Algorithms Mol. Biol.},
  volume    = {11},
  pages     = {26},
  year      = {2016},
  url       = {https://doi.org/10.1186/s13015-016-0088-2},
  doi       = {10.1186/s13015-016-0088-2},
  timestamp = {Sat, 05 Sep 2020 01:00:00 +0200},
  biburl    = {https://dblp.org/rec/journals/almob/ZhouLRHFT16.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/ZukurovNVOJA16,
  author    = {Jean P. Zukurov and
               Sieberth do Nascimento{-}Brito and
               Angela C. Volpini and
               Guilherme C. Oliveira and
               Luiz Mario R. Janini and
               Fernando Antoneli},
  title     = {Estimation of genetic diversity in viral populations from next generation
               sequencing data with extremely deep coverage},
  journal   = {Algorithms Mol. Biol.},
  volume    = {11},
  pages     = {2},
  year      = {2016},
  url       = {https://doi.org/10.1186/s13015-016-0064-x},
  doi       = {10.1186/s13015-016-0064-x},
  timestamp = {Fri, 27 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/ZukurovNVOJA16.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/AmberkarK15,
  author    = {Sandeep Amberkar and
               Lars Kaderali},
  title     = {An integrative approach for a network based meta-analysis of viral
               RNAi screens},
  journal   = {Algorithms Mol. Biol.},
  volume    = {10},
  pages     = {6},
  year      = {2015},
  url       = {https://doi.org/10.1186/s13015-015-0035-7},
  doi       = {10.1186/s13015-015-0035-7},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/AmberkarK15.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/Aumentado-Armstrong15,
  author    = {Tristan Aumentado{-}Armstrong and
               Bogdan Istrate and
               Robert A. Murgita},
  title     = {Algorithmic approaches to protein-protein interaction site prediction},
  journal   = {Algorithms Mol. Biol.},
  volume    = {10},
  pages     = {7},
  year      = {2015},
  url       = {https://doi.org/10.1186/s13015-015-0033-9},
  doi       = {10.1186/s13015-015-0033-9},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/Aumentado-Armstrong15.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/BandyopadhyayR015,
  author    = {Sanghamitra Bandyopadhyay and
               Sumanta Ray and
               Anirban Mukhopadhyay and
               Ujjwal Maulik},
  title     = {A multiobjective approach for identifying protein complexes and studying
               their association in multiple disorders},
  journal   = {Algorithms Mol. Biol.},
  volume    = {10},
  pages     = {24},
  year      = {2015},
  url       = {https://doi.org/10.1186/s13015-015-0056-2},
  doi       = {10.1186/s13015-015-0056-2},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/BandyopadhyayR015.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/BoyceSH15,
  author    = {Kieran Boyce and
               Fabian Sievers and
               Desmond G. Higgins},
  title     = {Instability in progressive multiple sequence alignment algorithms},
  journal   = {Algorithms Mol. Biol.},
  volume    = {10},
  pages     = {26},
  year      = {2015},
  url       = {https://doi.org/10.1186/s13015-015-0057-1},
  doi       = {10.1186/s13015-015-0057-1},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/BoyceSH15.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/BozaBV15,
  author    = {Vladim{\'{\i}}r Boza and
               Brona Brejov{\'{a}} and
               Tom{\'{a}}s Vinar},
  title     = {{GAML:} genome assembly by maximum likelihood},
  journal   = {Algorithms Mol. Biol.},
  volume    = {10},
  pages     = {18},
  year      = {2015},
  url       = {https://doi.org/10.1186/s13015-015-0052-6},
  doi       = {10.1186/s13015-015-0052-6},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/BozaBV15.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/BrucknerHK15,
  author    = {Sharon Bruckner and
               Falk H{\"{u}}ffner and
               Christian Komusiewicz},
  title     = {A graph modification approach for finding core-periphery structures
               in protein interaction networks},
  journal   = {Algorithms Mol. Biol.},
  volume    = {10},
  pages     = {16},
  year      = {2015},
  url       = {https://doi.org/10.1186/s13015-015-0043-7},
  doi       = {10.1186/s13015-015-0043-7},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/BrucknerHK15.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/CardonaPR15,
  author    = {Gabriel Cardona and
               Joan Carles Pons and
               Francesc Rossell{\'{o}}},
  title     = {A reconstruction problem for a class of phylogenetic networks with
               lateral gene transfers},
  journal   = {Algorithms Mol. Biol.},
  volume    = {10},
  pages     = {28},
  year      = {2015},
  url       = {https://doi.org/10.1186/s13015-015-0059-z},
  doi       = {10.1186/s13015-015-0059-z},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/CardonaPR15.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/ChoiPCC15,
  author    = {Jongpill Choi and
               Kiejung Park and
               Seong Beom Cho and
               Myungguen Chung},
  title     = {{HIA:} a genome mapper using hybrid index-based sequence alignment},
  journal   = {Algorithms Mol. Biol.},
  volume    = {10},
  pages     = {30},
  year      = {2015},
  url       = {https://doi.org/10.1186/s13015-015-0062-4},
  doi       = {10.1186/s13015-015-0062-4},
  timestamp = {Wed, 15 Apr 2020 01:00:00 +0200},
  biburl    = {https://dblp.org/rec/journals/almob/ChoiPCC15.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/CominLS15,
  author    = {Matteo Comin and
               Andrea Leoni and
               Michele Schimd},
  title     = {Clustering of reads with alignment-free measures and quality values},
  journal   = {Algorithms Mol. Biol.},
  volume    = {10},
  pages     = {4},
  year      = {2015},
  url       = {https://doi.org/10.1186/s13015-014-0029-x},
  doi       = {10.1186/s13015-014-0029-x},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/CominLS15.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/CrawfordSM15,
  author    = {Joseph Crawford and
               Yihan Sun and
               Tijana Milenkovic},
  title     = {Fair evaluation of global network aligners},
  journal   = {Algorithms Mol. Biol.},
  volume    = {10},
  pages     = {19},
  year      = {2015},
  url       = {https://doi.org/10.1186/s13015-015-0050-8},
  doi       = {10.1186/s13015-015-0050-8},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/CrawfordSM15.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/DonatiBSCS15,
  author    = {Beatrice Donati and
               Christian Baudet and
               Blerina Sinaimeri and
               Pierluigi Crescenzi and
               Marie{-}France Sagot},
  title     = {{EUCALYPT:} efficient tree reconciliation enumerator},
  journal   = {Algorithms Mol. Biol.},
  volume    = {10},
  pages     = {3},
  year      = {2015},
  url       = {https://doi.org/10.1186/s13015-014-0031-3},
  doi       = {10.1186/s13015-014-0031-3},
  timestamp = {Sat, 05 Sep 2020 01:00:00 +0200},
  biburl    = {https://dblp.org/rec/journals/almob/DonatiBSCS15.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/GalvaoLD15,
  author    = {Gustavo Rodrigues Galv{\~{a}}o and
               Orlando Lee and
               Zanoni Dias},
  title     = {Sorting signed permutations by short operations},
  journal   = {Algorithms Mol. Biol.},
  volume    = {10},
  pages     = {12},
  year      = {2015},
  url       = {https://doi.org/10.1186/s13015-015-0040-x},
  doi       = {10.1186/s13015-015-0040-x},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/GalvaoLD15.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/GoldsteinB15,
  author    = {Yaron A. B. Goldstein and
               Alexander Bockmayr},
  title     = {Double and multiple knockout simulations for genome-scale metabolic
               network reconstructions},
  journal   = {Algorithms Mol. Biol.},
  volume    = {10},
  pages     = {1},
  year      = {2015},
  url       = {https://doi.org/10.1186/s13015-014-0028-y},
  doi       = {10.1186/s13015-014-0028-y},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/GoldsteinB15.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/GonzalezWLJ15,
  author    = {Luis C. Gonz{\'{a}}lez and
               Hui Wang and
               Dennis R. Livesay and
               Donald J. Jacobs},
  title     = {A virtual pebble game to ensemble average graph rigidity},
  journal   = {Algorithms Mol. Biol.},
  volume    = {10},
  pages     = {11},
  year      = {2015},
  url       = {https://doi.org/10.1186/s13015-015-0039-3},
  doi       = {10.1186/s13015-015-0039-3},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/GonzalezWLJ15.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/GuYKWW15,
  author    = {Junfeng Gu and
               Xu Yang and
               Ling Kang and
               Jinying Wu and
               Xicheng Wang},
  title     = {MoDock: {A} multi-objective strategy improves the accuracy for molecular
               docking},
  journal   = {Algorithms Mol. Biol.},
  volume    = {10},
  pages     = {8},
  year      = {2015},
  url       = {https://doi.org/10.1186/s13015-015-0034-8},
  doi       = {10.1186/s13015-015-0034-8},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/GuYKWW15.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/HoffmannSS15,
  author    = {Steve Hoffmann and
               Peter F. Stadler and
               Korbinian Strimmer},
  title     = {A simple data-adaptive probabilistic variant calling model},
  journal   = {Algorithms Mol. Biol.},
  volume    = {10},
  pages     = {10},
  year      = {2015},
  url       = {https://doi.org/10.1186/s13015-015-0037-5},
  doi       = {10.1186/s13015-015-0037-5},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/HoffmannSS15.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/HordijkSS15,
  author    = {Wim Hordijk and
               Joshua I. Smith and
               Mike A. Steel},
  title     = {Algorithms for detecting and analysing autocatalytic sets},
  journal   = {Algorithms Mol. Biol.},
  volume    = {10},
  pages     = {15},
  year      = {2015},
  url       = {https://doi.org/10.1186/s13015-015-0042-8},
  doi       = {10.1186/s13015-015-0042-8},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/HordijkSS15.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/KhosraviGPLSBG15,
  author    = {Pegah Khosravi and
               Vahid H. Gazestani and
               Leila Pirhaji and
               Brian Law and
               Mehdi Sadeghi and
               Gary D. Bader and
               Bahram Goliaei},
  title     = {Erratum to: Inferring interaction type in gene regulatory networks
               using co-expression data},
  journal   = {Algorithms Mol. Biol.},
  volume    = {10},
  pages     = {25},
  year      = {2015},
  url       = {https://doi.org/10.1186/s13015-015-0055-3},
  doi       = {10.1186/s13015-015-0055-3},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/KhosraviGPLSBG15.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/KhosraviGPLSGB15,
  author    = {Pegah Khosravi and
               Vahid H. Gazestani and
               Leila Pirhaji and
               Brian Law and
               Mehdi Sadeghi and
               Bahram Goliaei and
               Gary D. Bader},
  title     = {Inferring interaction type in gene regulatory networks using co-expression
               data},
  journal   = {Algorithms Mol. Biol.},
  volume    = {10},
  pages     = {23},
  year      = {2015},
  url       = {https://doi.org/10.1186/s13015-015-0054-4},
  doi       = {10.1186/s13015-015-0054-4},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/KhosraviGPLSGB15.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/KopczynskiR15,
  author    = {Dominik Kopczynski and
               Sven Rahmann},
  title     = {An online peak extraction algorithm for ion mobility spectrometry
               data},
  journal   = {Algorithms Mol. Biol.},
  volume    = {10},
  pages     = {17},
  year      = {2015},
  url       = {https://doi.org/10.1186/s13015-015-0045-5},
  doi       = {10.1186/s13015-015-0045-5},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/KopczynskiR15.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/KrippahlB15,
  author    = {Ludwig Krippahl and
               Pedro Barahona},
  title     = {Protein docking with predicted constraints},
  journal   = {Algorithms Mol. Biol.},
  volume    = {10},
  pages     = {9},
  year      = {2015},
  url       = {https://doi.org/10.1186/s13015-015-0036-6},
  doi       = {10.1186/s13015-015-0036-6},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/KrippahlB15.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/Le15,
  author    = {Duc{-}Hau Le},
  title     = {A novel method for identifying disease associated protein complexes
               based on functional similarity protein complex networks},
  journal   = {Algorithms Mol. Biol.},
  volume    = {10},
  pages     = {14},
  year      = {2015},
  url       = {https://doi.org/10.1186/s13015-015-0044-6},
  doi       = {10.1186/s13015-015-0044-6},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/Le15.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/MartinezFBS15,
  author    = {F{\'{a}}bio Viduani Martinez and
               Pedro Feij{\~{a}}o and
               Mar{\'{\i}}lia D. V. Braga and
               Jens Stoye},
  title     = {On the family-free {DCJ} distance and similarity},
  journal   = {Algorithms Mol. Biol.},
  volume    = {10},
  pages     = {13},
  year      = {2015},
  url       = {https://doi.org/10.1186/s13015-015-0041-9},
  doi       = {10.1186/s13015-015-0041-9},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/MartinezFBS15.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/MorgensternZHL15,
  author    = {Burkhard Morgenstern and
               Binyao Zhu and
               Sebastian Horwege and
               Chris Leimeister},
  title     = {Estimating evolutionary distances between genomic sequences from spaced-word
               matches},
  journal   = {Algorithms Mol. Biol.},
  volume    = {10},
  pages     = {5},
  year      = {2015},
  url       = {https://doi.org/10.1186/s13015-015-0032-x},
  doi       = {10.1186/s13015-015-0032-x},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/MorgensternZHL15.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/NairJHZ15,
  author    = {Govind Nair and
               Christian Jungreuthmayer and
               Michael Hanscho and
               J{\"{u}}rgen Zanghellini},
  title     = {Designing minimal microbial strains of desired functionality using
               a genetic algorithm},
  journal   = {Algorithms Mol. Biol.},
  volume    = {10},
  pages     = {29},
  year      = {2015},
  url       = {https://doi.org/10.1186/s13015-015-0060-6},
  doi       = {10.1186/s13015-015-0060-6},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/NairJHZ15.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/PengWWP15,
  author    = {Wei Peng and
               Jianxin Wang and
               Fang{-}Xiang Wu and
               Yi Pan},
  title     = {Detecting conserved protein complexes using a dividing-and-matching
               algorithm and unequally lenient criteria for network comparison},
  journal   = {Algorithms Mol. Biol.},
  volume    = {10},
  pages     = {21},
  year      = {2015},
  url       = {https://doi.org/10.1186/s13015-015-0053-5},
  doi       = {10.1186/s13015-015-0053-5},
  timestamp = {Fri, 21 Aug 2020 01:00:00 +0200},
  biburl    = {https://dblp.org/rec/journals/almob/PengWWP15.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/Poleksic15,
  author    = {Aleksandar Poleksic},
  title     = {A polynomial time algorithm for computing the area under a {GDT} curve},
  journal   = {Algorithms Mol. Biol.},
  volume    = {10},
  pages     = {27},
  year      = {2015},
  url       = {https://doi.org/10.1186/s13015-015-0058-0},
  doi       = {10.1186/s13015-015-0058-0},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/Poleksic15.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/ReichelBMPMS15,
  author    = {Katja Reichel and
               Valentin Bahier and
               C{\'{e}}dric Midoux and
               Nicolas Parisey and
               Jean{-}Pierre Masson and
               Solenn Stoeckel},
  title     = {Interpretation and approximation tools for big, dense Markov chain
               transition matrices in population genetics},
  journal   = {Algorithms Mol. Biol.},
  volume    = {10},
  pages     = {31},
  year      = {2015},
  url       = {https://doi.org/10.1186/s13015-015-0061-5},
  doi       = {10.1186/s13015-015-0061-5},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/ReichelBMPMS15.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/SacomotoLS15,
  author    = {Gustavo Sacomoto and
               Vincent Lacroix and
               Marie{-}France Sagot},
  title     = {A polynomial delay algorithm for the enumeration of bubbles with length
               constraints in directed graphs},
  journal   = {Algorithms Mol. Biol.},
  volume    = {10},
  pages     = {20},
  year      = {2015},
  url       = {https://doi.org/10.1186/s13015-015-0046-4},
  doi       = {10.1186/s13015-015-0046-4},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/SacomotoLS15.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/SauleG15,
  author    = {C{\'{e}}dric Saule and
               Robert Giegerich},
  title     = {Pareto optimization in algebraic dynamic programming},
  journal   = {Algorithms Mol. Biol.},
  volume    = {10},
  pages     = {22},
  year      = {2015},
  url       = {https://doi.org/10.1186/s13015-015-0051-7},
  doi       = {10.1186/s13015-015-0051-7},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/SauleG15.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/VinhLBH15,
  author    = {Le Vinh and
               Tran Lang and
               Le Binh and
               Tran Hoai},
  title     = {A two-phase binning algorithm using l-mer frequency on groups of non-overlapping
               reads},
  journal   = {Algorithms Mol. Biol.},
  volume    = {10},
  pages     = {2},
  year      = {2015},
  url       = {https://doi.org/10.1186/s13015-014-0030-4},
  doi       = {10.1186/s13015-014-0030-4},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/VinhLBH15.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/BartonIP14,
  author    = {Carl Barton and
               Costas S. Iliopoulos and
               Solon P. Pissis},
  title     = {Fast algorithms for approximate circular string matching},
  journal   = {Algorithms Mol. Biol.},
  volume    = {9},
  pages     = {9},
  year      = {2014},
  url       = {https://doi.org/10.1186/1748-7188-9-9},
  doi       = {10.1186/1748-7188-9-9},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/BartonIP14.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/BartonIP14a,
  author    = {Carl Barton and
               Costas S. Iliopoulos and
               Solon P. Pissis},
  title     = {Optimal computation of all tandem repeats in a weighted sequence},
  journal   = {Algorithms Mol. Biol.},
  volume    = {9},
  pages     = {21},
  year      = {2014},
  url       = {https://doi.org/10.1186/s13015-014-0021-5},
  doi       = {10.1186/s13015-014-0021-5},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/BartonIP14a.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/CleynenKLRR14,
  author    = {Alice Cleynen and
               Michel Koskas and
               Emilie Lebarbier and
               Guillem Rigaill and
               St{\'{e}}phane Robin},
  title     = {Segmentor3IsBack: an {R} package for the fast and exact segmentation
               of Seq-data},
  journal   = {Algorithms Mol. Biol.},
  volume    = {9},
  pages     = {6},
  year      = {2014},
  url       = {https://doi.org/10.1186/1748-7188-9-6},
  doi       = {10.1186/1748-7188-9-6},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/CleynenKLRR14.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/DeepakF14,
  author    = {Akshay Deepak and
               David Fern{\'{a}}ndez{-}Baca},
  title     = {Enumerating all maximal frequent subtrees in collections of phylogenetic
               trees},
  journal   = {Algorithms Mol. Biol.},
  volume    = {9},
  pages     = {16},
  year      = {2014},
  url       = {https://doi.org/10.1186/1748-7188-9-16},
  doi       = {10.1186/1748-7188-9-16},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/DeepakF14.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/FangNY14,
  author    = {Chun Fang and
               Tamotsu Noguchi and
               Hayato Yamana},
  title     = {Simplified sequence-based method for ATP-binding prediction using
               contextual local evolutionary conservation},
  journal   = {Algorithms Mol. Biol.},
  volume    = {9},
  pages     = {7},
  year      = {2014},
  url       = {https://doi.org/10.1186/1748-7188-9-7},
  doi       = {10.1186/1748-7188-9-7},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/FangNY14.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/FilippovaPDK14,
  author    = {Darya Filippova and
               Robert Patro and
               Geet Duggal and
               Carl Kingsford},
  title     = {Identification of alternative topological domains in chromatin},
  journal   = {Algorithms Mol. Biol.},
  volume    = {9},
  pages     = {14},
  year      = {2014},
  url       = {https://doi.org/10.1186/1748-7188-9-14},
  doi       = {10.1186/1748-7188-9-14},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/FilippovaPDK14.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/HenriquesM14,
  author    = {Rui Henriques and
               Sara C. Madeira},
  title     = {BicPAM: Pattern-based biclustering for biomedical data analysis},
  journal   = {Algorithms Mol. Biol.},
  volume    = {9},
  pages     = {27},
  year      = {2014},
  url       = {https://doi.org/10.1186/s13015-014-0027-z},
  doi       = {10.1186/s13015-014-0027-z},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/HenriquesM14.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/KuppuswamyAWBG14,
  author    = {Usha Kuppuswamy and
               Seshan Ananthasubramanian and
               Yanli Wang and
               Narayanaswamy Balakrishnan and
               Madhavi Ganapathiraju},
  title     = {Predicting gene ontology annotations of orphan {GWAS} genes using
               protein-protein interactions},
  journal   = {Algorithms Mol. Biol.},
  volume    = {9},
  pages     = {10},
  year      = {2014},
  url       = {https://doi.org/10.1186/1748-7188-9-10},
  doi       = {10.1186/1748-7188-9-10},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/KuppuswamyAWBG14.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/LeibovichY14,
  author    = {Limor Leibovich and
               Zohar Yakhini},
  title     = {Mutual enrichment in ranked lists and the statistical assessment of
               position weight matrix motifs},
  journal   = {Algorithms Mol. Biol.},
  volume    = {9},
  pages     = {11},
  year      = {2014},
  url       = {https://doi.org/10.1186/1748-7188-9-11},
  doi       = {10.1186/1748-7188-9-11},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/LeibovichY14.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/MannNSBSF14,
  author    = {Martin Mann and
               Feras Nahar and
               Norah Schnorr and
               Rolf Backofen and
               Peter F. Stadler and
               Christoph Flamm},
  title     = {Atom mapping with constraint programming},
  journal   = {Algorithms Mol. Biol.},
  volume    = {9},
  pages     = {23},
  year      = {2014},
  url       = {https://doi.org/10.1186/s13015-014-0023-3},
  doi       = {10.1186/s13015-014-0023-3},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/MannNSBSF14.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/MazzaGFS14,
  author    = {Arnon Mazza and
               Irit Gat{-}Viks and
               Hesso Farhan and
               Roded Sharan},
  title     = {A minimum-labeling approach for reconstructing protein networks across
               multiple conditions},
  journal   = {Algorithms Mol. Biol.},
  volume    = {9},
  pages     = {1},
  year      = {2014},
  url       = {https://doi.org/10.1186/1748-7188-9-1},
  doi       = {10.1186/1748-7188-9-1},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/MazzaGFS14.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/MisofMRKPS14,
  author    = {Bernhard Misof and
               Karen Meusemann and
               Bj{\"{o}}rn Marcus von Reumont and
               Patrick K{\"{u}}ck and
               Sonja J. Prohaska and
               Peter F. Stadler},
  title     = {A priori assessment of data quality in molecular phylogenetics},
  journal   = {Algorithms Mol. Biol.},
  volume    = {9},
  pages     = {22},
  year      = {2014},
  url       = {https://doi.org/10.1186/s13015-014-0022-4},
  doi       = {10.1186/s13015-014-0022-4},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/MisofMRKPS14.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/ModzelewskiD14,
  author    = {Michal Modzelewski and
               Norbert Dojer},
  title     = {{MSARC:} Multiple sequence alignment by residue clustering},
  journal   = {Algorithms Mol. Biol.},
  volume    = {9},
  pages     = {12},
  year      = {2014},
  url       = {https://doi.org/10.1186/1748-7188-9-12},
  doi       = {10.1186/1748-7188-9-12},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/ModzelewskiD14.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/MohantyDV14,
  author    = {Anwoy Kumar Mohanty and
               Aniruddha Datta and
               Vijayanagaram Venkatraj},
  title     = {Using the message passing algorithm on discrete data to detect faults
               in boolean regulatory networks},
  journal   = {Algorithms Mol. Biol.},
  volume    = {9},
  pages     = {20},
  year      = {2014},
  url       = {https://doi.org/10.1186/s13015-014-0020-6},
  doi       = {10.1186/s13015-014-0020-6},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/MohantyDV14.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/MontaseriZC14,
  author    = {Soheila Montaseri and
               Fatemeh Zare{-}Mirakabad and
               Nasrollah Moghadam Charkari},
  title     = {{RNA-RNA} interaction prediction using genetic algorithm},
  journal   = {Algorithms Mol. Biol.},
  volume    = {9},
  pages     = {17},
  year      = {2014},
  url       = {https://doi.org/10.1186/1748-7188-9-17},
  doi       = {10.1186/1748-7188-9-17},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/MontaseriZC14.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/NanasiVB14,
  author    = {Michal N{\'{a}}n{\'{a}}si and
               Tom{\'{a}}s Vinar and
               Brona Brejov{\'{a}}},
  title     = {Probabilistic approaches to alignment with tandem repeats},
  journal   = {Algorithms Mol. Biol.},
  volume    = {9},
  pages     = {3},
  year      = {2014},
  url       = {https://doi.org/10.1186/1748-7188-9-3},
  doi       = {10.1186/1748-7188-9-3},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/NanasiVB14.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/PaisROC14,
  author    = {Fabiano Sviatopolk{-}Mirsky Pais and
               Patr{\'{\i}}cia de Ruy and
               Guilherme C. Oliveira and
               Roney Coimbra},
  title     = {Assessing the efficiency of multiple sequence alignment programs},
  journal   = {Algorithms Mol. Biol.},
  volume    = {9},
  pages     = {4},
  year      = {2014},
  url       = {https://doi.org/10.1186/1748-7188-9-4},
  doi       = {10.1186/1748-7188-9-4},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/PaisROC14.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/QinFMSB14,
  author    = {Jing Qin and
               Markus Fricke and
               Manja Marz and
               Peter F. Stadler and
               Rolf Backofen},
  title     = {Graph-distance distribution of the Boltzmann ensemble of {RNA} secondary
               structures},
  journal   = {Algorithms Mol. Biol.},
  volume    = {9},
  pages     = {19},
  year      = {2014},
  url       = {https://doi.org/10.1186/1748-7188-9-19},
  doi       = {10.1186/1748-7188-9-19},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/QinFMSB14.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/RegnierFYR14,
  author    = {Mireille R{\'{e}}gnier and
               Evgenia Furletova and
               Victor Yakovlev and
               Mikhail A. Roytberg},
  title     = {Analysis of pattern overlaps and exact computation of P-values of
               pattern occurrences numbers: case of Hidden Markov Models},
  journal   = {Algorithms Mol. Biol.},
  volume    = {9},
  pages     = {25},
  year      = {2014},
  url       = {https://doi.org/10.1186/s13015-014-0025-1},
  doi       = {10.1186/s13015-014-0025-1},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/RegnierFYR14.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/SalikhovSK14,
  author    = {Kamil Salikhov and
               Gustavo Sacomoto and
               Gregory Kucherov},
  title     = {Using cascading Bloom filters to improve the memory usage for de Brujin
               graphs},
  journal   = {Algorithms Mol. Biol.},
  volume    = {9},
  pages     = {2},
  year      = {2014},
  url       = {https://doi.org/10.1186/1748-7188-9-2},
  doi       = {10.1186/1748-7188-9-2},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/SalikhovSK14.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/SimhaS14,
  author    = {Ramanuja Simha and
               Hagit Shatkay},
  title     = {Protein (multi-)location prediction: using location inter-dependencies
               in a probabilistic framework},
  journal   = {Algorithms Mol. Biol.},
  volume    = {9},
  pages     = {8},
  year      = {2014},
  url       = {https://doi.org/10.1186/1748-7188-9-8},
  doi       = {10.1186/1748-7188-9-8},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/SimhaS14.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/Snir14,
  author    = {Sagi Snir},
  title     = {On the number of genomic pacemakers: a geometric approach},
  journal   = {Algorithms Mol. Biol.},
  volume    = {9},
  pages     = {26},
  year      = {2014},
  url       = {https://doi.org/10.1186/s13015-014-0026-0},
  doi       = {10.1186/s13015-014-0026-0},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/Snir14.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/SolimanFR14,
  author    = {Sylvain Soliman and
               Fran{\c{c}}ois Fages and
               Ovidiu Radulescu},
  title     = {A constraint solving approach to model reduction by tropical equilibration},
  journal   = {Algorithms Mol. Biol.},
  volume    = {9},
  pages     = {24},
  year      = {2014},
  url       = {https://doi.org/10.1186/s13015-014-0024-2},
  doi       = {10.1186/s13015-014-0024-2},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/SolimanFR14.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/Torda14,
  author    = {Andrew E. Torda},
  title     = {Not assessing the efficiency of multiple sequence alignment programs},
  journal   = {Algorithms Mol. Biol.},
  volume    = {9},
  pages     = {18},
  year      = {2014},
  url       = {https://doi.org/10.1186/1748-7188-9-18},
  doi       = {10.1186/1748-7188-9-18},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/Torda14.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/TsirogiannisS14,
  author    = {Constantinos Tsirogiannis and
               Brody Sandel},
  title     = {Computing the skewness of the phylogenetic mean pairwise distance
               in linear time},
  journal   = {Algorithms Mol. Biol.},
  volume    = {9},
  pages     = {15},
  year      = {2014},
  url       = {https://doi.org/10.1186/1748-7188-9-15},
  doi       = {10.1186/1748-7188-9-15},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/TsirogiannisS14.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/VakatiF14,
  author    = {Sudheer Vakati and
               David Fern{\'{a}}ndez{-}Baca},
  title     = {Characterizing compatibility and agreement of unrooted trees via cuts
               in graphs},
  journal   = {Algorithms Mol. Biol.},
  volume    = {9},
  pages     = {13},
  year      = {2014},
  url       = {https://doi.org/10.1186/1748-7188-9-13},
  doi       = {10.1186/1748-7188-9-13},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/VakatiF14.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/VenkatachalamGF14,
  author    = {Balaji Venkatachalam and
               Dan Gusfield and
               Yelena Frid},
  title     = {Faster algorithms for RNA-folding using the Four-Russians method},
  journal   = {Algorithms Mol. Biol.},
  volume    = {9},
  pages     = {5},
  year      = {2014},
  url       = {https://doi.org/10.1186/1748-7188-9-5},
  doi       = {10.1186/1748-7188-9-5},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/VenkatachalamGF14.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/ApostolicoCDP13,
  author    = {Alberto Apostolico and
               Matteo Comin and
               Andreas W. M. Dress and
               Laxmi Parida},
  title     = {Ultrametric networks: a new tool for phylogenetic analysis},
  journal   = {Algorithms Mol. Biol.},
  volume    = {8},
  pages     = {7},
  year      = {2013},
  url       = {https://doi.org/10.1186/1748-7188-8-7},
  doi       = {10.1186/1748-7188-8-7},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/ApostolicoCDP13.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/BharH0MBW13,
  author    = {Anirban Bhar and
               Martin Haubrock and
               Anirban Mukhopadhyay and
               Ujjwal Maulik and
               Sanghamitra Bandyopadhyay and
               Edgar Wingender},
  title     = {Coexpression and coregulation analysis of time-series gene expression
               data in estrogen-induced breast cancer cell},
  journal   = {Algorithms Mol. Biol.},
  volume    = {8},
  pages     = {9},
  year      = {2013},
  url       = {https://doi.org/10.1186/1748-7188-8-9},
  doi       = {10.1186/1748-7188-8-9},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/BharH0MBW13.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/CastellanaLRSPGV13,
  author    = {Natalie Castellana and
               Andrey Lushnikov and
               Piotr Rotkiewicz and
               Natasha Sefcovic and
               Pavel A. Pevzner and
               Adam Godzik and
               Kira Vyatkina},
  title     = {{MORPH-PRO:} a novel algorithm and web server for protein morphing},
  journal   = {Algorithms Mol. Biol.},
  volume    = {8},
  pages     = {19},
  year      = {2013},
  url       = {https://doi.org/10.1186/1748-7188-8-19},
  doi       = {10.1186/1748-7188-8-19},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/CastellanaLRSPGV13.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/CatanzaroRS13,
  author    = {Daniele Catanzaro and
               Ramamoorthi Ravi and
               Russell Schwartz},
  title     = {A mixed integer linear programming model to reconstruct phylogenies
               from single nucleotide polymorphism haplotypes under the maximum parsimony
               criterion},
  journal   = {Algorithms Mol. Biol.},
  volume    = {8},
  pages     = {3},
  year      = {2013},
  url       = {https://doi.org/10.1186/1748-7188-8-3},
  doi       = {10.1186/1748-7188-8-3},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/CatanzaroRS13.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/ChaudharyBF13,
  author    = {Ruchi Chaudhary and
               John Gordon Burleigh and
               David Fern{\'{a}}ndez{-}Baca},
  title     = {Inferring species trees from incongruent multi-copy gene trees using
               the Robinson-Foulds distance},
  journal   = {Algorithms Mol. Biol.},
  volume    = {8},
  pages     = {28},
  year      = {2013},
  url       = {https://doi.org/10.1186/1748-7188-8-28},
  doi       = {10.1186/1748-7188-8-28},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/ChaudharyBF13.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/ChikhiR13,
  author    = {Rayan Chikhi and
               Guillaume Rizk},
  title     = {Space-efficient and exact de Bruijn graph representation based on
               a Bloom filter},
  journal   = {Algorithms Mol. Biol.},
  volume    = {8},
  pages     = {22},
  year      = {2013},
  url       = {https://doi.org/10.1186/1748-7188-8-22},
  doi       = {10.1186/1748-7188-8-22},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/ChikhiR13.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/CloteKK13,
  author    = {Peter Clote and
               Evangelos Kranakis and
               Danny Krizanc},
  title     = {Asymptotic structural properties of quasi-random saturated structures
               of {RNA}},
  journal   = {Algorithms Mol. Biol.},
  volume    = {8},
  pages     = {24},
  year      = {2013},
  url       = {https://doi.org/10.1186/1748-7188-8-24},
  doi       = {10.1186/1748-7188-8-24},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/CloteKK13.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/Compeau13,
  author    = {Phillip E. C. Compeau},
  title     = {DCJ-Indel sorting revisited},
  journal   = {Algorithms Mol. Biol.},
  volume    = {8},
  pages     = {6},
  year      = {2013},
  url       = {https://doi.org/10.1186/1748-7188-8-6},
  doi       = {10.1186/1748-7188-8-6},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/Compeau13.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/CuiLBAL13,
  author    = {Xuefeng Cui and
               Shuai Cheng Li and
               Dongbo Bu and
               Babak Alipanahi and
               Ming Li},
  title     = {Protein Structure Idealization: How accurately is it possible to model
               protein structures with dihedral angles?},
  journal   = {Algorithms Mol. Biol.},
  volume    = {8},
  pages     = {5},
  year      = {2013},
  url       = {https://doi.org/10.1186/1748-7188-8-5},
  doi       = {10.1186/1748-7188-8-5},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/CuiLBAL13.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/DeepakFM13,
  author    = {Akshay Deepak and
               David Fern{\'{a}}ndez{-}Baca and
               Michelle M. McMahon},
  title     = {Extracting conflict-free information from multi-labeled trees},
  journal   = {Algorithms Mol. Biol.},
  volume    = {8},
  pages     = {18},
  year      = {2013},
  url       = {https://doi.org/10.1186/1748-7188-8-18},
  doi       = {10.1186/1748-7188-8-18},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/DeepakFM13.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/DeorowiczG13,
  author    = {Sebastian Deorowicz and
               Szymon Grabowski},
  title     = {Data compression for sequencing data},
  journal   = {Algorithms Mol. Biol.},
  volume    = {8},
  pages     = {25},
  year      = {2013},
  url       = {https://doi.org/10.1186/1748-7188-8-25},
  doi       = {10.1186/1748-7188-8-25},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/DeorowiczG13.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/Dexter013,
  author    = {Daniel Dexter and
               Daniel G. Brown},
  title     = {Fast half-sibling population reconstruction: theory and algorithms},
  journal   = {Algorithms Mol. Biol.},
  volume    = {8},
  pages     = {20},
  year      = {2013},
  url       = {https://doi.org/10.1186/1748-7188-8-20},
  doi       = {10.1186/1748-7188-8-20},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/Dexter013.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/DuggalPSWFKK13,
  author    = {Geet Duggal and
               Robert Patro and
               Emre Sefer and
               Hao Wang and
               Darya Filippova and
               Samir Khuller and
               Carl Kingsford},
  title     = {Resolving spatial inconsistencies in chromosome conformation measurements},
  journal   = {Algorithms Mol. Biol.},
  volume    = {8},
  pages     = {8},
  year      = {2013},
  url       = {https://doi.org/10.1186/1748-7188-8-8},
  doi       = {10.1186/1748-7188-8-8},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/DuggalPSWFKK13.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/DyrkaNK13,
  author    = {Witold Dyrka and
               Jean{-}Christophe Nebel and
               Malgorzata Kotulska},
  title     = {Probabilistic grammatical model for helix-helix contact site classification},
  journal   = {Algorithms Mol. Biol.},
  volume    = {8},
  pages     = {31},
  year      = {2013},
  url       = {https://doi.org/10.1186/1748-7188-8-31},
  doi       = {10.1186/1748-7188-8-31},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/DyrkaNK13.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/GavryushkinaWD13,
  author    = {Alexandra Gavryushkina and
               David Welch and
               Alexei J. Drummond},
  title     = {Recursive algorithms for phylogenetic tree counting},
  journal   = {Algorithms Mol. Biol.},
  volume    = {8},
  pages     = {26},
  year      = {2013},
  url       = {https://doi.org/10.1186/1748-7188-8-26},
  doi       = {10.1186/1748-7188-8-26},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/GavryushkinaWD13.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/HalldorssonBS13,
  author    = {Bjarni V. Halld{\'{o}}rsson and
               Dima Blokh and
               Roded Sharan},
  title     = {Estimating population size via line graph reconstruction},
  journal   = {Algorithms Mol. Biol.},
  volume    = {8},
  pages     = {17},
  year      = {2013},
  url       = {https://doi.org/10.1186/1748-7188-8-17},
  doi       = {10.1186/1748-7188-8-17},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/HalldorssonBS13.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/IslamR13,
  author    = {A. S. M. Sohidull Islam and
               Mohammad Sohel Rahman},
  title     = {On the protein folding problem in 2D-triangular lattices},
  journal   = {Algorithms Mol. Biol.},
  volume    = {8},
  pages     = {30},
  year      = {2013},
  url       = {https://doi.org/10.1186/1748-7188-8-30},
  doi       = {10.1186/1748-7188-8-30},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/IslamR13.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/KilpatrickWA13,
  author    = {Alastair M. Kilpatrick and
               Bruce Ward and
               Stuart Aitken},
  title     = {{MCOIN:} a novel heuristic for determining transcription factor binding
               site motif width},
  journal   = {Algorithms Mol. Biol.},
  volume    = {8},
  pages     = {16},
  year      = {2013},
  url       = {https://doi.org/10.1186/1748-7188-8-16},
  doi       = {10.1186/1748-7188-8-16},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/KilpatrickWA13.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/KourmpetisDB13,
  author    = {Yiannis Kourmpetis and
               Aalt D. J. van Dijk and
               Cajo J. F. ter Braak},
  title     = {Gene Ontology consistent protein function prediction: the {FALCON}
               algorithm applied to six eukaryotic genomes},
  journal   = {Algorithms Mol. Biol.},
  volume    = {8},
  pages     = {10},
  year      = {2013},
  url       = {https://doi.org/10.1186/1748-7188-8-10},
  doi       = {10.1186/1748-7188-8-10},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/KourmpetisDB13.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/Li13,
  author    = {Shuai Cheng Li},
  title     = {The Difficulty Of Protein Structure Alignment Under The {RMSD}},
  journal   = {Algorithms Mol. Biol.},
  volume    = {8},
  pages     = {1},
  year      = {2013},
  url       = {https://doi.org/10.1186/1748-7188-8-1},
  doi       = {10.1186/1748-7188-8-1},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/Li13.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/LuL13,
  author    = {Songjian Lu and
               Xinghua Lu},
  title     = {Using graph model to find transcription factor modules: the hitting
               set problem and an exact algorithm},
  journal   = {Algorithms Mol. Biol.},
  volume    = {8},
  pages     = {2},
  year      = {2013},
  url       = {https://doi.org/10.1186/1748-7188-8-2},
  doi       = {10.1186/1748-7188-8-2},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/LuL13.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/MiloZKBDZ13,
  author    = {Nimrod Milo and
               Shay Zakov and
               Erez Katzenelson and
               Eitan Bachmat and
               Yefim Dinitz and
               Michal Ziv{-}Ukelson},
  title     = {Unrooted unordered homeomorphic subtree alignment of {RNA} trees},
  journal   = {Algorithms Mol. Biol.},
  volume    = {8},
  pages     = {13},
  year      = {2013},
  url       = {https://doi.org/10.1186/1748-7188-8-13},
  doi       = {10.1186/1748-7188-8-13},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/MiloZKBDZ13.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/MohamadODYAI13,
  author    = {Mohd Saberi Mohamad and
               Sigeru Omatu and
               Safaai Deris and
               Michifumi Yoshioka and
               Afnizanfaizal Abdullah and
               Zuwairie Ibrahim},
  title     = {An enhancement of binary particle swarm optimization for gene selection
               in classifying cancer classes},
  journal   = {Algorithms Mol. Biol.},
  volume    = {8},
  pages     = {15},
  year      = {2013},
  url       = {https://doi.org/10.1186/1748-7188-8-15},
  doi       = {10.1186/1748-7188-8-15},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/MohamadODYAI13.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/NguyenRPCDB13,
  author    = {Thi Hau Nguyen and
               Vincent Ranwez and
               St{\'{e}}phanie Pointet and
               Anne{-}Muriel Arigon Chifolleau and
               Jean{-}Philippe Doyon and
               Vincent Berry},
  title     = {Reconciliation and local gene tree rearrangement can be of mutual
               profit},
  journal   = {Algorithms Mol. Biol.},
  volume    = {8},
  pages     = {12},
  year      = {2013},
  url       = {https://doi.org/10.1186/1748-7188-8-12},
  doi       = {10.1186/1748-7188-8-12},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/NguyenRPCDB13.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/PinhasZTZ13,
  author    = {Tamar Pinhas and
               Shay Zakov and
               Dekel Tsur and
               Michal Ziv{-}Ukelson},
  title     = {Efficient edit distance with duplications and contractions},
  journal   = {Algorithms Mol. Biol.},
  volume    = {8},
  pages     = {27},
  year      = {2013},
  url       = {https://doi.org/10.1186/1748-7188-8-27},
  doi       = {10.1186/1748-7188-8-27},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/PinhasZTZ13.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/PontesGA13,
  author    = {Beatriz Pontes and
               Ra{\'{u}}l Gir{\'{a}}ldez and
               Jes{\'{u}}s S. Aguilar{-}Ruiz},
  title     = {Configurable pattern-based evolutionary biclustering of gene expression
               data},
  journal   = {Algorithms Mol. Biol.},
  volume    = {8},
  pages     = {4},
  year      = {2013},
  url       = {https://doi.org/10.1186/1748-7188-8-4},
  doi       = {10.1186/1748-7188-8-4},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/PontesGA13.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/ShuttersVF13,
  author    = {Brad Shutters and
               Sudheer Vakati and
               David Fern{\'{a}}ndez{-}Baca},
  title     = {Incompatible quartets, triplets, and characters},
  journal   = {Algorithms Mol. Biol.},
  volume    = {8},
  pages     = {11},
  year      = {2013},
  url       = {https://doi.org/10.1186/1748-7188-8-11},
  doi       = {10.1186/1748-7188-8-11},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/ShuttersVF13.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/SilvaMDB13,
  author    = {Poly H. da Silva and
               Raphael Machado and
               Simone Dantas and
               Mar{\'{\i}}lia D. V. Braga},
  title     = {DCJ-indel and DCJ-substitution distances with distinct operation costs},
  journal   = {Algorithms Mol. Biol.},
  volume    = {8},
  pages     = {21},
  year      = {2013},
  url       = {http://www.almob.org/content/8/1/21},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/SilvaMDB13.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/SternM13,
  author    = {Harry A. Stern and
               David H. Mathews},
  title     = {Accelerating calculations of {RNA} secondary structure partition functions
               using GPUs},
  journal   = {Algorithms Mol. Biol.},
  volume    = {8},
  pages     = {29},
  year      = {2013},
  url       = {https://doi.org/10.1186/1748-7188-8-29},
  doi       = {10.1186/1748-7188-8-29},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/SternM13.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/VorontsovKM13,
  author    = {Ilya E. Vorontsov and
               Ivan V. Kulakovskiy and
               Vsevolod J. Makeev},
  title     = {Jaccard index based similarity measure to compare transcription factor
               binding site models},
  journal   = {Algorithms Mol. Biol.},
  volume    = {8},
  pages     = {23},
  year      = {2013},
  url       = {https://doi.org/10.1186/1748-7188-8-23},
  doi       = {10.1186/1748-7188-8-23},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/VorontsovKM13.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/WillSHESRB13,
  author    = {Sebastian Will and
               Michael F. Siebauer and
               Steffen Heyne and
               Jan Engelhardt and
               Peter F. Stadler and
               Kristin Reiche and
               Rolf Backofen},
  title     = {LocARNAscan: Incorporating thermodynamic stability in sequence and
               structure-based {RNA} homology search},
  journal   = {Algorithms Mol. Biol.},
  volume    = {8},
  pages     = {14},
  year      = {2013},
  url       = {https://doi.org/10.1186/1748-7188-8-14},
  doi       = {10.1186/1748-7188-8-14},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/WillSHESRB13.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/AlmeidaGMV12,
  author    = {Jonas S. Almeida and
               Alexander Gr{\"{u}}neberg and
               Wolfgang Maass and
               Susana Vinga},
  title     = {Fractal MapReduce decomposition of sequence alignment},
  journal   = {Algorithms Mol. Biol.},
  volume    = {7},
  pages     = {12},
  year      = {2012},
  url       = {https://doi.org/10.1186/1748-7188-7-12},
  doi       = {10.1186/1748-7188-7-12},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/AlmeidaGMV12.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/AviramVCB12,
  author    = {Iddo Aviram and
               Ilia Veltman and
               Alexander Churkin and
               Danny Barash},
  title     = {Efficient procedures for the numerical simulation of mid-size {RNA}
               kinetics},
  journal   = {Algorithms Mol. Biol.},
  volume    = {7},
  pages     = {24},
  year      = {2012},
  url       = {https://doi.org/10.1186/1748-7188-7-24},
  doi       = {10.1186/1748-7188-7-24},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/AviramVCB12.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/BaudetDS12,
  author    = {Christian Baudet and
               Zanoni Dias and
               Marie{-}France Sagot},
  title     = {Sampling solution traces for the problem of sorting permutations by
               signed reversals},
  journal   = {Algorithms Mol. Biol.},
  volume    = {7},
  pages     = {18},
  year      = {2012},
  url       = {https://doi.org/10.1186/1748-7188-7-18},
  doi       = {10.1186/1748-7188-7-18},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/BaudetDS12.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/CasanellasFK12,
  author    = {Marta Casanellas and
               Jes{\'{u}}s Fern{\'{a}}ndez{-}S{\'{a}}nchez and
               Anna M. Kedzierska},
  title     = {The space of phylogenetic mixtures for equivariant models},
  journal   = {Algorithms Mol. Biol.},
  volume    = {7},
  pages     = {33},
  year      = {2012},
  url       = {https://doi.org/10.1186/1748-7188-7-33},
  doi       = {10.1186/1748-7188-7-33},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/CasanellasFK12.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/CominV12,
  author    = {Matteo Comin and
               Davide Verzotto},
  title     = {Alignment-free phylogeny of whole genomes using underlying subwords},
  journal   = {Algorithms Mol. Biol.},
  volume    = {7},
  pages     = {34},
  year      = {2012},
  url       = {https://doi.org/10.1186/1748-7188-7-34},
  doi       = {10.1186/1748-7188-7-34},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/CominV12.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/DoerrGMY12,
  author    = {Daniel Doerr and
               Ilan Gronau and
               Shlomo Moran and
               Irad Yavneh},
  title     = {Stochastic errors vs. modeling errors in distance based phylogenetic
               reconstructions},
  journal   = {Algorithms Mol. Biol.},
  volume    = {7},
  pages     = {22},
  year      = {2012},
  url       = {https://doi.org/10.1186/1748-7188-7-22},
  doi       = {10.1186/1748-7188-7-22},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/DoerrGMY12.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/EnrothAAWGK12,
  author    = {Stefan Enroth and
               Claes R. Andersson and
               Robin Andersson and
               Claes Wadelius and
               Mats G. Gustafsson and
               Henryk Jan Komorowski},
  title     = {A strand specific high resolution normalization method for chip-sequencing
               data employing multiple experimental control measurements},
  journal   = {Algorithms Mol. Biol.},
  volume    = {7},
  pages     = {2},
  year      = {2012},
  url       = {https://doi.org/10.1186/1748-7188-7-2},
  doi       = {10.1186/1748-7188-7-2},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/EnrothAAWGK12.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/FarztdinovM12,
  author    = {Vadim Farztdinov and
               Fionnuala McDyer},
  title     = {Distributional fold change test - a statistical approach for detecting
               differential expression in microarray experiments},
  journal   = {Algorithms Mol. Biol.},
  volume    = {7},
  pages     = {29},
  year      = {2012},
  url       = {https://doi.org/10.1186/1748-7188-7-29},
  doi       = {10.1186/1748-7188-7-29},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/FarztdinovM12.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/FedericoLMV12,
  author    = {Maria Federico and
               Mauro Leoncini and
               Manuela Montangero and
               Paolo Valente},
  title     = {Direct vs 2-Stage Approaches to Structured Motif Finding},
  journal   = {Algorithms Mol. Biol.},
  volume    = {7},
  pages     = {20},
  year      = {2012},
  url       = {https://doi.org/10.1186/1748-7188-7-20},
  doi       = {10.1186/1748-7188-7-20},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/FedericoLMV12.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/FischerKNH12,
  author    = {Mareike Fischer and
               Steffen Klaere and
               Minh Anh Nguyen and
               Arndt von Haeseler},
  title     = {On the group theoretical background of assigning stepwise mutations
               onto phylogenies},
  journal   = {Algorithms Mol. Biol.},
  volume    = {7},
  pages     = {36},
  year      = {2012},
  url       = {https://doi.org/10.1186/1748-7188-7-36},
  doi       = {10.1186/1748-7188-7-36},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/FischerKNH12.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/FogolariCVE12,
  author    = {Federico Fogolari and
               Alessandra Corazza and
               Paolo Viglino and
               Gennaro Esposito},
  title     = {Fast structure similarity searches among protein models: efficient
               clustering of protein fragments},
  journal   = {Algorithms Mol. Biol.},
  volume    = {7},
  pages     = {16},
  year      = {2012},
  url       = {https://doi.org/10.1186/1748-7188-7-16},
  doi       = {10.1186/1748-7188-7-16},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/FogolariCVE12.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/GyselLG12,
  author    = {Rob Gysel and
               Fumei Lam and
               Dan Gusfield},
  title     = {Constructing perfect phylogenies and proper triangulations for three-state
               characters},
  journal   = {Algorithms Mol. Biol.},
  volume    = {7},
  pages     = {26},
  year      = {2012},
  url       = {https://doi.org/10.1186/1748-7188-7-26},
  doi       = {10.1186/1748-7188-7-26},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/GyselLG12.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/HuangR12,
  author    = {Fenix W. D. Huang and
               Christian M. Reidys},
  title     = {On the combinatorics of sparsification},
  journal   = {Algorithms Mol. Biol.},
  volume    = {7},
  pages     = {28},
  year      = {2012},
  url       = {https://doi.org/10.1186/1748-7188-7-28},
  doi       = {10.1186/1748-7188-7-28},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/HuangR12.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/KadotaNS12,
  author    = {Koji Kadota and
               Tomoaki Nishiyama and
               Kentaro Shimizu},
  title     = {A normalization strategy for comparing tag count data},
  journal   = {Algorithms Mol. Biol.},
  volume    = {7},
  pages     = {5},
  year      = {2012},
  url       = {https://doi.org/10.1186/1748-7188-7-5},
  doi       = {10.1186/1748-7188-7-5},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/KadotaNS12.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/KannanW12,
  author    = {Lavanya Kannan and
               Ward C. Wheeler},
  title     = {Maximum Parsimony on Phylogenetic networks},
  journal   = {Algorithms Mol. Biol.},
  volume    = {7},
  pages     = {9},
  year      = {2012},
  url       = {https://doi.org/10.1186/1748-7188-7-9},
  doi       = {10.1186/1748-7188-7-9},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/KannanW12.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/LinRM12,
  author    = {Yu Lin and
               Vaibhav Rajan and
               Bernard M. E. Moret},
  title     = {Bootstrapping phylogenies inferred from rearrangement data},
  journal   = {Algorithms Mol. Biol.},
  volume    = {7},
  pages     = {21},
  year      = {2012},
  url       = {https://doi.org/10.1186/1748-7188-7-21},
  doi       = {10.1186/1748-7188-7-21},
  timestamp = {Sat, 05 Sep 2020 01:00:00 +0200},
  biburl    = {https://dblp.org/rec/journals/almob/LinRM12.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/MarashiDB12,
  author    = {Sayed{-}Amir Marashi and
               L{\'{a}}szl{\'{o}} D{\'{a}}vid and
               Alexander Bockmayr},
  title     = {Analysis of Metabolic Subnetworks by Flux Cone Projection},
  journal   = {Algorithms Mol. Biol.},
  volume    = {7},
  pages     = {17},
  year      = {2012},
  url       = {https://doi.org/10.1186/1748-7188-7-17},
  doi       = {10.1186/1748-7188-7-17},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/MarashiDB12.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/MartynKMMS12,
  author    = {Iain Martyn and
               Tyler S. Kuhn and
               Arne O. Mooers and
               Vincent Moulton and
               Andreas Spillner},
  title     = {Computing evolutionary distinctiveness indices in large scale analysis},
  journal   = {Algorithms Mol. Biol.},
  volume    = {7},
  pages     = {6},
  year      = {2012},
  url       = {https://doi.org/10.1186/1748-7188-7-6},
  doi       = {10.1186/1748-7188-7-6},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/MartynKMMS12.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/MatsenE12,
  author    = {Frederick A. Matsen IV and
               Steven N. Evans},
  title     = {Ubiquity of synonymity: almost all large binary trees are not uniquely
               identified by their spectra or their immanantal polynomials},
  journal   = {Algorithms Mol. Biol.},
  volume    = {7},
  pages     = {14},
  year      = {2012},
  url       = {https://doi.org/10.1186/1748-7188-7-14},
  doi       = {10.1186/1748-7188-7-14},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/MatsenE12.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/MatsenG12,
  author    = {Frederick A. Matsen IV and
               Aaron Gallagher},
  title     = {Reconciling taxonomy and phylogenetic inference: formalism and algorithms
               for describing discord and inferring taxonomic roots},
  journal   = {Algorithms Mol. Biol.},
  volume    = {7},
  pages     = {8},
  year      = {2012},
  url       = {https://doi.org/10.1186/1748-7188-7-8},
  doi       = {10.1186/1748-7188-7-8},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/MatsenG12.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/MatsudaTI12,
  author    = {Hirokazu Matsuda and
               Yukio Taniguchi and
               Hiroaki Iwaisaki},
  title     = {QTL/microarray approach using pathway information},
  journal   = {Algorithms Mol. Biol.},
  volume    = {7},
  pages     = {1},
  year      = {2012},
  url       = {https://doi.org/10.1186/1748-7188-7-1},
  doi       = {10.1186/1748-7188-7-1},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/MatsudaTI12.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/NguyenMW12,
  author    = {Nam{-}phuong Nguyen and
               Siavash Mirarab and
               Tandy J. Warnow},
  title     = {{MRL} and SuperFine+MRL: new supertree methods},
  journal   = {Algorithms Mol. Biol.},
  volume    = {7},
  pages     = {3},
  year      = {2012},
  url       = {https://doi.org/10.1186/1748-7188-7-3},
  doi       = {10.1186/1748-7188-7-3},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/NguyenMW12.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/Ortiz-EstevezAR12,
  author    = {Maria Ortiz{-}Estevez and
               Ander Aramburu and
               Angel Rubio},
  title     = {Getting {DNA} copy numbers without control samples},
  journal   = {Algorithms Mol. Biol.},
  volume    = {7},
  pages     = {19},
  year      = {2012},
  url       = {https://doi.org/10.1186/1748-7188-7-19},
  doi       = {10.1186/1748-7188-7-19},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/Ortiz-EstevezAR12.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/PahikkalaOASA12,
  author    = {Tapio Pahikkala and
               Sebastian Okser and
               Antti Airola and
               Tapio Salakoski and
               Tero Aittokallio},
  title     = {Wrapper-based selection of genetic features in genome-wide association
               studies through fast matrix operations},
  journal   = {Algorithms Mol. Biol.},
  volume    = {7},
  pages     = {11},
  year      = {2012},
  url       = {https://doi.org/10.1186/1748-7188-7-11},
  doi       = {10.1186/1748-7188-7-11},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/PahikkalaOASA12.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/PatroSMMNK12,
  author    = {Robert Patro and
               Emre Sefer and
               Justin Malin and
               Guillaume Mar{\c{c}}ais and
               Saket Navlakha and
               Carl Kingsford},
  title     = {Parsimonious reconstruction of network evolution},
  journal   = {Algorithms Mol. Biol.},
  volume    = {7},
  pages     = {25},
  year      = {2012},
  url       = {https://doi.org/10.1186/1748-7188-7-25},
  doi       = {10.1186/1748-7188-7-25},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/PatroSMMNK12.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/RazmaraDP12,
  author    = {Jafar Razmara and
               Safaai Bin Deris and
               Sepideh Parvizpour},
  title     = {{TS-AMIR:} a topology string alignment method for intensive rapid
               protein structure comparison},
  journal   = {Algorithms Mol. Biol.},
  volume    = {7},
  pages     = {4},
  year      = {2012},
  url       = {https://doi.org/10.1186/1748-7188-7-4},
  doi       = {10.1186/1748-7188-7-4},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/RazmaraDP12.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/RusinkoH12,
  author    = {Joseph P. Rusinko and
               Brian Hipp},
  title     = {Invariant based quartet puzzling},
  journal   = {Algorithms Mol. Biol.},
  volume    = {7},
  pages     = {35},
  year      = {2012},
  url       = {https://doi.org/10.1186/1748-7188-7-35},
  doi       = {10.1186/1748-7188-7-35},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/RusinkoH12.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/Soliman12,
  author    = {Sylvain Soliman},
  title     = {Invariants and Other Structural Properties of Biochemical Models as
               a Constraint Satisfaction Problem},
  journal   = {Algorithms Mol. Biol.},
  volume    = {7},
  pages     = {15},
  year      = {2012},
  url       = {https://doi.org/10.1186/1748-7188-7-15},
  doi       = {10.1186/1748-7188-7-15},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/Soliman12.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/StadlerD12,
  author    = {Tanja Stadler and
               James H. Degnan},
  title     = {A polynomial time algorithm for calculating the probability of a ranked
               gene tree given a species tree},
  journal   = {Algorithms Mol. Biol.},
  volume    = {7},
  pages     = {7},
  year      = {2012},
  url       = {https://doi.org/10.1186/1748-7188-7-7},
  doi       = {10.1186/1748-7188-7-7},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/StadlerD12.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/SwensonDE12,
  author    = {Krister M. Swenson and
               Andrea Doroftei and
               Nadia El{-}Mabrouk},
  title     = {Gene tree correction for reconciliation and species tree inference},
  journal   = {Algorithms Mol. Biol.},
  volume    = {7},
  pages     = {31},
  year      = {2012},
  url       = {https://doi.org/10.1186/1748-7188-7-31},
  doi       = {10.1186/1748-7188-7-31},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/SwensonDE12.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/TanaseichukBJ12,
  author    = {Olga Tanaseichuk and
               James Borneman and
               Tao Jiang},
  title     = {Separating metagenomic short reads into genomes via clustering},
  journal   = {Algorithms Mol. Biol.},
  volume    = {7},
  pages     = {27},
  year      = {2012},
  url       = {https://doi.org/10.1186/1748-7188-7-27},
  doi       = {10.1186/1748-7188-7-27},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/TanaseichukBJ12.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/TruszkowskiH012,
  author    = {Jakub Truszkowski and
               Yanqi Hao and
               Daniel G. Brown},
  title     = {Towards a practical O(n log n) phylogeny algorithm},
  journal   = {Algorithms Mol. Biol.},
  volume    = {7},
  pages     = {32},
  year      = {2012},
  url       = {https://doi.org/10.1186/1748-7188-7-32},
  doi       = {10.1186/1748-7188-7-32},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/TruszkowskiH012.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/VandinUR12,
  author    = {Fabio Vandin and
               Eli Upfal and
               Benjamin J. Raphael},
  title     = {Finding Driver Pathways in Cancer: Models and Algorithms},
  journal   = {Algorithms Mol. Biol.},
  volume    = {7},
  pages     = {23},
  year      = {2012},
  url       = {https://doi.org/10.1186/1748-7188-7-23},
  doi       = {10.1186/1748-7188-7-23},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/VandinUR12.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/VingaCFRA12,
  author    = {Susana Vinga and
               Alexandra M. Carvalho and
               Alexandre P. Francisco and
               Lu{\'{\i}}s M. S. Russo and
               Jonas S. Almeida},
  title     = {Pattern matching through Chaos Game Representation: bridging numerical
               and discrete data structures for biological sequence analysis},
  journal   = {Algorithms Mol. Biol.},
  volume    = {7},
  pages     = {10},
  year      = {2012},
  url       = {https://doi.org/10.1186/1748-7188-7-10},
  doi       = {10.1186/1748-7188-7-10},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/VingaCFRA12.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/WandeltL12,
  author    = {Sebastian Wandelt and
               Ulf Leser},
  title     = {Adaptive efficient compression of genomes},
  journal   = {Algorithms Mol. Biol.},
  volume    = {7},
  pages     = {30},
  year      = {2012},
  url       = {https://doi.org/10.1186/1748-7188-7-30},
  doi       = {10.1186/1748-7188-7-30},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/WandeltL12.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/Willson12,
  author    = {Stephen J. Willson},
  title     = {Tree-average distances on certain phylogenetic networks have their
               weights uniquely determined},
  journal   = {Algorithms Mol. Biol.},
  volume    = {7},
  pages     = {13},
  year      = {2012},
  url       = {https://doi.org/10.1186/1748-7188-7-13},
  doi       = {10.1186/1748-7188-7-13},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/Willson12.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/AndreopoulosL11,
  author    = {Bill Andreopoulos and
               Dirk Labudde},
  title     = {Efficient unfolding pattern recognition in single molecule force spectroscopy
               data},
  journal   = {Algorithms Mol. Biol.},
  volume    = {6},
  pages     = {16},
  year      = {2011},
  url       = {https://doi.org/10.1186/1748-7188-6-16},
  doi       = {10.1186/1748-7188-6-16},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/AndreopoulosL11.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/ApostolicoPU11,
  author    = {Alberto Apostolico and
               Cinzia Pizzi and
               Esko Ukkonen},
  title     = {Efficient algorithms for the discovery of gapped factors},
  journal   = {Algorithms Mol. Biol.},
  volume    = {6},
  pages     = {5},
  year      = {2011},
  url       = {https://doi.org/10.1186/1748-7188-6-5},
  doi       = {10.1186/1748-7188-6-5},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/ApostolicoPU11.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/AzadSNL11,
  author    = {A. K. M. Azad and
               Saima Shahid and
               Nasimul Noman and
               Hyunju Lee},
  title     = {Prediction of plant promoters based on hexamers and random triplet
               pair analysis},
  journal   = {Algorithms Mol. Biol.},
  volume    = {6},
  pages     = {19},
  year      = {2011},
  url       = {https://doi.org/10.1186/1748-7188-6-19},
  doi       = {10.1186/1748-7188-6-19},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/AzadSNL11.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/BernhartMH11,
  author    = {Stephan H. Bernhart and
               Ulrike M{\"{u}}ckstein and
               Ivo L. Hofacker},
  title     = {{RNA} Accessibility in cubic time},
  journal   = {Algorithms Mol. Biol.},
  volume    = {6},
  pages     = {3},
  year      = {2011},
  url       = {https://doi.org/10.1186/1748-7188-6-3},
  doi       = {10.1186/1748-7188-6-3},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/BernhartMH11.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/CarvalhoO11,
  author    = {Alexandra M. Carvalho and
               Arlindo L. Oliveira},
  title     = {{GRISOTTO:} {A} greedy approach to improve combinatorial algorithms
               for motif discovery with prior knowledge},
  journal   = {Algorithms Mol. Biol.},
  volume    = {6},
  pages     = {13},
  year      = {2011},
  url       = {https://doi.org/10.1186/1748-7188-6-13},
  doi       = {10.1186/1748-7188-6-13},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/CarvalhoO11.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/DoanE11,
  author    = {Duong Dai Doan and
               Patricia A. Evans},
  title     = {An {FPT} haplotyping algorithm on pedigrees with a small number of
               sites},
  journal   = {Algorithms Mol. Biol.},
  volume    = {6},
  pages     = {8},
  year      = {2011},
  url       = {https://doi.org/10.1186/1748-7188-6-8},
  doi       = {10.1186/1748-7188-6-8},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/DoanE11.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/DornHKNU11,
  author    = {Britta Dorn and
               Falk H{\"{u}}ffner and
               Dominikus Kr{\"{u}}ger and
               Rolf Niedermeier and
               Johannes Uhlmann},
  title     = {Exploiting bounded signal flow for graph orientation based on cause-effect
               pairs},
  journal   = {Algorithms Mol. Biol.},
  volume    = {6},
  pages     = {21},
  year      = {2011},
  url       = {https://doi.org/10.1186/1748-7188-6-21},
  doi       = {10.1186/1748-7188-6-21},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/DornHKNU11.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/GiancarloU11,
  author    = {Raffaele Giancarlo and
               Filippo Utro},
  title     = {Speeding up the Consensus Clustering methodology for microarray data
               analysis},
  journal   = {Algorithms Mol. Biol.},
  volume    = {6},
  pages     = {1},
  year      = {2011},
  url       = {https://doi.org/10.1186/1748-7188-6-1},
  doi       = {10.1186/1748-7188-6-1},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/GiancarloU11.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/HackenbergCBBAO11,
  author    = {Michael Hackenberg and
               Pedro Carpena and
               Pedro Bernaola{-}Galv{\'{a}}n and
               Guillermo Barturen and
               {\'{A}}ngel M. Alganza and
               Jos{\'{e}} L. Oliver},
  title     = {WordCluster: detecting clusters of {DNA} words and genomic elements},
  journal   = {Algorithms Mol. Biol.},
  volume    = {6},
  pages     = {2},
  year      = {2011},
  url       = {https://doi.org/10.1186/1748-7188-6-2},
  doi       = {10.1186/1748-7188-6-2},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/HackenbergCBBAO11.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/Hosur0B11,
  author    = {Raghavendra Hosur and
               Rohit Singh and
               Bonnie Berger},
  title     = {Sparse estimation for structural variability},
  journal   = {Algorithms Mol. Biol.},
  volume    = {6},
  pages     = {12},
  year      = {2011},
  url       = {https://doi.org/10.1186/1748-7188-6-12},
  doi       = {10.1186/1748-7188-6-12},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/Hosur0B11.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/HsuCL11,
  author    = {Chen{-}Ming Hsu and
               Chien{-}Yu Chen and
               Baw{-}Jhiune Liu},
  title     = {WildSpan: mining structured motifs from protein sequences},
  journal   = {Algorithms Mol. Biol.},
  volume    = {6},
  pages     = {6},
  year      = {2011},
  url       = {https://doi.org/10.1186/1748-7188-6-6},
  doi       = {10.1186/1748-7188-6-6},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/HsuCL11.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/Kirkpatrick11,
  author    = {Bonnie Kirkpatrick},
  title     = {Haplotypes versus genotypes on pedigrees},
  journal   = {Algorithms Mol. Biol.},
  volume    = {6},
  pages     = {10},
  year      = {2011},
  url       = {https://doi.org/10.1186/1748-7188-6-10},
  doi       = {10.1186/1748-7188-6-10},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/Kirkpatrick11.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/LorenzBSTFSH11,
  author    = {Ronny Lorenz and
               Stephan H. Bernhart and
               Christian H{\"{o}}ner zu Siederdissen and
               Hakim Tafer and
               Christoph Flamm and
               Peter F. Stadler and
               Ivo L. Hofacker},
  title     = {ViennaRNA Package 2.0},
  journal   = {Algorithms Mol. Biol.},
  volume    = {6},
  pages     = {26},
  year      = {2011},
  url       = {https://doi.org/10.1186/1748-7188-6-26},
  doi       = {10.1186/1748-7188-6-26},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/LorenzBSTFSH11.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/MehmoodMSWS11,
  author    = {Tahir Mehmood and
               Harald Martens and
               Solve S{\ae}b{\o} and
               Jonas Warringer and
               Lars Snipen},
  title     = {A Partial Least Squares based algorithm for parsimonious variable
               selection},
  journal   = {Algorithms Mol. Biol.},
  volume    = {6},
  pages     = {27},
  year      = {2011},
  url       = {https://doi.org/10.1186/1748-7188-6-27},
  doi       = {10.1186/1748-7188-6-27},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/MehmoodMSWS11.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/NebelSW11,
  author    = {Markus E. Nebel and
               Anika Scheid and
               Frank Weinberg},
  title     = {Random generation of {RNA} secondary structures according to native
               distributions},
  journal   = {Algorithms Mol. Biol.},
  volume    = {6},
  pages     = {24},
  year      = {2011},
  url       = {https://doi.org/10.1186/1748-7188-6-24},
  doi       = {10.1186/1748-7188-6-24},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/NebelSW11.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/NicolaeMMZ11,
  author    = {Marius Nicolae and
               Serghei Mangul and
               Ion I. Mandoiu and
               Alex Zelikovsky},
  title     = {Estimation of alternative splicing isoform frequencies from RNA-Seq
               data},
  journal   = {Algorithms Mol. Biol.},
  volume    = {6},
  pages     = {9},
  year      = {2011},
  url       = {https://doi.org/10.1186/1748-7188-6-9},
  doi       = {10.1186/1748-7188-6-9},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/NicolaeMMZ11.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/NielsenKMP11,
  author    = {Jesper Nielsen and
               Anders K. Kristensen and
               Thomas Mailund and
               Christian N. S. Pedersen},
  title     = {A sub-cubic time algorithm for computing the quartet distance between
               two general trees},
  journal   = {Algorithms Mol. Biol.},
  volume    = {6},
  pages     = {15},
  year      = {2011},
  url       = {https://doi.org/10.1186/1748-7188-6-15},
  doi       = {10.1186/1748-7188-6-15},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/NielsenKMP11.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/OttoHGS11,
  author    = {Christian Otto and
               Steve Hoffmann and
               Jan Gorodkin and
               Peter F. Stadler},
  title     = {Fast local fragment chaining using sum-of-pair gap costs},
  journal   = {Algorithms Mol. Biol.},
  volume    = {6},
  pages     = {4},
  year      = {2011},
  url       = {https://doi.org/10.1186/1748-7188-6-4},
  doi       = {10.1186/1748-7188-6-4},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/OttoHGS11.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/PavlidisPS11,
  author    = {Stelios Pavlidis and
               Annette M. Payne and
               Stephen Swift},
  title     = {Multi-membership gene regulation in pathway based microarray analysis},
  journal   = {Algorithms Mol. Biol.},
  volume    = {6},
  pages     = {22},
  year      = {2011},
  url       = {https://doi.org/10.1186/1748-7188-6-22},
  doi       = {10.1186/1748-7188-6-22},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/PavlidisPS11.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/PolyanovskyRT11,
  author    = {Valery Polyanovsky and
               Mikhail A. Roytberg and
               Vladimir G. Tumanyan},
  title     = {Comparative analysis of the quality of a global algorithm and a local
               algorithm for alignment of two sequences},
  journal   = {Algorithms Mol. Biol.},
  volume    = {6},
  pages     = {25},
  year      = {2011},
  url       = {https://doi.org/10.1186/1748-7188-6-25},
  doi       = {10.1186/1748-7188-6-25},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/PolyanovskyRT11.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/RodionovBRT11,
  author    = {Alex Rodionov and
               Alexandr Bezginov and
               Jonathan Rose and
               Elisabeth R. M. Tillier},
  title     = {A new, fast algorithm for detecting protein coevolution using maximum
               compatible cliques},
  journal   = {Algorithms Mol. Biol.},
  volume    = {6},
  pages     = {17},
  year      = {2011},
  url       = {https://doi.org/10.1186/1748-7188-6-17},
  doi       = {10.1186/1748-7188-6-17},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/RodionovBRT11.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/SerinV11,
  author    = {Akdes Serin and
               Martin Vingron},
  title     = {DeBi: Discovering Differentially Expressed Biclusters using a Frequent
               Itemset Approach},
  journal   = {Algorithms Mol. Biol.},
  volume    = {6},
  pages     = {18},
  year      = {2011},
  url       = {https://doi.org/10.1186/1748-7188-6-18},
  doi       = {10.1186/1748-7188-6-18},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/SerinV11.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/SwensonBS11,
  author    = {Krister M. Swenson and
               Ghada Badr and
               David Sankoff},
  title     = {Listing all sorting reversals in quadratic time},
  journal   = {Algorithms Mol. Biol.},
  volume    = {6},
  pages     = {11},
  year      = {2011},
  url       = {https://doi.org/10.1186/1748-7188-6-11},
  doi       = {10.1186/1748-7188-6-11},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/SwensonBS11.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/SwensonSLW11,
  author    = {M. Shel Swenson and
               Rahul Suri and
               C. Randal Linder and
               Tandy J. Warnow},
  title     = {An experimental study of Quartets MaxCut and other supertree methods},
  journal   = {Algorithms Mol. Biol.},
  volume    = {6},
  pages     = {7},
  year      = {2011},
  url       = {https://doi.org/10.1186/1748-7188-6-7},
  doi       = {10.1186/1748-7188-6-7},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/SwensonSLW11.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/WangWLGFZ11,
  author    = {Huakun Wang and
               Zhenzhen Wang and
               Xia Li and
               Binsheng Gong and
               Lixin Feng and
               Ying Zhou},
  title     = {A robust approach based on Weibull distribution for clustering gene
               expression data},
  journal   = {Algorithms Mol. Biol.},
  volume    = {6},
  pages     = {14},
  year      = {2011},
  url       = {https://doi.org/10.1186/1748-7188-6-14},
  doi       = {10.1186/1748-7188-6-14},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/WangWLGFZ11.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/Yanovsky11,
  author    = {Vladimir Yanovsky},
  title     = {ReCoil - an algorithm for compression of extremely large datasets
               of dna data},
  journal   = {Algorithms Mol. Biol.},
  volume    = {6},
  pages     = {23},
  year      = {2011},
  url       = {https://doi.org/10.1186/1748-7188-6-23},
  doi       = {10.1186/1748-7188-6-23},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/Yanovsky11.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/ZakovTZ11,
  author    = {Shay Zakov and
               Dekel Tsur and
               Michal Ziv{-}Ukelson},
  title     = {Reducing the worst case running times of a family of {RNA} and {CFG}
               problems, using Valiant's approach},
  journal   = {Algorithms Mol. Biol.},
  volume    = {6},
  pages     = {20},
  year      = {2011},
  url       = {https://doi.org/10.1186/1748-7188-6-20},
  doi       = {10.1186/1748-7188-6-20},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/ZakovTZ11.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/ArnoldS10,
  author    = {Christian Arnold and
               Peter F. Stadler},
  title     = {Polynomial algorithms for the Maximal Pairing Problem: efficient phylogenetic
               targeting on arbitrary trees},
  journal   = {Algorithms Mol. Biol.},
  volume    = {5},
  pages     = {25},
  year      = {2010},
  url       = {https://doi.org/10.1186/1748-7188-5-25},
  doi       = {10.1186/1748-7188-5-25},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/ArnoldS10.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/BansalBEF10,
  author    = {Mukul S. Bansal and
               J. Gordon Burleigh and
               Oliver Eulenstein and
               David Fern{\'{a}}ndez{-}Baca},
  title     = {Robinson-Foulds Supertrees},
  journal   = {Algorithms Mol. Biol.},
  volume    = {5},
  pages     = {18},
  year      = {2010},
  url       = {https://doi.org/10.1186/1748-7188-5-18},
  doi       = {10.1186/1748-7188-5-18},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/BansalBEF10.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/BlackshieldsSSWH10,
  author    = {Gordon Blackshields and
               Fabian Sievers and
               Weifeng Shi and
               Andreas Wilm and
               Desmond G. Higgins},
  title     = {Sequence embedding for fast construction of guide trees for multiple
               sequence alignment},
  journal   = {Algorithms Mol. Biol.},
  volume    = {5},
  pages     = {21},
  year      = {2010},
  url       = {https://doi.org/10.1186/1748-7188-5-21},
  doi       = {10.1186/1748-7188-5-21},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/BlackshieldsSSWH10.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/BourguignonSKJM10,
  author    = {Pierre{-}Yves Bourguignon and
               Areejit Samal and
               Fran{\c{c}}ois K{\'{e}}p{\`{e}}s and
               J{\"{u}}rgen Jost and
               Olivier C. Martin},
  title     = {Challenges in experimental data integration within genome-scale metabolic
               models},
  journal   = {Algorithms Mol. Biol.},
  volume    = {5},
  pages     = {20},
  year      = {2010},
  url       = {https://doi.org/10.1186/1748-7188-5-20},
  doi       = {10.1186/1748-7188-5-20},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/BourguignonSKJM10.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/ChiaK10,
  author    = {Burton Chia and
               R. Krishna Murthy Karuturi},
  title     = {Differential co-expression framework to quantify goodness of biclusters
               and compare biclustering algorithms},
  journal   = {Algorithms Mol. Biol.},
  volume    = {5},
  pages     = {23},
  year      = {2010},
  url       = {https://doi.org/10.1186/1748-7188-5-23},
  doi       = {10.1186/1748-7188-5-23},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/ChiaK10.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/ConowFOL10,
  author    = {Chris Conow and
               Daniel Fielder and
               Yaniv Ovadia and
               Ran Libeskind{-}Hadas},
  title     = {Jane: a new tool for the cophylogeny reconstruction problem},
  journal   = {Algorithms Mol. Biol.},
  volume    = {5},
  pages     = {16},
  year      = {2010},
  url       = {https://doi.org/10.1186/1748-7188-5-16},
  doi       = {10.1186/1748-7188-5-16},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/ConowFOL10.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/DongFM10,
  author    = {Jianrong Dong and
               David Fern{\'{a}}ndez{-}Baca and
               Fred R. McMorris},
  title     = {Constructing majority-rule supertrees},
  journal   = {Algorithms Mol. Biol.},
  volume    = {5},
  pages     = {2},
  year      = {2010},
  url       = {https://doi.org/10.1186/1748-7188-5-2},
  doi       = {10.1186/1748-7188-5-2},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/DongFM10.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/FernandesKEWG10,
  author    = {Andrew D. Fernandes and
               Benjamin P. Kleinstiver and
               David R. Edgell and
               Lindi M. Wahl and
               Gregory B. Gloor},
  title     = {Estimating the evidence of selection and the reliability of inference
               in unigenic evolution},
  journal   = {Algorithms Mol. Biol.},
  volume    = {5},
  pages     = {35},
  year      = {2010},
  url       = {https://doi.org/10.1186/1748-7188-5-35},
  doi       = {10.1186/1748-7188-5-35},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/FernandesKEWG10.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/FridG10,
  author    = {Yelena Frid and
               Dan Gusfield},
  title     = {A simple, practical and complete O-time Algorithm for {RNA} folding
               using the Four-Russians Speedup},
  journal   = {Algorithms Mol. Biol.},
  volume    = {5},
  pages     = {13},
  year      = {2010},
  url       = {https://doi.org/10.1186/1748-7188-5-13},
  doi       = {10.1186/1748-7188-5-13},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/FridG10.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/GaoLR10,
  author    = {James Z. M. Gao and
               Linda Y. M. Li and
               Christian M. Reidys},
  title     = {Inverse folding of {RNA} pseudoknot structures},
  journal   = {Algorithms Mol. Biol.},
  volume    = {5},
  pages     = {27},
  year      = {2010},
  url       = {https://doi.org/10.1186/1748-7188-5-27},
  doi       = {10.1186/1748-7188-5-27},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/GaoLR10.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/GirdeaNK10,
  author    = {Marta G{\^{\i}}rdea and
               Laurent No{\'{e}} and
               Gregory Kucherov},
  title     = {Back-translation for discovering distant protein homologies in the
               presence of frameshift mutations},
  journal   = {Algorithms Mol. Biol.},
  volume    = {5},
  pages     = {6},
  year      = {2010},
  url       = {https://doi.org/10.1186/1748-7188-5-6},
  doi       = {10.1186/1748-7188-5-6},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/GirdeaNK10.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/Guerrero-FernandezBVCC10,
  author    = {Dar{\'{\i}}o Guerrero{-}Fern{\'{a}}ndez and
               Roc{\'{\i}}o Bautista and
               David P. Villalobos and
               Francisco R. Cant{\'{o}}n and
               M. Gonzalo Claros},
  title     = {AlignMiner: a Web-based tool for detection of divergent regions in
               multiple sequence alignments of conserved sequences},
  journal   = {Algorithms Mol. Biol.},
  volume    = {5},
  pages     = {24},
  year      = {2010},
  url       = {https://doi.org/10.1186/1748-7188-5-24},
  doi       = {10.1186/1748-7188-5-24},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/Guerrero-FernandezBVCC10.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/HancockM10,
  author    = {Timothy Hancock and
               Hiroshi Mamitsuka},
  title     = {A markov classification model for metabolic pathways},
  journal   = {Algorithms Mol. Biol.},
  volume    = {5},
  pages     = {10},
  year      = {2010},
  url       = {https://doi.org/10.1186/1748-7188-5-10},
  doi       = {10.1186/1748-7188-5-10},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/HancockM10.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/HansenESH10,
  author    = {Matthew Hansen and
               Logan Everett and
               Larry N. Singh and
               Sridhar Hannenhalli},
  title     = {Mimosa: Mixture model of co-expression to detect modulators of regulatory
               interaction},
  journal   = {Algorithms Mol. Biol.},
  volume    = {5},
  pages     = {4},
  year      = {2010},
  url       = {https://doi.org/10.1186/1748-7188-5-4},
  doi       = {10.1186/1748-7188-5-4},
  timestamp = {Sun, 21 Jun 2020 01:00:00 +0200},
  biburl    = {https://dblp.org/rec/journals/almob/HansenESH10.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/HusemannS10,
  author    = {Peter Husemann and
               Jens Stoye},
  title     = {Phylogenetic comparative assembly},
  journal   = {Algorithms Mol. Biol.},
  volume    = {5},
  pages     = {3},
  year      = {2010},
  url       = {https://doi.org/10.1186/1748-7188-5-3},
  doi       = {10.1186/1748-7188-5-3},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/HusemannS10.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/JunierHK10,
  author    = {Ivan Junier and
               Joan H{\'{e}}risson and
               Fran{\c{c}}ois K{\'{e}}p{\`{e}}s},
  title     = {Periodic pattern detection in sparse boolean sequences},
  journal   = {Algorithms Mol. Biol.},
  volume    = {5},
  pages     = {31},
  year      = {2010},
  url       = {https://doi.org/10.1186/1748-7188-5-31},
  doi       = {10.1186/1748-7188-5-31},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/JunierHK10.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/KahnMR10,
  author    = {Crystal L. Kahn and
               Shay Mozes and
               Benjamin J. Raphael},
  title     = {Efficient algorithms for analyzing segmental duplications with deletions
               and inversions in genomes},
  journal   = {Algorithms Mol. Biol.},
  volume    = {5},
  pages     = {11},
  year      = {2010},
  url       = {https://doi.org/10.1186/1748-7188-5-11},
  doi       = {10.1186/1748-7188-5-11},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/KahnMR10.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/KimSVB10,
  author    = {Ethan Kim and
               Ashish Sabharwal and
               Adrian Vetta and
               Mathieu Blanchette},
  title     = {Predicting direct protein interactions from affinity purification
               mass spectrometry data},
  journal   = {Algorithms Mol. Biol.},
  volume    = {5},
  pages     = {34},
  year      = {2010},
  url       = {https://doi.org/10.1186/1748-7188-5-34},
  doi       = {10.1186/1748-7188-5-34},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/KimSVB10.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/KristensenNP10,
  author    = {Thomas Greve Kristensen and
               Jesper Nielsen and
               Christian N. S. Pedersen},
  title     = {A tree-based method for the rapid screening of chemical fingerprints},
  journal   = {Algorithms Mol. Biol.},
  volume    = {5},
  pages     = {9},
  year      = {2010},
  url       = {https://doi.org/10.1186/1748-7188-5-9},
  doi       = {10.1186/1748-7188-5-9},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/KristensenNP10.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/KupczokSH10,
  author    = {Anne Kupczok and
               Heiko A. Schmidt and
               Arndt von Haeseler},
  title     = {Accuracy of phylogeny reconstruction methods combining overlapping
               gene data sets},
  journal   = {Algorithms Mol. Biol.},
  volume    = {5},
  pages     = {37},
  year      = {2010},
  url       = {https://doi.org/10.1186/1748-7188-5-37},
  doi       = {10.1186/1748-7188-5-37},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/KupczokSH10.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/LamM10,
  author    = {Tin Yin Lam and
               Irmtraud M. Meyer},
  title     = {Efficient algorithms for training the parameters of hidden Markov
               models using stochastic expectation maximization {(EM)} training and
               Viterbi training},
  journal   = {Algorithms Mol. Biol.},
  volume    = {5},
  pages     = {38},
  year      = {2010},
  url       = {https://doi.org/10.1186/1748-7188-5-38},
  doi       = {10.1186/1748-7188-5-38},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/LamM10.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/LiuMHM10,
  author    = {Zhenqiu Liu and
               Laurence S. Magder and
               Terry Hyslop and
               Li Mao},
  title     = {Survival associated pathway identification with group L\({}_{\mbox{p
               }}\)penalized global {AUC} maximization},
  journal   = {Algorithms Mol. Biol.},
  volume    = {5},
  pages     = {30},
  year      = {2010},
  url       = {https://doi.org/10.1186/1748-7188-5-30},
  doi       = {10.1186/1748-7188-5-30},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/LiuMHM10.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/MazinGMRRRK10,
  author    = {Pavel V. Mazin and
               Mikhail S. Gelfand and
               Andrey A. Mironov and
               Aleksandra B. Rakhmaninova and
               Anatoly R. Rubinov and
               Robert B. Russell and
               Olga V. Kalinina},
  title     = {An automated stochastic approach to the identification of the protein
               specificity determinants and functional subfamilies},
  journal   = {Algorithms Mol. Biol.},
  volume    = {5},
  pages     = {29},
  year      = {2010},
  url       = {https://doi.org/10.1186/1748-7188-5-29},
  doi       = {10.1186/1748-7188-5-29},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/MazinGMRRRK10.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/MohlSWBS10,
  author    = {Mathias M{\"{o}}hl and
               Raheleh Salari and
               Sebastian Will and
               Rolf Backofen and
               S{\"{u}}leyman Cenk Sahinalp},
  title     = {Sparsification of {RNA} structure prediction including pseudoknots},
  journal   = {Algorithms Mol. Biol.},
  volume    = {5},
  pages     = {39},
  year      = {2010},
  url       = {https://doi.org/10.1186/1748-7188-5-39},
  doi       = {10.1186/1748-7188-5-39},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/MohlSWBS10.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/NguyenSEM10,
  author    = {Binh T. Nguyen and
               Andreas Spillner and
               Brent C. Emerson and
               Vincent Moulton},
  title     = {Distinguishing between hot-spots and melting-pots of genetic diversity
               using haplotype connectivity},
  journal   = {Algorithms Mol. Biol.},
  volume    = {5},
  pages     = {19},
  year      = {2010},
  url       = {https://doi.org/10.1186/1748-7188-5-19},
  doi       = {10.1186/1748-7188-5-19},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/NguyenSEM10.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/NuelRMC10,
  author    = {Gr{\'{e}}gory Nuel and
               Leslie Regad and
               Juliette Martin and
               Anne{-}Claude Camproux},
  title     = {Exact distribution of a pattern in a set of random sequences generated
               by a Markov source: applications to biological data},
  journal   = {Algorithms Mol. Biol.},
  volume    = {5},
  pages     = {15},
  year      = {2010},
  url       = {https://doi.org/10.1186/1748-7188-5-15},
  doi       = {10.1186/1748-7188-5-15},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/NuelRMC10.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/PlanatscherSPSJTZ10,
  author    = {Hannes Planatscher and
               Jochen Supper and
               Oliver Poetz and
               Dieter Stoll and
               Thomas Joos and
               Markus F. Templin and
               Andreas Zell},
  title     = {Optimal selection of epitopes for TXP-immunoaffinity mass spectrometry},
  journal   = {Algorithms Mol. Biol.},
  volume    = {5},
  pages     = {28},
  year      = {2010},
  url       = {https://doi.org/10.1186/1748-7188-5-28},
  doi       = {10.1186/1748-7188-5-28},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/PlanatscherSPSJTZ10.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/SalariBS10,
  author    = {Raheleh Salari and
               Rolf Backofen and
               S{\"{u}}leyman Cenk Sahinalp},
  title     = {Fast prediction of {RNA-RNA} interaction},
  journal   = {Algorithms Mol. Biol.},
  volume    = {5},
  pages     = {5},
  year      = {2010},
  url       = {https://doi.org/10.1186/1748-7188-5-5},
  doi       = {10.1186/1748-7188-5-5},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/SalariBS10.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/SalemZB10,
  author    = {Saeed Salem and
               Mohammed J. Zaki and
               Chris Bystroff},
  title     = {FlexSnap: Flexible Non-sequential Protein Structure Alignment},
  journal   = {Algorithms Mol. Biol.},
  volume    = {5},
  pages     = {12},
  year      = {2010},
  url       = {https://doi.org/10.1186/1748-7188-5-12},
  doi       = {10.1186/1748-7188-5-12},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/SalemZB10.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/SeemannRGB10,
  author    = {Stefan E. Seemann and
               Andreas S. Richter and
               Jan Gorodkin and
               Rolf Backofen},
  title     = {Hierarchical folding of multiple sequence alignments for the prediction
               of structures and {RNA-RNA} interactions},
  journal   = {Algorithms Mol. Biol.},
  volume    = {5},
  pages     = {22},
  year      = {2010},
  url       = {https://doi.org/10.1186/1748-7188-5-22},
  doi       = {10.1186/1748-7188-5-22},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/SeemannRGB10.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/ShibuyaJS10,
  author    = {Tetsuo Shibuya and
               Jesper Jansson and
               Kunihiko Sadakane},
  title     = {Linear-time protein 3-D structure searching with insertions and deletions},
  journal   = {Algorithms Mol. Biol.},
  volume    = {5},
  pages     = {7},
  year      = {2010},
  url       = {https://doi.org/10.1186/1748-7188-5-7},
  doi       = {10.1186/1748-7188-5-7},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/ShibuyaJS10.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/SundbergCS10,
  author    = {Kenneth Sundberg and
               Mark J. Clement and
               Quinn Snell},
  title     = {On the use of cartographic projections in visualizing phylo-genetic
               tree space},
  journal   = {Algorithms Mol. Biol.},
  volume    = {5},
  pages     = {26},
  year      = {2010},
  url       = {https://doi.org/10.1186/1748-7188-5-26},
  doi       = {10.1186/1748-7188-5-26},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/SundbergCS10.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/SwensonBWL10,
  author    = {M. Shel Swenson and
               Fran{\c{c}}ois Barban{\c{c}}on and
               Tandy J. Warnow and
               C. Randal Linder},
  title     = {A simulation study comparing supertree and combined analysis methods
               using SMIDGen},
  journal   = {Algorithms Mol. Biol.},
  volume    = {5},
  pages     = {8},
  year      = {2010},
  url       = {https://doi.org/10.1186/1748-7188-5-8},
  doi       = {10.1186/1748-7188-5-8},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/SwensonBWL10.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/TianDK10,
  author    = {Ye Tian and
               Christopher Deutsch and
               Bala Krishnamoorthy},
  title     = {Scoring function to predict solubility mutagenesis},
  journal   = {Algorithms Mol. Biol.},
  volume    = {5},
  pages     = {33},
  year      = {2010},
  url       = {https://doi.org/10.1186/1748-7188-5-33},
  doi       = {10.1186/1748-7188-5-33},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/TianDK10.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/WaaijenborgZ10,
  author    = {Sandra Waaijenborg and
               Aeilko H. Zwinderman},
  title     = {Association of repeatedly measured intermediate risk factors for complex
               diseases with high dimensional {SNP} data},
  journal   = {Algorithms Mol. Biol.},
  volume    = {5},
  pages     = {17},
  year      = {2010},
  url       = {https://doi.org/10.1186/1748-7188-5-17},
  doi       = {10.1186/1748-7188-5-17},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/WaaijenborgZ10.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/XuBPT10,
  author    = {Gang Xu and
               Laura Bennett and
               Lazaros G. Papageorgiou and
               Sophia Tsoka},
  title     = {Module detection in complex networks using integer optimisation},
  journal   = {Algorithms Mol. Biol.},
  volume    = {5},
  pages     = {36},
  year      = {2010},
  url       = {https://doi.org/10.1186/1748-7188-5-36},
  doi       = {10.1186/1748-7188-5-36},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/XuBPT10.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/YaoL10,
  author    = {Bangpeng Yao and
               Shao Li},
  title     = {{ANMM4CBR:} a case-based reasoning method for gene expression data
               classification},
  journal   = {Algorithms Mol. Biol.},
  volume    = {5},
  pages     = {14},
  year      = {2010},
  url       = {https://doi.org/10.1186/1748-7188-5-14},
  doi       = {10.1186/1748-7188-5-14},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/YaoL10.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/ZhangM10,
  author    = {Xiuwei Zhang and
               Bernard M. E. Moret},
  title     = {Refining transcriptional regulatory networks using network evolutionary
               models and gene histories},
  journal   = {Algorithms Mol. Biol.},
  volume    = {5},
  pages     = {1},
  year      = {2010},
  url       = {https://doi.org/10.1186/1748-7188-5-1},
  doi       = {10.1186/1748-7188-5-1},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/ZhangM10.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/ZhengLZLW10,
  author    = {Ming Zheng and
               Guixia Liu and
               Chunguang Zhou and
               Yanchun Liang and
               Yan Wang},
  title     = {Gravitation field algorithm and its application in gene cluster},
  journal   = {Algorithms Mol. Biol.},
  volume    = {5},
  pages     = {32},
  year      = {2010},
  url       = {https://doi.org/10.1186/1748-7188-5-32},
  doi       = {10.1186/1748-7188-5-32},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/ZhengLZLW10.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/BhadraBCM09,
  author    = {Sahely Bhadra and
               Chiranjib Bhattacharyya and
               Nagasuma R. Chandra and
               I. Saira Mian},
  title     = {A linear programming approach for estimating the structure of a sparse
               linear genetic network from transcript profiling data},
  journal   = {Algorithms Mol. Biol.},
  volume    = {4},
  year      = {2009},
  url       = {https://doi.org/10.1186/1748-7188-4-5},
  doi       = {10.1186/1748-7188-4-5},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/BhadraBCM09.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/BragaGS09,
  author    = {Mar{\'{\i}}lia D. V. Braga and
               Christian Gautier and
               Marie{-}France Sagot},
  title     = {An asymmetric approach to preserve common intervals while sorting
               by reversals},
  journal   = {Algorithms Mol. Biol.},
  volume    = {4},
  pages     = {16},
  year      = {2009},
  url       = {https://doi.org/10.1186/1748-7188-4-16},
  doi       = {10.1186/1748-7188-4-16},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/BragaGS09.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/FariselliSMC09,
  author    = {Piero Fariselli and
               Castrense Savojardo and
               Pier Luigi Martelli and
               Rita Casadio},
  title     = {Grammatical-Restrained Hidden Conditional Random Fields for Bioinformatics
               applications},
  journal   = {Algorithms Mol. Biol.},
  volume    = {4},
  pages     = {13},
  year      = {2009},
  url       = {https://doi.org/10.1186/1748-7188-4-13},
  doi       = {10.1186/1748-7188-4-13},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/FariselliSMC09.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/HoJG09,
  author    = {Eric S. Ho and
               Christopher D. Jakubowski and
               Samuel I. Gunderson},
  title     = {iTriplet, a rule-based nucleic acid sequence motif finder},
  journal   = {Algorithms Mol. Biol.},
  volume    = {4},
  pages     = {14},
  year      = {2009},
  url       = {https://doi.org/10.1186/1748-7188-4-14},
  doi       = {10.1186/1748-7188-4-14},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/HoJG09.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/IvryMASB09,
  author    = {Tor Ivry and
               Shahar Michal and
               Assaf Avihoo and
               Guillermo Sapiro and
               Danny Barash},
  title     = {An image processing approach to computing distances between {RNA}
               secondary structures dot plots},
  journal   = {Algorithms Mol. Biol.},
  volume    = {4},
  year      = {2009},
  url       = {https://doi.org/10.1186/1748-7188-4-4},
  doi       = {10.1186/1748-7188-4-4},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/IvryMASB09.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/KadotaNS09,
  author    = {Koji Kadota and
               Yuji Nakai and
               Kentaro Shimizu},
  title     = {Ranking differentially expressed genes from Affymetrix gene expression
               data: methods with reproducibility, sensitivity, and specificity},
  journal   = {Algorithms Mol. Biol.},
  volume    = {4},
  year      = {2009},
  url       = {https://doi.org/10.1186/1748-7188-4-7},
  doi       = {10.1186/1748-7188-4-7},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/KadotaNS09.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/KimP09,
  author    = {Dae{-}Won Kim and
               Hong{-}Seog Park},
  title     = {Review of "Bioinformatics: {A} Computing Perspective" edited by Shuba
               Gopal, Anne Haake, Rhys Price Jones and Paul Tymann},
  journal   = {Algorithms Mol. Biol.},
  volume    = {4},
  year      = {2009},
  url       = {https://doi.org/10.1186/1748-7188-4-9},
  doi       = {10.1186/1748-7188-4-9},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/KimP09.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/KrollBC09,
  author    = {K. Myriam Kroll and
               Gerard T. Barkema and
               Enrico Carlon},
  title     = {Linear model for fast background subtraction in oligonucleotide microarrays},
  journal   = {Algorithms Mol. Biol.},
  volume    = {4},
  pages     = {15},
  year      = {2009},
  url       = {https://doi.org/10.1186/1748-7188-4-15},
  doi       = {10.1186/1748-7188-4-15},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/KrollBC09.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/LangdonH09,
  author    = {William B. Langdon and
               Andrew P. Harrison},
  title     = {Evolving {DNA} motifs to predict GeneChip probe performance},
  journal   = {Algorithms Mol. Biol.},
  volume    = {4},
  year      = {2009},
  url       = {https://doi.org/10.1186/1748-7188-4-6},
  doi       = {10.1186/1748-7188-4-6},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/LangdonH09.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/MadeiraO09,
  author    = {Sara C. Madeira and
               Arlindo L. Oliveira},
  title     = {A polynomial time biclustering algorithm for finding approximate expression
               patterns in gene expression time series},
  journal   = {Algorithms Mol. Biol.},
  volume    = {4},
  year      = {2009},
  url       = {https://doi.org/10.1186/1748-7188-4-8},
  doi       = {10.1186/1748-7188-4-8},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/MadeiraO09.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/MosigJWNEPC09,
  author    = {Axel Mosig and
               Stefan J{\"{a}}ger and
               Chaofeng Wang and
               Sumit Kumar Nath and
               Ilker Ersoy and
               Kannappan Palaniappan and
               Su{-}Shing Chen},
  title     = {Tracking cells in Life Cell Imaging videos using topological alignments},
  journal   = {Algorithms Mol. Biol.},
  volume    = {4},
  year      = {2009},
  url       = {https://doi.org/10.1186/1748-7188-4-10},
  doi       = {10.1186/1748-7188-4-10},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/MosigJWNEPC09.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/PeterlongoSLPS09,
  author    = {Pierre Peterlongo and
               Gustavo Akio Tominaga Sacomoto and
               Alair Pereira do Lago and
               Nadia Pisanti and
               Marie{-}France Sagot},
  title     = {Lossless filter for multiple repeats with bounded edit distance},
  journal   = {Algorithms Mol. Biol.},
  volume    = {4},
  year      = {2009},
  url       = {https://doi.org/10.1186/1748-7188-4-3},
  doi       = {10.1186/1748-7188-4-3},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/PeterlongoSLPS09.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/SainudiinY09,
  author    = {Raazesh Sainudiin and
               Thomas L. York},
  title     = {Auto-validating von Neumann rejection sampling from small phylogenetic
               tree spaces},
  journal   = {Algorithms Mol. Biol.},
  volume    = {4},
  year      = {2009},
  url       = {https://doi.org/10.1186/1748-7188-4-1},
  doi       = {10.1186/1748-7188-4-1},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/SainudiinY09.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/WangDYLL09,
  author    = {Zhen Wang and
               Guohui Ding and
               Zhong{-}Hao Yu and
               Lei Liu and
               Yixue Li},
  title     = {CHSMiner: a {GUI} tool to identify chromosomal homologous segments},
  journal   = {Algorithms Mol. Biol.},
  volume    = {4},
  year      = {2009},
  url       = {https://doi.org/10.1186/1748-7188-4-2},
  doi       = {10.1186/1748-7188-4-2},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/WangDYLL09.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/WenWBLCFWSKW09,
  author    = {Sheron Wen and
               Chenguang Wang and
               Arthur Berg and
               Yao Li and
               Myron M. Chang and
               Roger B. Fillingim and
               Margaret R. Wallace and
               Roland Staud and
               Lee Kaplan and
               Rongling Wu},
  title     = {Modeling genetic imprinting effects of {DNA} sequences with multilocus
               polymorphism data},
  journal   = {Algorithms Mol. Biol.},
  volume    = {4},
  year      = {2009},
  url       = {https://doi.org/10.1186/1748-7188-4-11},
  doi       = {10.1186/1748-7188-4-11},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/WenWBLCFWSKW09.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/ZahoranszkyKHMZZ09,
  author    = {L{\'{a}}szl{\'{o}} A. Zahor{\'{a}}nszky and
               Gyula Y. Katona and
               P{\'{e}}ter H{\'{a}}ri and
               Andr{\'{a}}s M{\'{a}}ln{\'{a}}si{-}Csizmadia and
               Katharina Anna Zweig and
               Gergely Zahor{\'{a}}nszky{-}K{\"{o}}halmi},
  title     = {Breaking the hierarchy - a new cluster selection mechanism for hierarchical
               clustering methods},
  journal   = {Algorithms Mol. Biol.},
  volume    = {4},
  pages     = {12},
  year      = {2009},
  url       = {https://doi.org/10.1186/1748-7188-4-12},
  doi       = {10.1186/1748-7188-4-12},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/ZahoranszkyKHMZZ09.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/ApostolicoD08,
  author    = {Alberto Apostolico and
               Olgert Denas},
  title     = {Fast algorithms for computing sequence distances by exhaustive substring
               composition},
  journal   = {Algorithms Mol. Biol.},
  volume    = {3},
  year      = {2008},
  url       = {https://doi.org/10.1186/1748-7188-3-13},
  doi       = {10.1186/1748-7188-3-13},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/ApostolicoD08.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/BinderKP08,
  author    = {Hans Binder and
               Knut Krohn and
               Stephan Preibisch},
  title     = {"Hook"-calibration of GeneChip-microarrays: Chip characteristics and
               expression measures},
  journal   = {Algorithms Mol. Biol.},
  volume    = {3},
  year      = {2008},
  url       = {https://doi.org/10.1186/1748-7188-3-11},
  doi       = {10.1186/1748-7188-3-11},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/BinderKP08.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/BinderP08,
  author    = {Hans Binder and
               Stephan Preibisch},
  title     = {"Hook"-calibration of GeneChip-microarrays: Theory and algorithm},
  journal   = {Algorithms Mol. Biol.},
  volume    = {3},
  year      = {2008},
  url       = {https://doi.org/10.1186/1748-7188-3-12},
  doi       = {10.1186/1748-7188-3-12},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/BinderP08.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/DressFFGKPS08,
  author    = {Andreas W. M. Dress and
               Christoph Flamm and
               Guido Fritzsch and
               Stefan Gr{\"{u}}newald and
               Matthias Kruspe and
               Sonja J. Prohaska and
               Peter F. Stadler},
  title     = {Noisy: Identification of problematic columns in multiple sequence
               alignments},
  journal   = {Algorithms Mol. Biol.},
  volume    = {3},
  year      = {2008},
  url       = {https://doi.org/10.1186/1748-7188-3-7},
  doi       = {10.1186/1748-7188-3-7},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/DressFFGKPS08.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/EickmeyerHPY08,
  author    = {Kord Eickmeyer and
               Peter Huggins and
               Lior Pachter and
               Ruriko Yoshida},
  title     = {On the optimality of the neighbor-joining algorithm},
  journal   = {Algorithms Mol. Biol.},
  volume    = {3},
  year      = {2008},
  url       = {https://doi.org/10.1186/1748-7188-3-5},
  doi       = {10.1186/1748-7188-3-5},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/EickmeyerHPY08.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/KadotaNS08,
  author    = {Koji Kadota and
               Yuji Nakai and
               Kentaro Shimizu},
  title     = {A weighted average difference method for detecting differentially
               expressed genes from microarray data},
  journal   = {Algorithms Mol. Biol.},
  volume    = {3},
  year      = {2008},
  url       = {https://doi.org/10.1186/1748-7188-3-8},
  doi       = {10.1186/1748-7188-3-8},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/KadotaNS08.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/MeinickeLKFGFKM08,
  author    = {Peter Meinicke and
               Thomas Lingner and
               Alexander Kaever and
               Kirstin Feussner and
               Cornelia G{\"{o}}bel and
               Ivo Feussner and
               Petr Karlovsky and
               Burkhard Morgenstern},
  title     = {Metabolite-based clustering and visualization of mass spectrometry
               data using one-dimensional self-organizing maps},
  journal   = {Algorithms Mol. Biol.},
  volume    = {3},
  year      = {2008},
  url       = {https://doi.org/10.1186/1748-7188-3-9},
  doi       = {10.1186/1748-7188-3-9},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/MeinickeLKFGFKM08.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/MoxonMK08,
  author    = {Simon Moxon and
               Vincent Moulton and
               Jan T. Kim},
  title     = {A scoring matrix approach to detecting miRNA target sites},
  journal   = {Algorithms Mol. Biol.},
  volume    = {3},
  year      = {2008},
  url       = {https://doi.org/10.1186/1748-7188-3-3},
  doi       = {10.1186/1748-7188-3-3},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/MoxonMK08.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/RodelspergerD08,
  author    = {Christian R{\"{o}}delsperger and
               Christoph Dieterich},
  title     = {Syntenator: Multiple gene order alignments with a gene-specific scoring
               function},
  journal   = {Algorithms Mol. Biol.},
  volume    = {3},
  year      = {2008},
  url       = {https://doi.org/10.1186/1748-7188-3-14},
  doi       = {10.1186/1748-7188-3-14},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/RodelspergerD08.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/RuanCKCKP08,
  author    = {Jishou Ruan and
               Hanzhe Chen and
               Lukasz A. Kurgan and
               Ke Chen and
               Chunsheng Kang and
               Peiyu Pu},
  title     = {HuMiTar: {A} sequence-based method for prediction of human microRNA
               targets},
  journal   = {Algorithms Mol. Biol.},
  volume    = {3},
  year      = {2008},
  url       = {https://doi.org/10.1186/1748-7188-3-16},
  doi       = {10.1186/1748-7188-3-16},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/RuanCKCKP08.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/SchenkMT08,
  author    = {Gundolf Schenk and
               Thomas Margraf and
               Andrew E. Torda},
  title     = {Protein sequence and structure alignments within one framework},
  journal   = {Algorithms Mol. Biol.},
  volume    = {3},
  year      = {2008},
  url       = {https://doi.org/10.1186/1748-7188-3-4},
  doi       = {10.1186/1748-7188-3-4},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/SchenkMT08.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/SubramanianKM08,
  author    = {Amarendran R. Subramanian and
               Michael Kaufmann and
               Burkhard Morgenstern},
  title     = {{DIALIGN-TX:} greedy and progressive approaches for segment-based
               multiple sequence alignment},
  journal   = {Algorithms Mol. Biol.},
  volume    = {3},
  year      = {2008},
  url       = {https://doi.org/10.1186/1748-7188-3-6},
  doi       = {10.1186/1748-7188-3-6},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/SubramanianKM08.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/Tostesen08,
  author    = {Eivind T{\o}stesen},
  title     = {A stitch in time: Efficient computation of genomic {DNA} melting bubbles},
  journal   = {Algorithms Mol. Biol.},
  volume    = {3},
  year      = {2008},
  url       = {https://doi.org/10.1186/1748-7188-3-10},
  doi       = {10.1186/1748-7188-3-10},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/Tostesen08.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/WagnerMD08,
  author    = {Holger Wagner and
               Burkhard Morgenstern and
               Andreas W. M. Dress},
  title     = {Stability of multiple alignments and phylogenetic trees: an analysis
               of ABC-transporter proteins family},
  journal   = {Algorithms Mol. Biol.},
  volume    = {3},
  year      = {2008},
  url       = {https://doi.org/10.1186/1748-7188-3-15},
  doi       = {10.1186/1748-7188-3-15},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/WagnerMD08.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/WuKLY08,
  author    = {Gang Wu and
               Ming{-}Yang Kao and
               Guohui Lin and
               Jia{-}Huai You},
  title     = {Reconstructing phylogenies from noisy quartets in polynomial time
               with a high success probability},
  journal   = {Algorithms Mol. Biol.},
  volume    = {3},
  year      = {2008},
  url       = {https://doi.org/10.1186/1748-7188-3-1},
  doi       = {10.1186/1748-7188-3-1},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/WuKLY08.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/YousefJSS08,
  author    = {Malik Yousef and
               Segun Jung and
               Louise C. Showe and
               Michael K. Showe},
  title     = {Learning from positive examples when the negative class is undetermined-
               microRNA gene identification},
  journal   = {Algorithms Mol. Biol.},
  volume    = {3},
  year      = {2008},
  url       = {https://doi.org/10.1186/1748-7188-3-2},
  doi       = {10.1186/1748-7188-3-2},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/YousefJSS08.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/BoevaCRRM07,
  author    = {Valentina Boeva and
               Julien Cl{\'{e}}ment and
               Mireille R{\'{e}}gnier and
               Mikhail A. Roytberg and
               Vsevolod J. Makeev},
  title     = {Exact p-value calculation for heterotypic clusters of regulatory motifs
               and its application in computational annotation of \emph{cis}-regulatory
               modules},
  journal   = {Algorithms Mol. Biol.},
  volume    = {2},
  year      = {2007},
  url       = {https://doi.org/10.1186/1748-7188-2-13},
  doi       = {10.1186/1748-7188-2-13},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/BoevaCRRM07.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/BryantMS07,
  author    = {David Bryant and
               Vincent Moulton and
               Andreas Spillner},
  title     = {Consistency of the Neighbor-Net Algorithm},
  journal   = {Algorithms Mol. Biol.},
  volume    = {2},
  year      = {2007},
  url       = {https://doi.org/10.1186/1748-7188-2-8},
  doi       = {10.1186/1748-7188-2-8},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/BryantMS07.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/CarmackMNL07,
  author    = {C. Steven Carmack and
               Lee Ann McCue and
               Lee Aaron Newberg and
               Charles E. Lawrence},
  title     = {PhyloScan: identification of transcription factor binding sites using
               cross-species evidence},
  journal   = {Algorithms Mol. Biol.},
  volume    = {2},
  year      = {2007},
  url       = {https://doi.org/10.1186/1748-7188-2-1},
  doi       = {10.1186/1748-7188-2-1},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/CarmackMNL07.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/DidierG07,
  author    = {Gilles Didier and
               Carito Guziolowski},
  title     = {Mapping sequences by parts},
  journal   = {Algorithms Mol. Biol.},
  volume    = {2},
  year      = {2007},
  url       = {https://doi.org/10.1186/1748-7188-2-11},
  doi       = {10.1186/1748-7188-2-11},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/DidierG07.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/FerreiraA07,
  author    = {Pedro Gabriel Ferreira and
               Paulo J. Azevedo},
  title     = {Evaluating deterministic motif significance measures in protein databases},
  journal   = {Algorithms Mol. Biol.},
  volume    = {2},
  year      = {2007},
  url       = {https://doi.org/10.1186/1748-7188-2-16},
  doi       = {10.1186/1748-7188-2-16},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/FerreiraA07.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/GiancarloSSU07,
  author    = {Raffaele Giancarlo and
               Alessandro Siragusa and
               Enrico Siragusa and
               Filippo Utro},
  title     = {A basic analysis toolkit for biological sequences},
  journal   = {Algorithms Mol. Biol.},
  volume    = {2},
  year      = {2007},
  url       = {https://doi.org/10.1186/1748-7188-2-10},
  doi       = {10.1186/1748-7188-2-10},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/GiancarloSSU07.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/Gouveia-OliveiraP07,
  author    = {Rodrigo Gouveia{-}Oliveira and
               Anders Gorm Pedersen},
  title     = {Finding coevolving amino acid residues using row and column weighting
               of mutual information and multi-dimensional amino acid representation},
  journal   = {Algorithms Mol. Biol.},
  volume    = {2},
  year      = {2007},
  url       = {https://doi.org/10.1186/1748-7188-2-12},
  doi       = {10.1186/1748-7188-2-12},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/Gouveia-OliveiraP07.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/KadotaANA07,
  author    = {Koji Kadota and
               Ryoko Araki and
               Yuji Nakai and
               Masumi Abe},
  title     = {{GOGOT:} a method for the identification of differentially expressed
               fragments from cDNA-AFLP data},
  journal   = {Algorithms Mol. Biol.},
  volume    = {2},
  year      = {2007},
  url       = {https://doi.org/10.1186/1748-7188-2-5},
  doi       = {10.1186/1748-7188-2-5},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/KadotaANA07.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/OoiCT07,
  author    = {Chia Huey Ooi and
               Madhu Chetty and
               Shyh Wei Teng},
  title     = {Characteristics of predictor sets found using differential prioritization},
  journal   = {Algorithms Mol. Biol.},
  volume    = {2},
  year      = {2007},
  url       = {https://doi.org/10.1186/1748-7188-2-7},
  doi       = {10.1186/1748-7188-2-7},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/OoiCT07.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/ReicheS07,
  author    = {Kristin Reiche and
               Peter F. Stadler},
  title     = {RNAstrand: reading direction of structured RNAs in multiple sequence
               alignments},
  journal   = {Algorithms Mol. Biol.},
  volume    = {2},
  year      = {2007},
  url       = {https://doi.org/10.1186/1748-7188-2-6},
  doi       = {10.1186/1748-7188-2-6},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/ReicheS07.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/Spillner07,
  author    = {Andreas Spillner},
  title     = {Review of "Reconstructing Evolution: New mathematical and computational
               advances" edited by Olivier Gascuel and Mike Steel},
  journal   = {Algorithms Mol. Biol.},
  volume    = {2},
  year      = {2007},
  url       = {https://doi.org/10.1186/1748-7188-2-14},
  doi       = {10.1186/1748-7188-2-14},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/Spillner07.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/SunTHESTO07,
  author    = {Jingjun Sun and
               Kagan Tuncay and
               Alaa Abi{-}Haidar and
               Lisa Ensman and
               Frank Stanley and
               Michael Trelinski and
               Peter J. Ortoleva},
  title     = {Transcriptional regulatory network discovery via multiple method integration:
               application to \emph{e. coli }K12},
  journal   = {Algorithms Mol. Biol.},
  volume    = {2},
  year      = {2007},
  url       = {https://doi.org/10.1186/1748-7188-2-2},
  doi       = {10.1186/1748-7188-2-2},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/SunTHESTO07.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/TouzetV07,
  author    = {H{\'{e}}l{\`{e}}ne Touzet and
               Jean{-}St{\'{e}}phane Varr{\'{e}}},
  title     = {Efficient and accurate P-value computation for Position Weight Matrices},
  journal   = {Algorithms Mol. Biol.},
  volume    = {2},
  year      = {2007},
  url       = {https://doi.org/10.1186/1748-7188-2-15},
  doi       = {10.1186/1748-7188-2-15},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/TouzetV07.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/WolfsheimerBH07,
  author    = {Stefan Wolfsheimer and
               Bernd Burghardt and
               Alexander K. Hartmann},
  title     = {Local sequence alignments statistics: deviations from Gumbel statistics
               in the rare-event tail},
  journal   = {Algorithms Mol. Biol.},
  volume    = {2},
  year      = {2007},
  url       = {https://doi.org/10.1186/1748-7188-2-9},
  doi       = {10.1186/1748-7188-2-9},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/WolfsheimerBH07.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/YangPU07,
  author    = {Hui Yang and
               Srinivasan Parthasarathy and
               Duygu Ucar},
  title     = {A spatio-temporal mining approach towards summarizing and analyzing
               protein folding trajectories},
  journal   = {Algorithms Mol. Biol.},
  volume    = {2},
  year      = {2007},
  url       = {https://doi.org/10.1186/1748-7188-2-3},
  doi       = {10.1186/1748-7188-2-3},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/YangPU07.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/ZakiKY07,
  author    = {Mohammed J. Zaki and
               George Karypis and
               Jiong Yang},
  title     = {Data Mining in Bioinformatics {(BIOKDD)}},
  journal   = {Algorithms Mol. Biol.},
  volume    = {2},
  year      = {2007},
  url       = {https://doi.org/10.1186/1748-7188-2-4},
  doi       = {10.1186/1748-7188-2-4},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/ZakiKY07.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/AllenS06,
  author    = {Jonathan E. Allen and
               Steven L. Salzberg},
  title     = {A phylogenetic generalized hidden Markov model for predicting alternatively
               spliced exons},
  journal   = {Algorithms Mol. Biol.},
  volume    = {1},
  year      = {2006},
  url       = {https://doi.org/10.1186/1748-7188-1-14},
  doi       = {10.1186/1748-7188-1-14},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/AllenS06.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/AlmeidaV06,
  author    = {Jonas S. Almeida and
               Susana Vinga},
  title     = {Computing distribution of scale independent motifs in biological sequences},
  journal   = {Algorithms Mol. Biol.},
  volume    = {1},
  year      = {2006},
  url       = {https://doi.org/10.1186/1748-7188-1-18},
  doi       = {10.1186/1748-7188-1-18},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/AlmeidaV06.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/ApostolicoCP06,
  author    = {Alberto Apostolico and
               Matteo Comin and
               Laxmi Parida},
  title     = {Mining, compressing and classifying with extensible motifs},
  journal   = {Algorithms Mol. Biol.},
  volume    = {1},
  year      = {2006},
  url       = {https://doi.org/10.1186/1748-7188-1-4},
  doi       = {10.1186/1748-7188-1-4},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/ApostolicoCP06.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/BernhartTMFSH06,
  author    = {Stephan H. Bernhart and
               Hakim Tafer and
               Ulrike M{\"{u}}ckstein and
               Christoph Flamm and
               Peter F. Stadler and
               Ivo L. Hofacker},
  title     = {Partition function and base pairing probabilities of {RNA} heterodimers},
  journal   = {Algorithms Mol. Biol.},
  volume    = {1},
  year      = {2006},
  url       = {https://doi.org/10.1186/1748-7188-1-3},
  doi       = {10.1186/1748-7188-1-3},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/BernhartTMFSH06.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/ChristiansenMPRS06,
  author    = {Chris Christiansen and
               Thomas Mailund and
               Christian N. S. Pedersen and
               Martin Randers and
               Martin Stig Stissing},
  title     = {Fast calculation of the quartet distance between trees of arbitrary
               degrees},
  journal   = {Algorithms Mol. Biol.},
  volume    = {1},
  year      = {2006},
  url       = {https://doi.org/10.1186/1748-7188-1-16},
  doi       = {10.1186/1748-7188-1-16},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/ChristiansenMPRS06.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/GrothausMM06,
  author    = {Gregory A. Grothaus and
               Adeel Mufti and
               T. M. Murali},
  title     = {Automatic layout and visualization of biclusters},
  journal   = {Algorithms Mol. Biol.},
  volume    = {1},
  year      = {2006},
  url       = {https://doi.org/10.1186/1748-7188-1-15},
  doi       = {10.1186/1748-7188-1-15},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/GrothausMM06.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/HwangCZR06,
  author    = {Woochang Hwang and
               Young{-}Rae Cho and
               Aidong Zhang and
               Murali Ramanathan},
  title     = {A novel functional module detection algorithm for protein-protein
               interaction networks},
  journal   = {Algorithms Mol. Biol.},
  volume    = {1},
  year      = {2006},
  url       = {https://doi.org/10.1186/1748-7188-1-24},
  doi       = {10.1186/1748-7188-1-24},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/HwangCZR06.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/LanciaR06,
  author    = {Giuseppe Lancia and
               Romeo Rizzi},
  title     = {The approximability of the String Barcoding problem},
  journal   = {Algorithms Mol. Biol.},
  volume    = {1},
  year      = {2006},
  url       = {https://doi.org/10.1186/1748-7188-1-12},
  doi       = {10.1186/1748-7188-1-12},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/LanciaR06.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/LehmannKSN06,
  author    = {Katharina Anna Lehmann and
               Michael Kaufmann and
               Stephan Steigele and
               Kay Nieselt},
  title     = {On the maximal cliques in \emph{c}-max-tolerance graphs and their
               application in clustering molecular sequences},
  journal   = {Algorithms Mol. Biol.},
  volume    = {1},
  year      = {2006},
  url       = {https://doi.org/10.1186/1748-7188-1-9},
  doi       = {10.1186/1748-7188-1-9},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/LehmannKSN06.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/LiT06,
  author    = {Nan Li and
               Martin Tompa},
  title     = {Analysis of computational approaches for motif discovery},
  journal   = {Algorithms Mol. Biol.},
  volume    = {1},
  year      = {2006},
  url       = {https://doi.org/10.1186/1748-7188-1-8},
  doi       = {10.1186/1748-7188-1-8},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/LiT06.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/LiuW06,
  author    = {Xiaowen Liu and
               Lusheng Wang},
  title     = {Finding the region of pseudo-periodic tandem repeats in biological
               sequences},
  journal   = {Algorithms Mol. Biol.},
  volume    = {1},
  year      = {2006},
  url       = {https://doi.org/10.1186/1748-7188-1-2},
  doi       = {10.1186/1748-7188-1-2},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/LiuW06.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/LuES06,
  author    = {James Lu and
               Heinz W. Engl and
               Peter Schuster},
  title     = {Inverse bifurcation analysis: application to simple gene systems},
  journal   = {Algorithms Mol. Biol.},
  volume    = {1},
  year      = {2006},
  url       = {https://doi.org/10.1186/1748-7188-1-11},
  doi       = {10.1186/1748-7188-1-11},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/LuES06.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/MeinickeBFW06,
  author    = {Peter Meinicke and
               Thomas Brodag and
               Wolfgang Florian Fricke and
               Stephan Waack},
  title     = {P-value based visualization of codon usage data},
  journal   = {Algorithms Mol. Biol.},
  volume    = {1},
  year      = {2006},
  url       = {https://doi.org/10.1186/1748-7188-1-10},
  doi       = {10.1186/1748-7188-1-10},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/MeinickeBFW06.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/MorgensternPPS06,
  author    = {Burkhard Morgenstern and
               Sonja J. Prohaska and
               Dirk P{\"{o}}hler and
               Peter F. Stadler},
  title     = {Multiple sequence alignment with user-defined anchor points},
  journal   = {Algorithms Mol. Biol.},
  volume    = {1},
  year      = {2006},
  url       = {https://doi.org/10.1186/1748-7188-1-6},
  doi       = {10.1186/1748-7188-1-6},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/MorgensternPPS06.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/MorgensternS06,
  author    = {Burkhard Morgenstern and
               Peter F. Stadler},
  title     = {New journal: Algorithms for Molecular Biology},
  journal   = {Algorithms Mol. Biol.},
  volume    = {1},
  year      = {2006},
  url       = {https://doi.org/10.1186/1748-7188-1-1},
  doi       = {10.1186/1748-7188-1-1},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/MorgensternS06.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/Nuel06,
  author    = {Gr{\'{e}}gory Nuel},
  title     = {Effective p-value computations using Finite Markov Chain Imbedding
               {(FMCI):} application to local score and to pattern statistics},
  journal   = {Algorithms Mol. Biol.},
  volume    = {1},
  year      = {2006},
  url       = {https://doi.org/10.1186/1748-7188-1-5},
  doi       = {10.1186/1748-7188-1-5},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/Nuel06.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/Nuel06a,
  author    = {Gr{\'{e}}gory Nuel},
  title     = {Pattern statistics on Markov chains and sensitivity to parameter estimation},
  journal   = {Algorithms Mol. Biol.},
  volume    = {1},
  year      = {2006},
  url       = {https://doi.org/10.1186/1748-7188-1-17},
  doi       = {10.1186/1748-7188-1-17},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/Nuel06a.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/PaluszewskiHW06,
  author    = {Martin Paluszewski and
               Thomas Hamelryck and
               Pawel Winter},
  title     = {Reconstructing protein structure from solvent exposure using tabu
               search},
  journal   = {Algorithms Mol. Biol.},
  volume    = {1},
  year      = {2006},
  url       = {https://doi.org/10.1186/1748-7188-1-20},
  doi       = {10.1186/1748-7188-1-20},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/PaluszewskiHW06.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/ReddyWC06,
  author    = {Chandan K. Reddy and
               Yao{-}Chung Weng and
               Hsiao{-}Dong Chiang},
  title     = {Refining motifs by improving information content scores using neighborhood
               profile search},
  journal   = {Algorithms Mol. Biol.},
  volume    = {1},
  year      = {2006},
  url       = {https://doi.org/10.1186/1748-7188-1-23},
  doi       = {10.1186/1748-7188-1-23},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/ReddyWC06.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/TournierFB06,
  author    = {Alexander L. Tournier and
               Paul W. Fitzjohn and
               Paul A. Bates},
  title     = {Probability-based model of protein-protein interactions on biological
               timescales},
  journal   = {Algorithms Mol. Biol.},
  volume    = {1},
  year      = {2006},
  url       = {https://doi.org/10.1186/1748-7188-1-25},
  doi       = {10.1186/1748-7188-1-25},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/TournierFB06.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/WilmMS06,
  author    = {Andreas Wilm and
               Indra Mainz and
               Gerhard Steger},
  title     = {An enhanced {RNA} alignment benchmark for sequence alignment programs},
  journal   = {Algorithms Mol. Biol.},
  volume    = {1},
  year      = {2006},
  url       = {https://doi.org/10.1186/1748-7188-1-19},
  doi       = {10.1186/1748-7188-1-19},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/WilmMS06.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/ZaslavskyS06,
  author    = {Elena Zaslavsky and
               Mona Singh},
  title     = {A combinatorial optimization approach for diverse motif finding applications},
  journal   = {Algorithms Mol. Biol.},
  volume    = {1},
  year      = {2006},
  url       = {https://doi.org/10.1186/1748-7188-1-13},
  doi       = {10.1186/1748-7188-1-13},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/ZaslavskyS06.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/ZhangZ06,
  author    = {Yongqiang Zhang and
               Mohammed J. Zaki},
  title     = {{EXMOTIF:} efficient structured motif extraction},
  journal   = {Algorithms Mol. Biol.},
  volume    = {1},
  year      = {2006},
  url       = {https://doi.org/10.1186/1748-7188-1-21},
  doi       = {10.1186/1748-7188-1-21},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/ZhangZ06.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/ZhangZ06a,
  author    = {Yongqiang Zhang and
               Mohammed J. Zaki},
  title     = {{SMOTIF:} efficient structured pattern and profile motif search},
  journal   = {Algorithms Mol. Biol.},
  volume    = {1},
  year      = {2006},
  url       = {https://doi.org/10.1186/1748-7188-1-22},
  doi       = {10.1186/1748-7188-1-22},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/ZhangZ06a.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/ZotenkoGJP06,
  author    = {Elena Zotenko and
               Katia S. Guimar{\~{a}}es and
               Raja Jothi and
               Teresa M. Przytycka},
  title     = {Decomposition of overlapping protein complexes: {A} graph theoretical
               method for analyzing static and dynamic protein associations},
  journal   = {Algorithms Mol. Biol.},
  volume    = {1},
  year      = {2006},
  url       = {https://doi.org/10.1186/1748-7188-1-7},
  doi       = {10.1186/1748-7188-1-7},
  timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl    = {https://dblp.org/rec/journals/almob/ZotenkoGJP06.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}
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