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ORCIDBibTeX records: Russell Schwartz
@inproceedings{DBLP:conf/recomb/WuJRRSSM24,
author = {Chih Hao Wu and
Suraj Joshi and
Welles Robinson and
Paul F. Robbins and
Russell Schwartz and
S{\"{u}}leyman Cenk Sahinalp and
Salem Malikic},
editor = {Jian Ma},
title = {Determining Optimal Placement of Copy Number Aberration Impacted Single
Nucleotide Variants in a Tumor Progression History},
booktitle = {Research in Computational Molecular Biology - 28th Annual International
Conference, {RECOMB} 2024, Cambridge, MA, USA, April 29 - May 2, 2024,
Proceedings},
series = {Lecture Notes in Computer Science},
volume = {14758},
pages = {438--443},
publisher = {Springer},
year = {2024},
url = {https://doi.org/10.1007/978-1-0716-3989-4\_48},
doi = {10.1007/978-1-0716-3989-4\_48},
timestamp = {Tue, 04 Jun 2024 16:20:52 +0200},
biburl = {https://dblp.org/rec/conf/recomb/WuJRRSSM24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/SrivatsaLS23,
author = {Arjun Srivatsa and
Haoyun Lei and
Russell Schwartz},
title = {A Clonal Evolution Simulator for Planning Somatic Evolution Studies},
journal = {J. Comput. Biol.},
volume = {30},
number = {8},
pages = {831--847},
year = {2023},
url = {https://doi.org/10.1089/cmb.2023.0086},
doi = {10.1089/CMB.2023.0086},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/SrivatsaLS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/PalagiSMO23,
author = {Patricia M. Palagi and
Russell Schwartz and
Scott Markel and
B. F. Francis Ouellette},
title = {Ten simple rules for writing a {PLOS} Computational Biology quick
tips article},
journal = {PLoS Comput. Biol.},
volume = {19},
number = {12},
year = {2023},
url = {https://doi.org/10.1371/journal.pcbi.1011689},
doi = {10.1371/JOURNAL.PCBI.1011689},
timestamp = {Sat, 16 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ploscb/PalagiSMO23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isbra/SrivatsaLS22,
author = {Arjun Srivatsa and
Haoyun Lei and
Russell Schwartz},
editor = {Mukul S. Bansal and
Zhipeng Cai and
Serghei Mangul},
title = {A Clonal Evolution Simulator for Planning Somatic Evolution Studies},
booktitle = {Bioinformatics Research and Applications - 18th International Symposium,
{ISBRA} 2022, Haifa, Israel, November 14-17, 2022, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {13760},
pages = {229--242},
publisher = {Springer},
year = {2022},
url = {https://doi.org/10.1007/978-3-031-23198-8\_21},
doi = {10.1007/978-3-031-23198-8\_21},
timestamp = {Mon, 09 Jan 2023 17:58:33 +0100},
biburl = {https://dblp.org/rec/conf/isbra/SrivatsaLS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LeiGSFTHTLXHWSD21,
author = {Haoyun Lei and
E. Michael Gertz and
Alejandro A. Sch{\"{a}}ffer and
Xuecong Fu and
Yifeng Tao and
Kerstin Heselmeyer{-}Haddad and
Irianna Torres and
Guibo Li and
Liqin Xu and
Yong Hou and
Kui Wu and
Xulian Shi and
Michael Dean and
Thomas Ried and
Russell Schwartz},
title = {Tumor heterogeneity assessed by sequencing and fluorescence in situ
hybridization {(FISH)} data},
journal = {Bioinform.},
volume = {37},
number = {24},
pages = {4704--4711},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab504},
doi = {10.1093/BIOINFORMATICS/BTAB504},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LeiGSFTHTLXHWSD21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/Schwartz21,
author = {Russell Schwartz},
title = {{RECOMB} 2020 Special Issue},
journal = {J. Comput. Biol.},
volume = {28},
number = {4},
pages = {345},
year = {2021},
url = {https://doi.org/10.1089/cmb.2021.29028.rs},
doi = {10.1089/CMB.2021.29028.RS},
timestamp = {Thu, 09 Sep 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/Schwartz21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/FuLTHTDRS21,
author = {Xuecong Fu and
Haoyun Lei and
Yifeng Tao and
Kerstin Heselmeyer{-}Haddad and
Irianna Torres and
Michael Dean and
Thomas Ried and
Russell Schwartz},
title = {Joint Clustering of Single-Cell Sequencing and Fluorescence In Situ
Hybridization Data for Reconstructing Clonal Heterogeneity in Cancers},
journal = {J. Comput. Biol.},
volume = {28},
number = {11},
pages = {1035--1051},
year = {2021},
url = {https://doi.org/10.1089/cmb.2021.0255},
doi = {10.1089/CMB.2021.0255},
timestamp = {Wed, 16 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/FuLTHTDRS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/TaoRCCCZEKMS21,
author = {Yifeng Tao and
Ashok Rajaraman and
Xiaoyue Cui and
Ziyi Cui and
Haoran Chen and
Yuanqi Zhao and
Jesse Eaton and
Hannah Kim and
Jian Ma and
Russell Schwartz},
title = {Assessing the contribution of tumor mutational phenotypes to cancer
progression risk},
journal = {PLoS Comput. Biol.},
volume = {17},
number = {3},
year = {2021},
url = {https://doi.org/10.1371/journal.pcbi.1008777},
doi = {10.1371/JOURNAL.PCBI.1008777},
timestamp = {Mon, 29 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ploscb/TaoRCCCZEKMS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibm/FuS21,
author = {Xuecong Fu and
Russell Schwartz},
editor = {Yufei Huang and
Lukasz A. Kurgan and
Feng Luo and
Xiaohua Hu and
Yidong Chen and
Edward R. Dougherty and
Andrzej Kloczkowski and
Yaohang Li},
title = {ConTreeDP: {A} consensus method of tumor trees based on maximum directed
partition support problem},
booktitle = {{IEEE} International Conference on Bioinformatics and Biomedicine,
{BIBM} 2021, Houston, TX, USA, December 9-12, 2021},
pages = {125--130},
publisher = {{IEEE}},
year = {2021},
url = {https://doi.org/10.1109/BIBM52615.2021.9669279},
doi = {10.1109/BIBM52615.2021.9669279},
timestamp = {Tue, 20 Aug 2024 07:54:45 +0200},
biburl = {https://dblp.org/rec/conf/bibm/FuS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WuIZS20,
author = {Zhenqin Wu and
Nilah M. Ioannidis and
James Zou and
Russell Schwartz},
title = {Predicting target genes of non-coding regulatory variants with {IRT}},
journal = {Bioinform.},
volume = {36},
number = {16},
pages = {4440--4448},
year = {2020},
url = {https://doi.org/10.1093/bioinformatics/btaa254},
doi = {10.1093/BIOINFORMATICS/BTAA254},
timestamp = {Thu, 29 Sep 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WuIZS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PriveLBMVS20,
author = {Florian Priv{\'{e}} and
Keurcien Luu and
Michael G. B. Blum and
John J. McGrath and
Bjarni J. Vilhj{\'{a}}lmsson and
Russell Schwartz},
title = {Efficient toolkit implementing best practices for principal component
analysis of population genetic data},
journal = {Bioinform.},
volume = {36},
number = {16},
pages = {4449--4457},
year = {2020},
url = {https://doi.org/10.1093/bioinformatics/btaa520},
doi = {10.1093/BIOINFORMATICS/BTAA520},
timestamp = {Sun, 25 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PriveLBMVS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhouBBS20,
author = {Ying Zhou and
Sharon R. Browning and
Brian L. Browning and
Russell Schwartz},
title = {IBDkin: fast estimation of kinship coefficients from identity by descent
segments},
journal = {Bioinform.},
volume = {36},
number = {16},
pages = {4519--4520},
year = {2020},
url = {https://doi.org/10.1093/bioinformatics/btaa569},
doi = {10.1093/BIOINFORMATICS/BTAA569},
timestamp = {Sun, 25 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhouBBS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/NolteS20,
author = {Ilja M. Nolte and
Russell Schwartz},
title = {Metasubtract: an R-package to analytically produce leave-one-out meta-analysis
{GWAS} summary statistics},
journal = {Bioinform.},
volume = {36},
number = {16},
pages = {4521--4522},
year = {2020},
url = {https://doi.org/10.1093/bioinformatics/btaa570},
doi = {10.1093/BIOINFORMATICS/BTAA570},
timestamp = {Fri, 14 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/NolteS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TaoLFLMS20,
author = {Yifeng Tao and
Haoyun Lei and
Xuecong Fu and
Adrian V. Lee and
Jian Ma and
Russell Schwartz},
title = {Robust and accurate deconvolution of tumor populations uncovers evolutionary
mechanisms of breast cancer metastasis},
journal = {Bioinform.},
volume = {36},
number = {Supplement-1},
pages = {i407--i416},
year = {2020},
url = {https://doi.org/10.1093/bioinformatics/btaa396},
doi = {10.1093/BIOINFORMATICS/BTAA396},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/TaoLFLMS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/LeiLGSSWLXHDS20,
author = {Haoyun Lei and
Bochuan Lyu and
E. Michael Gertz and
Alejandro A. Sch{\"{a}}ffer and
Xulian Shi and
Kui Wu and
Guibo Li and
Liqin Xu and
Yong Hou and
Michael Dean and
Russell Schwartz},
title = {Tumor Copy Number Deconvolution Integrating Bulk and Single-Cell Sequencing
Data},
journal = {J. Comput. Biol.},
volume = {27},
number = {4},
pages = {565--598},
year = {2020},
url = {https://doi.org/10.1089/cmb.2019.0302},
doi = {10.1089/CMB.2019.0302},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/LeiLGSSWLXHDS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/mlhc/TaoRDSL20,
author = {Yifeng Tao and
Shuangxia Ren and
Michael Q. Ding and
Russell Schwartz and
Xinghua Lu},
editor = {Finale Doshi{-}Velez and
Jim Fackler and
Ken Jung and
David C. Kale and
Rajesh Ranganath and
Byron C. Wallace and
Jenna Wiens},
title = {Predicting Drug Sensitivity of Cancer Cell Lines via Collaborative
Filtering with Contextual Attention},
booktitle = {Proceedings of the Machine Learning for Healthcare Conference, {MLHC}
2020, 7-8 August 2020, Virtual Event, Durham, NC, {USA}},
series = {Proceedings of Machine Learning Research},
volume = {126},
pages = {660--684},
publisher = {{PMLR}},
year = {2020},
url = {http://proceedings.mlr.press/v126/tao20a.html},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/mlhc/TaoRDSL20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/recomb/2020,
editor = {Russell Schwartz},
title = {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},
publisher = {Springer},
year = {2020},
url = {https://doi.org/10.1007/978-3-030-45257-5},
doi = {10.1007/978-3-030-45257-5},
isbn = {978-3-030-45256-8},
timestamp = {Tue, 21 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/2020.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2007-00100,
author = {Russell Schwartz and
Pratap Tokekar},
title = {Robust Multi-Agent Task Assignment in Failure-Prone and Adversarial
Environments},
journal = {CoRR},
volume = {abs/2007.00100},
year = {2020},
url = {https://arxiv.org/abs/2007.00100},
eprinttype = {arXiv},
eprint = {2007.00100},
timestamp = {Mon, 06 Jul 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2007-00100.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismco/TaoLLMS19,
author = {Yifeng Tao and
Haoyun Lei and
Adrian V. Lee and
Jian Ma and
Russell Schwartz},
editor = {George Bebis and
Takis Benos and
Ken Chen and
Katharina Jahn and
Ernesto Lima},
title = {Phylogenies Derived from Matched Transcriptome Reveal the Evolution
of Cell Populations and Temporal Order of Perturbed Pathways in Breast
Cancer Brain Metastases},
booktitle = {Mathematical and Computational Oncology - First International Symposium,
{ISMCO} 2019, Lake Tahoe, NV, USA, October 14-16, 2019, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {11826},
pages = {3--28},
publisher = {Springer},
year = {2019},
url = {https://doi.org/10.1007/978-3-030-35210-3\_1},
doi = {10.1007/978-3-030-35210-3\_1},
timestamp = {Thu, 09 Jun 2022 16:00:23 +0200},
biburl = {https://dblp.org/rec/conf/ismco/TaoLLMS19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/LeiLGSSWLXHDS19,
author = {Haoyun Lei and
Bochuan Lyu and
E. Michael Gertz and
Alejandro A. Sch{\"{a}}ffer and
Xulian Shi and
Kui Wu and
Guibo Li and
Liqin Xu and
Yong Hou and
Michael Dean and
Russell Schwartz},
editor = {Lenore J. Cowen},
title = {Tumor Copy Number Deconvolution Integrating Bulk and Single-Cell Sequencing
Data},
booktitle = {Research in Computational Molecular Biology - 23rd Annual International
Conference, {RECOMB} 2019, Washington, DC, USA, May 5-8, 2019, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {11467},
pages = {174--189},
publisher = {Springer},
year = {2019},
url = {https://doi.org/10.1007/978-3-030-17083-7\_11},
doi = {10.1007/978-3-030-17083-7\_11},
timestamp = {Tue, 15 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/LeiLGSSWLXHDS19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/EatonWS18,
author = {Jesse Eaton and
Jingyi Wang and
Russell Schwartz},
title = {Deconvolution and phylogeny inference of structural variations in
tumor genomic samples},
journal = {Bioinform.},
volume = {34},
number = {13},
pages = {i357--i365},
year = {2018},
url = {https://doi.org/10.1093/bioinformatics/bty270},
doi = {10.1093/BIOINFORMATICS/BTY270},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/EatonWS18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/ThomasS18,
author = {Marcus Thomas and
Russell Schwartz},
title = {A method for efficient Bayesian optimization of self-assembly systems
from scattering data},
journal = {{BMC} Syst. Biol.},
volume = {12},
number = {1},
pages = {65:1--65:17},
year = {2018},
url = {https://doi.org/10.1186/s12918-018-0592-8},
doi = {10.1186/S12918-018-0592-8},
timestamp = {Tue, 05 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcsb/ThomasS18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/MulderSBBGMPRRS18,
author = {Nicola J. Mulder and
Russell Schwartz and
Michelle D. Brazas and
Cath Brooksbank and
Bruno A. Ga{\"{e}}ta and
Sarah L. Morgan and
Mark A. Pauley and
Anne G. Rosenwald and
Gabriella Rustici and
Michael L. Sierk and
Tandy J. Warnow and
Lonnie R. Welch},
title = {The development and application of bioinformatics core competencies
to improve bioinformatics training and education},
journal = {PLoS Comput. Biol.},
volume = {14},
number = {2},
year = {2018},
url = {https://doi.org/10.1371/journal.pcbi.1005772},
doi = {10.1371/JOURNAL.PCBI.1005772},
timestamp = {Sat, 25 Dec 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ploscb/MulderSBBGMPRRS18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cocoon/Schwartz18,
author = {Russell Schwartz},
editor = {Lusheng Wang and
Daming Zhu},
title = {Reconstructing Tumor Evolution and Progression in Structurally Variant
Cancer Cells},
booktitle = {Computing and Combinatorics - 24th International Conference, {COCOON}
2018, Qing Dao, China, July 2-4, 2018, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {10976},
pages = {x},
publisher = {Springer},
year = {2018},
url = {https://link.springer.com/content/pdf/bfm\%3A978-3-319-94776-1\%2F1.pdf},
timestamp = {Thu, 20 Aug 2020 16:02:36 +0200},
biburl = {https://dblp.org/rec/conf/cocoon/Schwartz18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iccabs/LeiLGSS18,
author = {Haoyun Lei and
Bochuan Lyu and
E. Michael Gertz and
Alejandro A. Sch{\"{a}}ffer and
Russell Schwartz},
title = {Tumor Copy Number Data Deconvolution Integrating Bulk and Single-cell
Sequencing Data},
booktitle = {8th {IEEE} International Conference on Computational Advances in Bio
and Medical Sciences, {ICCABS} 2018, Las Vegas, NV, USA, October 18-20,
2018},
pages = {1},
publisher = {{IEEE} Computer Society},
year = {2018},
url = {https://doi.org/10.1109/ICCABS.2018.8542078},
doi = {10.1109/ICCABS.2018.8542078},
timestamp = {Thu, 23 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/iccabs/LeiLGSS18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/RomanXS17,
author = {Theodore Roman and
Lu Xie and
Russell Schwartz},
title = {Automated deconvolution of structured mixtures from heterogeneous
tumor genomic data},
journal = {PLoS Comput. Biol.},
volume = {13},
number = {10},
year = {2017},
url = {https://doi.org/10.1371/journal.pcbi.1005815},
doi = {10.1371/JOURNAL.PCBI.1005815},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/RomanXS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/XieSS17,
author = {Lu Xie and
Gregory R. Smith and
Russell Schwartz},
title = {Derivative-Free Optimization of Rate Parameters of Capsid Assembly
Models from Bulk in Vitro Data},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {14},
number = {4},
pages = {844--855},
year = {2017},
url = {https://doi.org/10.1109/TCBB.2016.2563421},
doi = {10.1109/TCBB.2016.2563421},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/XieSS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/wabi/2017,
editor = {Russell Schwartz and
Knut Reinert},
title = {17th International Workshop on Algorithms in Bioinformatics, {WABI}
2017, August 21-23, 2017, Boston, MA, {USA}},
series = {LIPIcs},
volume = {88},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2017},
url = {http://www.dagstuhl.de/dagpub/978-3-95977-050-7},
isbn = {978-3-95977-050-7},
timestamp = {Tue, 11 Feb 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/wabi/2017.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcgenomics/RomanXS16,
author = {Theodore Roman and
Lu Xie and
Russell Schwartz},
title = {Medoidshift clustering applied to genomic bulk tumor data},
journal = {{BMC} Genom.},
volume = {17},
number = {{S-1}},
pages = {6},
year = {2016},
url = {https://doi.org/10.1186/s12864-015-2302-x},
doi = {10.1186/S12864-015-2302-X},
timestamp = {Mon, 11 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcgenomics/RomanXS16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/WelchBSMGKMMMPP16,
author = {Lonnie R. Welch and
Cath Brooksbank and
Russell Schwartz and
Sarah L. Morgan and
Bruno A. Ga{\"{e}}ta and
Alastair M. Kilpatrick and
Daniel Mietchen and
Benjamin L. Moore and
Nicola J. Mulder and
Mark A. Pauley and
William R. Pearson and
Predrag Radivojac and
Naomi Rosenberg and
Anne G. Rosenwald and
Gabriella Rustici and
Tandy J. Warnow},
title = {Applying, Evaluating and Refining Bioinformatics Core Competencies
(An Update from the Curriculum Task Force of ISCB's Education Committee)},
journal = {PLoS Comput. Biol.},
volume = {12},
number = {5},
year = {2016},
url = {https://doi.org/10.1371/journal.pcbi.1004943},
doi = {10.1371/JOURNAL.PCBI.1004943},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/WelchBSMGKMMMPP16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/CatanzaroSSS16,
author = {Daniele Catanzaro and
Stanley E. Shackney and
Alejandro A. Sch{\"{a}}ffer and
Russell Schwartz},
title = {Classifying the Progression of Ductal Carcinoma from Single-Cell Sampled
Data via Integer Linear Programming: {A} Case Study},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {13},
number = {4},
pages = {643--655},
year = {2016},
url = {https://doi.org/10.1109/TCBB.2015.2476808},
doi = {10.1109/TCBB.2015.2476808},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/CatanzaroSSS16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iccabs/Schwartz16,
author = {Russell Schwartz},
title = {Computationally resolving heterogeneity in mixed genomic samples},
booktitle = {6th {IEEE} International Conference on Computational Advances in Bio
and Medical Sciences, {ICCABS} 2016, Atlanta, GA, USA, October 13-15,
2016},
pages = {1},
publisher = {{IEEE} Computer Society},
year = {2016},
url = {https://doi.org/10.1109/ICCABS.2016.7802796},
doi = {10.1109/ICCABS.2016.7802796},
timestamp = {Thu, 23 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/iccabs/Schwartz16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChowdhuryGWHRSS15,
author = {Salim Akhter Chowdhury and
E. Michael Gertz and
Darawalee Wangsa and
Kerstin Heselmeyer{-}Haddad and
Thomas Ried and
Alejandro A. Sch{\"{a}}ffer and
Russell Schwartz},
title = {Inferring models of multiscale copy number evolution for single-tumor
phylogenetics},
journal = {Bioinform.},
volume = {31},
number = {12},
pages = {258--267},
year = {2015},
url = {https://doi.org/10.1093/bioinformatics/btv233},
doi = {10.1093/BIOINFORMATICS/BTV233},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChowdhuryGWHRSS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/RomanNFS15,
author = {Theodore Roman and
Amir Nayyeri and
Brittany Fasy and
Russell Schwartz},
title = {A simplicial complex-based approach to unmixing tumor progression
data},
journal = {{BMC} Bioinform.},
volume = {16},
pages = {254:1--254:17},
year = {2015},
url = {https://doi.org/10.1186/s12859-015-0694-x},
doi = {10.1186/S12859-015-0694-X},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/RomanNFS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BatzoglouS14,
author = {Serafim Batzoglou and
Russell Schwartz},
title = {Editorial},
journal = {Bioinform.},
volume = {30},
number = {12},
pages = {1--2},
year = {2014},
url = {https://doi.org/10.1093/bioinformatics/btu304},
doi = {10.1093/BIOINFORMATICS/BTU304},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BatzoglouS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/WelchLSBRGS14,
author = {Lonnie R. Welch and
Fran Lewitter and
Russell Schwartz and
Catherine Brooksbank and
Predrag Radivojac and
Bruno A. Ga{\"{e}}ta and
Maria Victoria Schneider},
title = {Bioinformatics Curriculum Guidelines: Toward a Definition of Core
Competencies},
journal = {PLoS Comput. Biol.},
volume = {10},
number = {3},
year = {2014},
url = {https://doi.org/10.1371/journal.pcbi.1003496},
doi = {10.1371/JOURNAL.PCBI.1003496},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/WelchLSBRGS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/ChowdhurySHRSS14,
author = {Salim Akhter Chowdhury and
Stanley E. Shackney and
Kerstin Heselmeyer{-}Haddad and
Thomas Ried and
Alejandro A. Sch{\"{a}}ffer and
Russell Schwartz},
title = {Algorithms to Model Single Gene, Single Chromosome, and Whole Genome
Copy Number Changes Jointly in Tumor Phylogenetics},
journal = {PLoS Comput. Biol.},
volume = {10},
number = {7},
year = {2014},
url = {https://doi.org/10.1371/journal.pcbi.1003740},
doi = {10.1371/JOURNAL.PCBI.1003740},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/ChowdhurySHRSS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/TanSTSY14,
author = {Cheemeng Tan and
Robert Phillip Smith and
Ming{-}Chi Tsai and
Russell Schwartz and
Lingchong You},
title = {Phenotypic Signatures Arising from Unbalanced Bacterial Growth},
journal = {PLoS Comput. Biol.},
volume = {10},
number = {8},
year = {2014},
url = {https://doi.org/10.1371/journal.pcbi.1003751},
doi = {10.1371/JOURNAL.PCBI.1003751},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/TanSTSY14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iccabs/SubramanianS14,
author = {Ayshwarya Subramanian and
Russell Schwartz},
title = {Reference-free inference of tumor phylogenies from single-cell sequencing
data},
booktitle = {{IEEE} 4th International Conference on Computational Advances in Bio
and Medical Sciences, {ICCABS} 2014, Miami, FL, USA, June 2-4, 2014},
pages = {1},
publisher = {{IEEE} Computer Society},
year = {2014},
url = {https://doi.org/10.1109/ICCABS.2014.6863944},
doi = {10.1109/ICCABS.2014.6863944},
timestamp = {Thu, 23 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/iccabs/SubramanianS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/CatanzaroRS13,
author = {Daniele Catanzaro and
Ramamoorthi Ravi and
Russell Schwartz},
title = {A mixed integer linear programming model to reconstruct phylogenies
from single nucleotide polymorphism haplotypes under the maximum parsimony
criterion},
journal = {Algorithms Mol. Biol.},
volume = {8},
pages = {3},
year = {2013},
url = {https://doi.org/10.1186/1748-7188-8-3},
doi = {10.1186/1748-7188-8-3},
timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/almob/CatanzaroRS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChowdhurySHRSS13,
author = {Salim Akhter Chowdhury and
Stanley Shackney and
Kerstin Heselmeyer{-}Haddad and
Thomas Ried and
Alejandro A. Sch{\"{a}}ffer and
Russell Schwartz},
title = {Phylogenetic analysis of multiprobe fluorescence \emph{in situ} hybridization
data from tumor cell populations},
journal = {Bioinform.},
volume = {29},
number = {13},
pages = {189--198},
year = {2013},
url = {https://doi.org/10.1093/bioinformatics/btt205},
doi = {10.1093/BIOINFORMATICS/BTT205},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChowdhurySHRSS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/TsaiBRS13,
author = {Ming{-}Chi Tsai and
Guy E. Blelloch and
R. Ravi and
Russell Schwartz},
title = {Coalescent-Based Method for Learning Parameters of Admixture Events
from Large-Scale Genetic Variation Data},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {10},
number = {5},
pages = {1137--1149},
year = {2013},
url = {https://doi.org/10.1109/TCBB.2013.98},
doi = {10.1109/TCBB.2013.98},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/TsaiBRS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/SubramanianSS13,
author = {Ayshwarya Subramanian and
Stanley Shackney and
Russell Schwartz},
title = {Novel Multisample Scheme for Inferring Phylogenetic Markers from Whole
Genome Tumor Profiles},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {10},
number = {6},
pages = {1422--1431},
year = {2013},
url = {https://doi.org/10.1109/TCBB.2013.33},
doi = {10.1109/TCBB.2013.33},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/SubramanianSS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/WelchSL12,
author = {Lonnie R. Welch and
Russell Schwartz and
Fran Lewitter},
title = {A Report of the Curriculum Task Force of the {ISCB} Education Committee},
journal = {PLoS Comput. Biol.},
volume = {8},
number = {6},
year = {2012},
url = {https://doi.org/10.1371/journal.pcbi.1002570},
doi = {10.1371/JOURNAL.PCBI.1002570},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/WelchSL12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bcb/TsaiBSR12,
author = {Ming{-}Chi Tsai and
Guy E. Blelloch and
Russell Schwartz and
R. Ravi},
editor = {Sanjay Ranka and
Tamer Kahveci and
Mona Singh},
title = {Coalescent-based method for learning parameters of admixture events
from large-scale genetic variation data},
booktitle = {{ACM} International Conference on Bioinformatics, Computational Biology
and Biomedicine, BCB' 12, Orlando, FL, {USA} - October 08 - 10, 2012},
pages = {90--97},
publisher = {{ACM}},
year = {2012},
url = {https://doi.org/10.1145/2382936.2382948},
doi = {10.1145/2382936.2382948},
timestamp = {Sun, 02 Jun 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bcb/TsaiBSR12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isbra/SubramanianSS12,
author = {Ayshwarya Subramanian and
Stanley Shackney and
Russell Schwartz},
editor = {Leonidas G. Bleris and
Ion I. Mandoiu and
Russell Schwartz and
Jianxin Wang},
title = {Novel Multi-sample Scheme for Inferring Phylogenetic Markers from
Whole Genome Tumor Profiles},
booktitle = {Bioinformatics Research and Applications - 8th International Symposium,
{ISBRA} 2012, Dallas, TX, USA, May 21-23, 2012. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {7292},
pages = {250--262},
publisher = {Springer},
year = {2012},
url = {https://doi.org/10.1007/978-3-642-30191-9\_24},
doi = {10.1007/978-3-642-30191-9\_24},
timestamp = {Sun, 02 Jun 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/isbra/SubramanianSS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/isbra/2012,
editor = {Leonidas G. Bleris and
Ion I. Mandoiu and
Russell Schwartz and
Jianxin Wang},
title = {Bioinformatics Research and Applications - 8th International Symposium,
{ISBRA} 2012, Dallas, TX, USA, May 21-23, 2012. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {7292},
publisher = {Springer},
year = {2012},
url = {https://doi.org/10.1007/978-3-642-30191-9},
doi = {10.1007/978-3-642-30191-9},
isbn = {978-3-642-30190-2},
timestamp = {Tue, 14 May 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/isbra/2012.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/MisraBRS11,
author = {Navodit Misra and
Guy E. Blelloch and
R. Ravi and
Russell Schwartz},
title = {Generalized Buneman Pruning for Inferring the Most Parsimonious Multi-State
Phylogeny},
journal = {J. Comput. Biol.},
volume = {18},
number = {3},
pages = {445--457},
year = {2011},
url = {https://doi.org/10.1089/cmb.2010.0254},
doi = {10.1089/CMB.2010.0254},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/MisraBRS11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/MisraBRS11a,
author = {Navodit Misra and
Guy E. Blelloch and
R. Ravi and
Russell Schwartz},
title = {An Optimization-Based Sampling Scheme for Phylogenetic Trees},
journal = {J. Comput. Biol.},
volume = {18},
number = {11},
pages = {1599--1609},
year = {2011},
url = {https://doi.org/10.1089/cmb.2011.0164},
doi = {10.1089/CMB.2011.0164},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/MisraBRS11a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jea/TsourakakisPTMS11,
author = {Charalampos E. Tsourakakis and
Richard Peng and
Maria A. Tsiarli and
Gary L. Miller and
Russell Schwartz},
title = {Approximation algorithms for speeding up dynamic programming and denoising
aCGH data},
journal = {{ACM} J. Exp. Algorithmics},
volume = {16},
year = {2011},
url = {https://doi.org/10.1145/1963190.2063517},
doi = {10.1145/1963190.2063517},
timestamp = {Mon, 01 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jea/TsourakakisPTMS11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/TsaiBRS11,
author = {Ming{-}Chi Tsai and
Guy E. Blelloch and
R. Ravi and
Russell Schwartz},
title = {A Consensus Tree Approach for Reconstructing Human Evolutionary History
and Detecting Population Substructure},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {8},
number = {4},
pages = {918--928},
year = {2011},
url = {https://doi.org/10.1109/TCBB.2011.23},
doi = {10.1109/TCBB.2011.23},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/TsaiBRS11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bcb/SubramanianSS11,
author = {Ayshwarya Subramanian and
Stanley Shackney and
Russell Schwartz},
editor = {Robert Grossman and
Andrey Rzhetsky and
Sun Kim and
Wei Wang},
title = {Inference of tumor phylogenies from genomic assays on heterogeneous
samples},
booktitle = {{ACM} International Conference on Bioinformatics, Computational Biology
and Biomedicine, BCB' 11, Chicago, IL, {USA} - July 31 - August 03,
2011},
pages = {172--181},
publisher = {{ACM}},
year = {2011},
url = {https://doi.org/10.1145/2147805.2147824},
doi = {10.1145/2147805.2147824},
timestamp = {Sun, 02 Jun 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bcb/SubramanianSS11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isbra/Schwartz11,
author = {Russell Schwartz},
editor = {Jianer Chen and
Jianxin Wang and
Alexander Zelikovsky},
title = {Phylogenetics of Heterogeneous Samples - (Keynote Talk)},
booktitle = {Bioinformatics Research and Applications - 7th International Symposium,
{ISBRA} 2011, Changsha, China, May 27-29, 2011. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {6674},
pages = {1},
publisher = {Springer},
year = {2011},
url = {https://doi.org/10.1007/978-3-642-21260-4\_1},
doi = {10.1007/978-3-642-21260-4\_1},
timestamp = {Fri, 21 Aug 2020 17:12:20 +0200},
biburl = {https://dblp.org/rec/conf/isbra/Schwartz11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/MisraBRS11,
author = {Navodit Misra and
Guy E. Blelloch and
R. Ravi and
Russell Schwartz},
editor = {Vineet Bafna and
S{\"{u}}leyman Cenk Sahinalp},
title = {An Optimization-Based Sampling Scheme for Phylogenetic Trees},
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 = {252--266},
publisher = {Springer},
year = {2011},
url = {https://doi.org/10.1007/978-3-642-20036-6\_23},
doi = {10.1007/978-3-642-20036-6\_23},
timestamp = {Sun, 02 Jun 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/MisraBRS11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/soda/MillerPST11,
author = {Gary L. Miller and
Richard Peng and
Russell Schwartz and
Charalampos E. Tsourakakis},
editor = {Dana Randall},
title = {Approximate Dynamic Programming using Halfspace Queries and Multiscale
Monge Decomposition},
booktitle = {Proceedings of the Twenty-Second Annual {ACM-SIAM} Symposium on Discrete
Algorithms, {SODA} 2011, San Francisco, California, USA, January 23-25,
2011},
pages = {1675--1682},
publisher = {{SIAM}},
year = {2011},
url = {https://doi.org/10.1137/1.9781611973082.129},
doi = {10.1137/1.9781611973082.129},
timestamp = {Mon, 01 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/soda/MillerPST11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TolliverTSSS10,
author = {David Tolliver and
Charalampos E. Tsourakakis and
Ayshwarya Subramanian and
Stanley Shackney and
Russell Schwartz},
title = {Robust unmixing of tumor states in array comparative genomic hybridization
data},
journal = {Bioinform.},
volume = {26},
number = {12},
pages = {106--114},
year = {2010},
url = {https://doi.org/10.1093/bioinformatics/btq213},
doi = {10.1093/BIOINFORMATICS/BTQ213},
timestamp = {Mon, 01 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/TolliverTSSS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SchwartzS10,
author = {Russell Schwartz and
Stanley Shackney},
title = {Applying unmixing to gene expression data for tumor phylogeny inference},
journal = {{BMC} Bioinform.},
volume = {11},
pages = {42},
year = {2010},
url = {https://doi.org/10.1186/1471-2105-11-42},
doi = {10.1186/1471-2105-11-42},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/SchwartzS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cominfsys/Schwartz10,
author = {Russell Schwartz},
title = {Theory and Algorithms for the Haplotype Assembly Problem},
journal = {Commun. Inf. Syst.},
volume = {10},
number = {1},
pages = {23--38},
year = {2010},
url = {https://doi.org/10.4310/cis.2010.v10.n1.a2},
doi = {10.4310/CIS.2010.V10.N1.A2},
timestamp = {Wed, 16 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/cominfsys/Schwartz10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isbra/TsaiBRS10,
author = {Ming{-}Chi Tsai and
Guy E. Blelloch and
R. Ravi and
Russell Schwartz},
editor = {Mark Borodovsky and
Johann Peter Gogarten and
Teresa M. Przytycka and
Sanguthevar Rajasekaran},
title = {A Consensus Tree Approach for Reconstructing Human Evolutionary History
and Detecting Population Substructure},
booktitle = {Bioinformatics Research and Applications, 6th International Symposium,
{ISBRA} 2010, Storrs, CT, USA, May 23-26, 2010. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {6053},
pages = {167--178},
publisher = {Springer},
year = {2010},
url = {https://doi.org/10.1007/978-3-642-13078-6\_20},
doi = {10.1007/978-3-642-13078-6\_20},
timestamp = {Sun, 02 Jun 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/isbra/TsaiBRS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/MisraBRS10,
author = {Navodit Misra and
Guy E. Blelloch and
R. Ravi and
Russell Schwartz},
editor = {Bonnie Berger},
title = {Generalized Buneman Pruning for Inferring the Most Parsimonious Multi-state
Phylogeny},
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 = {369--383},
publisher = {Springer},
year = {2010},
url = {https://doi.org/10.1007/978-3-642-12683-3\_24},
doi = {10.1007/978-3-642-12683-3\_24},
timestamp = {Sun, 02 Jun 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/MisraBRS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/stringology/LanciaRS10,
author = {Giuseppe Lancia and
Romeo Rizzi and
Russell Schwartz},
editor = {Jan Holub and
Jan Zd{\'{a}}rek},
title = {Tiling Binary Matrices in Haplotyping: Complexity, Models and Algorithms},
booktitle = {Proceedings of the Prague Stringology Conference 2010, Prague, Czech
Republic, August 30 - September 1, 2010},
pages = {89--102},
publisher = {Prague Stringology Club, Department of Theoretical Computer Science,
Faculty of Information Technology, Czech Technical University in Prague},
year = {2010},
url = {http://www.stringology.org/event/2010/p08.html},
timestamp = {Wed, 10 Feb 2021 08:42:22 +0100},
biburl = {https://dblp.org/rec/conf/stringology/LanciaRS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1003-4942,
author = {Gary L. Miller and
Richard Peng and
Russell Schwartz and
Charalampos E. Tsourakakis},
title = {Approximate Dynamic Programming for Fast Denoising of aCGH Data},
journal = {CoRR},
volume = {abs/1003.4942},
year = {2010},
url = {http://arxiv.org/abs/1003.4942},
eprinttype = {arXiv},
eprint = {1003.4942},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1003-4942.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/ParkSS09,
author = {Yongjin Park and
Stanley Shackney and
Russell Schwartz},
title = {Network-Based Inference of Cancer Progression from Microarray Data},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {6},
number = {2},
pages = {200--212},
year = {2009},
url = {https://doi.org/10.1109/TCBB.2008.126},
doi = {10.1109/TCBB.2008.126},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/ParkSS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/SridharLBRS08,
author = {Srinath Sridhar and
Fumei Lam and
Guy E. Blelloch and
R. Ravi and
Russell Schwartz},
title = {Mixed Integer Linear Programming for Maximum-Parsimony Phylogeny Inference},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {5},
number = {3},
pages = {323--331},
year = {2008},
url = {https://doi.org/10.1109/TCBB.2008.26},
doi = {10.1109/TCBB.2008.26},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/SridharLBRS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icls/GrayHLJJSFWDS08,
author = {Steven Gray and
Cindy E. Hmelo{-}Silver and
Lei Liu and
Rebecca Jordan and
Heisawn Jeong and
Russell Schwartz and
Heather Finkelstein and
Daniel Wolsten and
Marylee Demeter and
Suparna Sinha},
editor = {Paul A. Kirschner and
Jeroen J. G. van Merri{\"{e}}nboer and
Ton de Jong},
title = {Learning with ecosystem models: a tale of two classrooms},
booktitle = {Cre8ing a learning world: Proceedings of the 8th International Conference
for the Learning Sciences, {ICLS} 2008, Utrecht, The Netherlands,
June 23-28, 2008, Volume 1},
pages = {289--296},
publisher = {International Society of the Learning Sciences},
year = {2008},
url = {https://repository.isls.org/handle/1/3107},
timestamp = {Mon, 10 May 2021 16:29:15 +0200},
biburl = {https://dblp.org/rec/conf/icls/GrayHLJJSFWDS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isbra/ParkSS08,
author = {Yongjin Park and
Stanley Shackney and
Russell Schwartz},
editor = {Ion I. Mandoiu and
Raj Sunderraman and
Alexander Zelikovsky},
title = {Network-Based Inference of Cancer Progression from Microarray Data},
booktitle = {Bioinformatics Research and Applications, Fourth International Symposium,
{ISBRA} 2008, Atlanta, GA, USA, May 6-9, 2008. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {4983},
pages = {268--279},
publisher = {Springer},
year = {2008},
url = {https://doi.org/10.1007/978-3-540-79450-9\_25},
doi = {10.1007/978-3-540-79450-9\_25},
timestamp = {Sun, 02 Jun 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/isbra/ParkSS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/Schwartz07,
author = {Russell Schwartz},
title = {Stochastic Modelling for Systems Biology: Darren J. Wilkinson},
journal = {Briefings Bioinform.},
volume = {8},
number = {3},
pages = {204--205},
year = {2007},
url = {https://doi.org/10.1093/bib/bbm001},
doi = {10.1093/BIB/BBM001},
timestamp = {Thu, 04 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/Schwartz07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SridharLBRS07,
author = {Srinath Sridhar and
Fumei Lam and
Guy E. Blelloch and
R. Ravi and
Russell Schwartz},
title = {Direct maximum parsimony phylogeny reconstruction from genotype data},
journal = {{BMC} Bioinform.},
volume = {8},
year = {2007},
url = {https://doi.org/10.1186/1471-2105-8-472},
doi = {10.1186/1471-2105-8-472},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/SridharLBRS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbcb/PenningtonSSS07,
author = {Gregory Pennington and
Charles A. Smith and
Stanley Shackney and
Russell Schwartz},
title = {Reconstructing Tumor phylogenies from Heterogeneous Single-Cell Data},
journal = {J. Bioinform. Comput. Biol.},
volume = {5},
number = {2a},
pages = {407--427},
year = {2007},
url = {https://doi.org/10.1142/S021972000700259X},
doi = {10.1142/S021972000700259X},
timestamp = {Thu, 04 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jbcb/PenningtonSSS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/SridharDBHRS07,
author = {Srinath Sridhar and
Kedar Dhamdhere and
Guy E. Blelloch and
Eran Halperin and
R. Ravi and
Russell Schwartz},
title = {Algorithms for Efficient Near-Perfect Phylogenetic Tree Reconstruction
in Theory and Practice},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {4},
number = {4},
pages = {561--571},
year = {2007},
url = {https://doi.org/10.1109/TCBB.2007.1070},
doi = {10.1109/TCBB.2007.1070},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/SridharDBHRS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isbra/SridharLBRS07,
author = {Srinath Sridhar and
Fumei Lam and
Guy E. Blelloch and
R. Ravi and
Russell Schwartz},
editor = {Ion I. Mandoiu and
Alexander Zelikovsky},
title = {Efficiently Finding the Most Parsimonious Phylogenetic Tree Via Linear
Programming},
booktitle = {Bioinformatics Research and Applications, Third International Symposium,
{ISBRA} 2007, Atlanta, GA, USA, May 7-10, 2007, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {4463},
pages = {37--48},
publisher = {Springer},
year = {2007},
url = {https://doi.org/10.1007/978-3-540-72031-7\_4},
doi = {10.1007/978-3-540-72031-7\_4},
timestamp = {Tue, 14 May 2019 10:00:51 +0200},
biburl = {https://dblp.org/rec/conf/isbra/SridharLBRS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icalp/BlellochDHRSS06,
author = {Guy E. Blelloch and
Kedar Dhamdhere and
Eran Halperin and
R. Ravi and
Russell Schwartz and
Srinath Sridhar},
editor = {Michele Bugliesi and
Bart Preneel and
Vladimiro Sassone and
Ingo Wegener},
title = {Fixed Parameter Tractability of Binary Near-Perfect Phylogenetic Tree
Reconstruction},
booktitle = {Automata, Languages and Programming, 33rd International Colloquium,
{ICALP} 2006, Venice, Italy, July 10-14, 2006, Proceedings, Part {I}},
series = {Lecture Notes in Computer Science},
volume = {4051},
pages = {667--678},
publisher = {Springer},
year = {2006},
url = {https://doi.org/10.1007/11786986\_58},
doi = {10.1007/11786986\_58},
timestamp = {Sun, 02 Jun 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/icalp/BlellochDHRSS06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iccS/SridharDBHRS06,
author = {Srinath Sridhar and
Kedar Dhamdhere and
Guy E. Blelloch and
Eran Halperin and
R. Ravi and
Russell Schwartz},
editor = {Vassil N. Alexandrov and
G. Dick van Albada and
Peter M. A. Sloot and
Jack J. Dongarra},
title = {Simple Reconstruction of Binary Near-Perfect Phylogenetic Trees},
booktitle = {Computational Science - {ICCS} 2006, 6th International Conference,
Reading, UK, May 28-31, 2006, Proceedings, Part {II}},
series = {Lecture Notes in Computer Science},
volume = {3992},
pages = {799--806},
publisher = {Springer},
year = {2006},
url = {https://doi.org/10.1007/11758525\_107},
doi = {10.1007/11758525\_107},
timestamp = {Sun, 02 Jun 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/iccS/SridharDBHRS06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/CastellanaDSS06,
author = {Natalie Castellana and
Kedar Dhamdhere and
Srinath Sridhar and
Russell Schwartz},
editor = {Russ B. Altman and
Tiffany Murray and
Teri E. Klein and
A. Keith Dunker and
Lawrence Hunter},
title = {Relaxing Haplotype Block Models for Association Testing},
booktitle = {Biocomputing 2006, Proceedings of the Pacific Symposium, Maui, Hawaii,
USA, 3-7 January 2006},
pages = {454--466},
publisher = {World Scientific},
year = {2006},
url = {http://psb.stanford.edu/psb-online/proceedings/psb06/castellana.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/CastellanaDSS06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wsc/ZhangRS05,
author = {Tiequan Zhang and
Rori Rohlfs and
Russell Schwartz},
title = {Implementation of a discrete event simulator for biological self-assembly
systems},
booktitle = {Proceedings of the 37th Winter Simulation Conference, Orlando, FL,
USA, December 4-7, 2005},
pages = {2223--2231},
publisher = {{IEEE} Computer Society},
year = {2005},
url = {https://doi.org/10.1109/WSC.2005.1574510},
doi = {10.1109/WSC.2005.1574510},
timestamp = {Thu, 10 Jun 2021 22:18:45 +0200},
biburl = {https://dblp.org/rec/conf/wsc/ZhangRS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/csb/Schwartz04,
author = {Russell Schwartz},
title = {Algorithms for Association Study Design Using a Generalized Model
of Haplotype Conservation},
booktitle = {3rd International {IEEE} Computer Society Computational Systems Bioinformatics
Conference, {CSB} 2004, Stanford, CA, USA, August 16-19, 2004},
pages = {90--97},
publisher = {{IEEE} Computer Society},
year = {2004},
url = {https://doi.org/10.1109/CSB.2004.1332421},
doi = {10.1109/CSB.2004.1332421},
timestamp = {Thu, 23 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/csb/Schwartz04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/SchwartzHBCI03,
author = {Russell Schwartz and
Bjarni V. Halld{\'{o}}rsson and
Vineet Bafna and
Andrew G. Clark and
Sorin Istrail},
title = {Robustness of Inference of Haplotype Block Structure},
journal = {J. Comput. Biol.},
volume = {10},
number = {1},
pages = {13--19},
year = {2003},
url = {https://doi.org/10.1089/106652703763255642},
doi = {10.1089/106652703763255642},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/SchwartzHBCI03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/csb/FloreaHKSHI03,
author = {Liliana Florea and
Bjarni V. Halld{\'{o}}rsson and
Oliver Kohlbacher and
Russell Schwartz and
Stephen Hoffman and
Sorin Istrail},
title = {Epitope Prediction Algorithms for Peptide based Vaccine Design},
booktitle = {2nd {IEEE} Computer Society Bioinformatics Conference, {CSB} 2003,
Stanford, CA, USA, August 11-14, 2003},
pages = {17--26},
publisher = {{IEEE} Computer Society},
year = {2003},
url = {https://doi.org/10.1109/CSB.2003.1227293},
doi = {10.1109/CSB.2003.1227293},
timestamp = {Thu, 23 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/csb/FloreaHKSHI03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/csb/Schwartz03,
author = {Russell Schwartz},
title = {Haplotype Motifs: An Algorithmic Approach to Locating Evolutionarily
Conserved Patterns in Haploid Sequences},
booktitle = {2nd {IEEE} Computer Society Bioinformatics Conference, {CSB} 2003,
Stanford, CA, USA, August 11-14, 2003},
pages = {306--315},
publisher = {{IEEE} Computer Society},
year = {2003},
url = {https://doi.org/10.1109/CSB.2003.1227331},
doi = {10.1109/CSB.2003.1227331},
timestamp = {Thu, 23 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/csb/Schwartz03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/BafnaHSCI03,
author = {Vineet Bafna and
Bjarni V. Halld{\'{o}}rsson and
Russell Schwartz and
Andrew G. Clark and
Sorin Istrail},
editor = {Martin Vingron and
Sorin Istrail and
Pavel A. Pevzner and
Michael S. Waterman and
Webb Miller},
title = {Haplotypes and informative {SNP} selection algorithms: don't block
out information},
booktitle = {Proceedings of the Sventh Annual International Conference on Computational
Biology, {RECOMB} 2003, Berlin, Germany, April 10-13, 2003},
pages = {19--27},
publisher = {{ACM}},
year = {2003},
url = {https://doi.org/10.1145/640075.640078},
doi = {10.1145/640075.640078},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/BafnaHSCI03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LippertSLI02,
author = {Ross Lippert and
Russell Schwartz and
Giuseppe Lancia and
Sorin Istrail},
title = {Algorithmic strategies for the single nucleotide polymorphism haplotype
assembly problem},
journal = {Briefings Bioinform.},
volume = {3},
number = {1},
pages = {23--31},
year = {2002},
url = {https://doi.org/10.1093/bib/3.1.23},
doi = {10.1093/BIB/3.1.23},
timestamp = {Tue, 29 Dec 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LippertSLI02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/SchwartzCI02,
author = {Russell Schwartz and
Andrew G. Clark and
Sorin Istrail},
editor = {Sorin Istrail and
Michael S. Waterman and
Andrew G. Clark},
title = {Inferring Piecewise Ancestral History from Haploid Sequences},
booktitle = {Computational Methods for SNPs and Haplotype Inference, {DIMACS/RECOMB}
Satellite Workshop, Piscataway, NJ, USA, November 21-22, 2002, Revised
Papers},
series = {Lecture Notes in Computer Science},
volume = {2983},
pages = {62--73},
publisher = {Springer},
year = {2002},
url = {https://doi.org/10.1007/978-3-540-24719-7\_5},
doi = {10.1007/978-3-540-24719-7\_5},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/SchwartzCI02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/SchwartzCI02,
author = {Russell Schwartz and
Andrew G. Clark and
Sorin Istrail},
editor = {Roderic Guig{\'{o}} and
Dan Gusfield},
title = {Methods for Inferring Block-Wise Ancestral History from Haploid Sequences},
booktitle = {Algorithms in Bioinformatics, Second International Workshop, {WABI}
2002, Rome, Italy, September 17-21, 2002, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {2452},
pages = {44--59},
publisher = {Springer},
year = {2002},
url = {https://doi.org/10.1007/3-540-45784-4\_4},
doi = {10.1007/3-540-45784-4\_4},
timestamp = {Sun, 25 Oct 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wabi/SchwartzCI02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/esa/LanciaBILS01,
author = {Giuseppe Lancia and
Vineet Bafna and
Sorin Istrail and
Ross Lippert and
Russell Schwartz},
editor = {Friedhelm Meyer auf der Heide},
title = {SNPs Problems, Complexity, and Algorithms},
booktitle = {Algorithms - {ESA} 2001, 9th Annual European Symposium, Aarhus, Denmark,
August 28-31, 2001, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {2161},
pages = {182--193},
publisher = {Springer},
year = {2001},
url = {https://doi.org/10.1007/3-540-44676-1\_15},
doi = {10.1007/3-540-44676-1\_15},
timestamp = {Tue, 29 Dec 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/esa/LanciaBILS01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/pvg/TurnerCEFHHKMRRSWYI01,
author = {Russell J. Turner and
Kabir Chaturvedi and
Nathan Edwards and
Daniel P. Fasulo and
Aaron L. Halpern and
Daniel H. Huson and
Oliver Kohlbacher and
Jason R. Miller and
Knut Reinert and
Karin A. Remington and
Russell Schwartz and
Brian Walenz and
Shibu Yooseph and
Sorin Istrail},
editor = {David E. Breen and
Alan Heirich and
Anton H. J. Koning},
title = {Visualization challenges for a new cyberpharmaceutical computing paradigm},
booktitle = {Proceedings of the {IEEE} 2001 Symposium on Parallel and Large-Data
Visualization and Graphics, {PVG} 2001, San Diego, California, USA,
October 22-23, 2001},
pages = {7--18},
publisher = {{IEEE}},
year = {2001},
url = {https://dl.acm.org/doi/10.5555/502125.502127},
doi = {10.5555/502125.502127},
timestamp = {Thu, 02 Jun 2022 12:38:21 +0200},
biburl = {https://dblp.org/rec/conf/pvg/TurnerCEFHHKMRRSWYI01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@phdthesis{DBLP:phd/ndltd/Schwartz00,
author = {Russell Schwartz},
title = {The local rules dynamics model for self-assembly simulation},
school = {Massachusetts Institute of Technology, Cambridge, MA, {USA}},
year = {2000},
url = {https://hdl.handle.net/1721.1/86426},
timestamp = {Wed, 04 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/phd/ndltd/Schwartz00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dam/BergerKSS00,
author = {Bonnie Berger and
Jonathan A. King and
Russell Schwartz and
Peter W. Shor},
title = {Local rule mechanism for selecting icosahedral shell geometry},
journal = {Discret. Appl. Math.},
volume = {104},
number = {1-3},
pages = {97--111},
year = {2000},
url = {https://doi.org/10.1016/S0166-218X(00)00187-6},
doi = {10.1016/S0166-218X(00)00187-6},
timestamp = {Thu, 11 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/dam/BergerKSS00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/IstrailSK99,
author = {Sorin Istrail and
Russell Schwartz and
Jonathan A. King},
title = {Lattice Simulations of Aggregation Funnels for Protein Folding},
journal = {J. Comput. Biol.},
volume = {6},
number = {2},
pages = {143--162},
year = {1999},
url = {https://doi.org/10.1089/cmb.1999.6.143},
doi = {10.1089/CMB.1999.6.143},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/IstrailSK99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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