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ORCIDRussell Schwartz
Person information
- affiliation: Carnegie Mellon University, Pittsburgh, USA
- award (2004): Presidential Early Career Award for Scientists and Engineers
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Books and Theses
- 2000
[b1]Russell Schwartz:
The local rules dynamics model for self-assembly simulation. Massachusetts Institute of Technology, Cambridge, MA, USA, 2000
Journal Articles
- 2023
- [j50]Arjun Srivatsa
, Haoyun Lei, Russell Schwartz:
A Clonal Evolution Simulator for Planning Somatic Evolution Studies. J. Comput. Biol. 30(8): 831-847 (2023) - [j49]Patricia M. Palagi, Russell Schwartz, Scott Markel, B. F. Francis Ouellette:
Ten simple rules for writing a PLOS Computational Biology quick tips article. PLoS Comput. Biol. 19(12) (2023) - 2022
- [j48]Xuecong Fu, Haoyun Lei, Yifeng Tao, Russell Schwartz:
Reconstructing tumor clonal lineage trees incorporating single-nucleotide variants, copy number alterations and structural variations. Bioinform. 38(Supplement_1): i125-i133 (2022) - [j47]Haoyun Lei, Xiaoyan A. Guo, Yifeng Tao, Kai Ding, Xuecong Fu, Steffi Oesterreich, Adrian V. Lee, Russell Schwartz:
Semi-deconvolution of bulk and single-cell RNA-seq data with application to metastatic progression in breast cancer. Bioinform. 38(Supplement_1): i386-i394 (2022) - 2021
- [j46]Haoyun Lei, E. Michael Gertz, Alejandro A. Schäffer, Xuecong Fu, Yifeng Tao, Kerstin Heselmeyer-Haddad, Irianna Torres, Guibo Li, Liqin Xu, Yong Hou, Kui Wu, Xulian Shi, Michael Dean, Thomas Ried, Russell Schwartz:
Tumor heterogeneity assessed by sequencing and fluorescence in situ hybridization (FISH) data. Bioinform. 37(24): 4704-4711 (2021) - [j45]Russell Schwartz:
RECOMB 2020 Special Issue. J. Comput. Biol. 28(4): 345 (2021) - [j44]Xuecong Fu, Haoyun Lei, Yifeng Tao, Kerstin Heselmeyer-Haddad, Irianna Torres, Michael Dean, Thomas Ried, Russell Schwartz:
Joint Clustering of Single-Cell Sequencing and Fluorescence In Situ Hybridization Data for Reconstructing Clonal Heterogeneity in Cancers. J. Comput. Biol. 28(11): 1035-1051 (2021) - [j43]Yifeng Tao, Ashok Rajaraman, Xiaoyue Cui, Ziyi Cui, Haoran Chen, Yuanqi Zhao, Jesse Eaton, Hannah Kim, Jian Ma, Russell Schwartz:
Assessing the contribution of tumor mutational phenotypes to cancer progression risk. PLoS Comput. Biol. 17(3) (2021) - 2020
- [j42]Zhenqin Wu, Nilah M. Ioannidis, James Zou, Russell Schwartz:
Predicting target genes of non-coding regulatory variants with IRT. Bioinform. 36(16): 4440-4448 (2020) - [j41]Florian Privé, Keurcien Luu, Michael G. B. Blum, John J. McGrath, Bjarni J. Vilhjálmsson, Russell Schwartz:
Efficient toolkit implementing best practices for principal component analysis of population genetic data. Bioinform. 36(16): 4449-4457 (2020) - [j40]Ying Zhou, Sharon R. Browning, Brian L. Browning, Russell Schwartz:
IBDkin: fast estimation of kinship coefficients from identity by descent segments. Bioinform. 36(16): 4519-4520 (2020) - [j39]Ilja M. Nolte, Russell Schwartz:
Metasubtract: an R-package to analytically produce leave-one-out meta-analysis GWAS summary statistics. Bioinform. 36(16): 4521-4522 (2020) - [j38]Yifeng Tao, Haoyun Lei, Xuecong Fu, Adrian V. Lee, Jian Ma, Russell Schwartz:
Robust and accurate deconvolution of tumor populations uncovers evolutionary mechanisms of breast cancer metastasis. Bioinform. 36(Supplement-1): i407-i416 (2020) - [j37]Haoyun Lei, Bochuan Lyu, E. Michael Gertz, Alejandro A. Schäffer, Xulian Shi, Kui Wu, Guibo Li, Liqin Xu, Yong Hou, Michael Dean, Russell Schwartz:
Tumor Copy Number Deconvolution Integrating Bulk and Single-Cell Sequencing Data. J. Comput. Biol. 27(4): 565-598 (2020) - 2018
- [j36]Jesse Eaton, Jingyi Wang, Russell Schwartz:
Deconvolution and phylogeny inference of structural variations in tumor genomic samples. Bioinform. 34(13): i357-i365 (2018) - [j35]Marcus Thomas, Russell Schwartz:
A method for efficient Bayesian optimization of self-assembly systems from scattering data. BMC Syst. Biol. 12(1): 65:1-65:17 (2018) - [j34]Nicola J. Mulder, Russell Schwartz, Michelle D. Brazas, Cath Brooksbank, Bruno A. Gaëta, Sarah L. Morgan, Mark A. Pauley, Anne G. Rosenwald, Gabriella Rustici, Michael L. Sierk, Tandy J. Warnow, Lonnie R. Welch:
The development and application of bioinformatics core competencies to improve bioinformatics training and education. PLoS Comput. Biol. 14(2) (2018) - 2017
- [j33]Theodore Roman, Lu Xie, Russell Schwartz:
Automated deconvolution of structured mixtures from heterogeneous tumor genomic data. PLoS Comput. Biol. 13(10) (2017) - [j32]Lu Xie, Gregory R. Smith, Russell Schwartz:
Derivative-Free Optimization of Rate Parameters of Capsid Assembly Models from Bulk in Vitro Data. IEEE ACM Trans. Comput. Biol. Bioinform. 14(4): 844-855 (2017) - 2016
- [j31]Theodore Roman, Lu Xie, Russell Schwartz:
Medoidshift clustering applied to genomic bulk tumor data. BMC Genom. 17(S-1): 6 (2016) - [j30]Lonnie R. Welch, Cath Brooksbank, Russell Schwartz, Sarah L. Morgan, Bruno A. Gaëta, Alastair M. Kilpatrick, Daniel Mietchen, Benjamin L. Moore, Nicola J. Mulder, Mark A. Pauley, William R. Pearson, Predrag Radivojac, Naomi Rosenberg, Anne G. Rosenwald, Gabriella Rustici, Tandy J. Warnow:
Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB's Education Committee). PLoS Comput. Biol. 12(5) (2016) - [j29]Daniele Catanzaro, Stanley E. Shackney, Alejandro A. Schäffer, Russell Schwartz:
Classifying the Progression of Ductal Carcinoma from Single-Cell Sampled Data via Integer Linear Programming: A Case Study. IEEE ACM Trans. Comput. Biol. Bioinform. 13(4): 643-655 (2016) - 2015
- [j28]Salim Akhter Chowdhury, E. Michael Gertz, Darawalee Wangsa, Kerstin Heselmeyer-Haddad, Thomas Ried, Alejandro A. Schäffer, Russell Schwartz:
Inferring models of multiscale copy number evolution for single-tumor phylogenetics. Bioinform. 31(12): 258-267 (2015) - [j27]Theodore Roman, Amir Nayyeri, Brittany Fasy, Russell Schwartz:
A simplicial complex-based approach to unmixing tumor progression data. BMC Bioinform. 16: 254:1-254:17 (2015) - 2014
- [j26]Serafim Batzoglou, Russell Schwartz:
Editorial. Bioinform. 30(12): 1-2 (2014) - [j25]Lonnie R. Welch, Fran Lewitter, Russell Schwartz, Catherine Brooksbank, Predrag Radivojac, Bruno A. Gaëta, Maria Victoria Schneider:
Bioinformatics Curriculum Guidelines: Toward a Definition of Core Competencies. PLoS Comput. Biol. 10(3) (2014) - [j24]Salim Akhter Chowdhury, Stanley E. Shackney, Kerstin Heselmeyer-Haddad, Thomas Ried, Alejandro A. Schäffer, Russell Schwartz:
Algorithms to Model Single Gene, Single Chromosome, and Whole Genome Copy Number Changes Jointly in Tumor Phylogenetics. PLoS Comput. Biol. 10(7) (2014) - [j23]Cheemeng Tan, Robert Phillip Smith, Ming-Chi Tsai, Russell Schwartz, Lingchong You:
Phenotypic Signatures Arising from Unbalanced Bacterial Growth. PLoS Comput. Biol. 10(8) (2014) - 2013
- [j22]Daniele Catanzaro, Ramamoorthi Ravi, Russell Schwartz:
A mixed integer linear programming model to reconstruct phylogenies from single nucleotide polymorphism haplotypes under the maximum parsimony criterion. Algorithms Mol. Biol. 8: 3 (2013) - [j21]Salim Akhter Chowdhury, Stanley Shackney, Kerstin Heselmeyer-Haddad, Thomas Ried, Alejandro A. Schäffer, Russell Schwartz:
Phylogenetic analysis of multiprobe fluorescence in situ hybridization data from tumor cell populations. Bioinform. 29(13): 189-198 (2013) - [j20]Ming-Chi Tsai, Guy E. Blelloch, R. Ravi, Russell Schwartz:
Coalescent-Based Method for Learning Parameters of Admixture Events from Large-Scale Genetic Variation Data. IEEE ACM Trans. Comput. Biol. Bioinform. 10(5): 1137-1149 (2013) - [j19]Ayshwarya Subramanian, Stanley Shackney, Russell Schwartz:
Novel Multisample Scheme for Inferring Phylogenetic Markers from Whole Genome Tumor Profiles. IEEE ACM Trans. Comput. Biol. Bioinform. 10(6): 1422-1431 (2013) - 2012
- [j18]Lonnie R. Welch, Russell Schwartz, Fran Lewitter:
A Report of the Curriculum Task Force of the ISCB Education Committee. PLoS Comput. Biol. 8(6) (2012) - 2011
- [j17]Navodit Misra, Guy E. Blelloch, R. Ravi, Russell Schwartz:
Generalized Buneman Pruning for Inferring the Most Parsimonious Multi-State Phylogeny. J. Comput. Biol. 18(3): 445-457 (2011) - [j16]Navodit Misra, Guy E. Blelloch, R. Ravi, Russell Schwartz:
An Optimization-Based Sampling Scheme for Phylogenetic Trees. J. Comput. Biol. 18(11): 1599-1609 (2011) - [j15]Charalampos E. Tsourakakis, Richard Peng, Maria A. Tsiarli, Gary L. Miller, Russell Schwartz:
Approximation algorithms for speeding up dynamic programming and denoising aCGH data. ACM J. Exp. Algorithmics 16 (2011) - [j14]Ming-Chi Tsai, Guy E. Blelloch, R. Ravi, Russell Schwartz:
A Consensus Tree Approach for Reconstructing Human Evolutionary History and Detecting Population Substructure. IEEE ACM Trans. Comput. Biol. Bioinform. 8(4): 918-928 (2011) - 2010
- [j13]David Tolliver, Charalampos E. Tsourakakis, Ayshwarya Subramanian, Stanley Shackney, Russell Schwartz:
Robust unmixing of tumor states in array comparative genomic hybridization data. Bioinform. 26(12): 106-114 (2010) - [j12]Russell Schwartz, Stanley Shackney:
Applying unmixing to gene expression data for tumor phylogeny inference. BMC Bioinform. 11: 42 (2010) - [j11]Russell Schwartz:
Theory and Algorithms for the Haplotype Assembly Problem. Commun. Inf. Syst. 10(1): 23-38 (2010) - 2009
- [j10]Yongjin Park, Stanley Shackney, Russell Schwartz:
Network-Based Inference of Cancer Progression from Microarray Data. IEEE ACM Trans. Comput. Biol. Bioinform. 6(2): 200-212 (2009) - 2008
- [j9]Srinath Sridhar, Fumei Lam, Guy E. Blelloch, R. Ravi, Russell Schwartz:
Mixed Integer Linear Programming for Maximum-Parsimony Phylogeny Inference. IEEE ACM Trans. Comput. Biol. Bioinform. 5(3): 323-331 (2008) - 2007
- [j8]Russell Schwartz:
Stochastic Modelling for Systems Biology: Darren J. Wilkinson. Briefings Bioinform. 8(3): 204-205 (2007) - [j7]Srinath Sridhar, Fumei Lam, Guy E. Blelloch, R. Ravi, Russell Schwartz:
Direct maximum parsimony phylogeny reconstruction from genotype data. BMC Bioinform. 8 (2007) - [j6]Gregory Pennington, Charles A. Smith, Stanley Shackney, Russell Schwartz:
Reconstructing Tumor phylogenies from Heterogeneous Single-Cell Data. J. Bioinform. Comput. Biol. 5(2a): 407-427 (2007) - [j5]Srinath Sridhar, Kedar Dhamdhere, Guy E. Blelloch, Eran Halperin, R. Ravi, Russell Schwartz:
Algorithms for Efficient Near-Perfect Phylogenetic Tree Reconstruction in Theory and Practice. IEEE ACM Trans. Comput. Biol. Bioinform. 4(4): 561-571 (2007) - 2003
- [j4]Russell Schwartz, Bjarni V. Halldórsson, Vineet Bafna, Andrew G. Clark, Sorin Istrail:
Robustness of Inference of Haplotype Block Structure. J. Comput. Biol. 10(1): 13-19 (2003) - 2002
- [j3]Ross Lippert, Russell Schwartz, Giuseppe Lancia, Sorin Istrail:
Algorithmic strategies for the single nucleotide polymorphism haplotype assembly problem. Briefings Bioinform. 3(1): 23-31 (2002) - 2000
- [j2]Bonnie Berger, Jonathan A. King, Russell Schwartz, Peter W. Shor:
Local rule mechanism for selecting icosahedral shell geometry. Discret. Appl. Math. 104(1-3): 97-111 (2000) - 1999
- [j1]Sorin Istrail, Russell Schwartz, Jonathan A. King:
Lattice Simulations of Aggregation Funnels for Protein Folding. J. Comput. Biol. 6(2): 143-162 (1999)
Conference and Workshop Papers
- 2024
- [c34]Chih Hao Wu, Suraj Joshi, Welles Robinson, Paul F. Robbins, Russell Schwartz, Süleyman Cenk Sahinalp, Salem Malikic:
Determining Optimal Placement of Copy Number Aberration Impacted Single Nucleotide Variants in a Tumor Progression History. RECOMB 2024: 438-443 - 2022
- [c33]Arjun Srivatsa, Haoyun Lei, Russell Schwartz:
A Clonal Evolution Simulator for Planning Somatic Evolution Studies. ISBRA 2022: 229-242 - 2021
- [c32]Xuecong Fu, Russell Schwartz:
ConTreeDP: A consensus method of tumor trees based on maximum directed partition support problem. BIBM 2021: 125-130 - 2020
- [c31]Yifeng Tao, Shuangxia Ren, Michael Q. Ding, Russell Schwartz, Xinghua Lu:
Predicting Drug Sensitivity of Cancer Cell Lines via Collaborative Filtering with Contextual Attention. MLHC 2020: 660-684 - 2019
- [c30]Yifeng Tao, Haoyun Lei, Adrian V. Lee, Jian Ma, Russell Schwartz:
Phylogenies Derived from Matched Transcriptome Reveal the Evolution of Cell Populations and Temporal Order of Perturbed Pathways in Breast Cancer Brain Metastases. ISMCO 2019: 3-28 - [c29]Haoyun Lei, Bochuan Lyu, E. Michael Gertz, Alejandro A. Schäffer, Xulian Shi, Kui Wu, Guibo Li, Liqin Xu, Yong Hou, Michael Dean, Russell Schwartz:
Tumor Copy Number Deconvolution Integrating Bulk and Single-Cell Sequencing Data. RECOMB 2019: 174-189 - 2018
- [c28]Russell Schwartz:
Reconstructing Tumor Evolution and Progression in Structurally Variant Cancer Cells. COCOON 2018: x- - [c27]Haoyun Lei, Bochuan Lyu, E. Michael Gertz, Alejandro A. Schäffer, Russell Schwartz:
Tumor Copy Number Data Deconvolution Integrating Bulk and Single-cell Sequencing Data. ICCABS 2018: 1 - 2016
- [c26]Russell Schwartz:
Computationally resolving heterogeneity in mixed genomic samples. ICCABS 2016: 1 - 2014
- [c25]Ayshwarya Subramanian, Russell Schwartz:
Reference-free inference of tumor phylogenies from single-cell sequencing data. ICCABS 2014: 1 - 2012
- [c24]Ming-Chi Tsai, Guy E. Blelloch, Russell Schwartz, R. Ravi:
Coalescent-based method for learning parameters of admixture events from large-scale genetic variation data. BCB 2012: 90-97 - [c23]Ayshwarya Subramanian, Stanley Shackney, Russell Schwartz:
Novel Multi-sample Scheme for Inferring Phylogenetic Markers from Whole Genome Tumor Profiles. ISBRA 2012: 250-262 - 2011
- [c22]Ayshwarya Subramanian, Stanley Shackney, Russell Schwartz:
Inference of tumor phylogenies from genomic assays on heterogeneous samples. BCB 2011: 172-181 - [c21]Russell Schwartz:
Phylogenetics of Heterogeneous Samples - (Keynote Talk). ISBRA 2011: 1 - [c20]Navodit Misra, Guy E. Blelloch, R. Ravi, Russell Schwartz:
An Optimization-Based Sampling Scheme for Phylogenetic Trees. RECOMB 2011: 252-266 - [c19]Gary L. Miller, Richard Peng, Russell Schwartz, Charalampos E. Tsourakakis:
Approximate Dynamic Programming using Halfspace Queries and Multiscale Monge Decomposition. SODA 2011: 1675-1682 - 2010
- [c18]Ming-Chi Tsai, Guy E. Blelloch, R. Ravi, Russell Schwartz:
A Consensus Tree Approach for Reconstructing Human Evolutionary History and Detecting Population Substructure. ISBRA 2010: 167-178 - [c17]Navodit Misra, Guy E. Blelloch, R. Ravi, Russell Schwartz:
Generalized Buneman Pruning for Inferring the Most Parsimonious Multi-state Phylogeny. RECOMB 2010: 369-383 - [c16]Giuseppe Lancia, Romeo Rizzi, Russell Schwartz:
Tiling Binary Matrices in Haplotyping: Complexity, Models and Algorithms. Stringology 2010: 89-102 - 2008
- [c15]Steven Gray, Cindy E. Hmelo-Silver, Lei Liu, Rebecca Jordan, Heisawn Jeong, Russell Schwartz, Heather Finkelstein, Daniel Wolsten, Marylee Demeter, Suparna Sinha:
Learning with ecosystem models: a tale of two classrooms. ICLS (1) 2008: 289-296 - [c14]Yongjin Park, Stanley Shackney, Russell Schwartz:
Network-Based Inference of Cancer Progression from Microarray Data. ISBRA 2008: 268-279 - 2007
- [c13]Srinath Sridhar, Fumei Lam, Guy E. Blelloch, R. Ravi, Russell Schwartz:
Efficiently Finding the Most Parsimonious Phylogenetic Tree Via Linear Programming. ISBRA 2007: 37-48 - 2006
- [c12]Guy E. Blelloch, Kedar Dhamdhere, Eran Halperin, R. Ravi, Russell Schwartz, Srinath Sridhar:
Fixed Parameter Tractability of Binary Near-Perfect Phylogenetic Tree Reconstruction. ICALP (1) 2006: 667-678 - [c11]Srinath Sridhar, Kedar Dhamdhere, Guy E. Blelloch, Eran Halperin, R. Ravi, Russell Schwartz:
Simple Reconstruction of Binary Near-Perfect Phylogenetic Trees. International Conference on Computational Science (2) 2006: 799-806 - [c10]Natalie Castellana, Kedar Dhamdhere, Srinath Sridhar, Russell Schwartz:
Relaxing Haplotype Block Models for Association Testing. Pacific Symposium on Biocomputing 2006: 454-466 - 2005
- [c9]Tiequan Zhang, Rori Rohlfs, Russell Schwartz:
Implementation of a discrete event simulator for biological self-assembly systems. WSC 2005: 2223-2231 - 2004
- [c8]Russell Schwartz:
Algorithms for Association Study Design Using a Generalized Model of Haplotype Conservation. CSB 2004: 90-97 - 2003
- [c7]Liliana Florea, Bjarni V. Halldórsson, Oliver Kohlbacher, Russell Schwartz, Stephen Hoffman, Sorin Istrail:
Epitope Prediction Algorithms for Peptide based Vaccine Design. CSB 2003: 17-26 - [c6]Russell Schwartz:
Haplotype Motifs: An Algorithmic Approach to Locating Evolutionarily Conserved Patterns in Haploid Sequences. CSB 2003: 306-315 - [c5]Vineet Bafna, Bjarni V. Halldórsson, Russell Schwartz, Andrew G. Clark, Sorin Istrail:
Haplotypes and informative SNP selection algorithms: don't block out information. RECOMB 2003: 19-27 - 2002
- [c4]Russell Schwartz, Andrew G. Clark, Sorin Istrail:
Inferring Piecewise Ancestral History from Haploid Sequences. Computational Methods for SNPs and Haplotype Inference 2002: 62-73 - [c3]Russell Schwartz, Andrew G. Clark, Sorin Istrail:
Methods for Inferring Block-Wise Ancestral History from Haploid Sequences. WABI 2002: 44-59 - 2001
- [c2]Giuseppe Lancia, Vineet Bafna, Sorin Istrail, Ross Lippert, Russell Schwartz:
SNPs Problems, Complexity, and Algorithms. ESA 2001: 182-193 - [c1]Russell J. Turner, Kabir Chaturvedi, Nathan Edwards, Daniel P. Fasulo, Aaron L. Halpern, Daniel H. Huson, Oliver Kohlbacher, Jason R. Miller, Knut Reinert, Karin A. Remington, Russell Schwartz, Brian Walenz, Shibu Yooseph, Sorin Istrail:
Visualization challenges for a new cyberpharmaceutical computing paradigm. IEEE Symposium on Parallel and Large-Data Visualization and Graphics 2001: 7-18
Editorship
- 2020
- [e3]Russell Schwartz:
Research in Computational Molecular Biology - 24th Annual International Conference, RECOMB 2020, Padua, Italy, May 10-13, 2020, Proceedings. Lecture Notes in Computer Science 12074, Springer 2020, ISBN 978-3-030-45256-8 [contents] - 2017
- [e2]Russell Schwartz, Knut Reinert:
17th International Workshop on Algorithms in Bioinformatics, WABI 2017, August 21-23, 2017, Boston, MA, USA. LIPIcs 88, Schloss Dagstuhl - Leibniz-Zentrum für Informatik 2017, ISBN 978-3-95977-050-7 [contents] - 2012
- [e1]Leonidas G. Bleris, Ion I. Mandoiu, Russell Schwartz, Jianxin Wang:
Bioinformatics Research and Applications - 8th International Symposium, ISBRA 2012, Dallas, TX, USA, May 21-23, 2012. Proceedings. Lecture Notes in Computer Science 7292, Springer 2012, ISBN 978-3-642-30190-2 [contents]
Informal and Other Publications
- 2020
- [i2]Russell Schwartz, Pratap Tokekar:
Robust Multi-Agent Task Assignment in Failure-Prone and Adversarial Environments. CoRR abs/2007.00100 (2020) - 2010
- [i1]Gary L. Miller, Richard Peng, Russell Schwartz, Charalampos E. Tsourakakis:
Approximate Dynamic Programming for Fast Denoising of aCGH Data. CoRR abs/1003.4942 (2010)
Coauthor Index
Stanley Shackney
aka: Stanley E. Shackney
aka: Stanley E. Shackney
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