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ORCIDBibTeX records: Carl Kingsford
@article{DBLP:journals/jcb/ZhengMK23,
author = {Hongyu Zheng and
Guillaume Mar{\c{c}}ais and
Carl Kingsford},
title = {Creating and Using Minimizer Sketches in Computational Genomics},
journal = {J. Comput. Biol.},
volume = {30},
number = {12},
pages = {1251--1276},
year = {2023},
url = {https://doi.org/10.1089/cmb.2023.0094},
doi = {10.1089/CMB.2023.0094},
timestamp = {Fri, 26 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/ZhengMK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/automl/ShenK23,
author = {Yihang Shen and
Carl Kingsford},
editor = {Aleksandra Faust and
Roman Garnett and
Colin White and
Frank Hutter and
Jacob R. Gardner},
title = {Computationally Efficient High-Dimensional Bayesian Optimization via
Variable Selection},
booktitle = {International Conference on Automated Machine Learning, 12-15 November
2023, Hasso Plattner Institute, Potsdam, Germany},
series = {Proceedings of Machine Learning Research},
volume = {224},
pages = {15/1--27},
publisher = {{PMLR}},
year = {2023},
url = {https://proceedings.mlr.press/v224/shen23a.html},
timestamp = {Wed, 10 Apr 2024 18:16:37 +0200},
biburl = {https://dblp.org/rec/conf/automl/ShenK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/QiuSK23,
author = {Yutong Qiu and
Yihang Shen and
Carl Kingsford},
editor = {Djamal Belazzougui and
A{\"{\i}}da Ouangraoua},
title = {Revisiting the Complexity of and Algorithms for the Graph Traversal
Edit Distance and Its Variants},
booktitle = {23rd International Workshop on Algorithms in Bioinformatics, {WABI}
2023, September 4-6, 2023, Houston, TX, {USA}},
series = {LIPIcs},
volume = {273},
pages = {11:1--11:22},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2023},
url = {https://doi.org/10.4230/LIPIcs.WABI.2023.11},
doi = {10.4230/LIPICS.WABI.2023.11},
timestamp = {Tue, 29 Aug 2023 16:25:19 +0200},
biburl = {https://dblp.org/rec/conf/wabi/QiuSK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/FerdosiGK23,
author = {Mohsen Ferdosi and
Yuejun Ge and
Carl Kingsford},
editor = {Djamal Belazzougui and
A{\"{\i}}da Ouangraoua},
title = {Reinforcement Learning for Robotic Liquid Handler Planning},
booktitle = {23rd International Workshop on Algorithms in Bioinformatics, {WABI}
2023, September 4-6, 2023, Houston, TX, {USA}},
series = {LIPIcs},
volume = {273},
pages = {23:1--23:16},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2023},
url = {https://doi.org/10.4230/LIPIcs.WABI.2023.23},
doi = {10.4230/LIPICS.WABI.2023.23},
timestamp = {Tue, 29 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wabi/FerdosiGK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2305-10577,
author = {Yutong Qiu and
Yihang Shen and
Carl Kingsford},
title = {Revisiting the Complexity of and Algorithms for the Graph Traversal
Edit Distance and Its Variants},
journal = {CoRR},
volume = {abs/2305.10577},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2305.10577},
doi = {10.48550/ARXIV.2305.10577},
eprinttype = {arXiv},
eprint = {2305.10577},
timestamp = {Thu, 25 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2305-10577.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2311-03592,
author = {Guillaume Mar{\c{c}}ais and
Dan F. DeBlasio and
Carl Kingsford},
title = {Sketching methods with small window guarantee using minimum decycling
sets},
journal = {CoRR},
volume = {abs/2311.03592},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2311.03592},
doi = {10.48550/ARXIV.2311.03592},
eprinttype = {arXiv},
eprint = {2311.03592},
timestamp = {Tue, 14 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2311-03592.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/ZhengMK22,
author = {Hongyu Zheng and
Cong Ma and
Carl Kingsford},
title = {Deriving Ranges of Optimal Estimated Transcript Expression due to
Nonidentifiability},
journal = {J. Comput. Biol.},
volume = {29},
number = {2},
pages = {121--139},
year = {2022},
url = {https://doi.org/10.1089/cmb.2021.0444},
doi = {10.1089/CMB.2021.0444},
timestamp = {Wed, 22 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/ZhengMK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/HoangZK22,
author = {Minh Hoang and
Hongyu Zheng and
Carl Kingsford},
title = {Differentiable Learning of Sequence-Specific Minimizer Schemes with
DeepMinimizer},
journal = {J. Comput. Biol.},
volume = {29},
number = {12},
pages = {1288--1304},
year = {2022},
url = {https://doi.org/10.1089/cmb.2022.0275},
doi = {10.1089/CMB.2022.0275},
timestamp = {Tue, 31 Jan 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/HoangZK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/HoangZK22,
author = {Minh Hoang and
Hongyu Zheng and
Carl Kingsford},
editor = {Itsik Pe'er},
title = {DeepMinimizer: {A} Differentiable Framework for Optimizing Sequence-Specific
Minimizer Schemes},
booktitle = {Research in Computational Molecular Biology - 26th Annual International
Conference, {RECOMB} 2022, San Diego, CA, USA, May 22-25, 2022, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {13278},
pages = {52--69},
publisher = {Springer},
year = {2022},
url = {https://doi.org/10.1007/978-3-031-04749-7\_4},
doi = {10.1007/978-3-031-04749-7\_4},
timestamp = {Wed, 22 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/HoangZK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/MaZK21,
author = {Cong Ma and
Hongyu Zheng and
Carl Kingsford},
title = {Exact transcript quantification over splice graphs},
journal = {Algorithms Mol. Biol.},
volume = {16},
number = {1},
pages = {5},
year = {2021},
url = {https://doi.org/10.1186/s13015-021-00184-7},
doi = {10.1186/S13015-021-00184-7},
timestamp = {Wed, 22 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/almob/MaZK21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RajanZKZ21,
author = {Vaibhav Rajan and
Ziqi Zhang and
Carl Kingsford and
Xiuwei Zhang},
title = {Maximum likelihood reconstruction of ancestral networks by integer
linear programming},
journal = {Bioinform.},
volume = {37},
number = {8},
pages = {1083--1092},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btaa931},
doi = {10.1093/BIOINFORMATICS/BTAA931},
timestamp = {Sat, 31 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RajanZKZ21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhengKM21,
author = {Hongyu Zheng and
Carl Kingsford and
Guillaume Mar{\c{c}}ais},
title = {Sequence-specific minimizers via polar sets},
journal = {Bioinform.},
volume = {37},
number = {Supplement},
pages = {187--195},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab313},
doi = {10.1093/BIOINFORMATICS/BTAB313},
timestamp = {Wed, 22 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhengKM21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/QiuK21,
author = {Yutong Qiu and
Carl Kingsford},
title = {Constructing small genome graphs via string compression},
journal = {Bioinform.},
volume = {37},
number = {Supplement},
pages = {205--213},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab281},
doi = {10.1093/BIOINFORMATICS/BTAB281},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/QiuK21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TungK21,
author = {Laura H. Tung and
Carl Kingsford},
title = {Practical selection of representative sets of RNA-seq samples using
a hierarchical approach},
journal = {Bioinform.},
volume = {37},
number = {Supplement},
pages = {334--341},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab315},
doi = {10.1093/BIOINFORMATICS/BTAB315},
timestamp = {Tue, 21 Dec 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/TungK21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/FrisbyBMHKL21,
author = {Trevor S. Frisby and
Shawn J. Baker and
Guillaume Mar{\c{c}}ais and
Quang Minh Hoang and
Carl Kingsford and
Christopher J. Langmead},
title = {Harvestman: a framework for hierarchical feature learning and selection
from whole genome sequencing data},
journal = {{BMC} Bioinform.},
volume = {22},
number = {1},
pages = {174},
year = {2021},
url = {https://doi.org/10.1186/s12859-021-04096-6},
doi = {10.1186/S12859-021-04096-6},
timestamp = {Tue, 16 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/FrisbyBMHKL21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/ZhengKM21,
author = {Hongyu Zheng and
Carl Kingsford and
Guillaume Mar{\c{c}}ais},
title = {Lower Density Selection Schemes via Small Universal Hitting Sets with
Short Remaining Path Length},
journal = {J. Comput. Biol.},
volume = {28},
number = {4},
pages = {395--409},
year = {2021},
url = {https://doi.org/10.1089/cmb.2020.0432},
doi = {10.1089/CMB.2020.0432},
timestamp = {Wed, 22 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/ZhengKM21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/stoc/BalcanDDKSV21,
author = {Maria{-}Florina Balcan and
Dan F. DeBlasio and
Travis Dick and
Carl Kingsford and
Tuomas Sandholm and
Ellen Vitercik},
editor = {Samir Khuller and
Virginia Vassilevska Williams},
title = {How much data is sufficient to learn high-performing algorithms? generalization
guarantees for data-driven algorithm design},
booktitle = {{STOC} '21: 53rd Annual {ACM} {SIGACT} Symposium on Theory of Computing,
Virtual Event, Italy, June 21-25, 2021},
pages = {919--932},
publisher = {{ACM}},
year = {2021},
url = {https://doi.org/10.1145/3406325.3451036},
doi = {10.1145/3406325.3451036},
timestamp = {Sat, 08 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/stoc/BalcanDDKSV21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2109-09264,
author = {Yihang Shen and
Carl Kingsford},
title = {Computationally Efficient High-Dimensional Bayesian Optimization via
Variable Selection},
journal = {CoRR},
volume = {abs/2109.09264},
year = {2021},
url = {https://arxiv.org/abs/2109.09264},
eprinttype = {arXiv},
eprint = {2109.09264},
timestamp = {Mon, 27 Sep 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2109-09264.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/QiuMXK20,
author = {Yutong Qiu and
Cong Ma and
Han Xie and
Carl Kingsford},
title = {Detecting transcriptomic structural variants in heterogeneous contexts
via the Multiple Compatible Arrangements Problem},
journal = {Algorithms Mol. Biol.},
volume = {15},
number = {1},
pages = {9},
year = {2020},
url = {https://doi.org/10.1186/s13015-020-00170-5},
doi = {10.1186/S13015-020-00170-5},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/almob/QiuMXK20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/XinSK20,
author = {Hongyi Xin and
Mingfu Shao and
Carl Kingsford},
title = {Context-aware seeds for read mapping},
journal = {Algorithms Mol. Biol.},
volume = {15},
number = {1},
pages = {10},
year = {2020},
url = {https://doi.org/10.1186/s13015-020-00172-3},
doi = {10.1186/S13015-020-00172-3},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/almob/XinSK20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhengKM20,
author = {Hongyu Zheng and
Carl Kingsford and
Guillaume Mar{\c{c}}ais},
title = {Improved design and analysis of practical minimizers},
journal = {Bioinform.},
volume = {36},
number = {Supplement-1},
pages = {i119--i127},
year = {2020},
url = {https://doi.org/10.1093/bioinformatics/btaa472},
doi = {10.1093/BIOINFORMATICS/BTAA472},
timestamp = {Wed, 22 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhengKM20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/DeBlasioKK20,
author = {Dan F. DeBlasio and
Kwanho Kim and
Carl Kingsford},
title = {More Accurate Transcript Assembly via Parameter Advising},
journal = {J. Comput. Biol.},
volume = {27},
number = {8},
pages = {1181--1189},
year = {2020},
url = {https://doi.org/10.1089/cmb.2019.0286},
doi = {10.1089/CMB.2019.0286},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/DeBlasioKK20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icml/HoangK20,
author = {Minh Hoang and
Carleton Kingsford},
title = {Optimizing Dynamic Structures with Bayesian Generative Search},
booktitle = {Proceedings of the 37th International Conference on Machine Learning,
{ICML} 2020, 13-18 July 2020, Virtual Event},
series = {Proceedings of Machine Learning Research},
volume = {119},
pages = {4271--4281},
publisher = {{PMLR}},
year = {2020},
url = {http://proceedings.mlr.press/v119/hoang20a.html},
timestamp = {Tue, 15 Dec 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/icml/HoangK20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/ZhengKM20,
author = {Hongyu Zheng and
Carl Kingsford and
Guillaume Mar{\c{c}}ais},
editor = {Russell Schwartz},
title = {Lower Density Selection Schemes via Small Universal Hitting Sets with
Short Remaining Path Length},
booktitle = {Research in Computational Molecular Biology - 24th Annual International
Conference, {RECOMB} 2020, Padua, Italy, May 10-13, 2020, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {12074},
pages = {202--217},
publisher = {Springer},
year = {2020},
url = {https://doi.org/10.1007/978-3-030-45257-5\_13},
doi = {10.1007/978-3-030-45257-5\_13},
timestamp = {Wed, 22 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/ZhengKM20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/MaZK20,
author = {Cong Ma and
Hongyu Zheng and
Carl Kingsford},
editor = {Carl Kingsford and
Nadia Pisanti},
title = {Exact Transcript Quantification Over Splice Graphs},
booktitle = {20th International Workshop on Algorithms in Bioinformatics, {WABI}
2020, September 7-9, 2020, Pisa, Italy (Virtual Conference)},
series = {LIPIcs},
volume = {172},
pages = {12:1--12:18},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2020},
url = {https://doi.org/10.4230/LIPIcs.WABI.2020.12},
doi = {10.4230/LIPICS.WABI.2020.12},
timestamp = {Wed, 22 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wabi/MaZK20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/wabi/2020,
editor = {Carl Kingsford and
Nadia Pisanti},
title = {20th International Workshop on Algorithms in Bioinformatics, {WABI}
2020, September 7-9, 2020, Pisa, Italy (Virtual Conference)},
series = {LIPIcs},
volume = {172},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2020},
url = {https://www.dagstuhl.de/dagpub/978-3-95977-161-0},
isbn = {978-3-95977-161-0},
timestamp = {Mon, 21 Dec 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/wabi/2020.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2001-06550,
author = {Hongyu Zheng and
Carl Kingsford and
Guillaume Mar{\c{c}}ais},
title = {Lower density selection schemes via small universal hitting sets with
short remaining path length},
journal = {CoRR},
volume = {abs/2001.06550},
year = {2020},
url = {https://arxiv.org/abs/2001.06550},
eprinttype = {arXiv},
eprint = {2001.06550},
timestamp = {Wed, 22 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2001-06550.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/SeferK19,
author = {Emre Sefer and
Carl Kingsford},
title = {Semi-nonparametric modeling of topological domain formation from epigenetic
data},
journal = {Algorithms Mol. Biol.},
volume = {14},
number = {1},
pages = {4:1--4:11},
year = {2019},
url = {https://doi.org/10.1186/s13015-019-0142-y},
doi = {10.1186/S13015-019-0142-Y},
timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/almob/SeferK19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MarcaisDPK19,
author = {Guillaume Mar{\c{c}}ais and
Dan F. DeBlasio and
Prashant Pandey and
Carl Kingsford},
title = {Locality-sensitive hashing for the edit distance},
journal = {Bioinform.},
volume = {35},
number = {14},
pages = {i127--i135},
year = {2019},
url = {https://doi.org/10.1093/bioinformatics/btz354},
doi = {10.1093/BIOINFORMATICS/BTZ354},
timestamp = {Tue, 06 Sep 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MarcaisDPK19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nature/SnyderLPARRRGHS19,
author = {Michael P. Snyder and
Shin Lin and
Amanda Posgai and
Mark Atkinson and
Aviv Regev and
Jennifer Rood and
Orit Rozenblatt{-}Rosen and
Leslie Gaffney and
Anna Hupalowska and
Rahul Satija and
Nils Gehlenborg and
Jay Shendure and
Julia Laskin and
Pehr Harbury and
Nicholas A. Nystrom and
Jonathan C. Silverstein and
Ziv Bar{-}Joseph and
Kun Zhang and
Katy B{\"{o}}rner and
Yiing Lin and
Richard Conroy and
Dena Procaccini and
Ananda L. Roy and
Ajay Pillai and
Marishka Brown and
Zorina S. Galis and
Long Cai and
Cole Trapnell and
Dana Jackson and
Garry P. Nolan and
William James Greenleaf and
Sylvia K. Plevritis and
Sara Ahadi and
Stephanie A. Nevins and
Hayan Lee and
Christian Martijn Schuerch and
Sarah Black and
Vishal Gautham Venkataraaman and
Ed Esplin and
Aaron Horning and
Amir Bahmani and
Xin Sun and
Sanjay Jain and
James S. Hagood and
Gloria Pryhuber and
Peter V. Kharchenko and
Bernd Bodenmiller and
Todd Brusko and
Michael Clare{-}Salzler and
Harry Nick and
Kevin Otto and
Clive Wasserfall and
Marda Jorgensen and
Maigan Brusko and
Sergio Maffioletti and
Richard M. Caprioli and
Jeffrey M. Spraggins and
Danielle Gutierrez and
Nathan Heath Patterson and
Elizabeth K. Neumann and
Raymond Harris and
Mark P. de Caestecker and
Agnes B. Fogo and
Raf Van de Plas and
Ken Lau and
Guo{-}Cheng Yuan and
Qian Zhu and
Ruben Dries and
Peng Yin and
Sinem K. Saka and
Jocelyn Y. Kishi and
Yu Wang and
Isabel Goldaracena and
Dong Hye Ye and
Kristin E. Burnum{-}Johnson and
Paul D. Piehowski and
Charles Ansong and
Ying Zhu and
Tushar Desai and
Jay Mulye and
Peter Chou and
Monica Nagendran and
Sarah A. Teichmann and
Benedict Paten and
Robert F. Murphy and
Jian Ma and
Vladimir Yu. Kiselev and
Carl Kingsford and
Allyson Ricarte and
Maria Keays and
Sushma Anand Akoju and
Matthew Ruffalo and
Margaret Vella and
Chuck McCallum and
Leonard E. Cross and
Samuel H. Friedman and
Randy W. Heiland and
Bruce William Herr II and
Paul Macklin and
Ellen M. Quardokus and
Lisel Record and
James P. Sluka and
Griffin M. Weber and
Philip D. Blood and
Alexander Ropelewski and
William Shirey and
Robin M. Scibek and
Paula M. Mabee and
W. Christopher Lenhardt and
Kimberly Robasky and
Stavros Michailidis and
John C. Marioni and
Andrew Butler and
Tim Stuart and
Eyal Fisher and
Shila Ghazanfar and
G{\"{o}}kcen Eraslan and
Tommaso Biancalani and
Eeshit D. Vaishnav and
Pothur Srinivas and
Aaron Pawlyk and
Salvatore Sechi and
Elizabeth L. Wilder and
James Anderson},
title = {The human body at cellular resolution: the {NIH} Human Biomolecular
Atlas Program},
journal = {Nat.},
volume = {574},
number = {7777},
pages = {187--192},
year = {2019},
url = {https://doi.org/10.1038/s41586-019-1629-x},
doi = {10.1038/S41586-019-1629-X},
timestamp = {Fri, 22 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nature/SnyderLPARRRGHS19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/ShaoK19,
author = {Mingfu Shao and
Carl Kingsford},
title = {Theory and {A} Heuristic for the Minimum Path Flow Decomposition Problem},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {16},
number = {2},
pages = {658--670},
year = {2019},
url = {https://doi.org/10.1109/TCBB.2017.2779509},
doi = {10.1109/TCBB.2017.2779509},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/ShaoK19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bcb/DeBlasioGKM19,
author = {Dan F. DeBlasio and
Fiyinfoluwa Gbosibo and
Carl Kingsford and
Guillaume Mar{\c{c}}ais},
editor = {Xinghua Mindy Shi and
Michael Buck and
Jian Ma and
Pierangelo Veltri},
title = {Practical Universal k-mer Sets for Minimizer Schemes},
booktitle = {Proceedings of the 10th {ACM} International Conference on Bioinformatics,
Computational Biology and Health Informatics, {BCB} 2019, Niagara
Falls, NY, USA, September 7-10, 2019},
pages = {167--176},
publisher = {{ACM}},
year = {2019},
url = {https://doi.org/10.1145/3307339.3342144},
doi = {10.1145/3307339.3342144},
timestamp = {Sat, 05 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bcb/DeBlasioGKM19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icml/HoangHLK19,
author = {Quang Minh Hoang and
Trong Nghia Hoang and
Bryan Kian Hsiang Low and
Carl Kingsford},
editor = {Kamalika Chaudhuri and
Ruslan Salakhutdinov},
title = {Collective Model Fusion for Multiple Black-Box Experts},
booktitle = {Proceedings of the 36th International Conference on Machine Learning,
{ICML} 2019, 9-15 June 2019, Long Beach, California, {USA}},
series = {Proceedings of Machine Learning Research},
volume = {97},
pages = {2742--2750},
publisher = {{PMLR}},
year = {2019},
url = {http://proceedings.mlr.press/v97/hoang19a.html},
timestamp = {Tue, 11 Jun 2019 15:37:38 +0200},
biburl = {https://dblp.org/rec/conf/icml/HoangHLK19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/XinSK19,
author = {Hongyi Xin and
Mingfu Shao and
Carl Kingsford},
editor = {Katharina T. Huber and
Dan Gusfield},
title = {Context-Aware Seeds for Read Mapping},
booktitle = {19th International Workshop on Algorithms in Bioinformatics, {WABI}
2019, September 8-10, 2019, Niagara Falls, NY, {USA}},
series = {LIPIcs},
volume = {143},
pages = {15:1--15:13},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2019},
url = {https://doi.org/10.4230/LIPIcs.WABI.2019.15},
doi = {10.4230/LIPICS.WABI.2019.15},
timestamp = {Tue, 03 Sep 2019 17:17:23 +0200},
biburl = {https://dblp.org/rec/conf/wabi/XinSK19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/QiuMXK19,
author = {Yutong Qiu and
Cong Ma and
Han Xie and
Carl Kingsford},
editor = {Katharina T. Huber and
Dan Gusfield},
title = {Detecting Transcriptomic Structural Variants in Heterogeneous Contexts
via the Multiple Compatible Arrangements Problem},
booktitle = {19th International Workshop on Algorithms in Bioinformatics, {WABI}
2019, September 8-10, 2019, Niagara Falls, NY, {USA}},
series = {LIPIcs},
volume = {143},
pages = {18:1--18:19},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2019},
url = {https://doi.org/10.4230/LIPIcs.WABI.2019.18},
doi = {10.4230/LIPICS.WABI.2019.18},
timestamp = {Tue, 03 Sep 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wabi/QiuMXK19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/SauerwaldSK19,
author = {Natalie Sauerwald and
Yihang Shen and
Carl Kingsford},
editor = {Katharina T. Huber and
Dan Gusfield},
title = {Topological Data Analysis Reveals Principles of Chromosome Structure
in Cellular Differentiation},
booktitle = {19th International Workshop on Algorithms in Bioinformatics, {WABI}
2019, September 8-10, 2019, Niagara Falls, NY, {USA}},
series = {LIPIcs},
volume = {143},
pages = {23:1--23:16},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2019},
url = {https://doi.org/10.4230/LIPIcs.WABI.2019.23},
doi = {10.4230/LIPICS.WABI.2019.23},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wabi/SauerwaldSK19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1908-02894,
author = {Maria{-}Florina Balcan and
Dan F. DeBlasio and
Travis Dick and
Carl Kingsford and
Tuomas Sandholm and
Ellen Vitercik},
title = {How much data is sufficient to learn high-performing algorithms?},
journal = {CoRR},
volume = {abs/1908.02894},
year = {2019},
url = {http://arxiv.org/abs/1908.02894},
eprinttype = {arXiv},
eprint = {1908.02894},
timestamp = {Fri, 09 Aug 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1908-02894.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MarcaisDK18,
author = {Guillaume Mar{\c{c}}ais and
Dan F. DeBlasio and
Carl Kingsford},
title = {Asymptotically optimal minimizers schemes},
journal = {Bioinform.},
volume = {34},
number = {13},
pages = {i13--i22},
year = {2018},
url = {https://doi.org/10.1093/bioinformatics/bty258},
doi = {10.1093/BIOINFORMATICS/BTY258},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MarcaisDK18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SauerwaldK18,
author = {Natalie Sauerwald and
Carl Kingsford},
title = {Quantifying the similarity of topological domains across normal and
cancer human cell types},
journal = {Bioinform.},
volume = {34},
number = {13},
pages = {i475--i483},
year = {2018},
url = {https://doi.org/10.1093/bioinformatics/bty265},
doi = {10.1093/BIOINFORMATICS/BTY265},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SauerwaldK18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/SolomonK18,
author = {Brad Solomon and
Carl Kingsford},
title = {Improved Search of Large Transcriptomic Sequencing Databases Using
Split Sequence Bloom Trees},
journal = {J. Comput. Biol.},
volume = {25},
number = {7},
pages = {755--765},
year = {2018},
url = {https://doi.org/10.1089/cmb.2017.0265},
doi = {10.1089/CMB.2017.0265},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/SolomonK18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MarcaisPBOSK17,
author = {Guillaume Mar{\c{c}}ais and
David Pellow and
Daniel Bork and
Yaron Orenstein and
Ron Shamir and
Carl Kingsford},
title = {Improving the performance of minimizers and winnowing schemes},
journal = {Bioinform.},
volume = {33},
number = {14},
pages = {i110--i117},
year = {2017},
url = {https://doi.org/10.1093/bioinformatics/btx235},
doi = {10.1093/BIOINFORMATICS/BTX235},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MarcaisPBOSK17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/WangMK17,
author = {Hao Wang and
Joel McManus and
Carl Kingsford},
title = {Accurate Recovery of Ribosome Positions Reveals Slow Translation of
Wobble-Pairing Codons in Yeast},
journal = {J. Comput. Biol.},
volume = {24},
number = {6},
pages = {486--500},
year = {2017},
url = {https://doi.org/10.1089/cmb.2016.0147},
doi = {10.1089/CMB.2016.0147},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/WangMK17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/PellowFK17,
author = {David Pellow and
Darya Filippova and
Carl Kingsford},
title = {Improving Bloom Filter Performance on Sequence Data Using \emph{k}-mer
Bloom Filters},
journal = {J. Comput. Biol.},
volume = {24},
number = {6},
pages = {547--557},
year = {2017},
url = {https://doi.org/10.1089/cmb.2016.0155},
doi = {10.1089/CMB.2016.0155},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/PellowFK17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/OrensteinPMSK17,
author = {Yaron Orenstein and
David Pellow and
Guillaume Mar{\c{c}}ais and
Ron Shamir and
Carl Kingsford},
title = {Designing small universal k-mer hitting sets for improved analysis
of high-throughput sequencing},
journal = {PLoS Comput. Biol.},
volume = {13},
number = {10},
year = {2017},
url = {https://doi.org/10.1371/journal.pcbi.1005777},
doi = {10.1371/JOURNAL.PCBI.1005777},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/OrensteinPMSK17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/SolomonK17,
author = {Brad Solomon and
Carl Kingsford},
editor = {S{\"{u}}leyman Cenk Sahinalp},
title = {Improved Search of Large Transcriptomic Sequencing Databases Using
Split Sequence Bloom Trees},
booktitle = {Research in Computational Molecular Biology - 21st Annual International
Conference, {RECOMB} 2017, Hong Kong, China, May 3-7, 2017, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {10229},
pages = {257--271},
year = {2017},
url = {https://doi.org/10.1007/978-3-319-56970-3\_16},
doi = {10.1007/978-3-319-56970-3\_16},
timestamp = {Sat, 30 May 2020 20:04:52 +0200},
biburl = {https://dblp.org/rec/conf/recomb/SolomonK17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/XinNZEPKAM16,
author = {Hongyi Xin and
Sunny Nahar and
Richard L. Zhu and
John Emmons and
Gennady Pekhimenko and
Carl Kingsford and
Can Alkan and
Onur Mutlu},
title = {Optimal seed solver: optimizing seed selection in read mapping},
journal = {Bioinform.},
volume = {32},
number = {11},
pages = {1632--1642},
year = {2016},
url = {https://doi.org/10.1093/bioinformatics/btv670},
doi = {10.1093/BIOINFORMATICS/BTV670},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/XinNZEPKAM16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangMK16,
author = {Hao Wang and
Joel McManus and
Carl Kingsford},
title = {Isoform-level ribosome occupancy estimation guided by transcript abundance
with Ribomap},
journal = {Bioinform.},
volume = {32},
number = {12},
pages = {1880--1882},
year = {2016},
url = {https://doi.org/10.1093/bioinformatics/btw085},
doi = {10.1093/BIOINFORMATICS/BTW085},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangMK16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/PatroNPSLSZLBTB16,
author = {Rob Patro and
Raquel Norel and
Robert J. Prill and
Julio Saez{-}Rodriguez and
Peter Lorenz and
Felix Steinbeck and
Bjoern Ziems and
Mitja Lustrek and
Nicola Barbarini and
Alessandra Tiengo and
Riccardo Bellazzi and
Hans{-}J{\"{u}}rgen Thiesen and
Gustavo Stolovitzky and
Carl Kingsford},
title = {A computational method for designing diverse linear epitopes including
citrullinated peptides with desired binding affinities to intravenous
immunoglobulin},
journal = {{BMC} Bioinform.},
volume = {17},
pages = {155},
year = {2016},
url = {https://doi.org/10.1186/s12859-016-1008-7},
doi = {10.1186/S12859-016-1008-7},
timestamp = {Tue, 03 Nov 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/PatroNPSLSZLBTB16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cse/Kingsford16,
author = {Carl Kingsford},
title = {Teaching Computation to Biologists},
journal = {Comput. Sci. Eng.},
volume = {18},
number = {1},
pages = {4--5},
year = {2016},
url = {https://doi.org/10.1109/MCSE.2016.11},
doi = {10.1109/MCSE.2016.11},
timestamp = {Tue, 16 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/cse/Kingsford16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/SeferDK16,
author = {Emre Sefer and
Geet Duggal and
Carl Kingsford},
title = {Deconvolution of Ensemble Chromatin Interaction Data Reveals the Latent
Mixing Structures in Cell Subpopulations},
journal = {J. Comput. Biol.},
volume = {23},
number = {6},
pages = {425--438},
year = {2016},
url = {https://doi.org/10.1089/cmb.2015.0210},
doi = {10.1089/CMB.2015.0210},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/SeferDK16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/kais/SeferK16,
author = {Emre Sefer and
Carl Kingsford},
title = {Diffusion archeology for diffusion progression history reconstruction},
journal = {Knowl. Inf. Syst.},
volume = {49},
number = {2},
pages = {403--427},
year = {2016},
url = {https://doi.org/10.1007/s10115-015-0904-x},
doi = {10.1007/S10115-015-0904-X},
timestamp = {Wed, 14 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/kais/SeferK16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/HormozdiariHKMV16,
author = {Farhad Hormozdiari and
Fereydoun Hormozdiari and
Carl Kingsford and
Paul Medvedev and
Fabio Vandin},
editor = {Mona Singh},
title = {The Second Decade of the International Conference on Research in Computational
Molecular Biology {(RECOMB)}},
booktitle = {Research in Computational Molecular Biology - 20th Annual Conference,
{RECOMB} 2016, Santa Monica, CA, USA, April 17-21, 2016, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {9649},
pages = {3--16},
publisher = {Springer},
year = {2016},
url = {https://doi.org/10.1007/978-3-319-31957-5\_1},
doi = {10.1007/978-3-319-31957-5\_1},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/HormozdiariHKMV16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/WangMK16,
author = {Hao Wang and
Joel McManus and
Carl Kingsford},
editor = {Mona Singh},
title = {Accurate Recovery of Ribosome Positions Reveals Slow Translation of
Wobble-Pairing Codons in Yeast},
booktitle = {Research in Computational Molecular Biology - 20th Annual Conference,
{RECOMB} 2016, Santa Monica, CA, USA, April 17-21, 2016, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {9649},
pages = {37--52},
publisher = {Springer},
year = {2016},
url = {https://doi.org/10.1007/978-3-319-31957-5\_3},
doi = {10.1007/978-3-319-31957-5\_3},
timestamp = {Mon, 13 May 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/WangMK16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/PellowFK16,
author = {David Pellow and
Darya Filippova and
Carl Kingsford},
editor = {Mona Singh},
title = {Improving Bloom Filter Performance on Sequence Data Using k -mer Bloom
Filters},
booktitle = {Research in Computational Molecular Biology - 20th Annual Conference,
{RECOMB} 2016, Santa Monica, CA, USA, April 17-21, 2016, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {9649},
pages = {137--151},
publisher = {Springer},
year = {2016},
url = {https://doi.org/10.1007/978-3-319-31957-5\_10},
doi = {10.1007/978-3-319-31957-5\_10},
timestamp = {Mon, 13 May 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/PellowFK16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/OrensteinPMSK16,
author = {Yaron Orenstein and
David Pellow and
Guillaume Mar{\c{c}}ais and
Ron Shamir and
Carl Kingsford},
editor = {Martin C. Frith and
Christian N{\o}rgaard Storm Pedersen},
title = {Compact Universal k-mer Hitting Sets},
booktitle = {Algorithms in Bioinformatics - 16th International Workshop, {WABI}
2016, Aarhus, Denmark, August 22-24, 2016. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {9838},
pages = {257--268},
publisher = {Springer},
year = {2016},
url = {https://doi.org/10.1007/978-3-319-43681-4\_21},
doi = {10.1007/978-3-319-43681-4\_21},
timestamp = {Tue, 14 May 2019 10:00:40 +0200},
biburl = {https://dblp.org/rec/conf/wabi/OrensteinPMSK16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/GuptaSWKP16,
author = {Nitish Gupta and
Komal Sanjeev and
Tim Wall and
Carl Kingsford and
Rob Patro},
title = {Efficient Index Maintenance Under Dynamic Genome Modification},
journal = {CoRR},
volume = {abs/1604.03132},
year = {2016},
url = {http://arxiv.org/abs/1604.03132},
eprinttype = {arXiv},
eprint = {1604.03132},
timestamp = {Tue, 03 Nov 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/GuptaSWKP16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/XinGEPKAM15,
author = {Hongyi Xin and
John Greth and
John Emmons and
Gennady Pekhimenko and
Carl Kingsford and
Can Alkan and
Onur Mutlu},
title = {Shifted Hamming distance: a fast and accurate SIMD-friendly filter
to accelerate alignment verification in read mapping},
journal = {Bioinform.},
volume = {31},
number = {10},
pages = {1553--1560},
year = {2015},
url = {https://doi.org/10.1093/bioinformatics/btu856},
doi = {10.1093/BIOINFORMATICS/BTU856},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/XinGEPKAM15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KingsfordP15,
author = {Carl Kingsford and
Rob Patro},
title = {Reference-based compression of short-read sequences using path encoding},
journal = {Bioinform.},
volume = {31},
number = {12},
pages = {1920--1928},
year = {2015},
url = {https://doi.org/10.1093/bioinformatics/btv071},
doi = {10.1093/BIOINFORMATICS/BTV071},
timestamp = {Tue, 03 Nov 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KingsfordP15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PatroK15,
author = {Rob Patro and
Carl Kingsford},
title = {Data-dependent bucketing improves reference-free compression of sequencing
reads},
journal = {Bioinform.},
volume = {31},
number = {17},
pages = {2770--2777},
year = {2015},
url = {https://doi.org/10.1093/bioinformatics/btv248},
doi = {10.1093/BIOINFORMATICS/BTV248},
timestamp = {Tue, 03 Nov 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PatroK15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bcb/FilippovaK15,
author = {Darya Filippova and
Carl Kingsford},
title = {Rapid, separable compression enables fast analyses of sequence alignments},
booktitle = {Proceedings of the 6th {ACM} Conference on Bioinformatics, Computational
Biology and Health Informatics, {BCB} 2015, Atlanta, GA, USA, September
9-12, 2015},
pages = {194--201},
publisher = {{ACM}},
year = {2015},
url = {https://doi.org/10.1145/2808719.2808739},
doi = {10.1145/2808719.2808739},
timestamp = {Tue, 06 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/bcb/FilippovaK15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icde/SeferK15,
author = {Emre Sefer and
Carl Kingsford},
editor = {Johannes Gehrke and
Wolfgang Lehner and
Kyuseok Shim and
Sang Kyun Cha and
Guy M. Lohman},
title = {Convex Risk Minimization to Infer Networks from probabilistic diffusion
data at multiple scales},
booktitle = {31st {IEEE} International Conference on Data Engineering, {ICDE} 2015,
Seoul, South Korea, April 13-17, 2015},
pages = {663--674},
publisher = {{IEEE} Computer Society},
year = {2015},
url = {https://doi.org/10.1109/ICDE.2015.7113323},
doi = {10.1109/ICDE.2015.7113323},
timestamp = {Sun, 25 Oct 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/icde/SeferK15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/SeferDK15,
author = {Emre Sefer and
Geet Duggal and
Carl Kingsford},
editor = {Teresa M. Przytycka},
title = {Deconvolution of Ensemble Chromatin Interaction Data Reveals the Latent
Mixing Structures in Cell Subpopulations},
booktitle = {Research in Computational Molecular Biology - 19th Annual International
Conference, {RECOMB} 2015, Warsaw, Poland, April 12-15, 2015, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {9029},
pages = {293--308},
publisher = {Springer},
year = {2015},
url = {https://doi.org/10.1007/978-3-319-16706-0\_30},
doi = {10.1007/978-3-319-16706-0\_30},
timestamp = {Sun, 25 Oct 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/SeferDK15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/SeferK15,
author = {Emre Sefer and
Carl Kingsford},
editor = {Mihai Pop and
H{\'{e}}l{\`{e}}ne Touzet},
title = {Semi-nonparametric Modeling of Topological Domain Formation from Epigenetic
Data},
booktitle = {Algorithms in Bioinformatics - 15th International Workshop, {WABI}
2015, Atlanta, GA, USA, September 10-12, 2015, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {9289},
pages = {148--161},
publisher = {Springer},
year = {2015},
url = {https://doi.org/10.1007/978-3-662-48221-6\_11},
doi = {10.1007/978-3-662-48221-6\_11},
timestamp = {Thu, 14 Oct 2021 10:34:16 +0200},
biburl = {https://dblp.org/rec/conf/wabi/SeferK15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/XinZNEPKAM15,
author = {Hongyi Xin and
Richard L. Zhu and
Sunny Nahar and
John Emmons and
Gennady Pekhimenko and
Carl Kingsford and
Can Alkan and
Onur Mutlu},
title = {Optimal Seed Solver: Optimizing Seed Selection in Read Mapping},
journal = {CoRR},
volume = {abs/1506.08235},
year = {2015},
url = {http://arxiv.org/abs/1506.08235},
eprinttype = {arXiv},
eprint = {1506.08235},
timestamp = {Thu, 13 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/XinZNEPKAM15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/FilippovaPDK14,
author = {Darya Filippova and
Rob Patro and
Geet Duggal and
Carl Kingsford},
title = {Identification of alternative topological domains in chromatin},
journal = {Algorithms Mol. Biol.},
volume = {9},
pages = {14},
year = {2014},
url = {https://doi.org/10.1186/1748-7188-9-14},
doi = {10.1186/1748-7188-9-14},
timestamp = {Tue, 03 Nov 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/almob/FilippovaPDK14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icdm/SeferK14,
author = {Emre Sefer and
Carl Kingsford},
editor = {Ravi Kumar and
Hannu Toivonen and
Jian Pei and
Joshua Zhexue Huang and
Xindong Wu},
title = {Diffusion Archaeology for Diffusion Progression History Reconstruction},
booktitle = {2014 {IEEE} International Conference on Data Mining, {ICDM} 2014,
Shenzhen, China, December 14-17, 2014},
pages = {530--539},
publisher = {{IEEE} Computer Society},
year = {2014},
url = {https://doi.org/10.1109/ICDM.2014.135},
doi = {10.1109/ICDM.2014.135},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/icdm/SeferK14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/DuggalPSWFKK13,
author = {Geet Duggal and
Rob Patro and
Emre Sefer and
Hao Wang and
Darya Filippova and
Samir Khuller and
Carl Kingsford},
title = {Resolving spatial inconsistencies in chromosome conformation measurements},
journal = {Algorithms Mol. Biol.},
volume = {8},
pages = {8},
year = {2013},
url = {https://doi.org/10.1186/1748-7188-8-8},
doi = {10.1186/1748-7188-8-8},
timestamp = {Tue, 03 Nov 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/almob/DuggalPSWFKK13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PatroK13,
author = {Rob Patro and
Carl Kingsford},
title = {Predicting protein interactions via parsimonious network history inference},
journal = {Bioinform.},
volume = {29},
number = {13},
pages = {237--246},
year = {2013},
url = {https://doi.org/10.1093/bioinformatics/btt224},
doi = {10.1093/BIOINFORMATICS/BTT224},
timestamp = {Tue, 03 Nov 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PatroK13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bcb/WangDPGHK13,
author = {Hao Wang and
Geet Duggal and
Rob Patro and
Michelle Girvan and
Sridhar Hannenhalli and
Carl Kingsford},
editor = {Jing Gao},
title = {Topological properties of chromosome conformation graphs reflect spatial
proximities within chromatin},
booktitle = {{ACM} Conference on Bioinformatics, Computational Biology and Biomedical
Informatics. {ACM-BCB} 2013, Washington, DC, USA, September 22-25,
2013},
pages = {306},
publisher = {{ACM}},
year = {2013},
url = {https://doi.org/10.1145/2506583.2506633},
doi = {10.1145/2506583.2506633},
timestamp = {Tue, 03 Nov 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/bcb/WangDPGHK13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/FilippovaPDK13,
author = {Darya Filippova and
Rob Patro and
Geet Duggal and
Carl Kingsford},
editor = {Aaron E. Darling and
Jens Stoye},
title = {Multiscale Identification of Topological Domains in Chromatin},
booktitle = {Algorithms in Bioinformatics - 13th International Workshop, {WABI}
2013, Sophia Antipolis, France, September 2-4, 2013. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {8126},
pages = {300--312},
publisher = {Springer},
year = {2013},
url = {https://doi.org/10.1007/978-3-642-40453-5\_23},
doi = {10.1007/978-3-642-40453-5\_23},
timestamp = {Tue, 21 Mar 2023 21:00:29 +0100},
biburl = {https://dblp.org/rec/conf/wabi/FilippovaPDK13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/PatroMK13,
author = {Rob Patro and
Stephen M. Mount and
Carl Kingsford},
title = {Sailfish: Alignment-free Isoform Quantification from RNA-seq Reads
using Lightweight Algorithms},
journal = {CoRR},
volume = {abs/1308.3700},
year = {2013},
url = {http://arxiv.org/abs/1308.3700},
eprinttype = {arXiv},
eprint = {1308.3700},
timestamp = {Tue, 03 Nov 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/PatroMK13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/PatroSMMNK12,
author = {Rob Patro and
Emre Sefer and
Justin Malin and
Guillaume Mar{\c{c}}ais and
Saket Navlakha and
Carl Kingsford},
title = {Parsimonious reconstruction of network evolution},
journal = {Algorithms Mol. Biol.},
volume = {7},
pages = {25},
year = {2012},
url = {https://doi.org/10.1186/1748-7188-7-25},
doi = {10.1186/1748-7188-7-25},
timestamp = {Tue, 03 Nov 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/almob/PatroSMMNK12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PatroK12,
author = {Rob Patro and
Carl Kingsford},
title = {Global network alignment using multiscale spectral signatures},
journal = {Bioinform.},
volume = {28},
number = {23},
pages = {3105--3114},
year = {2012},
url = {https://doi.org/10.1093/bioinformatics/bts592},
doi = {10.1093/BIOINFORMATICS/BTS592},
timestamp = {Tue, 03 Nov 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/PatroK12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/DuggalK12,
author = {Geet Duggal and
Carl Kingsford},
title = {Graph rigidity reveals well-constrained regions of chromosome conformation
embeddings},
journal = {{BMC} Bioinform.},
volume = {13},
pages = {241},
year = {2012},
url = {https://doi.org/10.1186/1471-2105-13-241},
doi = {10.1186/1471-2105-13-241},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/DuggalK12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/FilippovaGK12,
author = {Darya Filippova and
Aashish Gadani and
Carl Kingsford},
title = {Coral: an integrated suite of visualizations for comparing clusterings},
journal = {{BMC} Bioinform.},
volume = {13},
pages = {276},
year = {2012},
url = {https://doi.org/10.1186/1471-2105-13-276},
doi = {10.1186/1471-2105-13-276},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/FilippovaGK12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/kdd/PatroDSWFK12,
author = {Rob Patro and
Geet Duggal and
Emre Sefer and
Hao Wang and
Darya Filippova and
Carl Kingsford},
editor = {Qiang Yang and
Deepak Agarwal and
Jian Pei},
title = {The missing models: a data-driven approach for learning how networks
grow},
booktitle = {The 18th {ACM} {SIGKDD} International Conference on Knowledge Discovery
and Data Mining, {KDD} '12, Beijing, China, August 12-16, 2012},
pages = {42--50},
publisher = {{ACM}},
year = {2012},
url = {https://doi.org/10.1145/2339530.2339541},
doi = {10.1145/2339530.2339541},
timestamp = {Tue, 03 Nov 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/kdd/PatroDSWFK12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/socialcom/FilippovaFKB12,
author = {Darya Filippova and
Michael Fitzgerald and
Carl Kingsford and
Fernando Benadon},
title = {Dynamic Exploration of Recording Sessions between Jazz Musicians over
Time},
booktitle = {2012 International Conference on Privacy, Security, Risk and Trust,
{PASSAT} 2012, and 2012 International Confernece on Social Computing,
SocialCom 2012, Amsterdam, Netherlands, September 3-5, 2012},
pages = {368--376},
publisher = {{IEEE} Computer Society},
year = {2012},
url = {https://doi.org/10.1109/SocialCom-PASSAT.2012.78},
doi = {10.1109/SOCIALCOM-PASSAT.2012.78},
timestamp = {Thu, 23 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/socialcom/FilippovaFKB12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/DuggalPSWFKK12,
author = {Geet Duggal and
Rob Patro and
Emre Sefer and
Hao Wang and
Darya Filippova and
Samir Khuller and
Carl Kingsford},
editor = {Benjamin J. Raphael and
Jijun Tang},
title = {Resolving Spatial Inconsistencies in Chromosome Conformation Data},
booktitle = {Algorithms in Bioinformatics - 12th International Workshop, {WABI}
2012, Ljubljana, Slovenia, September 10-12, 2012. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {7534},
pages = {288--300},
publisher = {Springer},
year = {2012},
url = {https://doi.org/10.1007/978-3-642-33122-0\_23},
doi = {10.1007/978-3-642-33122-0\_23},
timestamp = {Tue, 03 Nov 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/wabi/DuggalPSWFKK12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MarcaisK11,
author = {Guillaume Mar{\c{c}}ais and
Carl Kingsford},
title = {A fast, lock-free approach for efficient parallel counting of occurrences
of \emph{k}-mers},
journal = {Bioinform.},
volume = {27},
number = {6},
pages = {764--770},
year = {2011},
url = {https://doi.org/10.1093/bioinformatics/btr011},
doi = {10.1093/BIOINFORMATICS/BTR011},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MarcaisK11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/WetzelKP11,
author = {Joshua L. Wetzel and
Carl Kingsford and
Mihai Pop},
title = {Assessing the benefits of using mate-pairs to resolve repeats in de
novo short-read prokaryotic assemblies},
journal = {{BMC} Bioinform.},
volume = {12},
pages = {95},
year = {2011},
url = {https://doi.org/10.1186/1471-2105-12-95},
doi = {10.1186/1471-2105-12-95},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/WetzelKP11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/KelleyK11,
author = {David R. Kelley and
Carl Kingsford},
title = {Extracting Between-Pathway Models from {E-MAP} Interactions Using
Expected Graph Compression},
journal = {J. Comput. Biol.},
volume = {18},
number = {3},
pages = {379--390},
year = {2011},
url = {https://doi.org/10.1089/cmb.2010.0268},
doi = {10.1089/CMB.2010.0268},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/KelleyK11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jda/KingsfordZS11,
author = {Carl Kingsford and
Elena Zaslavsky and
Mona Singh},
title = {A cost-aggregating integer linear program for motif finding},
journal = {J. Discrete Algorithms},
volume = {9},
number = {4},
pages = {326--334},
year = {2011},
url = {https://doi.org/10.1016/j.jda.2011.04.001},
doi = {10.1016/J.JDA.2011.04.001},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jda/KingsfordZS11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/NavlakhaK11,
author = {Saket Navlakha and
Carl Kingsford},
title = {Network Archaeology: Uncovering Ancient Networks from Present-Day
Interactions},
journal = {PLoS Comput. Biol.},
volume = {7},
number = {4},
year = {2011},
url = {https://doi.org/10.1371/journal.pcbi.1001119},
doi = {10.1371/JOURNAL.PCBI.1001119},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/NavlakhaK11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/sigact/Kingsford11,
author = {Carl Kingsford},
title = {Review of Complex social networks by Fernando Vega-Redondo},
journal = {{SIGACT} News},
volume = {42},
number = {1},
pages = {29--31},
year = {2011},
url = {https://doi.org/10.1145/1959045.1959052},
doi = {10.1145/1959045.1959052},
timestamp = {Tue, 06 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/sigact/Kingsford11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/SeferK11,
author = {Emre Sefer and
Carl Kingsford},
editor = {Vineet Bafna and
S{\"{u}}leyman Cenk Sahinalp},
title = {Metric Labeling and Semi-metric Embedding for Protein Annotation Prediction},
booktitle = {Research in Computational Molecular Biology - 15th Annual International
Conference, {RECOMB} 2011, Vancouver, BC, Canada, March 28-31, 2011.
Proceedings},
series = {Lecture Notes in Computer Science},
volume = {6577},
pages = {392--407},
publisher = {Springer},
year = {2011},
url = {https://doi.org/10.1007/978-3-642-20036-6\_37},
doi = {10.1007/978-3-642-20036-6\_37},
timestamp = {Sun, 25 Oct 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/SeferK11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/PatroSMMNK11,
author = {Rob Patro and
Emre Sefer and
Justin Malin and
Guillaume Mar{\c{c}}ais and
Saket Navlakha and
Carl Kingsford},
editor = {Teresa M. Przytycka and
Marie{-}France Sagot},
title = {Parsimonious Reconstruction of Network Evolution},
booktitle = {Algorithms in Bioinformatics - 11th International Workshop, {WABI}
2011, Saarbr{\"{u}}cken, Germany, September 5-7, 2011. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {6833},
pages = {237--249},
publisher = {Springer},
year = {2011},
url = {https://doi.org/10.1007/978-3-642-23038-7\_21},
doi = {10.1007/978-3-642-23038-7\_21},
timestamp = {Tue, 03 Nov 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/wabi/PatroSMMNK11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/NavlakhaK10,
author = {Saket Navlakha and
Carl Kingsford},
title = {The power of protein interaction networks for associating genes with
diseases},
journal = {Bioinform.},
volume = {26},
number = {8},
pages = {1057--1063},
year = {2010},
url = {https://doi.org/10.1093/bioinformatics/btq076},
doi = {10.1093/BIOINFORMATICS/BTQ076},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/NavlakhaK10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KingsfordSP10,
author = {Carl Kingsford and
Michael C. Schatz and
Mihai Pop},
title = {Assembly complexity of prokaryotic genomes using short reads},
journal = {{BMC} Bioinform.},
volume = {11},
pages = {21},
year = {2010},
url = {https://doi.org/10.1186/1471-2105-11-21},
doi = {10.1186/1471-2105-11-21},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/KingsfordSP10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/WhiteNNGKP10,
author = {James Robert White and
Saket Navlakha and
Niranjan Nagarajan and
Mohammadreza Ghodsi and
Carl Kingsford and
Mihai Pop},
title = {Alignment and clustering of phylogenetic markers - implications for
microbial diversity studies},
journal = {{BMC} Bioinform.},
volume = {11},
pages = {152},
year = {2010},
url = {https://doi.org/10.1186/1471-2105-11-152},
doi = {10.1186/1471-2105-11-152},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/WhiteNNGKP10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/NavlakhaWNPK10,
author = {Saket Navlakha and
James Robert White and
Niranjan Nagarajan and
Mihai Pop and
Carl Kingsford},
title = {Finding Biologically Accurate Clusterings in Hierarchical Tree Decompositions
Using the Variation of Information},
journal = {J. Comput. Biol.},
volume = {17},
number = {3},
pages = {503--516},
year = {2010},
url = {https://doi.org/10.1089/cmb.2009.0173},
doi = {10.1089/CMB.2009.0173},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/NavlakhaWNPK10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cec/Lapizco-EncinasKR10,
author = {Grecia Lapizco{-}Encinas and
Carl Kingsford and
James A. Reggia},
title = {Particle Swarm Optimization for multimodal combinatorial problems
and its application to protein design},
booktitle = {Proceedings of the {IEEE} Congress on Evolutionary Computation, {CEC}
2010, Barcelona, Spain, 18-23 July 2010},
pages = {1--8},
publisher = {{IEEE}},
year = {2010},
url = {https://doi.org/10.1109/CEC.2010.5586157},
doi = {10.1109/CEC.2010.5586157},
timestamp = {Thu, 16 Dec 2021 14:02:32 +0100},
biburl = {https://dblp.org/rec/conf/cec/Lapizco-EncinasKR10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/NavlakhaK10,
author = {Saket Navlakha and
Carl Kingsford},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Tiffany Murray and
Teri E. Klein},
title = {Exploring Biological Network Dynamics with Ensembles of Graph Partitions},
booktitle = {Biocomputing 2010: Proceedings of the Pacific Symposium, Kamuela,
Hawaii, USA, 4-8 January 2010},
pages = {166--177},
publisher = {World Scientific Publishing},
year = {2010},
url = {http://psb.stanford.edu/psb-online/proceedings/psb10/navlakha.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/NavlakhaK10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/KelleyK10,
author = {David R. Kelley and
Carl Kingsford},
editor = {Bonnie Berger},
title = {Extracting Between-Pathway Models from {E-MAP} Interactions Using
Expected Graph Compression},
booktitle = {Research in Computational Molecular Biology, 14th Annual International
Conference, {RECOMB} 2010, Lisbon, Portugal, April 25-28, 2010. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {6044},
pages = {248--262},
publisher = {Springer},
year = {2010},
url = {https://doi.org/10.1007/978-3-642-12683-3\_16},
doi = {10.1007/978-3-642-12683-3\_16},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/KelleyK10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1008-5166,
author = {Saket Navlakha and
Carl Kingsford},
title = {Network Archaeology: Uncovering Ancient Networks from Present-day
Interactions},
journal = {CoRR},
volume = {abs/1008.5166},
year = {2010},
url = {http://arxiv.org/abs/1008.5166},
eprinttype = {arXiv},
eprint = {1008.5166},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1008-5166.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/NavlakhaSK09,
author = {Saket Navlakha and
Michael C. Schatz and
Carl Kingsford},
title = {Revealing Biological Modules via Graph Summarization},
journal = {J. Comput. Biol.},
volume = {16},
number = {2},
pages = {253--264},
year = {2009},
url = {https://doi.org/10.1089/cmb.2008.11TT},
doi = {10.1089/CMB.2008.11TT},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/NavlakhaSK09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/NavlakhaWNPK09,
author = {Saket Navlakha and
James Robert White and
Niranjan Nagarajan and
Mihai Pop and
Carl Kingsford},
editor = {Serafim Batzoglou},
title = {Finding Biologically Accurate Clusterings in Hierarchical Tree Decompositions
Using the Variation of Information},
booktitle = {Research in Computational Molecular Biology, 13th Annual International
Conference, {RECOMB} 2009, Tucson, AZ, USA, May 18-21, 2009. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5541},
pages = {400--417},
publisher = {Springer},
year = {2009},
url = {https://doi.org/10.1007/978-3-642-02008-7\_29},
doi = {10.1007/978-3-642-02008-7\_29},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/NavlakhaWNPK09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/swis/Lapizco-EncinasKR09,
author = {Grecia Lapizco{-}Encinas and
Carl Kingsford and
James A. Reggia},
title = {A cooperative combinatorial Particle Swarm Optimization algorithm
for side-chain packing},
booktitle = {2009 {IEEE} Swarm Intelligence Symposium, {SIS} 2009, Nashville, TN,
USA, April 1-2, 2009},
pages = {22--29},
publisher = {{IEEE}},
year = {2009},
url = {https://doi.org/10.1109/SIS.2009.4937840},
doi = {10.1109/SIS.2009.4937840},
timestamp = {Wed, 16 Oct 2019 14:14:48 +0200},
biburl = {https://dblp.org/rec/conf/swis/Lapizco-EncinasKR09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibm/NagarajanK08,
author = {Niranjan Nagarajan and
Carl Kingsford},
editor = {Xue{-}wen Chen and
Xiaohua Hu and
Sun Kim},
title = {Uncovering Genomic Reassortments among Influenza Strains by Enumerating
Maximal Bicliques},
booktitle = {2008 {IEEE} International Conference on Bioinformatics and Biomedicine,
{BIBM} 2008, Philadephia, Pennsylvania, USA, November 3-5, 2008},
pages = {223--230},
publisher = {{IEEE} Computer Society},
year = {2008},
url = {https://doi.org/10.1109/BIBM.2008.78},
doi = {10.1109/BIBM.2008.78},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/bibm/NagarajanK08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cpm/KingsfordZS06,
author = {Carl Kingsford and
Elena Zaslavsky and
Mona Singh},
editor = {Moshe Lewenstein and
Gabriel Valiente},
title = {A Compact Mathematical Programming Formulation for {DNA} Motif Finding},
booktitle = {Combinatorial Pattern Matching, 17th Annual Symposium, {CPM} 2006,
Barcelona, Spain, July 5-7, 2006, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {4009},
pages = {233--245},
publisher = {Springer},
year = {2006},
url = {https://doi.org/10.1007/11780441\_22},
doi = {10.1007/11780441\_22},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/cpm/KingsfordZS06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KingsfordCS05,
author = {Carleton Kingsford and
Bernard Chazelle and
Mona Singh},
title = {Solving and analyzing side-chain positioning problems using linear
and integer programming},
journal = {Bioinform.},
volume = {21},
number = {7},
pages = {1028--1039},
year = {2005},
url = {https://doi.org/10.1093/bioinformatics/bti144},
doi = {10.1093/BIOINFORMATICS/BTI144},
timestamp = {Sat, 14 Jan 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KingsfordCS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/informs/ChazelleKS04,
author = {Bernard Chazelle and
Carl Kingsford and
Mona Singh},
title = {A Semidefinite Programming Approach to Side Chain Positioning with
New Rounding Strategies},
journal = {{INFORMS} J. Comput.},
volume = {16},
number = {4},
pages = {380--392},
year = {2004},
url = {https://doi.org/10.1287/ijoc.1040.0096},
doi = {10.1287/IJOC.1040.0096},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/informs/ChazelleKS04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/birthday/ChazelleKS03,
author = {Bernard Chazelle and
Carl Kingsford and
Mona Singh},
editor = {Dina Q. Goldin and
Alexander A. Shvartsman and
Scott A. Smolka and
Jeffrey Scott Vitter and
Stanley B. Zdonik},
title = {The Side-Chain Positioning Problem: {A} Semidefinite Programming Formulation
With New Rounding Schemes},
booktitle = {{PCK50} - Principles of Computing {\&} Knowledge, Paris C. Kanellakis
Memorial Workshop, San Diego, California, USA, June 8th, 2003},
pages = {86--94},
publisher = {{ACM}},
year = {2003},
url = {https://doi.org/10.1145/778348.778360},
doi = {10.1145/778348.778360},
timestamp = {Thu, 17 Feb 2022 16:43:16 +0100},
biburl = {https://dblp.org/rec/conf/birthday/ChazelleKS03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/dna/ReifLPRGKW01,
author = {John H. Reif and
Thomas H. LaBean and
Michael Pirrung and
Vipul S. Rana and
Bo Guo and
Carl Kingsford and
Gene S. Wickham},
editor = {Natasa Jonoska and
Nadrian C. Seeman},
title = {Experimental Construction of Very Large Scale {DNA} Databases with
Associative Search Capability},
booktitle = {{DNA} Computing, 7th International Workshop on DNA-Based Computers,
DNA7, Tampa, Florida, USA, June 10-13, 2001, Revised Papers},
series = {Lecture Notes in Computer Science},
volume = {2340},
pages = {231--247},
publisher = {Springer},
year = {2001},
url = {https://doi.org/10.1007/3-540-48017-X\_22},
doi = {10.1007/3-540-48017-X\_22},
timestamp = {Tue, 14 May 2019 10:00:40 +0200},
biburl = {https://dblp.org/rec/conf/dna/ReifLPRGKW01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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