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ORCIDBioinformatics, Volume 30
Volume 30, Number 1, January 2014
- Christos Kozanitis, Andrew Heiberg, George Varghese, Vineet Bafna
:
Using Genome Query Language to uncover genetic variation. 1-8
- Sven H. Giese, Franziska Zickmann, Bernhard Y. Renard:
Specificity control for read alignments using an artificial reference genome-guided false discovery rate. 9-16 - Daniel Alonso-Alemany, Aurélien Barré, Stefano Beretta, Paola Bonizzoni, Macha Nikolski, Gabriel Valiente:
Further Steps in TANGO: improved taxonomic assignment in metagenomics. 17-23 - Lilian Janin, Giovanna Rosone, Anthony J. Cox:
Adaptive reference-free compression of sequence quality scores. 24-30 - Rayan Chikhi, Paul Medvedev:
Informed and automated k-mer size selection for genome assembly. 31-37 - Daniel H. Huson, Chao Xie:
A poor man's BLASTX - high-throughput metagenomic protein database search using PAUDA. 38-39
- David Hernández, Ryan Tewhey, Jean-Baptiste Veyrieras, Laurent Farinelli, Magne Østerås, Patrice François, Jacques Schrenzel:
De novo finished 2.8 Mbp Staphylococcus aureus genome assembly from 100 bp short and long range paired-end reads. 40-49 - Noemi Andor, Julie V. Harness, Sabine Müller, Hans-Werner Mewes, Claudia Petritsch:
EXPANDS: expanding ploidy and allele frequency on nested subpopulations. 50-60
- Paulo Vieira Milreu, Cecilia Coimbra Klein, Ludovic Cottret, Vicente Acuña, Etienne Birmelé, Michele Borassi, Christophe Junot, Alberto Marchetti-Spaccamela, Andrea Marino, Leen Stougie, Fabien Jourdan, Pierluigi Crescenzi, Vincent Lacroix, Marie-France Sagot:
Telling metabolic stories to explore metabolomics data: a case study on the yeast response to cadmium exposure. 61-70 - Mingjun Wang, Xing-Ming Zhao, Hao Tan, Tatsuya Akutsu, James C. Whisstock, Jiangning Song:
Cascleave 2.0, a new approach for predicting caspase and granzyme cleavage targets. 71-80
- Yijie Wang, Xiaoning Qian:
Functional module identification in protein interaction networks by interaction patterns. 81-93 - Yungang Xu, Maozu Guo, Xiaoyan Liu, Chun-yu Wang, Yang Liu:
Inferring the soybean (Glycine max) microRNA functional network based on target gene network. 94-103
- Songhua Xu, Hong-Jun Yoon, Georgia D. Tourassi:
A user-oriented web crawler for selectively acquiring online content in e-health research. 104-114
- Sebastian Bartschat, Stephanie Kehr, Hakim Tafer, Peter F. Stadler, Jana Hertel:
snoStrip: a snoRNA annotation pipeline. 115-116
- Armando J. Pinho, Diogo Pratas:
MFCompress: a compression tool for FASTA and multi-FASTA data. 117-118 - André Schumacher, Luca Pireddu, Matti Niemenmaa, Aleksi Kallio, Eija Korpelainen, Gianluigi Zanetti, Keijo Heljanko:
SeqPig: simple and scalable scripting for large sequencing data sets in Hadoop. 119-120 - Christoph Gille, Birgit Weyand, Andreas Gille:
Sequence alignment visualization in HTML5 without Java. 121-122
- Michael J. Landis, Trevor Bedford:
Phylowood: interactive web-based animations of biogeographic and phylogeographic histories. 123-124
- Shannon L. N. Mayne, Hugh-George Patterton:
AnchorMS: a bioinformatics tool to derive structural information from the mass spectra of cross-linked protein complexes. 125-126
- Thomas Sandmann, Sarah K. Kummerfeld, Robert Gentleman, Richard Bourgon:
gCMAP: user-friendly connectivity mapping with R. 127-128
- Maxwell Lewis Neal, Michal Galdzicki, J. T. Gallimore, Herbert M. Sauro:
A C library for retrieving specific reactions from the BioModels database. 129-130 - Matthias Bock, Till Scharp, Chaitanya Talnikar, Edda Klipp:
BooleSim: an interactive Boolean network simulator. 131-132 - Grant Hughes, Charmion Cruickshank-Quinn, Richard Reisdorph, Sharon Lutz, Irina Petrache, Nichole Reisdorph, Russell Bowler, Katerina J. Kechris:
MSPrep - Summarization, normalization and diagnostics for processing of mass spectrometry-based metabolomic data. 133-134 - Minji Jeon, Sunwon Lee, Kyubum Lee, Aik Choon Tan, Jaewoo Kang:
BEReX: Biomedical Entity-Relationship eXplorer. 135-136 - Tomasz Jetka, Agata Charzynska, Anna Gambin, Michael P. H. Stumpf, Michal Komorowski:
StochDecomp - Matlab package for noise decomposition in stochastic biochemical systems. 137-138
- Özgün Babur, Bülent Arman Aksoy, Igor V. Rodchenkov, Selçuk Onur Sümer, Chris Sander, Emek Demir:
Pattern search in BioPAX models. 139-140 - Jianfei Hu, Hee-Sool Rho, Robert H. Newman, Jin Zhang, Heng Zhu, Jiang Qian:
PhosphoNetworks: a database for human phosphorylation networks. 141-142
- Burkhard Rost:
ISCB: past-present perspective for the International Society for Computational Biology. 143-145 - Andreas W. M. Dress, Michal Linial, Olga G. Troyanskaya, Martin Vingron:
ISCB/SPRINGER series in computational biology. 146-147 - Jim Cavalcoli, Lonnie R. Welch, Bruce J. Aronow, Sorin Draghici, Daisuke Kihara:
The International Society of Computational Biology presents: the Great Lakes Bioinformatics Conference, May 16-18, 2014, Cincinnati, Ohio. 148-149
Volume 30, Number 2, January 2014
- Laurence O. W. Wilson, Andrew Spriggs, Jennifer M. Taylor, Aude M. Fahrer:
A novel splicing outcome reveals more than 2000 new mammalian protein isoforms. 151-156 - Dandi Qiao, Michael H. Cho, Heide Loehlein Fier, Per S. Bakke, Amund Gulsvik, Edwin K. Silverman, Christoph Lange:
On the simultaneous association analysis of large genomic regions: a massive multi-locus association test. 157-164 - Sebastian M. Waszak, Helena Kilpinen, Andreas R. Gschwind, Andrea Orioli, Sunil K. Raghav, Robert M. Witwicki, Eugenia Migliavacca, Alisa Yurovsky, Tuuli Lappalainen, Nouria Hernandez, Alexandre Reymond, Emmanouil T. Dermitzakis, Bart Deplancke:
Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data. 165-171 - Longjie Cheng, Yu Zhu:
A classification approach for DNA methylation profiling with bisulfite next-generation sequencing data. 172-179
- Ernest Turro, William J. Astle, Simon Tavaré:
Flexible analysis of RNA-seq data using mixed effects models. 180-188 - Kevin Lim, Limsoon Wong:
Finding consistent disease subnetworks using PFSNet. 189-196 - Yaqing Si, Peng Liu, Pinghua Li, Thomas P. Brutnell:
Model-based clustering for RNA-seq data. 197-205
- Buhm Han, Eun Yong Kang, Soumya Raychaudhuri, Paul I. W. de Bakker, Eleazar Eskin:
Fast pairwise IBD association testing in genome-wide association studies. 206-213
- Simina M. Boca, Rashmi Sinha, Amanda J. Cross, Steven C. Moore, Joshua N. Sampson:
Testing multiple biological mediators simultaneously. 214-220 - Mikael Sunnåker, Elías Zamora-Sillero, Adrián López García de Lomana, Florian Rudroff, Uwe Sauer, Jörg Stelling, Andreas Wagner:
Topological augmentation to infer hidden processes in biological systems. 221-227 - Marianna De Santis, Francesco Rinaldi, Emmanuela Falcone, Stefano Lucidi, Giulia Piaggio, Aymone Gurtner, Lorenzo Farina:
Combining optimization and machine learning techniques for genome-wide prediction of human cell cycle-regulated genes. 228-233
- Attila Kertész-Farkas, Beáta Reiz, Roberto Vera, Michael P. Myers, Sándor Pongor:
PTMTreeSearch: a novel two-stage tree-search algorithm with pruning rules for the identification of post-translational modification of proteins in MS/MS spectra. 234-241 - Mohammad Shahrokh Esfahani, Edward R. Dougherty:
Effect of separate sampling on classification accuracy. 242-250
- Mandy L. Wilson, Sakiko Okumoto, Laura Adam, Jean Peccoud:
Development of a domain-specific genetic language to design Chlamydomonas reinhardtii expression vectors. 251-257 - Álvaro Sebastián, Bruno Contreras-Moreira:
footprintDB: a database of transcription factors with annotated cis elements and binding interfaces. 258-265
- Lei Yuan, Cheng Pan, Shuiwang Ji, Michael McCutchan, Zhi-Hua Zhou, Stuart J. Newfeld, Sudhir Kumar, Jieping Ye:
Automated annotation of developmental stages of Drosophila embryos in images containing spatial patterns of expression. 266-273
- Nicolas Terrapon, January 3rd Weiner, Sonja Grath, Andrew D. Moore, Erich Bornberg-Bauer:
Rapid similarity search of proteins using alignments of domain arrangements. 274-281
- Andrew D. Moore, Andreas Held, Nicolas Terrapon, January 3rd Weiner, Erich Bornberg-Bauer:
DoMosaics: software for domain arrangement visualization and domain-centric analysis of proteins. 282-283 - Matthias Lienhard, Christina Grimm, Markus Morkel, Ralf Herwig, Lukas Chavez:
MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments. 284-286 - João F. Matias Rodrigues, Christian von Mering:
HPC-CLUST: distributed hierarchical clustering for large sets of nucleotide sequences. 287-288
- Toma Tebaldi, Erik Dassi, Galena Kostoska, Gabriella Viero, Alessandro Quattrone:
tRanslatome: an R/Bioconductor package to portray translational control. 289-291
- Michael L. Blinov, James C. Schaff, Oliver Ruebenacker, Xintao Wei, Dan Vasilescu, Fei Gao, Frank Morgan, Li Ye, Anuradha Lakshminarayana, Ion I. Moraru, Leslie M. Loew:
Pathway Commons at Virtual Cell: use of pathway data for mathematical modeling. 292-294
- Luke E. Ulrich, Igor B. Zhulin:
SeqDepot: streamlined database of biological sequences and precomputed features. 295-297 - Rodrigo Ochoa, Mark Davies, George Papadatos, Francis Atkinson, John P. Overington:
myChEMBL: a virtual machine implementation of open data and cheminformatics tools. 298-300
Volume 30, Number 3, February 2014
- Yuwen Liu, Jie Zhou, Kevin P. White:
RNA-seq differential expression studies: more sequence or more replication? 301-304
- Min Xiong, Bin Li, Qiang Zhu, Yun-Xing Wang, Hong-yu Zhang:
Identification of transcription factors for drug-associated gene modules and biomedical implications. 305-309
- Dror Hibsh, Hadas Schori, Sol Efroni, Orit Shefi:
Spatial regulation dominates gene function in the ganglia chain. 310-316
- Kazunori D. Yamada, Kentaro Tomii:
Revisiting amino acid substitution matrices for identifying distantly related proteins. 317-325
- Ali May, René Pool, Erik van Dijk, Jochem Bijlard, Sanne Abeln, Jaap Heringa, K. Anton Feenstra:
Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins. 326-334 - Douglas E. V. Pires, David B. Ascher, Tom L. Blundell:
mCSM: predicting the effects of mutations in proteins using graph-based signatures. 335-342 - Luke Day, Ouala Abdelhadi Ep Souki, Andreas Alexander Albrecht, Kathleen Steinhöfel:
Accessibility of microRNA binding sites in metastable RNA secondary structures in the presence of SNPs. 343-352 - Hamidreza Khataee, Alan Wee-Chung Liew:
A mathematical model describing the mechanical kinetics of kinesin stepping. 353-359
- Yasir Rahmatallah, Frank Emmert-Streib, Galina V. Glazko:
Gene Sets Net Correlations Analysis (GSNCA): a multivariate differential coexpression test for gene sets. 360-368 - Chuan Gao, Nicole L. Tignor, Jacqueline Salit, Yael Strulovici-Barel, Neil R. Hackett, Ronald G. Crystal, Jason G. Mezey:
HEFT: eQTL analysis of many thousands of expressed genes while simultaneously controlling for hidden factors. 369-376 - Hari Krishna Yalamanchili, Bin Yan, Mulin Jun Li, Jing Qin, Zhongying Zhao, Francis Y. L. Chin, Junwen Wang:
DDGni: Dynamic delay gene-network inference from high-temporal data using gapped local alignment. 377-383
- Barbara Di Camillo, Francesco Sambo, Gianna Toffolo, Claudio Cobelli:
ABACUS: an entropy-based cumulative bivariate statistic robust to rare variants and different direction of genotype effect. 384-391
- Søren Mørk, Sune Pletscher-Frankild, Albert Pallejà Caro, Jan Gorodkin, Lars Juhl Jensen:
Protein-driven inference of miRNA-disease associations. 392-397 - Jianlong Peng, Jing Lu, Qiancheng Shen, Mingyue Zheng, Xiaomin Luo, Weiliang Zhu, Hualiang Jiang, Kaixian Chen:
In silico site of metabolism prediction for human UGT-catalyzed reactions. 398-405 - Matan Bodaker, Eran Meshorer, Eduardo Mitrani, Yoram Louzoun:
Genes related to differentiation are correlated with the gene regulatory network structure. 406-413 - Sebastian Dümcke, Johannes Bräuer, Benedict Anchang, Rainer Spang, Niko Beerenwinkel, Achim Tresch:
Exact likelihood computation in Boolean networks with probabilistic time delays, and its application in signal network reconstruction. 414-419
- Violeta N. Kovacheva, Adnan Mujahid Khan, Michael Khan, David B. A. Epstein, Nasir M. Rajpoot:
DiSWOP: a novel measure for cell-level protein network analysis in localized proteomics image data. 420-427
- Tiffany J. Morris, Lee M. Butcher, Andrew Feber, Andrew E. Teschendorff, Ankur R. Chakravarthy, Tomasz K. Wojdacz, Stephan Beck:
ChAMP: 450k Chip Analysis Methylation Pipeline. 428-430 - Bai Zhang, Xuchu Hou, Xiguo Yuan, Ie-Ming Shih, Zhen Zhang, Robert Clarke, Roger R. Wang, Yi Fu, Subha Madhavan, Yue Joseph Wang, Guoqiang Yu:
AISAIC: a software suite for accurate identification of significant aberrations in cancers. 431-433
- Guan-Zheng Luo, Wei Yang, Ying-Ke Ma, Xiu-Jie Wang:
ISRNA: an integrative online toolkit for short reads from high-throughput sequencing data. 434-436
- Esteban López-Camacho, María Jesús García-Godoy, Antonio J. Nebro, José Francisco Aldana Montes:
jMetalCpp: optimizing molecular docking problems with a C++ metaheuristic framework. 437-438 - Mohammad Mehdi Ghahremanpour, Seyed Shahriar Arab, Saman Biook Aghazadeh, Jin Zhang, David van der Spoel:
MemBuilder: a web-based graphical interface to build heterogeneously mixed membrane bilayers for the GROMACS biomolecular simulation program. 439-441
- Biao Li, Gao T. Wang, Suzanne M. Leal:
PhenoMan: phenotypic data exploration, selection, management and quality control for association studies of rare and common variants. 442-444
- Zeliha Görmez, Burcu Bakir-Gungor, Mahmut Samil Sagiroglu:
HomSI: a homozygous stretch identifier from next-generation sequencing data. 445-447
Volume 30, Number 4, February 2014
- Olga Tanaseichuk, James Borneman, Tao Jiang:
Phylogeny-based classification of microbial communities. 449-456 - Ruslan A. Soldatov, Svetlana V. Vinogradova, Andrey A. Mironov:
RNASurface: fast and accurate detection of locally optimal potentially structured RNA segments. 457-463 - Francisco Fernandes, Ana T. Freitas:
slaMEM: efficient retrieval of maximal exact matches using a sampled LCP array. 464-471 - Bin Liu, Deyuan Zhang, Ruifeng Xu, Jinghao Xu, Xiaolong Wang, Qingcai Chen, Qiwen Dong, Kuo-Chen Chou:
Combining evolutionary information extracted from frequency profiles with sequence-based kernels for protein remote homology detection. 472-479 - Song Yan, Yun Li:
BETASEQ: a powerful novel method to control type-I error inflation in partially sequenced data for rare variant association testing. 480-487
- Nicolas Lartillot:
A phylogenetic Kalman filter for ancestral trait reconstruction using molecular data. 488-496
- Hua Zhang, Lukasz A. Kurgan:
Sequence-based Gaussian network model for protein dynamics. 497-505
- Chen Suo, Stefano Calza, Agus Salim, Yudi Pawitan:
Joint estimation of isoform expression and isoform-specific read distribution using multisample RNA-Seq data. 506-513 - Hongjie Zhu, Man Luo:
Chemical structure informing statistical hypothesis testing in metabolomics. 514-522
- Andreas Krämer, Jeff Green, Jack Pollard Jr., Stuart Tugendreich:
Causal analysis approaches in Ingenuity Pathway Analysis. 523-530 - Ferhat Alkan, Cesim Erten:
BEAMS: backbone extraction and merge strategy for the global many-to-many alignment of multiple PPI networks. 531-539 - Jialu Hu, Birte Kehr, Knut Reinert:
NetCoffee: a fast and accurate global alignment approach to identify functionally conserved proteins in multiple networks. 540-548 - Cong Zhou, Michael J. Walker, Andrew J. K. Williamson, Andrew Pierce, Carlo Berzuini, Caroline Dive, Anthony D. Whetton:
A hierarchical statistical modeling approach to analyze proteomic isobaric tag for relative and absolute quantitation data. 549-558
- Tomaz Hocevar, Janez Demsar:
A combinatorial approach to graphlet counting. 559-565
- Richard M. Leggett, Bernardo J. Clavijo, Leah Clissold, Matthew D. Clark, Mario Cáccamo:
NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries. 566-568
- José Colmenares, Jesús Ortiz, Walter Rocchia:
GPU linear and non-linear Poisson-Boltzmann solver module for DelPhi. 569-570
- Nicolas Jung, Frédéric Bertrand, Seiamak Bahram, Laurent Vallat, Myriam Maumy-Bertrand:
Cascade: a R package to study, predict and simulate the diffusion of a signal through a temporal gene network. 571-573 - Raghavendra Hosur, Suzanne Szak, Alice Thai, Norm Allaire, Jadwiga R. Bienkowska:
ProbeSelect: selecting differentially expressed probes in transcriptional profile data. 574-575
- Darren Kessner, John Novembre:
forqs: forward-in-time simulation of recombination, quantitative traits and selection. 576-577 - Michel Petitjean, Anne Vanet:
VIRAPOPS: a forward simulator dedicated to rapidly evolved viral populations. 578-580
- Jiarui Zhou, Ralf J. M. Weber, James William Allwood, Robert Mistrik, Zexuan Zhu, Zhen Ji, Siping Chen, Warwick B. Dunn, Shan He, Mark R. Viant:
HAMMER: automated operation of mass frontier to construct in silico mass spectral fragmentation libraries. 581-583 - Longfei Mao, Wynand S. Verwoerd:
ORCA: a COBRA toolbox extension for model-driven discovery and analysis. 584-585 - Cheng Chang, Jiyang Zhang, Mingfei Han, Jie Ma, Wei Zhang, Songfeng Wu, Kehui Liu, Hongwei Xie, Fuchu He, Yunping Zhu:
SILVER: an efficient tool for stable isotope labeling LC-MS data quantitative analysis with quality control methods. 586-587
- Denis Fourches, Maria F. Sassano, Bryan L. Roth, Alexander Tropsha:
HTS navigator: freely accessible cheminformatics software for analyzing high-throughput screening data. 588-589
- Muhammad A. Shah, Emily Denton, Lihua Liu, Matthieu Schapira:
ChromoHub V2: cancer genomics. 590-592 - Dennis Bromley, Steven J. Rysavy, Robert Su, Rudesh D. Toofanny, Tom Schmidlin, Valerie Daggett:
DIVE: a data intensive visualization engine. 593-595
- Sarah Sheppard, Nathan D. Lawson, Lihua Julie Zhu:
Accurate identification of polyadenylation sites from 3′ end deep sequencing using a naïve Bayes classifier. 596
Volume 30, Number 5, March 2014
- Balamurugan Palanisamy, Rajasekaran Ekambaram, Klaus Heese:
Thymine distribution in genes provides novel insight into the functional significance of the proteome of the malaria parasite Plasmodium falciparum 3D7. 597-600
- Douglas D. Baumann, Rebecca W. Doerge:
Robust adjustment of sequence tag abundance. 601-605 - Franziska Zickmann, Martin S. Lindner, Bernhard Y. Renard:
GIIRA - RNA-Seq driven gene finding incorporating ambiguous reads. 606-613 - Jiajie Zhang, Kassian Kobert, Tomás Flouri, Alexandros Stamatakis:
PEAR: a fast and accurate Illumina Paired-End reAd mergeR. 614-620 - Yue Li, Anna Goldenberg, Ka-Chun Wong, Zhaolei Zhang:
A probabilistic approach to explore human miRNA targetome by integrating miRNA-overexpression data and sequence information. 621-628
- Luis Miguel Rodriguez-Rojas, Konstantinos T. Konstantinidis:
Nonpareil: a redundancy-based approach to assess the level of coverage in metagenomic datasets. 629-635 - Matthew Levinson, Qing Zhou:
A penalized Bayesian approach to predicting sparse protein-DNA binding landscapes. 636-643 - Phuong Dao, Ibrahim Numanagic, Yen-Yi Lin, Faraz Hach, Emre Karakoç, Nilgun Donmez, Colin C. Collins, Evan E. Eichler, Süleyman Cenk Sahinalp:
ORMAN: Optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms. 644-651 - Hongseok Tae, Dong-Yun Kim, John McCormick, Robert E. Settlage, Harold R. Garner:
Discretized Gaussian mixture for genotyping of microsatellite loci containing homopolymer runs. 652-659
- Dong Xu, Lukasz Jaroszewski, Zhanwen Li, Adam Godzik:
FFAS-3D: improving fold recognition by including optimized structural features and template re-ranking. 660-667 - Giuseppe Maccari, Giulia L. B. Spampinato, Valentina Tozzini:
SecStAnT: secondary structure analysis tool for data selection, statistics and models building. 668-674
- Ben Teng, Ting Huang, Zengyou He:
Decoy-free protein-level false discovery rate estimation. 675-681 - David A. Liebner, Kun Huang, Jeffrey D. Parvin:
MMAD: microarray microdissection with analysis of differences is a computational tool for deconvoluting cell type-specific contributions from tissue samples. 682-689
- Marina Evangelou, Frank Dudbridge, Lorenz Wernisch:
Two novel pathway analysis methods based on a hierarchical model. 690-697
- Emily Rose Holzinger, Scott M. Dudek, Alex T. Frase, Sarah A. Pendergrass, Marylyn D. Ritchie:
ATHENA: the analysis tool for heritable and environmental network associations. 698-705 - Tomomi Ichimiya, Shoko Nishihara, Sayaka Takase-Yoden, Hiroshi Kida, Kiyoko F. Aoki-Kinoshita:
Frequent glycan structure mining of influenza virus data revealed a sulfated glycan motif that increased viral infection. 706-711 - Joseph Geraci, Moyez Dharsee, Paulo A. S. Nuin, Alexandria Haslehurst, Madhuri Koti, Harriet E. Feilotter, Kenneth R. Evans:
Exploring high dimensional data with Butterfly: a novel classification algorithm based on discrete dynamical systems. 712-718 - Robert Hoehndorf, Tanya Hiebert, Nigel W. Hardy, Paul N. Schofield, Georgios V. Gkoutos, Michel Dumontier:
Mouse model phenotypes provide information about human drug targets. 719-725
- Johannes Stegmaier, Maryam Shahid, Masanari Takamiya, Lixin Yang, Sepand Rastegar, Markus Reischl, Uwe Strähle, Ralf Mikut:
Automated prior knowledge-based quantification of neuronal patterns in the spinal cord of zebrafish. 726-733
- Ole Kristian Ekseth, Martin Kuiper, Vladimir Mironov:
orthAgogue: an agile tool for the rapid prediction of orthology relations. 734-736
- Haoqi Sun, Haiping Wang, Ruixin Zhu, Kailin Tang, Qin Gong, Juan Cui, Zhiwei Cao, Qi Liu:
iPEAP: integrating multiple omics and genetic data for pathway enrichment analysis. 737-739
- Sébastien Harispe, Sylvie Ranwez, Stefan Janaqi, Jacky Montmain:
The semantic measures library and toolkit: fast computation of semantic similarity and relatedness using biomedical ontologies. 740-742
- Eric C. Anderson, Thomas C. Ng:
Comment on 'Bayesian parentage analysis with systematic accountability of genotyping error, missing data and false matching'. 743-745
Volume 30, Number 6, March 2014
- Gong-Hua Li, Jing-Fei Huang:
Inferring therapeutic targets from heterogeneous data: HKDC1 is a novel potential therapeutic target for cancer. 748-752
- Chandler Zuo, Sündüz Keles:
A statistical framework for power calculations in ChIP-seq experiments. 753-760 - Jung-Hsien Chiang, Chan-Hsien Lin:
NCS: incorporating positioning data to quantify nucleosome stability in yeast. 761-767
- Carson Holt, Bojan Losic, Deepa Pai, Zhen Zhao, Quang Trinh, Sujata Syam, Niloofar Arshadi, Gun Ho Jang, Johar Ali, Tim Beck, John D. McPherson, Lakshmi B. Muthuswamy:
WaveCNV: allele-specific copy number alterations in primary tumors and xenograft models from next-generation sequencing. 768-774 - Zizhen Yao, Kyle L. MacQuarrie, Abraham P. Fong, Stephen J. Tapscott, Walter L. Ruzzo, Robert Gentleman:
Discriminative motif analysis of high-throughput dataset. 775-783
- Frédéric Guyon, Pierre Tufféry:
Fast protein fragment similarity scoring using a Binet-Cauchy kernel. 784-791 - Lydia Benkaidali, François André, Boubekeur Maouche, Pridi Siregar, Mohamed Benyettou, François Maurel, Michel Petitjean:
Computing cavities, channels, pores and pockets in proteins from non-spherical ligands models. 792-800
- Yufei Xiao, Tzu-Hung Hsiao, Uthra Suresh, Hung-I Harry Chen, Xiaowu Wu, Steven E. Wolf, Yidong Chen:
A novel significance score for gene selection and ranking. 801-807 - Pengyi Yang, Ellis Patrick, Shi-Xiong Tan, Daniel J. Fazakerley, James G. Burchfield, Christopher Gribben, Matthew J. Prior, David E. James, Yee Hwa Yang:
Direction pathway analysis of large-scale proteomics data reveals novel features of the insulin action pathway. 808-814
- Koichiro Doi, Taku Monjo, Pham H. Hoang, Jun Yoshimura, Hideaki Yurino, Jun Mitsui, Hiroyuki Ishiura, Yuji Takahashi, Yaeko Ichikawa, Jun Goto, Shoji Tsuji, Shinichi Morishita:
Rapid detection of expanded short tandem repeats in personal genomics using hybrid sequencing. 815-822
- Pengzhan Hu, Zhongchao Shen, Haibo Tu, Li Zhang, Tieliu Shi:
Integrating multiple resources to identify specific transcriptional cooperativity with a Bayesian approach. 823-830 - Tanya P. Garcia, Samuel Müller, Raymond J. Carroll, Rosemary L. Walzem:
Identification of important regressor groups, subgroups and individuals via regularization methods: application to gut microbiome data. 831-837 - José A. Seoane, Ian N. M. Day, Tom R. Gaunt, Colin Campbell:
A pathway-based data integration framework for prediction of disease progression. 838-845 - Ivan Dimitrov, Lyudmila Naneva, Irini A. Doytchinova, Ivan Bangov:
AllergenFP: allergenicity prediction by descriptor fingerprints. 846-851 - Xiangtian Yu, Guojun Li, Luonan Chen:
Prediction and early diagnosis of complex diseases by edge-network. 852-859 - Senol Isci, Haluk Dogan, Cengizhan Ozturk, Hasan H. Otu:
Bayesian network prior: network analysis of biological data using external knowledge. 860-867
- Sampo Pyysalo, Sophia Ananiadou:
Anatomical entity mention recognition at literature scale. 868-875
- Samuel Croset, John P. Overington, Dietrich Rebholz-Schuhmann:
The functional therapeutic chemical classification system. 876-883
- Ulrich Omasits, Christian H. Ahrens, Sebastian Müller, Bernd Wollscheid:
Protter: interactive protein feature visualization and integration with experimental proteomic data. 884-886 - Sutharzan Sreeskandarajan, Michelle M. Flowers, John E. Karro, Chun Liang:
A MATLAB-based tool for accurate detection of perfect overlapping and nested inverted repeats in DNA sequences. 887-888
- Anton A. Polyansky, Anton O. Chugunov, Pavel E. Volynsky, Nikolay A. Krylov, Dmitry E. Nolde, Roman G. Efremov:
PREDDIMER: a web server for prediction of transmembrane helical dimers. 889-890
- Xavier Rogé, Xuegong Zhang:
RNAseqViewer: visualization tool for RNA-Seq data. 891-892
- Joram M. Posma, Steven L. Robinette, Elaine Holmes, Jeremy K. Nicholson:
MetaboNetworks, an interactive Matlab-based toolbox for creating, customizing and exploring sub-networks from KEGG. 893-895
- Daniel Jaeger, Johannes Barth, Anna Niehues, Christian Fufezan:
pyGCluster, a novel hierarchical clustering approach. 896-898
Volume 30, Number 7, April 2014
- Kenneth B. Schou, Jens S. Andersen, Lotte B. Pedersen:
A divergent calponin homology (NN-CH) domain defines a novel family: implications for evolution of ciliary IFT complex B proteins. 899-902
- Lucian P. Smith, Erik Butterworth, James B. Bassingthwaighte, Herbert M. Sauro:
SBML and CellML translation in Antimony and JSim. 903-907
- Nha Nguyen, An P. N. Vo, Kyoung-Jae Won:
A wavelet-based method to exploit epigenomic language in the regulatory region. 908-914 - Yu Qian, Brian L. Browning, Sharon R. Browning:
Efficient clustering of identity-by-descent between multiple individuals. 915-922
- Yang Liao, Gordon K. Smyth, Wei Shi:
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. 923-930 - Dan Ofer, Michal Linial:
NeuroPID: a predictor for identifying neuropeptide precursors from metazoan proteomes. 931-940 - Ronak Y. Patel, Gary D. Stormo:
Discriminative motif optimization based on perceptron training. 941-948
- Xuefeng Cui, Shuai Cheng Li, Lin He, Ming Li:
Fingerprinting protein structures effectively and efficiently. 949-955
- Amit G. Deshwar, Quaid Morris:
PLIDA: cross-platform gene expression normalization using perturbed topic models. 956-961 - Krzysztof Polanski, Johanna Rhodes, Claire Hill, Peijun Zhang, Dafyd J. Jenkins, Steven J. Kiddle, Aleksey Jironkin, Jim Beynon, Vicky Buchanan-Wollaston, Sascha Ott, Katherine J. Denby:
Wigwams: identifying gene modules co-regulated across multiple biological conditions. 962-970 - Hadi Jorjani, Mihaela Zavolan:
TSSer: an automated method to identify transcription start sites in prokaryotic genomes from differential RNA sequencing data. 971-974
- Jon Pey, Francisco J. Planes, John E. Beasley:
Refining carbon flux paths using atomic trace data. 975-980 - Satoshi Ohno, Hiroshi Shimizu, Chikara Furusawa:
FastPros: screening of reaction knockout strategies for metabolic engineering. 981-987 - Nils Hoffmann, Mathias Wilhelm, Anja Doebbe, Karsten Niehaus, Jens Stoye:
BiPACE 2D - graph-based multiple alignment for comprehensive 2D gas chromatography-mass spectrometry. 988-995
- Lin Yang, Xin Qi, Fuyong Xing, Tahsin M. Kurç, Joel H. Saltz, David J. Foran:
Parallel content-based sub-image retrieval using hierarchical searching. 996-1002
- Brian J. Raney, Timothy R. Dreszer, Galt P. Barber, Hiram Clawson, Pauline A. Fujita, Ting Wang, Ngan Nguyen, Benedict Paten, Ann S. Zweig, Donna Karolchik, W. James Kent:
Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser. 1003-1005 - Hao Zhao, Zhifu Sun, Jing Wang, Haojie Huang, Jean-Pierre A. Kocher, Liguo Wang:
CrossMap: a versatile tool for coordinate conversion between genome assemblies. 1006-1007 - Daniel R. Zerbino, Nathan Johnson, Thomas Juettemann, Steven P. Wilder, Paul Flicek:
WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis. 1008-1009
- Jaebum Kim, Jian Ma:
PSAR-Align: improving multiple sequence alignment using probabilistic sampling. 1010-1012 - Hue Vuong, Robert M. Stephens, Natalia Volfovsky:
AVIA: an interactive web-server for annotation, visualization and impact analysis of genomic variations. 1013-1014 - Beifang Niu, Kai Ye, Qunyuan Zhang, Charles Lu, Mingchao Xie, Michael D. McLellan, Michael C. Wendl, Li Ding:
MSIsensor: microsatellite instability detection using paired tumor-normal sequence data. 1015-1016
- Sebastián Duchêne, Martyna Molak, Simon Y. W. Ho:
ClockstaR: choosing the number of relaxed-clock models in molecular phylogenetic analysis. 1017-1019 - Nicolas Rodrigue, Nicolas Lartillot:
Site-heterogeneous mutation-selection models within the PhyloBayes-MPI package. 1020-1021
- Silvia Caprari, Daniele Toti, Le Viet Hung, Maurizio Di Stefano, Fabio Polticelli:
ASSIST: a fast versatile local structural comparison tool. 1022-1024
- Eric Wu, Tracy Nance, Stephen B. Montgomery:
SplicePlot: a utility for visualizing splicing quantitative trait loci. 1025-1026
- Ida Moltke, Anders Albrechtsen:
RelateAdmix: a software tool for estimating relatedness between admixed individuals. 1027-1028
- Charles Winterhalter, Pawel Widera, Natalio Krasnogor:
JEPETTO: a Cytoscape plugin for gene set enrichment and topological analysis based on interaction networks. 1029-1030 - Xiaoquan Su, Xuetao Wang, Gongchao Jing, Kang Ning:
GPU-Meta-Storms: computing the structure similarities among massive amount of microbial community samples using GPU. 1031-1033 - Jan Taubert, Keywan Hassani-Pak, Nathalie Castells-Brooke, Christopher J. Rawlings:
Ondex Web: web-based visualization and exploration of heterogeneous biological networks. 1034-1035 - John T. Sauls, Joerg M. Buescher:
Assimilating genome-scale metabolic reconstructions with modelBorgifier. 1036-1038
- Anabel Usie, Rui Alves, Francesc Solsona, Miguel Vazquez, Alfonso Valencia:
CheNER: chemical named entity recognizer. 1039-1040 - Rodrigo Aldecoa, Ignacio Marín:
SurpriseMe: an integrated tool for network community structure characterization using Surprise maximization. 1041-1042
- Mengyuan Fan, Hong Sang Low, Hufeng Zhou, Markus R. Wenk, Limsoon Wong:
LipidGO: database for lipid-related GO terms and applications. 1043-1044 - Changqing Zhang, Guangping Li, Shinong Zhu, Shuo Zhang, Jinggui Fang:
tasiRNAdb: a database of ta-siRNA regulatory pathways. 1045-1046
- Nestoras Karathanasis, Ioannis Tsamardinos, Panayiota Poirazi:
Don't use a cannon to kill the ... miRNA mosquito. 1047-1048
Volume 30, Number 8, April 2014
- Xihao Hu, Thomas K. F. Wong, Zhi John Lu, Ting-Fung Chan, Terrence Chi-Kong Lau, Siu-Ming Yiu, Kevin Y. Yip:
Computational identification of protein binding sites on RNAs using high-throughput RNA structure-probing data. 1049-1055 - Lei Bao, Minya Pu, Karen Messer:
AbsCN-seq: a statistical method to estimate tumor purity, ploidy and absolute copy numbers from next-generation sequencing data. 1056-1063 - Jan Schröder, Arthur L. Hsu, Samantha E. Boyle, Geoff MacIntyre, Marek Cmero, Richard W. Tothill, Ricky W. Johnstone, Mark Shackleton, Anthony T. Papenfuss:
Socrates: identification of genomic rearrangements in tumour genomes by re-aligning soft clipped reads. 1064-1072 - Wanding Zhou, Tenghui Chen, Hao Zhao, Agda Karina Eterovic, Funda Meric-Bernstam, Gordon B. Mills, Ken Chen:
Bias from removing read duplication in ultra-deep sequencing experiments. 1073-1080
- Kamil S. Jaron, Jirí C. Moravec, Natália Martínková:
SigHunt: horizontal gene transfer finder optimized for eukaryotic genomes. 1081-1086 - Joao C. Guimaraes, Miguel Rocha, Adam P. Arkin, Guillaume Cambray:
D-Tailor: automated analysis and design of DNA sequences. 1087-1094 - Atsushi Kurotani, Alexander A. Tokmakov, Yutaka Kuroda, Yasuo Fukami, Kazuo Shinozaki, Tetsuya Sakurai:
Correlations between predicted protein disorder and post-translational modifications in plants. 1095-1103 - Josep Gregori, Miquel Salicru, Esteban Domingo, Alex Sánchez-Pla, Juan I. Esteban, Francisco Rodríguez-Frías, Josep Quer:
Inference with viral quasispecies diversity indices: clonal and NGS approaches. 1104-1111 - Ka-Chun Wong, Zhaolei Zhang:
SNPdryad: predicting deleterious non-synonymous human SNPs using only orthologous protein sequences. 1112-1119 - Ha X. Dang, Christopher B. Lawrence:
Allerdictor: fast allergen prediction using text classification techniques. 1120-1128
- Mario Valle, Hannes Schabauer, Christoph Pacher, Heinz Stockinger, Alexandros Stamatakis, Marc Robinson-Rechavi, Nicolas Salamin:
Optimization strategies for fast detection of positive selection on phylogenetic trees. 1129-1137
- Derek J. Pitman, Christian D. Schenkelberg, Yao-ming Huang, Frank D. Teets, Daniel J. DiTursi, Christopher Bystroff:
Improving computational efficiency and tractability of protein design using a piecemeal approach. A strategy for parallel and distributed protein design. 1138-1145
- Antti Häkkinen, Meenakshisundaram Kandhavelu, Stefania Garasto, Andre S. Ribeiro:
Estimation of fluorescence-tagged RNA numbers from spot intensities. 1146-1153 - Hans-Ulrich Klein, Martin Schäfer, Bo T. Porse, Marie S. Hasemann, Katja Ickstadt, Martin Dugas:
Integrative analysis of histone ChIP-seq and transcription data using Bayesian mixture models. 1154-1162
- Ming Wu, Christina Chan:
Prediction of therapeutic microRNA based on the human metabolic network. 1163-1171
- Hamid Younesy, Torsten Möller, Alireza Heravi Moussavi, Jeffrey B. Cheng, Joseph F. Costello, Matthew C. Lorincz, Mohammad M. Karimi, Steven J. M. Jones:
ALEA: a toolbox for allele-specific epigenomics analysis. 1172-1174 - Jianchao Yao, Kelvin Xi Zhang, Melissa Kramer, Matteo Pellegrini, W. Richard McCombie:
FamAnn: an automated variant annotation pipeline to facilitate target discovery for family-based sequencing studies. 1175-1176 - Luis Cebamanos, Alan Gray, I. Stewart, Albert Tenesa:
Regional heritability advanced complex trait analysis for GPU and traditional parallel architectures. 1177-1179 - An Xiao, Zhenchao Cheng, Lei Kong, Zuoyan Zhu, Shuo Lin, Ge Gao, Bo Zhang:
CasOT: a genome-wide Cas9/gRNA off-target searching tool. 1180-1182
- Emmanuel Dimont, Oliver Hofmann, Shannan J. Ho Sui, Alistair R. R. Forrest, Hideya Kawaji, Winston Hide:
CAGExploreR: an R package for the analysis and visualization of promoter dynamics across multiple experiments. 1183-1184
- Peter J. van der Most, Ahmad Vaez, Bram P. Prins, M. Loretto Munoz, Harold Snieder, Behrooz Z. Alizadeh, Ilja M. Nolte:
QCGWAS: A flexible R package for automated quality control of genome-wide association results. 1185-1186 - Jean-Marie Cornuet, Pierre Pudlo, Julien Veyssier, Alexandre Dehne-Garcia, Mathieu Gautier, Raphaël Leblois, Jean-Michel Marin, Arnaud Estoup:
DIYABC v2.0: a software to make approximate Bayesian computation inferences about population history using single nucleotide polymorphism, DNA sequence and microsatellite data. 1187-1189
- Daogang Guan, Jiaofang Shao, Youping Deng, Panwen Wang, Zhongying Zhao, Yan Liang, Junwen Wang, Bin Yan:
CMGRN: a web server for constructing multilevel gene regulatory networks using ChIP-seq and gene expression data. 1190-1192
Volume 30, Number 9, May 2014
- Joseph P. Cornish, Neus Sanchez-Alberola, Patrick K. O'Neill, Ronald O'Keefe, Jameel Gheba, Ivan Erill:
Characterization of the SOS meta-regulon in the human gut microbiome. 1193-1197
- Moritz Gerstung, Elli Papaemmanuil, Peter J. Campbell:
Subclonal variant calling with multiple samples and prior knowledge. 1198-1204
- Hannes Planatscher, Frederik Weiß, David Eisen, B. H. J. van den Berg, Andreas Zell, Thomas Joos, Oliver Poetz:
Identification of short terminal motifs enriched by antibodies using peptide mass fingerprinting. 1205-1213 - Chengxi Ye, Chiaowen Hsiao, Héctor Corrada Bravo:
BlindCall: ultra-fast base-calling of high-throughput sequencing data by blind deconvolution. 1214-1219 - Gorka Prieto, Asier Fullaondo, Jose A. Rodriguez:
Prediction of nuclear export signals using weighted regular expressions (Wregex). 1220-1227 - Jared T. Simpson:
Exploring genome characteristics and sequence quality without a reference. 1228-1235 - Philip Jones, David Binns, Hsin-Yu Chang, Matthew Fraser, Weizhong Li, Craig McAnulla, Hamish McWilliam, John Maslen, Alex L. Mitchell, Gift Nuka, Sebastien Pesseat, Antony F. Quinn, Amaia Sangrador-Vegas, Maxim Scheremetjew, Siew-Yit Yong, Rodrigo Lopez, Sarah Hunter:
InterProScan 5: genome-scale protein function classification. 1236-1240
- Linda Dib, Daniele Silvestro, Nicolas Salamin:
Evolutionary footprint of coevolving positions in genes. 1241-1249
- Ali Esmaili-Taheri, Mohammad Ganjtabesh, Morteza Mohammad Noori:
Evolutionary solution for the RNA design problem. 1250-1258 - Noël Malod-Dognin, Natasa Przulj:
GR-Align: fast and flexible alignment of protein 3D structures using graphlet degree similarity. 1259-1265
- Richard Durbin:
Efficient haplotype matching and storage using the positional Burrows-Wheeler transform (PBWT). 1266-1272
- Stefan Maetschke, Mark A. Ragan:
Characterizing cancer subtypes as attractors of Hopfield networks. 1273-1279
- Pierre Mahé, Maud Arsac, Sonia Chatellier, Valérie Monnin, Nadine Perrot, Sandrine Mailler, Victoria Girard, Mahendrasingh Ramjeet, Jérémy Surre, Bruno Lacroix, Alex van Belkum, Jean-Baptiste Veyrieras:
Automatic identification of mixed bacterial species fingerprints in a MALDI-TOF mass-spectrum. 1280-1286
- Burcu Bakir-Gungor, Ece Egemen, Osman Ugur Sezerman:
PANOGA: a web server for identification of SNP-targeted pathways from genome-wide association study data. 1287-1289 - David Sims, Nicholas E. Ilott, Stephen N. Sansom, Ian M. Sudbery, Jethro S. Johnson, Katherine A. Fawcett, Antonio J. Berlanga-Taylor, Sebastian Luna-Valero, Chris P. Ponting, Andreas Heger:
CGAT: computational genomics analysis toolkit. 1290-1291 - Samuel A. Assefa, Mark D. Preston, Susana G. Campino, Harold Ocholla, Colin J. Sutherland, Taane G. Clark:
estMOI: estimating multiplicity of infection using parasite deep sequencing data. 1292-1294 - Xin Lu, Roman K. Thomas, Martin Peifer:
CGARS: cancer genome analysis by rank sums. 1295-1296 - Yongbing Zhao, Xinmiao Jia, Junhui Yang, Yunchao Ling, Zhang Zhang, Jun Yu, Jiayan Wu, Jing-Fa Xiao:
PanGP: A tool for quickly analyzing bacterial pan-genome profile. 1297-1299
- Vipin T. Sreedharan, Sebastian J. Schultheiß, Géraldine Jean, André Kahles, Regina Bohnert, Philipp Drewe, Pramod Mudrakarta, Nico Görnitz, Georg Zeller, Gunnar Rätsch:
Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis. 1300-1301 - Michael T. McCarthy, Christopher A. O'Callaghan:
PeaKDEck: a kernel density estimator-based peak calling program for DNaseI-seq data. 1302-1304 - Glen Stecher, Li Liu, Maxwell D. Sanderford, Daniel Peterson, Koichiro Tamura, Sudhir Kumar:
MEGA-MD: molecular evolutionary genetics analysis software with mutational diagnosis of amino acid variation. 1305-1307
- Garry Jolley-Rogers, Temi Varghese, Paul Harvey, Nick dos Remedios, Joseph T. Miller:
PhyloJIVE: Integrating biodiversity data with the Tree of Life. 1308-1309 - Jose Manuel Santorum, Diego Darriba, Guillermo L. Taboada, David Posada:
jmodeltest.org: selection of nucleotide substitution models on the cloud. 1310-1311 - Alexandros Stamatakis:
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. 1312-1313
- Alejandro Panjkovich, Xavier Daura:
PARS: a web server for the prediction of Protein Allosteric and Regulatory Sites. 1314-1315
- Qiang Fu, Ana Carolina Fierro, Pieter Meysman, Aminael Sánchez-Rodríguez, Klaas Vandepoele, Kathleen Marchal, Kristof Engelen:
MAGIC: access portal to a cross-platform gene expression compendium for maize. 1316-1318 - Ivan Montiel, Charlotte Konikoff, Bremen L. Braun, Mary Packard, L. Sian Gramates, Qian Sun, Jieping Ye, Sudhir Kumar:
myFX: a turn-key software for laboratory desktops to analyze spatial patterns of gene expression in Drosophila embryos. 1319-1321 - Laurent Gatto, Lisa M. Breckels, Samuel Wieczorek, Thomas Burger, Kathryn S. Lilley:
Mass-spectrometry-based spatial proteomics data analysis using pRoloc and pRolocdata. 1322-1324 - Yupeng Cun, Holger Fröhlich:
netClass: an R-package for network based, integrative biomarker signature discovery. 1325-1326
- Paul A. Jensen, Jason A. Papin:
MetDraw: automated visualization of genome-scale metabolic network reconstructions and high-throughput data. 1327-1328 - Kieran O'Neill, Adrin Jalali, Nima Aghaeepour, Holger H. Hoos, Ryan Remy Brinkman:
Enhanced flowType/RchyOptimyx: a Bioconductor pipeline for discovery in high-dimensional cytometry data. 1329-1330 - Jörn Starruß, Walter de Back, Lutz Brusch, Andreas Deutsch:
Morpheus: a user-friendly modeling environment for multiscale and multicellular systems biology. 1331-1332 - Jamey D. Young:
INCA: a computational platform for isotopically non-stationary metabolic flux analysis. 1333-1335 - Ricardo Roberto da Silva, Fabien Jourdan, Diego M. Salvanha, Fabien Létisse, Emilien L. Jamin, Simone Guidetti-Gonzalez, Carlos A. Labate, Ricardo Z. N. Vêncio:
ProbMetab: an R package for Bayesian probabilistic annotation of LC-MS-based metabolomics. 1336-1337
- Simon Jupp, James Malone, Jerven T. Bolleman, Marco Brandizi, Mark Davies, Leyla J. García, Anna Gaulton, Sebastien Gehant, Camille Laibe, Nicole Redaschi, Sarala M. Wimalaratne, Maria Jesus Martin, Nicolas Le Novère, Helen E. Parkinson, Ewan Birney, Andrew M. Jenkinson:
The EBI RDF platform: linked open data for the life sciences. 1338-1339 - Jie Zheng, Zuoshuang Xiang, Christian J. Stoeckert Jr., Yongqun He:
Ontodog: a web-based ontology community view generation tool. 1340-1342
Volume 30, Number 10, May 2014
- Clara Pizzuti, Simona E. Rombo:
Algorithms and tools for protein-protein interaction networks clustering, with a special focus on population-based stochastic methods. 1343-1352
- Robert F. Murphy:
A new era in bioimage informatics. 1353
- Yun Heo, Xiaolong Wu, Deming Chen, Jian Ma, Wen-mei W. Hwu:
BLESS: Bloom filter-based error correction solution for high-throughput sequencing reads. 1354-1362 - Martin J. Aryee, Andrew E. Jaffe, Héctor Corrada Bravo, Christine Ladd-Acosta, Andrew P. Feinberg, Kasper D. Hansen, Rafael A. Irizarry:
Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays. 1363-1369 - Priyadip Ray, Lingling Zheng, Joseph E. Lucas, Lawrence Carin:
Bayesian joint analysis of heterogeneous genomics data. 1370-1376
- Xiaowei Wang:
Composition of seed sequence is a major determinant of microRNA targeting patterns. 1377-1383 - Kaiyong Zhao, Xiaowen Chu:
G-BLASTN: accelerating nucleotide alignment by graphics processors. 1384-1391
- Marta Rosikiewicz, Marc Robinson-Rechavi:
IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics. 1392-1399 - Iwona Pawlikowska, Gang Wu, Michael N. Edmonson, Zhifa Liu, Tanja Gruber, Jinghui Zhang, Stan Pounds:
The most informative spacing test effectively discovers biologically relevant outliers or multiple modes in expression. 1400-1408 - Bogdan Mirauta, Pierre Nicolas, Hugues Richard:
Parseq: reconstruction of microbial transcription landscape from RNA-Seq read counts using state-space models. 1409-1416 - Martin Vincent, Katharina Perell, Finn Cilius Nielsen, Gedske Daugaard, Niels Richard Hansen:
Modeling tissue contamination to improve molecular identification of the primary tumor site of metastases. 1417-1423 - Klaus Jung, Hassan Dihazi, Asima Bibi, Gry H. Dihazi, Tim Beißbarth:
Adaption of the global test idea to proteomics data with missing values. 1424-1430
- Eugene Andres Houseman, John Molitor, Carmen J. Marsit:
Reference-free cell mixture adjustments in analysis of DNA methylation data. 1431-1439
- Andreas Raue, Johan Karlsson, Maria Pia Saccomani, Mats Jirstrand, Jens Timmer:
Comparison of approaches for parameter identifiability analysis of biological systems. 1440-1448 - Dana Silverbush, Roded Sharan:
Network orientation via shortest paths. 1449-1455 - Kaifang Pang, Ying-Wooi Wan, William T. Choi, Lawrence A. Donehower, Jingchun Sun, Dhruv Pant, Zhandong Liu:
Combinatorial therapy discovery using mixed integer linear programming. 1456-1463
- Paul Theodor Pyl, Julian Gehring, Bernd Fischer, Wolfgang Huber:
h5vc: scalable nucleotide tallies with HDF5. 1464-1466 - Alex Chun-Hong Fok, Sunny Siu-Nam Mok, Sau Dan Lee, Kevin Y. Yip:
ECplot: an online tool for making standardized plots from large datasets for bioinformatics publications. 1467-1468 - Andrey Tovchigrechko, Pratap Venepally, Samuel H. Payne:
PGP: parallel prokaryotic proteogenomics pipeline for MPI clusters, high-throughput batch clusters and multicore workstations. 1469-1470
- Fabian A. Buske, Hugh J. French, Martin A. Smith, Susan J. Clark, Denis C. Bauer:
NGSANE: a lightweight production informatics framework for high-throughput data analysis. 1471-1472 - Sangsu Bae, Jeongbin Park, Jin-Soo Kim:
Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases. 1473-1475
- Fernando Izquierdo-Carrasco, John Cazes, Stephen A. Smith, Alexandros Stamatakis:
PUmPER: phylogenies updated perpetually. 1476-1477
- Ramon Guixà-González, Ismael Rodriguez-Espigares, Juan Manuel Ramírez-Anguita, Pau Carrió-Gaspar, Hector Martinez-Seara, Toni Giorgino, Jana Selent:
MEMBPLUGIN: studying membrane complexity in VMD. 1478-1480 - Jamel Meslamani, Steven G. Smith, Roberto Sanchez, Ming-Ming Zhou:
ChEpiMod: a knowledgebase for chemical modulators of epigenome reader domains. 1481-1483
- Sander Bollen, Mathias Leddin, Miguel A. Andrade-Navarro, Nancy Mah:
CAFE: an R package for the detection of gross chromosomal abnormalities from gene expression microarray data. 1484-1485
- Matteo Fumagalli, Filipe G. Vieira, Tyler Linderoth, Rasmus Nielsen:
ngsTools: methods for population genetics analyses from next-generation sequencing data. 1486-1487 - James T. Monacell, Ignazio Carbone:
Mobyle SNAP Workbench: a web-based analysis portal for population genetics and evolutionary genomics. 1488-1490
- Michael Pedersen, Nicolas Oury, Colin Gravill, Andrew Phillips:
Bio Simulators: a web UI for biological simulation. 1491-1492
Volume 30, Number 11, June 2014
- Charles C. Berry, Karen E. Ocwieja, Nirav Malani, Frederic D. Bushman:
Comparing DNA integration site clusters with scan statistics. 1493-1500 - Jun Hu, Jung-Ying Tzeng:
Integrative gene set analysis of multi-platform data with sample heterogeneity. 1501-1507 - Megan J. Puckelwartz, Lorenzo L. Pesce, Viswateja Nelakuditi, Lisa Dellefave-Castillo, Jessica R. Golbus, Sharlene M. Day, Thomas P. Cappola, Gerald W. Dorn II, Ian T. Foster, Elizabeth M. McNally:
Supercomputing for the parallelization of whole genome analysis. 1508-1513
- Eitan Halper-Stromberg, Jared Steranka, Kathleen H. Burns, Sarven Sabunciyan, Rafael A. Irizarry:
Visualization and probability-based scoring of structural variants within repetitive sequences. 1514-1521 - Shou-Hui Guo, En-Ze Deng, Liqin Xu, Hui Ding, Hao Lin, Wei Chen, Kuo-Chen Chou:
iNuc-PseKNC: a sequence-based predictor for predicting nucleosome positioning in genomes with pseudo k-tuple nucleotide composition. 1522-1529 - Ali May, Sanne Abeln, Wim Crielaard, Jaap Heringa, Bernd W. Brandt:
Unraveling the outcome of 16S rDNA-based taxonomy analysis through mock data and simulations. 1530-1538
- Toby Dylan Hocking, Valentina Boeva, Guillem Rigaill, Gudrun Schleiermacher, Isabelle Janoueix-Lerosey, Olivier Delattre, Wilfrid Richer, Franck Bourdeaut, Miyuki Suguro, Masao Seto, Francis R. Bach, Jean-Philippe Vert:
SegAnnDB: interactive Web-based genomic segmentation. 1539-1546 - Peng Yu, Chad A. Shaw:
An efficient algorithm for accurate computation of the Dirichlet-multinomial log-likelihood function. 1547-1554 - Daniah Trabzuni, Peter C. Thomson:
Analysis of gene expression data using a linear mixed model/finite mixture model approach: application to regional differences in the human brain. 1555-1561
- David C. Kessler, Jack A. Taylor, David B. Dunson:
Learning phenotype densities conditional on many interacting predictors. 1562-1568
- Kristopher A. Hunt, James P. Folsom, Reed L. Taffs, Ross P. Carlson:
Complete enumeration of elementary flux modes through scalable demand-based subnetwork definition. 1569-1578 - Rui Liu, Xiangtian Yu, Xiaoping Liu, Dong Xu, Kazuyuki Aihara, Luonan Chen:
Identifying critical transitions of complex diseases based on a single sample. 1579-1586
- Deyu Zhou, Dayou Zhong, Yulan He:
Event trigger identification for biomedical events extraction using domain knowledge. 1587-1594
- Clinton J. Mielke, Lawrence J. Mandarino, Valentin Dinu:
AMASS: a database for investigating protein structures. 1595-1600
- Petr Klus, Benedetta Bolognesi, Federico Agostini, Domenica Marchese, Andreas Zanzoni, Gian Gaetano Tartaglia:
The cleverSuite approach for protein characterization: predictions of structural properties, solubility, chaperone requirements and RNA-binding abilities. 1601-1608
- Martin Maska, Vladimír Ulman, David Svoboda, Pavel Matula, Petr Matula, Cristina Ederra, Ainhoa Urbiola, Tomás España, Subramanian Venkatesan, Deepak M. W. Balak, Pavel Karas, Tereza Bolcková, Markéta Streitová, Craig Carthel, Stefano Coraluppi, Nathalie Harder, Karl Rohr, Klas E. G. Magnusson, Joakim Jaldén, Helen M. Blau, Oleh Dzyubachyk, Pavel Krízek, Guy M. Hagen, David Pastor-Escuredo, Daniel Jimenez-Carretero, María J. Ledesma-Carbayo, Arrate Muñoz-Barrutia, Erik Meijering, Michal Kozubek, Carlos Ortiz-de-Solorzano:
A benchmark for comparison of cell tracking algorithms. 1609-1617
- Andy Pohl, Miguel Beato:
bwtool: a tool for bigWig files. 1618-1619 - Jonas Paulsen, Geir Kjetil Sandve, Sveinung Gundersen, Tonje Lien, Kai Trengereid, Eivind Hovig:
HiBrowse: multi-purpose statistical analysis of genome-wide chromatin 3D organization. 1620-1622 - Jeffrey B. Endelman, Christophe Plomion:
LPmerge: an R package for merging genetic maps by linear programming. 1623-1624
- Paul C. Lott, Ian Korf:
StochHMM: a flexible hidden Markov model tool and C++ library. 1625-1626 - Travis M. Drucker, Sarah H. Johnson, Stephen J. Murphy, Kendall W. Cradic, Terry M. Therneau, George Vasmatzis:
BIMA V3: an aligner customized for mate pair library sequencing. 1627-1629
- Raúl Aguirre-Gamboa, Victor Trevino:
SurvMicro: assessment of miRNA-based prognostic signatures for cancer clinical outcomes by multivariate survival analysis. 1630-1632
- Pete Donnell, Murad Banaji, Anca Marginean, Casian Pantea:
CoNtRol: an open source framework for the analysis of chemical reaction networks. 1633-1634
- Natalia Novoselova, Cristina Della Beffa, Junxi Wang, Jialiang Li, Frank Pessler, Frank Klawonn:
HUM calculator and HUM package for R: easy-to-use software tools for multicategory receiver operating characteristic analysis. 1635-1636
- Mark Maienschein-Cline, Zhengdeng Lei, Vincent Gardeux, Taimur Abbasi, Roberto F. Machado, Victor Gordeuk, Ankit A. Desai, Santosh Saraf, Neil Bahroos, Yves A. Lussier:
ARTS: automated randomization of multiple traits for study design. 1637-1639 - Chao Li, Xiao Dong, Haiwei Fan, Chuan Wang, Guohui Ding, Yixue Li:
The 3DGD: a database of genome 3D structure. 1640-1642
Volume 30, Number 12, June 2014
- Serafim Batzoglou, Russell Schwartz:
Editorial. 1-2
- Cristina G. Ghiurcuta, Bernard M. E. Moret:
Evaluating synteny for improved comparative studies. 9-18 - Ya'ara Arkin, Elior Rahmani, Marcus E. Kleber, Reijo Laaksonen, Winfried März, Eran Halperin:
EPIQ - efficient detection of SNP-SNP epistatic interactions for quantitative traits. 19-25 - Nelle Varoquaux, Ferhat Ay, William Stafford Noble, Jean-Philippe Vert:
A statistical approach for inferring the 3D structure of the genome. 26-33 - Michael Kramer, Janusz Dutkowski, Michael Yu, Vineet Bafna, Trey Ideker:
Inferring gene ontologies from pairwise similarity data. 34-42 - Terumasa Tokunaga, Osamu Hirose, Shotaro Kawaguchi, Yu Toyoshima, Takayuki Teramoto, Hisaki Ikebata, Sayuri Kuge, Takeshi Ishihara, Yuichi Iino, Ryo Yoshida:
Automated detection and tracking of many cells by using 4D live-cell imaging data. 43-51 - Anika Oellrich, Julius O. B. Jacobsen, Irene Papatheodorou, Damian Smedley:
Using association rule mining to determine promising secondary phenotyping hypotheses. 52-59 - Nagarajan Natarajan, Inderjit S. Dhillon:
Inductive matrix completion for predicting gene-disease associations. 60-68 - Kourosh Zarringhalam, Ahmed Enayetallah, Padmalatha Reddy, Daniel Ziemek:
Robust clinical outcome prediction based on Bayesian analysis of transcriptional profiles and prior causal networks. 69-77 - Iman Hajirasouliha, Ahmad Mahmoody, Benjamin J. Raphael:
A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data. 78-86 - Ran Libeskind-Hadas, Yi-Chieh Wu, Mukul S. Bansal, Manolis Kellis:
Pareto-optimal phylogenetic tree reconciliation. 87-95 - Andrei Todor, Haitham Gabr, Alin Dobra, Tamer Kahveci:
Large scale analysis of signal reachability. 96-104 - Christoph Bernau, Markus Riester, Anne-Laure Boulesteix, Giovanni Parmigiani, Curtis Huttenhower, Levi Waldron, Lorenzo Trippa:
Cross-study validation for the assessment of prediction algorithms. 105-112 - Tarmo Äijö, Vincent Butty, Zhi Jane Chen, Verna Salo, Subhash Tripathi, Christopher B. Burge, Riitta Lahesmaa, Harri Lähdesmäki:
Methods for time series analysis of RNA-seq data with application to human Th17 cell differentiation. 113-120 - Michael K. K. Leung, Hui Yuan Xiong, Leo J. Lee, Brendan J. Frey:
Deep learning of the tissue-regulated splicing code. 121-129 - Matthew Studham, Andreas Tjärnberg, Torbjörn E. M. Nordling, Sven Nelander, Erik L. L. Sonnhammer:
Functional association networks as priors for gene regulatory network inference. 130-138 - Wei Cheng, Xiang Zhang, Zhishan Guo, Yu Shi, Wei Wang:
Graph-regularized dual Lasso for robust eQTL mapping. 139-148 - Anke Penzlin, Martin S. Lindner, Joerg Doellinger, Piotr Wojtek Dabrowski, Andreas Nitsche, Bernhard Y. Renard:
Pipasic: similarity and expression correction for strain-level identification and quantification in metaproteomics. 149-156 - Huibin Shen, Kai Dührkop, Sebastian Böcker, Juho Rousu:
Metabolite identification through multiple kernel learning on fragmentation trees. 157-164 - Masaaki Kotera, Yasuo Tabei, Yoshihiro Yamanishi, Ai Muto, Yuki Moriya, Toshiaki Tokimatsu, Susumu Goto:
Metabolome-scale prediction of intermediate compounds in multistep metabolic pathways with a recursive supervised approach. 165-174 - A. Ercüment Çiçek, Kathryn Roeder, Gultekin Özsoyoglu:
MIRA: mutual information-based reporter algorithm for metabolic networks. 175-184 - Richard Leslie, Christopher J. O'Donnell, Andrew D. Johnson:
GRASP: analysis of genotype-phenotype results from 1390 genome-wide association studies and corresponding open access database. 185-194 - Hsin-Ta Wu, Iman Hajirasouliha, Benjamin J. Raphael:
Detecting independent and recurrent copy number aberrations using interval graphs. 195-203 - Farhad Hormozdiari, Jong Wha J. Joo, Akshay Wadia, Feng Guan, Rafail Ostrovsky, Amit Sahai, Eleazar Eskin:
Privacy preserving protocol for detecting genetic relatives using rare variants. 204-211 - Ladislav Rampásek, Aryan Arbabi, Michael Brudno:
Probabilistic method for detecting copy number variation in a fetal genome using maternal plasma sequencing. 212-218 - Mengfei Cao, Christopher M. Pietras, Xian Feng, Kathryn J. Doroschak, Thomas Schaffner, Jisoo Park, Hao Zhang, Lenore J. Cowen, Benjamin J. Hescott:
New directions for diffusion-based network prediction of protein function: incorporating pathways with confidence. 219-227 - Lei Huang, Fuhai Li, Jianting Sheng, Xiaofeng Xia, Jinwen Ma, Ming Zhan, Stephen T. C. Wong:
DrugComboRanker: drug combination discovery based on target network analysis. 228-236 - Marc Hulsman, Christos Dimitrakopoulos, Jeroen de Ridder:
Scale-space measures for graph topology link protein network architecture to function. 237-245 - Marinka Zitnik, Blaz Zupan:
Gene network inference by probabilistic scoring of relationships from a factorized model of interactions. 246-254 - Yichao Zhou, Wei Xu, Bruce Randall Donald, Jianyang Zeng:
An efficient parallel algorithm for accelerating computational protein design. 255-263 - Jing Ren, Qian Liu, John T. Ellis, Jinyan Li:
Tertiary structure-based prediction of conformational B-cell epitopes through B factors. 264-273 - Pavankumar Videm, Dominic Rose, Fabrizio Costa, Rolf Backofen:
BlockClust: efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles. 274-282 - Zhaojun Zhang, Wei Wang:
RNA-Skim: a rapid method for RNA-Seq quantification at transcript level. 283-292 - Andrey D. Prjibelski, Irina Vasilinetc, Anton Bankevich, Alexey A. Gurevich, Tatiana Krivosheeva, Sergey Nurk, Son K. Pham, Anton I. Korobeynikov, Alla L. Lapidus, Pavel A. Pevzner:
ExSPAnder: a universal repeat resolver for DNA fragment assembly. 293-301 - Mikhail Kolmogorov, Brian J. Raney, Benedict Paten, Son K. Pham:
Ragout - a reference-assisted assembly tool for bacterial genomes. 302-309 - Alastair M. Kilpatrick, Bruce Ward, Stuart Aitken:
Stochastic EM-based TFBS motif discovery with MITSU. 310-318 - Ergude Bao, Tao Jiang, Thomas Girke:
AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references. 319-328 - Serghei Mangul, Nicholas C. Wu, Nicholas Mancuso, Alex Zelikovsky, Ren Sun, Eleazar Eskin:
Accurate viral population assembly from ultra-deep sequencing data. 329-337
- Guofeng Meng, Martin Vingron:
Condition-specific target prediction from motifs and expression. 1643-1650 - Seyed Yahya Anvar, Kristiaan J. van der Gaag, Jaap W. F. van der Heijden, Marcel H. A. M. Veltrop, Rolf H. A. M. Vossen, Rick H. de Leeuw, Cor Breukel, Henk P. J. Buermans, J. Sjef Verbeek, Peter de Knijff, Johan T. den Dunnen, Jeroen F. J. Laros:
TSSV: a tool for characterization of complex allelic variants in pure and mixed genomes. 1651-1659
- Yinlong Xie, Gengxiong Wu, Jingbo Tang, Ruibang Luo, Jordan Patterson, Shanlin Liu, Weihua Huang, Guangzhu He, Shengchang Gu, Shengkang Li, Xin Zhou, Tak Wah Lam, Yingrui Li, Xun Xu, Gane Ka-Shu Wong, Jun Wang:
SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads. 1660-1666 - Daniel Quang, Xiaohui Xie:
EXTREME: an online EM algorithm for motif discovery. 1667-1673
- Yang Cao, Lei Li:
Improved protein-ligand binding affinity prediction by using a curvature-dependent surface-area model. 1674-1680 - Ken Nagata, Arlo Z. Randall, Pierre Baldi:
Incorporating post-translational modifications and unnatural amino acids into high-throughput modeling of protein structures. 1681-1689
- Kevin H. Eng, Bret M. Hanlon:
Discrete mixture modeling to address genetic heterogeneity in time-to-event regression. 1690-1697 - H. Robert Frost, Jason H. Moore:
Optimization of gene set annotations via entropy minimization over variable clusters (EMVC). 1698-1706
- Anthony Youzhi Cheng, Yik-Ying Teo, Rick Twee-Hee Ong:
Assessing single nucleotide variant detection and genotype calling on whole-genome sequenced individuals. 1707-1713 - Jin Zhou, Erwin Tantoso, Lai-Ping Wong, Rick Twee-Hee Ong, Jin-Xin Bei, Yi Li, Jianjun Liu, Chiea-Chuen Khor, Yik-Ying Teo:
iCall: a genotype-calling algorithm for rare, low-frequency and common variants on the Illumina exome array. 1714-1720
- Fazle Elahi Faisal, Tijana Milenkovic:
Dynamic networks reveal key players in aging. 1721-1729 - Nikhil Prakash Damle, Debasisa Mohanty:
Deciphering kinase-substrate relationships by analysis of domain-specific phosphorylation network. 1730-1738
- Hsiu-Sen Chiang, Dong-Her Shih, Binshan Lin, Ming-Hung Shih:
An APN model for Arrhythmic beat classification. 1739-1746
- Eduard Hermann, Stephanie Bleicken, Yamunadevi Subburaj, Ana J. García-Sáez:
Automated analysis of giant unilamellar vesicles using circular Hough transformation. 1747-1754
- Yeonok Lee, Debashis Ghosh, Ross C. Hardison, Yu Zhang:
MRHMMs: Multivariate Regression Hidden Markov Models and the variantS. 1755-1756 - Jordi Deu-Pons, Michael P. Schroeder, Núria López-Bigas:
jHeatmap: an interactive heatmap viewer for the web. 1757-1758 - Ramón Díaz-Uriarte:
ADaCGH2: parallelized analysis of (big) CNA data. 1759-1761 - Adrian Lärkeryd, Kerstin Myrtennäs, Edvin Karlsson, Chinmay Kumar Dwibedi, Mats Forsman, Pär Larsson, Anders Johansson, Andreas Sjödin:
CanSNPer: a hierarchical genotype classifier of clonal pathogens. 1762-1764
- Maxim I. Pyatkov, Anton N. Pankratov:
SBARS: fast creation of dotplots for DNA sequences on different scales using GA-, GC-content. 1765-1766 - Francisco J. López-Domingo, Javier Perez-Florido, Antonio Rueda, Joaquín Dopazo, Javier Santoyo-Lopez:
ngsCAT: a tool to assess the efficiency of targeted enrichment sequencing. 1767-1768
- Tim Seifert, Andreas Lund, Benny Kneissl, Sabine C. Mueller, Christofer S. Tautermann, Andreas Hildebrandt:
SKINK: a web server for string kernel based kink prediction in α-helices. 1769-1770 - Brian G. Pierce, Kevin Wiehe, Howook Hwang, Bong-Hyun Kim, Thom Vreven, Zhiping Weng:
ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers. 1771-1773 - Ling-Hong Hung, Ram Samudrala:
fast_protein_cluster: parallel and optimized clustering of large-scale protein modeling data. 1774-1776
- Xi Wang, Murray J. Cairns:
SeqGSEA: a Bioconductor package for gene set enrichment analysis of RNA-Seq data integrating differential expression and splicing. 1777-1779 - Mario Huerta, Marc Munyi, David Expósito, Enric Querol, Juan Cedano:
MGDB: crossing the marker genes of a user microarray with a database of public-microarrays marker genes. 1780-1781 - Matias D. Butti, Hernan Chanfreau, Diego Martínez, Diego García, Ezequiel Lacunza, Martin C. Abba:
BioPlat: a software for human cancer biomarker discovery. 1782-1784 - Rodrigo Santamaría, Roberto Therón, Luis Quintales:
BicOverlapper 2.0: visual analysis for gene expression. 1785-1786
- Diego Carrella, Francesco Napolitano, Rossella Rispoli, Mario Miglietta, Annamaria Carissimo, Luisa Cutillo, Francesco Sirci, Francesco Gregoretti, Diego di Bernardo:
Mantra 2.0: an online collaborative resource for drug mode of action and repurposing by network analysis. 1787-1788 - Emre Guney, Javier García-García, Baldo Oliva:
GUILDify: a web server for phenotypic characterization of genes through biological data integration and network-based prioritization algorithms. 1789-1790
- Kim M. Rutherford, Midori A. Harris, Antonia Lock, Stephen G. Oliver, Valerie Wood:
Canto: an online tool for community literature curation. 1791-1792
Volume 30, Number 13, July 2014
- Manja Marz, Niko Beerenwinkel, Christian Drosten, Markus Fricke, Dmitrij Frishman, Ivo L. Hofacker, Dieter Hoffmann, Martin Middendorf, Thomas Rattei, Peter F. Stadler, Armin Töpfer:
Challenges in RNA virus bioinformatics. 1793-1799
- Max T. B. Clabbers, René C. L. Olsthoorn, Alexander P. Gultyaev:
Tospovirus ambisense genomic RNA segments use almost complete repertoire of stable tetraloops in the intergenic region. 1800-1804
- Ambarish Biswas, Peter C. Fineran, Chris M. Brown:
Accurate computational prediction of the transcribed strand of CRISPR non-coding RNAs. 1805-1813 - Peter A. Stockwell, Aniruddha Chatterjee, Euan J. Rodger, Ian M. Morison:
DMAP: differential methylation analysis package for RRBS and WGBS data. 1814-1822
- Arief Gusnanto, Charles C. Taylor, Ibrahim Nafisah, Henry M. Wood, Pamela Rabbitts, Stefano Berri:
Estimating optimal window size for analysis of low-coverage next-generation sequence data. 1823-1829 - Yongzhuang Liu, Bingshan Li, Renjie Tan, Xiaolin Zhu, Yadong Wang:
A gradient-boosting approach for filtering de novo mutations in parent-offspring trios. 1830-1836 - Christian Otto, Peter F. Stadler, Steve Hoffmann:
Lacking alignments? The next-generation sequencing mapper segemehl revisited. 1837-1843
- Deren A. R. Eaton:
PyRAD: assembly of de novo RADseq loci for phylogenetic analyses. 1844-1849
- Pooya Zakeri, Ben Jeuris, Raf Vandebril, Yves Moreau:
Protein fold recognition using geometric kernel data fusion. 1850-1857
- Md. Jamiul Jahid, Tim Hui-Ming Huang, Jianhua Ruan:
A personalized committee classification approach to improving prediction of breast cancer metastasis. 1858-1866 - Florian Buettner, Victoria Moignard, Berthold Göttgens, Fabian J. Theis:
Probabilistic PCA of censored data: accounting for uncertainties in the visualization of high-throughput single-cell qPCR data. 1867-1875
- Lei Zhang, Yu-Fang Pei, Xiaoying Fu, Yong Lin, Yu-Ping Wang, Hong-Wen Deng:
FISH: fast and accurate diploid genotype imputation via segmental hidden Markov model. 1876-1883
- Francesco Pappalardo, Marzio Pennisi, Alessia Ricupito, Francesco Topputo, Matteo Bellone:
Induction of T-cell memory by a dendritic cell vaccine: a computational model. 1884-1891 - Justina Zurauskiene, Paul D. W. Kirk, Thomas Thorne, John Pinney, Michael P. H. Stumpf:
Derivative processes for modelling metabolic fluxes. 1892-1898 - Huiming Peng, Tao Peng, Jianguo Wen, David A. Engler, Risë K. Matsunami, Jing Su, Le Zhang, Chung-Che Jeff Chang, Xiaobo Zhou:
Characterization of p38 MAPK isoforms for drug resistance study using systems biology approach. 1899-1907
- Suh-Yuen Liang, Sz-Wei Wu, Tsung-Hsien Pu, Fang-Yu Chang, Kay-Hooi Khoo:
An adaptive workflow coupled with Random Forest algorithm to identify intact N-glycopeptides detected from mass spectrometry. 1908-1916
- Daniel J. Blankenberg, James E. Johnson, The Galaxy Team, James Taylor, Anton Nekrutenko:
Wrangling Galaxy's reference data. 1917-1919 - Jean-Pierre A. Kocher, Daniel J. Quest, Patrick H. Duffy, Michael A. Meiners, Raymond M. Moore, David N. Rider, Asif Hossain, Steven N. Hart, Valentin Dinu:
The Biological Reference Repository (BioR): a rapid and flexible system for genomics annotation. 1920-1922
- Chih Lee, Chun-Hsi Huang:
LASAGNA-Search 2.0: integrated transcription factor binding site search and visualization in a browser. 1923-1925 - Florent E. Angly, Christopher J. Fields, Gene W. Tyson:
The Bio-Community Perl toolkit for microbial ecology. 1926-1927 - Gianmauro Cuccuru, Massimiliano Orsini, Andrea Pinna, Andrea Sbardellati, Nicola Soranzo, Antonella Travaglione, Paolo Uva, Gianluigi Zanetti, Giorgio Fotia:
Orione, a web-based framework for NGS analysis in microbiology. 1928-1929 - Jason A. Vander Heiden, Gur Yaari, Mohamed Uduman, Joel N. H. Stern, Kevin C. O'Connor, David A. Hafler, Francois Vigneault, Steven H. Kleinstein:
pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires. 1930-1932 - Kemal Akman, Thomas Haaf, Silvia Gravina, Jan Vijg, Achim Tresch:
Genome-wide quantitative analysis of DNA methylation from bisulfite sequencing data. 1933-1934
- Jaume Bonet, Joan Segura, Joan Planas-Iglesias, Baldomero Oliva, Narcis Fernandez-Fuentes:
Frag'r'Us: knowledge-based sampling of protein backbone conformations for de novo structure-based protein design. 1935-1936
- Francesc Fernández-Albert, Rafael Llorach, Cristina Andres-Lacueva, Alexandre Perera:
An R package to analyse LC/MS metabolomic data: MAIT (Metabolite Automatic Identification Toolkit). 1937-1939
- Steven Gazal, Mourad Sahbatou, Marie-Claude Babron, Emmanuelle Génin, Anne-Louise Leutenegger:
FSuite: exploiting inbreeding in dense SNP chip and exome data. 1940-1941
- Carito Guziolowski, Santiago Videla, Federica Eduati, Sven Thiele, Thomas Cokelaer, Anne Siegel, Julio Saez-Rodriguez:
Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming. 1942
Volume 30, Number 14, July 2014
Genome Analysis
- Xiaowei Zhou, Jiming Liu, Xiang Wan, Weichuan Yu:
Piecewise-constant and low-rank approximation for identification of recurrent copy number variations. 1943-1949
- Rajat Shuvro Roy, Debashish Bhattacharya, Alexander Schliep:
Turtle: Identifying frequent k-mers with cache-efficient algorithms. 1950-1957 - William H. Majoros, Niel Lebeck, Uwe Ohler, Song Li:
Improved transcript isoform discovery using ORF graphs. 1958-1964 - Emi Tanaka, Timothy L. Bailey, Uri Keich:
Improving MEME via a two-tiered significance analysis. 1965-1973 - Christophe Charpilloz, Anne-Lise Veuthey, Bastien Chopard, Jean-Luc Falcone:
Motifs tree: a new method for predicting post-translational modifications. 1974-1982 - A. Mary Thangakani, Sandeep Kumar, Raju Nagarajan, Devadasan Velmurugan, M. Michael Gromiha:
GAP: towards almost 100 percent prediction for β-strand-mediated aggregating peptides with distinct morphologies. 1983-1990 - Chris-André Leimeister, Marcus Boden, Sebastian Horwege, Sebastian Lindner, Burkhard Morgenstern:
Fast alignment-free sequence comparison using spaced-word frequencies. 1991-1999 - Chris-André Leimeister, Burkhard Morgenstern:
kmacs: the k-mismatch average common substring approach to alignment-free sequence comparison. 2000-2008
- Marcel Kucharík, Ivo L. Hofacker, Peter F. Stadler, Jing Qin:
Basin Hopping Graph: a computational framework to characterize RNA folding landscapes. 2009-2017
- Yuan-De Tan, Hongyan Xu:
A general method for accurate estimation of false discovery rates in identification of differentially expressed genes. 2018-2025
- Pekka Marttinen, Matti Pirinen, Antti-Pekka Sarin, Jussi Gillberg, Johannes Kettunen, Ida Surakka, Antti J. Kangas, Pasi Soininen, Paul F. O'Reilly, Marika Kaakinen, Mika Kähönen, Terho Lehtimäki, Mika Ala-Korpela, Olli T. Raitakari, Veikko Salomaa, Marjo-Riitta Järvelin, Samuli Ripatti, Samuel Kaski:
Assessing multivariate gene-metabolome associations with rare variants using Bayesian reduced rank regression. 2026-2034 - Amir R. Kermany, Laure Segurel, Tiffany R. Oliver, Molly Przeworski:
TroX: a new method to learn about the genesis of aneuploidy from trisomic products of conception. 2035-2042
- Mario Latendresse, Markus Krummenacker, Peter D. Karp:
Optimal metabolic route search based on atom mappings. 2043-2050 - Bülent Arman Aksoy, Emek Demir, Özgün Babur, Weiqing Wang, Xiaohong Jing, Nikolaus Schultz, Chris Sander:
Prediction of individualized therapeutic vulnerabilities in cancer from genomic profiles. 2051-2059
- Davide Rambaldi, Salvatore Pece, Pier Paolo Di Fiore:
flowFit: a Bioconductor package to estimate proliferation in cell-tracking dye studies. 2060-2065
Genome Analysis
- Uciel Chorostecki, Javier F. Palatnik:
comTAR: a web tool for the prediction and characterization of conserved microRNA targets in plants. 2066-2067 - Torsten Seemann:
Prokka: rapid prokaryotic genome annotation. 2068-2069
- Peter Audano, Fredrik Vannberg:
KAnalyze: a fast versatile pipelined K-mer toolkit. 2070-2072 - Zhenpeng Li, Yang Huang, Yabo Ouyang, Yang Jiao, Hui Xing, Lingjie Liao, Shibo Jiang, Yiming Shao, Liying Ma:
CorMut: an R/Bioconductor package for computing correlated mutations based on selection pressure. 2073-2075 - Valerie Obenchain, Michael F. Lawrence, Vincent J. Carey, Stephanie M. Gogarten, Paul Shannon, Martin Morgan:
VariantAnnotation: a Bioconductor package for exploration and annotation of genetic variants. 2076-2078
- Andreas Sand, Morten Kragelund Holt, Jens Johansen, Gerth Stølting Brodal, Thomas Mailund, Christian N. S. Pedersen:
tqDist: a library for computing the quartet and triplet distances between binary or general trees. 2079-2080
- Dario Ghersi, Mona Singh:
molBLOCKS: decomposing small molecule sets and uncovering enriched fragments. 2081-2083
- Sam Buckberry, Stephen J. Bent, Tina Bianco-Miotto, Claire T. Roberts:
massiR: a method for predicting the sex of samples in gene expression microarray datasets. 2084-2085
- Dale R. Nyholt:
SECA: SNP effect concordance analysis using genome-wide association summary results. 2086-2088
Genetics and Population Analysis
- So Young Ryu, Samuel H. Payne, Christoph Schaab, Wenzhong Xiao:
Beyond the proteome: Mass Spectrometry Special Interest Group (MS-SIG) at ISMB/ECCB 2013. 2089-2090 - Mark N. Wass, Sean D. Mooney, Michal Linial, Predrag Radivojac, Iddo Friedberg:
The automated function prediction SIG looks back at 2013 and prepares for 2014. 2091-2092
Volume 30, Number 15, August 2014
Sequence Analysis
- Darius Kazlauskas, Ceslovas Venclovas:
Herpesviral helicase-primase subunit UL8 is inactivated B-family polymerase. 2093-2097
Genome Analysis
- Rong W. Zablocki, Andrew J. Schork, Richard A. Levine, Ole A. Andreassen, Anders M. Dale, Wesley K. Thompson:
Covariate-modulated local false discovery rate for genome-wide association studies. 2098-2104 - Hervé Marie-Nelly, Martial Marbouty, Axel Cournac, Gianni Liti, Gilles Fischer, Christophe Zimmer, Romain Koszul:
Filling annotation gaps in yeast genomes using genome-wide contact maps. 2105-2113 - Anthony M. Bolger, Marc Lohse, Björn Usadel:
Trimmomatic: a flexible trimmer for Illumina sequence data. 2114-2120 - Yi Li, Xiaohui Xie:
Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity. 2121-2129
- Rodrigo Cánovas, Alistair Moffat, Andrew Turpin:
Lossy compression of quality scores in genomic data. 2130-2136 - Amir Toporik, Itamar Borukhov, Avihay Apatoff, Doron Gerber, Yossef Kliger:
Computational identification of natural peptides based on analysis of molecular evolution. 2137-2141
- Zeyneb Kurt, Nizamettin Aydin, Gökmen Altay:
A comprehensive comparison of association estimators for gene network inference algorithms. 2142-2149 - Michal Jamróz, Andrzej Kolinski, Sebastian Kmiecik:
CABS-flex predictions of protein flexibility compared with NMR ensembles. 2150-2154
- Alexandra Jauhiainen, Basetti Madhu, Masako Narita, Masashi Narita, John Griffiths, Simon Tavaré:
Normalization of metabolomics data with applications to correlation maps. 2155-2161 - Wei Wang, Zhi Wei, Hongzhe Li:
A change-point model for identifying 3′UTR switching by next-generation RNA sequencing. 2162-2170
- Han Zhang, William Wheeler, Zhaoming Wang, Philip R. Taylor, Kai Yu:
A fast and powerful tree-based association test for detecting complex joint effects in case-control studies. 2171-2178 - Andriy Derkach, Theodore Chiang, Jiafen Gong, Laura Addis, Sara E. Dobbins, Ian Tomlinson, Richard S. Houlston, Deb K. Pal, Lisa J. Strug:
Association analysis using next-generation sequence data from publicly available control groups: the robust variance score statistic. 2179-2188 - Alexandre Bureau, Samuel G. Younkin, Margaret M. Parker, Joan E. Bailey-Wilson, Mary L. Marazita, Jeffrey C. Murray, Elisabeth Mangold, Hasan Albacha-Hejazi, Terri H. Beaty, Ingo Ruczinski:
Inferring rare disease risk variants based on exact probabilities of sharing by multiple affected relatives. 2189-2196
- Jon Pey, Francisco J. Planes:
Direct calculation of elementary flux modes satisfying several biological constraints in genome-scale metabolic networks. 2197-2203
Genome Analysis
- Sylvain Mareschal, Sydney Dubois, Thierry Lecroq, Fabrice Jardin:
Rgb: a scriptable genome browser for R. 2204-2205 - Xin Zhou, Daofeng Li, Rebecca F. Lowdon, Joseph F. Costello, Ting Wang:
methylC Track: visual integration of single-base resolution DNA methylation data on the WashU EpiGenome Browser. 2206-2207
- Sung Kyu Robin Park, Aaron Aslanian, Daniel B. McClatchy, Xuemei Han, Harshil Shah, Meha Singh, Navin Rauniyar, James J. Moresco, Antonio F. M. Pinto, Jolene K. Diedrich, Claire Delahunty, John R. Yates III:
Census 2: isobaric labeling data analysis. 2208-2209 - Ju Xin Chin, Bevan Kai-Sheng Chung, Dong-Yup Lee:
Codon Optimization OnLine (COOL): a web-based multi-objective optimization platform for synthetic gene design. 2210-2212 - Lukasz Roguski, Sebastian Deorowicz:
DSRC 2 - Industry-oriented compression of FASTQ files. 2213-2215
- Matthew W. Pennell, Jonathan M. Eastman, Graham J. Slater, Joseph W. Brown, Josef C. Uyeda, Richard G. FitzJohn, Michael E. Alfaro, Luke J. Harmon:
geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees. 2216-2218
- Sébastien Morin, Troels E. Linnet, Mathilde Lescanne, Paul Schanda, Gary S. Thompson, Martin Tollinger, Kaare Teilum, Stéphane Gagné, Dominique Marion, Christian Griesinger, Martin Blackledge, Edward J. d'Auvergne:
relax: the analysis of biomolecular kinetics and thermodynamics using NMR relaxation dispersion data. 2219-2220 - Björn Wallner:
ProQM-resample: improved model quality assessment for membrane proteins by limited conformational sampling. 2221-2223
- Wandaliz Torres-García, Siyuan Zheng, Andrey Sivachenko, Rahulsimham Vegesna, Qianghu Wang, Rong Yao, Michael F. Berger, John N. Weinstein, Gad Getz, Roel G. W. Verhaak:
PRADA: pipeline for RNA sequencing data analysis. 2224-2226
- Raeece Naeem, Lailatul Hidayah, Mark D. Preston, Taane G. Clark, Arnab Pain:
SVAMP: sequence variation analysis, maps and phylogeny. 2227-2229
- Alvin Leung, Gary D. Bader, Jüri Reimand:
HyperModules: identifying clinically and phenotypically significant network modules with disease mutations for biomarker discovery. 2230-2232 - Frédéric Fournier, Charles Joly Beauparlant, René Paradis, Arnaud Droit:
rTANDEM, an R/Bioconductor package for MS/MS protein identification. 2233-2234
- Horacio Caniza, Alfonso E. Romero, Samuel Heron, Haixuan Yang, Alessandra Devoto, Marco Frasca, Marco Mesiti, Giorgio Valentini, Alberto Paccanaro:
GOssTo: a stand-alone application and a web tool for calculating semantic similarities on the Gene Ontology. 2235-2236 - Dongfang Wang, Jin Gu, Ting Wang, Zijian Ding:
OncomiRDB: a database for the experimentally verified oncogenic and tumor-suppressive microRNAs. 2237-2238 - William Duren, Terry E. Weymouth, Tim Hull, Gilbert S. Omenn, Brian D. Athey, Charles F. Burant, Alla Karnovsky:
MetDisease - connecting metabolites to diseases via literature. 2239-2241
Databases and Ontologies
- Jinghua Gu, Jianhua Xuan, Rebecca B. Riggins, Li Chen, Yue Joseph Wang, Robert Clarke:
Robust identification of transcriptional regulatory networks using a Gibbs sampler on outlier sum statistic. 2242
Volume 30, Number 16, August 2014
Genome Analysis
- Laurent F. Thomas, Pål Sætrom:
Circular RNAs are depleted of polymorphisms at microRNA binding sites. 2243-2246
Genome Analysis
- Rolf Hilker, Kai Bernd Stadermann, Daniel Doppmeier, Jörn Kalinowski, Jens Stoye, Jasmin Straube, Jörn Winnebald, Alexander Goesmann:
ReadXplorer - visualization and analysis of mapped sequences. 2247-2254
- Andreas Futschik, Thomas Hotz, Axel Munk, Hannes Sieling:
Multiscale DNA partitioning: statistical evidence for segments. 2255-2262 - Maria Cha, Qing Zhou:
Detecting clustering and ordering binding patterns among transcription factors via point process models. 2263-2271
- Timothy G. Vaughan, Denise Kühnert, Alex Popinga, David Welch, Alexei J. Drummond:
Efficient Bayesian inference under the structured coalescent. 2272-2279 - Grady Weyenberg, Peter Huggins, Christopher L. Schardl, Daniel K. Howe, Ruriko Yoshida:
kdetrees: non-parametric estimation of phylogenetic tree distributions. 2280-2287
- Konrad Krawczyk, Xiaofeng Liu, Terry Baker, Jiye Shi, Charlotte M. Deane:
Improving B-cell epitope prediction and its application to global antibody-antigen docking. 2288-2294 - Chen Yanover, Natalia Vanetik, Michael Levitt, Rachel Kolodny, Chen Keasar:
Redundancy-weighting for better inference of protein structural features. 2295-2301 - Praveen Nedumpully-Govindan, Lin Li, Emil Alexov, Mark A. Blenner, Feng Ding:
Structural and energetic determinants of tyrosylprotein sulfotransferase sulfation specificity. 2302-2309
- Matthew N. McCall, Helene R. McMurray, Hartmut Land, Anthony Almudevar:
On non-detects in qPCR data. 2310-2316
- Hokeun Sun, Shuang Wang:
A power set-based statistical selection procedure to locate susceptible rare variants associated with complex traits with sequencing data. 2317-2323 - Trisevgeni Rapakoulia, Konstantinos A. Theofilatos, Dimitris Kleftogiannis, Spiridon Likothanasis, Athanasios K. Tsakalidis, Seferina Mavroudi:
EnsembleGASVR: a novel ensemble method for classifying missense single nucleotide polymorphisms. 2324-2333
- Shibin Mathew, Sankaramanivel Sundararaj, Hikaru Mamiya, Ipsita Banerjee:
Regulatory interactions maintaining self-renewal of human embryonic stem cells as revealed through a systems analysis of PI3K/AKT pathway. 2334-2342 - Xiaoke Ma, Long Gao, Kai Tan:
Modeling disease progression using dynamics of pathway connectivity. 2343-2350 - Connor Clark, Jugal Kalita:
A comparison of algorithms for the pairwise alignment of biological networks. 2351-2359 - Yinming Jiao, Martin Widschwendter, Andrew E. Teschendorff:
A systems-level integrative framework for genome-wide DNA methylation and gene expression data identifies differential gene expression modules under epigenetic control. 2360-2366
- James P. Sluka, Abbas Shirinifard, Maciej Swat, Alin Cosmanescu, Randy W. Heiland, James A. Glazier:
The cell behavior ontology: describing the intrinsic biological behaviors of real and model cells seen as active agents. 2367-2374
Genetics and Population Analysis
- Robert J. Carroll, Lisa Bastarache, Joshua C. Denny:
R PheWAS: data analysis and plotting tools for phenome-wide association studies in the R environment. 2375-2376 - Gao T. Wang, Biao Li, Regie P. Lyn Santos-Cortez, Bo Peng, Suzanne M. Leal:
Power analysis and sample size estimation for sequence-based association studies. 2377-2378
- Hiroshi Tsugawa, Mitsuhiro Kanazawa, Atsushi Ogiwara, Masanori Arita:
MRMPROBS suite for metabolomics using large-scale MRM assays. 2379-2380 - Stephen J. Goodswen, Paul J. Kennedy, John T. Ellis:
Vacceed: a high-throughput in silico vaccine candidate discovery pipeline for eukaryotic pathogens based on reverse vaccinology. 2381-2383
- Matthew Horridge, Tania Tudorache, Csongor Nyulas, Jennifer Vendetti, Natalya Fridman Noy, Mark A. Musen:
WebProtégé: a collaborative Web-based platform for editing biomedical ontologies. 2384-2385 - Yi-Ju Chen, Cheng-Tsung Lu, Tzong-Yi Lee, Yu-Ju Chen:
dbGSH: a database of S-glutathionylation. 2386-2388
- Martin Ovesný, Pavel Krízek, Josef Borkovec, Zdenek Svindrych, Guy M. Hagen:
ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging. 2389-2390
Volume 30, Number 17, September 2014
Editorial
- Marie-Dominique Devignes, Yves Moreau:
ECCB 2014: The 13th European Conference on Computational Biology. 345-348
- Hannes Hauswedell, Jochen Singer, Knut Reinert:
Lambda: the local aligner for massive biological data. 349-355 - Marcel H. Schulz, David Weese, Manuel Holtgrewe, Viktoria Dimitrova, Sijia Niu, Knut Reinert, Hugues Richard:
Fiona: a parallel and automatic strategy for read error correction. 356-363 - Jocelyn Brayet, Farida Zehraoui, Laurence Jeanson-Leh, David Israeli, Fariza Tahi:
Towards a piRNA prediction using multiple kernel fusion and support vector machine. 364-370 - Sepideh Mazrouee, Wei Wang:
FastHap: fast and accurate single individual haplotype reconstruction using fuzzy conflict graphs. 371-378 - Volodymyr Kuleshov:
Probabilistic single-individual haplotyping. 379-385 - Céline Lévy-Leduc, Maud Delattre, Tristan Mary-Huard, Stéphane Robin:
Two-dimensional segmentation for analyzing Hi-C data. 386-392 - Raymond G. Cavalcante, Chee Lee, Ryan P. Welch, Snehal Patil, Terry E. Weymouth, Laura J. Scott, Maureen A. Sartor:
Broad-Enrich: functional interpretation of large sets of broad genomic regions. 393-400 - Theresa Schacht, Marcus Oswald, Roland Eils, Stefan B. Eichmüller, Rainer König:
Estimating the activity of transcription factors by the effect on their target genes. 401-407 - John A. Capra, Dennis Kostka:
Modeling DNA methylation dynamics with approaches from phylogenetics. 408-414 - Thorsten Will, Volkhard Helms:
Identifying transcription factor complexes and their roles. 415-421 - TaeJin Ahn, Eunjin Lee, Nam Huh, Taesung Park:
Personalized identification of altered pathways in cancer using accumulated normal tissue data. 422-429 - Waqar Ali, Tiago Rito, Gesine Reinert, Fengzhu Sun, Charlotte M. Deane:
Alignment-free protein interaction network comparison. 430-437 - Somaye Hashemifar, Jinbo Xu:
HubAlign: an accurate and efficient method for global alignment of protein-protein interaction networks. 438-444 - Nir Atias, Michal Gershenzon, Katia Labazin, Roded Sharan:
Experimental design schemes for learning Boolean network models. 445-452 - Yongsoo Kim, Jin-Hyeok Jang, Seungjin Choi, Daehee Hwang:
TEMPI: probabilistic modeling time-evolving differential PPI networks with multiPle information. 453-460 - Tommi Suvitaival, Simon Rogers, Samuel Kaski:
Stronger findings for metabolomics through Bayesian modeling of multiple peaks and compound correlations. 461-467 - Chris J. Oates, Frank Dondelinger, Nora Bayani, James Korkola, Joe W. Gray, Sach Mukherjee:
Causal network inference using biochemical kinetics. 468-474 - Peter Kreyssig, Christian Wozar, Stephan Peter, Tomas Veloz, Bashar Ibrahim, Peter Dittrich:
Effects of small particle numbers on long-term behaviour in discrete biochemical systems. 475-481 - Mirco Michel, Sikander Hayat, Marcin J. Skwark, Chris Sander, Debora S. Marks, Arne Elofsson:
PconsFold: improved contact predictions improve protein models. 482-488 - Omer S. Alkhnbashi, Fabrizio Costa, Shiraz A. Shah, Roger A. Garrett, Sita J. Saunders, Rolf Backofen:
CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci. 489-496 - Suleiman A. Khan, Seppo Virtanen, Olli-P. Kallioniemi, Krister Wennerberg, Antti Poso, Samuel Kaski:
Identification of structural features in chemicals associated with cancer drug response: a systematic data-driven analysis. 497-504 - Gabriel Studer, Marco Biasini, Torsten Schwede:
Assessing the local structural quality of transmembrane protein models using statistical potentials (QMEANBrane). 505-511 - James H. Collier, Lloyd Allison, Arthur M. Lesk, Maria Garcia de la Banda, Arun Siddharth Konagurthu:
A new statistical framework to assess structural alignment quality using information compression. 512-518 - Manuel Lafond, Cédric Chauve, Riccardo Dondi, Nadia El-Mabrouk:
Polytomy refinement for the correction of dubious duplications in gene trees. 519-526 - Christina Kratsch, Alice Carolyn McHardy:
RidgeRace: ridge regression for continuous ancestral character estimation on phylogenetic trees. 527-533 - Philipp Benner, Miroslav Bacák, Pierre-Yves Bourguignon:
Point estimates in phylogenetic reconstructions. 534-540 - Siavash Mirarab, Rezwana Reaz, Md. Shamsuzzoha Bayzid, Théo Zimmermann, M. Shel Swenson, Tandy J. Warnow:
ASTRAL: genome-scale coalescent-based species tree estimation. 541-548 - Michael P. Schroeder, Carlota Rubio-Perez, David Tamborero, Abel Gonzalez-Perez, Núria López-Bigas:
OncodriveROLE classifies cancer driver genes in loss of function and activating mode of action. 549-555 - Mehmet Gönen, Adam A. Margolin:
Drug susceptibility prediction against a panel of drugs using kernelized Bayesian multitask learning. 556-563 - Jingwen Yan, Lei Du, Sungeun Kim, Shannon L. Risacher, Heng Huang, Jason H. Moore, Andrew J. Saykin, Li Shen:
Transcriptome-guided amyloid imaging genetic analysis via a novel structured sparse learning algorithm. 564-571 - Rui Tian, Malay Kumar Basu, Emidio Capriotti:
ContrastRank: a new method for ranking putative cancer driver genes and classification of tumor samples. 572-578 - Xueping Liu, Mónica Campillos:
Unveiling new biological relationships using shared hits of chemical screening assay pairs. 579-586 - Paolo Frasconi, Ludovico Silvestri, Paolo Soda, Roberto Cortini, Francesco Pavone, Giulio Iannello:
Large-scale automated identification of mouse brain cells in confocal light sheet microscopy images. 587-593 - Vladimir Gligorijevic, Vuk Janjic, Natasa Przulj:
Integration of molecular network data reconstructs Gene Ontology. 594-600 - Geraint Duck, Goran Nenadic, Andy Brass, David L. Robertson, Robert Stevens:
Extracting patterns of database and software usage from the bioinformatics literature. 601-608 - Yuxiang Jiang, Wyatt T. Clark, Iddo Friedberg, Predrag Radivojac:
The impact of incomplete knowledge on the evaluation of protein function prediction: a structured-output learning perspective. 609-616 - Andrea Gobbi, Francesco Iorio, Kevin J. Dawson, David C. Wedge, David Tamborero, Ludmil B. Alexandrov, Núria López-Bigas, Mathew Garnett, Giuseppe Jurman, Julio Saez-Rodriguez:
Fast randomization of large genomic datasets while preserving alteration counts. 617-623 - Nadav Rappoport, Amos Stern, Nathan Linial, Michal Linial:
Entropy-driven partitioning of the hierarchical protein space. 624-630 - Markus List, Ines Block, Marlene Lemvig Pedersen, Helle Christiansen, Steffen Schmidt, Mads Thomassen, Qihua Tan, Jan Baumbach, Jan Mollenhauer:
Microarray R-based analysis of complex lysate experiments with MIRACLE. 631-638 - Evangelos Bellos, Lachlan J. M. Coin:
cnvOffSeq: detecting intergenic copy number variation using off-target exome sequencing data. 639-645
- Jihye Kim, Vihas T. Vasu, Rangnath Mishra, Katherine R. Singleton, Minjae Yoo, Sonia M. Leach, Eveline Farias-Hesson, Robert J. Mason, Jaewoo Kang, Preveen Ramamoorthy, Jeffrey A. Kern, Lynn E. Heasley, James H. Finigan, Aik Choon Tan:
Bioinformatics-driven discovery of rational combination for overcoming EGFR-mutant lung cancer resistance to EGFR therapy. 2393-2398
- Rotem Ben-Hamo, Moriah Gidoni, Sol Efroni:
PhenoNet: identification of key networks associated with disease phenotype. 2399-2405 - Nishanth Ulhas Nair, Sunil Kumar, Bernard M. E. Moret, Philipp Bucher:
Probabilistic partitioning methods to find significant patterns in ChIP-Seq data. 2406-2413 - Yongseok Park, Maria E. Figueroa, Laura S. Rozek, Maureen A. Sartor:
MethylSig: a whole genome DNA methylation analysis pipeline. 2414-2422 - Saikat Chatterjee, David Koslicki, Siyuan Dong, Nicolas Innocenti, Lu Cheng, Yueheng Lan, Mikko Vehkaperä, Mikael Skoglund, Lars K. Rasmussen, Erik Aurell, Jukka Corander:
SEK: sparsity exploiting k-mer-based estimation of bacterial community composition. 2423-2431 - Walyd Khenoussi, Renaud Vanhoutrève, Olivier Poch, Julie Dawn Thompson:
SIBIS: a Bayesian model for inconsistent protein sequence estimation. 2432-2439 - Lizong Deng, Aiping Wu, Wentao Dai, Tingrui Song, Ya Cui, Taijiao Jiang:
Exploring protein domain organization by recognition of secondary structure packing interfaces. 2440-2446 - Elsa Bernard, Laurent Jacob, Julien Mairal, Jean-Philippe Vert:
Efficient RNA isoform identification and quantification from RNA-Seq data with network flows. 2447-2455 - Navodit Misra, Ewa Szczurek, Martin Vingron:
Inferring the paths of somatic evolution in cancer. 2456-2463 - Mehrab Ghanat Bari, Xuepo Ma, Jianqiu Zhang:
PeakLink: a new peptide peak linking method in LC-MS/MS using wavelet and SVM. 2464-2470 - Sohan Seth, Niko Välimäki, Samuel Kaski, Antti Honkela:
Exploration and retrieval of whole-metagenome sequencing samples. 2471-2479 - Charny Park, Namhee Yu, Ikjung Choi, Wan Kyu Kim, Sanghyuk Lee:
lncRNAtor: a comprehensive resource for functional investigation of long non-coding RNAs. 2480-2485 - Florian Gomez, Ralph Lukas Stoop, Ruedi Stoop:
Universal dynamical properties preclude standard clustering in a large class of biochemical data. 2486-2493
- Jan De Neve, Joris Meys, Jean-Pierre Ottoy, Lieven Clement, Olivier Thas:
unifiedWMWqPCR: the unified Wilcoxon-Mann-Whitney test for analyzing RT-qPCR data in R. 2494-2495 - Kamil Slowikowski, Xinli Hu, Soumya Raychaudhuri:
SNPsea: an algorithm to identify cell types, tissues and pathways affected by risk loci. 2496-2497 - Weixin Wang, Panwen Wang, Feng Xu, Ruibang Luo, Maria P. Wong, Tak Wah Lam, Junwen Wang:
FaSD-somatic: a fast and accurate somatic SNV detection algorithm for cancer genome sequencing data. 2498-2500 - Alex Lancaster, Andrew Nutter-Upham, Susan Lindquist, Oliver D. King:
PLAAC: a web and command-line application to identify proteins with prion-like amino acid composition. 2501-2502 - Gregory G. Faust, Ira M. Hall:
SAMBLASTER: fast duplicate marking and structural variant read extraction. 2503-2505 - Michael J. Sanderson:
Ceiba: scalable visualization of phylogenies and 2D/3D image collections. 2506-2507 - Guillermo Rodrigo, Alfonso Jaramillo:
RiboMaker: computational design of conformation-based riboregulation. 2508-2510 - George Rosenberger, Christina Ludwig, Hannes L. Röst, Ruedi Aebersold, Lars Malmström:
aLFQ: an R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data. 2511-2513 - Francesco Russo, Claudia Angelini:
RNASeqGUI: a GUI for analysing RNA-Seq data. 2514-2516 - Charlotte Soneson:
compcodeR - an R package for benchmarking differential expression methods for RNA-seq data. 2517-2518 - Thomas Nussbaumer, Karl G. Kugler, Kai Christian Bader, Sapna Sharma, Michael Seidel, Klaus F. X. Mayer:
RNASeqExpressionBrowser - a web interface to browse and visualize high-throughput expression data. 2519-2520 - Daniel Broudy, Trevor Killeen, Meena Choi, Nicholas Shulman, Deepak R. Mani, Susan E. Abbatiello, Deepak Mani, Rushdy Ahmad, Alexandria K. Sahu, Birgit Schilling, Kaipo Tamura, Yuval Boss, Vagisha Sharma, Bradford W. Gibson, Steven A. Carr, Olga Vitek, Michael J. MacCoss, Brendan MacLean:
A framework for installable external tools in Skyline. 2521-2523 - Meena Choi, Ching-Yun Chang, Timothy Clough, Daniel Broudy, Trevor Killeen, Brendan MacLean, Olga Vitek:
MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments. 2524-2526 - Ken-Chi Yang, Chia-Lang Hsu, Chen-Ching Lin, Hsueh-Fen Juan, Hsuan-Cheng Huang:
Mirin: identifying microRNA regulatory modules in protein-protein interaction networks. 2527-2528 - Ines Thiele, Nikos Vlassis, Ronan M. T. Fleming:
fastGapFill: efficient gap filling in metabolic networks. 2529-2531 - Paul Müller, Petra Schwille, Thomas Weidemann:
PyCorrFit - generic data evaluation for fluorescence correlation spectroscopy. 2532-2533 - Jia-Hong Wang, Ling-Feng Zhao, Pei Lin, Xiao-Rong Su, Shi-Jun Chen, Li-Qiang Huang, Hua-Feng Wang, Hai Zhang, Zhen-Fu Hu, Kai-Tai Yao, Zhong-Xi Huang:
GenCLiP 2.0: a web server for functional clustering of genes and construction of molecular networks based on free terms. 2534-2536 - Jordan Plieskatt, Gabriel Rinaldi, Paul J. Brindley, Xinying Jia, Jeremy Potriquet, Jeffrey Bethony, Jason P. Mulvenna:
Bioclojure: a functional library for the manipulation of biological sequences. 2537-2539 - Daeun Ryu, SeongBeom Cho, Hun Kim, Sanghyuk Lee, Wan Kyu Kim:
GEPdb: a database for investigating the ternary association of genotype, gene expression and phenotype. 2540-2542
Volume 30, Number 18, September 2014
Genome Analysis
- Huy Hoang Do, Wing-Kin Sung:
CWig: compressed representation of Wiggle/BedGraph format. 2543-2550 - Israel T. da Silva, Rafael Rosales, Adriano J. Holanda, Michel C. Nussenzweig, Mila Jankovic:
Identification of chromosomal translocation hotspots via scan statistics. 2551-2558 - Edward Wijaya, Kana Shimizu, Kiyoshi Asai, Michiaki Hamada:
Reference-free prediction of rearrangement breakpoint reads. 2559-2567 - Yan-Xiao Zhang, Yu-Hsuan Lin, Timothy D. Johnson, Laura S. Rozek, Maureen A. Sartor:
PePr: a peak-calling prioritization pipeline to identify consistent or differential peaks from replicated ChIP-Seq data. 2568-2575
- Zhenhua Yu, Yuanning Liu, Yi Shen, Minghui Wang, Ao Li:
CLImAT: accurate detection of copy number alteration and loss of heterozygosity in impure and aneuploid tumor samples using whole-genome sequencing data. 2576-2583
- Martin Mann, Marcel Kucharík, Christoph Flamm, Michael T. Wolfinger:
Memory-efficient RNA energy landscape exploration. 2584-2591 - Christophe N. Magnan, Pierre Baldi:
SSpro/ACCpro 5: almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, machine learning and structural similarity. 2592-2597
- María José Nueda, Sonia Tarazona, Ana Conesa:
Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series. 2598-2602 - Andrew Quinn, Punita Juneja, Francis M. Jiggins:
Estimates of allele-specific expression in Drosophila with a single genome sequence and RNA-seq data. 2603-2610
- Meng Wang, Shili Lin:
FamLBL: detecting rare haplotype disease association based on common SNPs using case-parent triads. 2611-2618
- Boon-Siew Seah, Sourav S. Bhowmick, C. Forbes Dewey Jr.:
DualAligner: a dual alignment-based strategy to align protein interaction networks. 2619-2626 - Yue Li, Cheng Liang, Ka-Chun Wong, Jiawei Luo, Zhaolei Zhang:
Mirsynergy: detecting synergistic miRNA regulatory modules by overlapping neighbourhood expansion. 2627-2635
- Christopher J. Conley, Robert Smith, Ralf J. O. Torgrip, Ryan M. Taylor, Ralf Tautenhahn, John T. Prince:
Massifquant: open-source Kalman filter-based XC-MS isotope trace feature detection. 2636-2643