Russell Schwartz

ORCID

Publication Activity (10 Years)

Years Active: 1999-2024
Publications (10 Years): 30

Top Venues

Massachusetts Institute of Technology, Cambridge, MA, USA (PHD)

Education History

Massachusetts Institute of Technology, Cambridge, MA, USA

PHD

Publications

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)
Arjun Srivatsa, Haoyun Lei, Russell Schwartz
A Clonal Evolution Simulator for Planning Somatic Evolution Studies. J. Comput. Biol. 30 (8) (2023)
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)
Arjun Srivatsa, Haoyun Lei, Russell Schwartz
A Clonal Evolution Simulator for Planning Somatic Evolution Studies. ISBRA (2022)
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) (2021)
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)
Xuecong Fu, Russell Schwartz
ConTreeDP: A consensus method of tumor trees based on maximum directed partition support problem. BIBM (2021)
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) (2021)
Russell Schwartz
RECOMB 2020 Special Issue. J. Comput. Biol. 28 (4) (2021)
Ying Zhou, Sharon R. Browning, Brian L. Browning, Russell Schwartz
IBDkin: fast estimation of kinship coefficients from identity by descent segments. Bioinform. 36 (16) (2020)
Zhenqin Wu, Nilah M. Ioannidis, James Zou, Russell Schwartz
Predicting target genes of non-coding regulatory variants with IRT. Bioinform. 36 (16) (2020)
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) (2020)
Russell Schwartz, Pratap Tokekar
Robust Multi-Agent Task Assignment in Failure-Prone and Adversarial Environments. CoRR (2020)
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) (2020)
Ilja M. Nolte, Russell Schwartz
Metasubtract: an R-package to analytically produce leave-one-out meta-analysis GWAS summary statistics. Bioinform. 36 (16) (2020)
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) (2020)
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)
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)
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)
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)
Russell Schwartz
Reconstructing Tumor Evolution and Progression in Structurally Variant Cancer Cells. COCOON (2018)
Marcus Thomas, Russell Schwartz
A method for efficient Bayesian optimization of self-assembly systems from scattering data. BMC Syst. Biol. 12 (1) (2018)
Jesse Eaton, Jingyi Wang, Russell Schwartz
Deconvolution and phylogeny inference of structural variations in tumor genomic samples. Bioinform. 34 (13) (2018)
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)
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) (2017)
Theodore Roman, Lu Xie, Russell Schwartz
Automated deconvolution of structured mixtures from heterogeneous tumor genomic data. PLoS Comput. Biol. 13 (10) (2017)
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)
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) (2016)
Russell Schwartz
Computationally resolving heterogeneity in mixed genomic samples. ICCABS (2016)
Theodore Roman, Lu Xie, Russell Schwartz
Medoidshift clustering applied to genomic bulk tumor data. BMC Genom. 17 (S-1) (2016)
Theodore Roman, Amir Nayyeri, Brittany Fasy, Russell Schwartz
A simplicial complex-based approach to unmixing tumor progression data. BMC Bioinform. 16 (2015)
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) (2015)
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)
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)
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)
Serafim Batzoglou, Russell Schwartz
Editorial. Bioinform. 30 (12) (2014)
Ayshwarya Subramanian, Russell Schwartz
Reference-free inference of tumor phylogenies from single-cell sequencing data. ICCABS (2014)
Salim Akhter Chowdhury, Stanley Shackney, Kerstin Heselmeyer-Haddad, Thomas Ried, Alejandro A. Schäffer, Russell Schwartz
hybridization data from tumor cell populations. Bioinform. 29 (13) (2013)
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 (2013)
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) (2013)
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) (2013)
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)
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)
Ayshwarya Subramanian, Stanley Shackney, Russell Schwartz
Novel Multi-sample Scheme for Inferring Phylogenetic Markers from Whole Genome Tumor Profiles. ISBRA (2012)
Ayshwarya Subramanian, Stanley Shackney, Russell Schwartz
Inference of tumor phylogenies from genomic assays on heterogeneous samples. BCB (2011)
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)
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) (2011)
Navodit Misra, Guy E. Blelloch, R. Ravi, Russell Schwartz
An Optimization-Based Sampling Scheme for Phylogenetic Trees. J. Comput. Biol. 18 (11) (2011)
Gary L. Miller, Richard Peng, Russell Schwartz, Charalampos E. Tsourakakis
Approximate Dynamic Programming using Halfspace Queries and Multiscale Monge Decomposition. SODA (2011)
Russell Schwartz
Phylogenetics of Heterogeneous Samples - (Keynote Talk). ISBRA (2011)
Navodit Misra, Guy E. Blelloch, R. Ravi, Russell Schwartz
An Optimization-Based Sampling Scheme for Phylogenetic Trees. RECOMB (2011)
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) (2011)
Navodit Misra, Guy E. Blelloch, R. Ravi, Russell Schwartz
Generalized Buneman Pruning for Inferring the Most Parsimonious Multi-state Phylogeny. RECOMB (2010)
Russell Schwartz
Theory and Algorithms for the Haplotype Assembly Problem. Commun. Inf. Syst. 10 (1) (2010)
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)
Giuseppe Lancia, Romeo Rizzi, Russell Schwartz
Tiling Binary Matrices in Haplotyping: Complexity, Models and Algorithms. Stringology (2010)
Gary L. Miller, Richard Peng, Russell Schwartz, Charalampos E. Tsourakakis
Approximate Dynamic Programming for Fast Denoising of aCGH Data CoRR (2010)
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) (2010)
Russell Schwartz, Stanley Shackney
Applying unmixing to gene expression data for tumor phylogeny inference. BMC Bioinform. 11 (2010)
Yongjin Park, Stanley Shackney, Russell Schwartz
Network-Based Inference of Cancer Progression from Microarray Data. IEEE ACM Trans. Comput. Biol. Bioinform. 6 (2) (2009)
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)
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) (2008)
Yongjin Park, Stanley Shackney, Russell Schwartz
Network-Based Inference of Cancer Progression from Microarray Data. ISBRA (2008)
Gregory Pennington, Charles A. Smith, Stanley Shackney, Russell Schwartz
Reconstructing Tumor phylogenies from Heterogeneous Single-Cell Data. J. Bioinform. Comput. Biol. 5 (2a) (2007)
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) (2007)
Russell Schwartz
Stochastic Modelling for Systems Biology: Darren J. Wilkinson. Briefings Bioinform. 8 (3) (2007)
Srinath Sridhar, Fumei Lam, Guy E. Blelloch, R. Ravi, Russell Schwartz
Efficiently Finding the Most Parsimonious Phylogenetic Tree Via Linear Programming. ISBRA (2007)
Srinath Sridhar, Fumei Lam, Guy E. Blelloch, R. Ravi, Russell Schwartz
Direct maximum parsimony phylogeny reconstruction from genotype data. BMC Bioinform. 8 (2007)
Natalie Castellana, Kedar Dhamdhere, Srinath Sridhar, Russell Schwartz
Relaxing Haplotype Block Models for Association Testing. Pacific Symposium on Biocomputing (2006)
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)
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)
Tiequan Zhang, Rori Rohlfs, Russell Schwartz
Implementation of a discrete event simulator for biological self-assembly systems. WSC (2005)
Russell Schwartz
Algorithms for Association Study Design Using a Generalized Model of Haplotype Conservation. CSB (2004)
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)
Russell Schwartz
Haplotype Motifs: An Algorithmic Approach to Locating Evolutionarily Conserved Patterns in Haploid Sequences. CSB (2003)
Russell Schwartz, Bjarni V. Halldórsson, Vineet Bafna, Andrew G. Clark, Sorin Istrail
Robustness of Inference of Haplotype Block Structure. J. Comput. Biol. 10 (1) (2003)
Liliana Florea, Bjarni V. Halldórsson, Oliver Kohlbacher, Russell Schwartz, Stephen Hoffman, Sorin Istrail
Epitope Prediction Algorithms for Peptide based Vaccine Design. CSB (2003)
Russell Schwartz, Andrew G. Clark, Sorin Istrail
Inferring Piecewise Ancestral History from Haploid Sequences. Computational Methods for SNPs and Haplotype Inference (2002)
Russell Schwartz, Andrew G. Clark, Sorin Istrail
Methods for Inferring Block-Wise Ancestral History from Haploid Sequences. WABI (2002)
Ross Lippert, Russell Schwartz, Giuseppe Lancia, Sorin Istrail
Algorithmic strategies for the single nucleotide polymorphism haplotype assembly problem. Briefings Bioinform. 3 (1) (2002)
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)
Giuseppe Lancia, Vineet Bafna, Sorin Istrail, Ross Lippert, Russell Schwartz
SNPs Problems, Complexity, and Algorithms. ESA (2001)
Bonnie Berger, Jonathan A. King, Russell Schwartz, Peter W. Shor
Local rule mechanism for selecting icosahedral shell geometry. Discret. Appl. Math. 104 (1-3) (2000)
Sorin Istrail, Russell Schwartz, Jonathan A. King
Lattice Simulations of Aggregation Funnels for Protein Folding. J. Comput. Biol. 6 (2) (1999)

Russell Schwartz.css-eqlu8i{font-size:small;padding-left:4px;}

Publication Activity (10 Years)

Top Topics

Top Venues

Russell Schwartz