Russell Schwartz

93 papers A* 1A 1B 6C 2Misc 5Journal 54Unranked 22
YearRankTypeTitle / Venue / Authors
2025 — conf
Computationally Reconstructing the Evolution of Cancer Progression Risk.
ICCABS
Kefan Cao, Russell Schwartz
2025 J jnl
Marker selection strategies for circulating tumor DNA guided by phylogenetic inference.
Bioinform.
Xuecong Fu, Zhicheng Luo, Yueqian Deng, William Laframboise, David Bartlett, Russell Schwartz
2025 J jnl
Sc-TUSV-Ext: Single-Cell Clonal Lineage Inference from Single Nucleotide Variants, Copy Number Alterations, and Structural Variants.
J. Comput. Biol.
Nishat Anjum Bristy, Xuecong Fu, Russell Schwartz
2024 B conf
Determining Optimal Placement of Copy Number Aberration Impacted Single Nucleotide Variants in a Tumor Progression History.
RECOMB
Chih Hao Wu, Suraj Joshi, Welles Robinson, Paul F. Robbins, Russell Schwartz, Süleyman Cenk Sahinalp, Salem Malikic
2023 J jnl
A Clonal Evolution Simulator for Planning Somatic Evolution Studies.
J. Comput. Biol.
Arjun Srivatsa, Haoyun Lei, Russell Schwartz
2023 J jnl
Ten simple rules for writing a PLOS Computational Biology quick tips article.
PLoS Comput. Biol.
Patricia M. Palagi, Russell Schwartz, Scott Markel, B. F. Francis Ouellette
2022 — conf
A Clonal Evolution Simulator for Planning Somatic Evolution Studies.
ISBRA
Arjun Srivatsa, Haoyun Lei, Russell Schwartz
2022 J jnl
Reconstructing tumor clonal lineage trees incorporating single-nucleotide variants, copy number alterations and structural variations.
Bioinform.
Xuecong Fu, Haoyun Lei, Yifeng Tao, Russell Schwartz
2022 J jnl
Semi-deconvolution of bulk and single-cell RNA-seq data with application to metastatic progression in breast cancer.
Bioinform.
Haoyun Lei, Xiaoyan A. Guo, Yifeng Tao, Kai Ding, Xuecong Fu, Steffi Oesterreich, Adrian V. Lee, Russell Schwartz
2021 J jnl
Assessing the contribution of tumor mutational phenotypes to cancer progression risk.
PLoS Comput. Biol.
Yifeng Tao, Ashok Rajaraman, Xiaoyue Cui, Ziyi Cui, Haoran Chen, Yuanqi Zhao, Jesse Eaton, Hannah Kim, Jian Ma, Russell Schwartz
2021 — conf
ConTreeDP: A consensus method of tumor trees based on maximum directed partition support problem.
BIBM
Xuecong Fu, Russell Schwartz
2021 J jnl
Joint Clustering of Single-Cell Sequencing and Fluorescence In Situ Hybridization Data for Reconstructing Clonal Heterogeneity in Cancers.
J. Comput. Biol.
Xuecong Fu, Haoyun Lei, Yifeng Tao, Kerstin Heselmeyer-Haddad, Irianna Torres, Michael Dean, Thomas Ried, Russell Schwartz
2021 J jnl
RECOMB 2020 Special Issue.
J. Comput. Biol.
Russell Schwartz
2021 J jnl
Tumor heterogeneity assessed by sequencing and fluorescence in situ hybridization (FISH) data.
Bioinform.
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
2020 J jnl
Efficient toolkit implementing best practices for principal component analysis of population genetic data.
Bioinform.
Florian Privé, Keurcien Luu, Michael G. B. Blum, John J. McGrath, Bjarni J. Vilhjálmsson, Russell Schwartz
2020 J jnl
IBDkin: fast estimation of kinship coefficients from identity by descent segments.
Bioinform.
Ying Zhou, Sharon R. Browning, Brian L. Browning, Russell Schwartz
2020 J jnl
Metasubtract: an R-package to analytically produce leave-one-out meta-analysis GWAS summary statistics.
Bioinform.
Ilja M. Nolte, Russell Schwartz
2020 — conf
Predicting Drug Sensitivity of Cancer Cell Lines via Collaborative Filtering with Contextual Attention.
MLHC
Yifeng Tao, Shuangxia Ren, Michael Q. Ding, Russell Schwartz, Xinghua Lu
2020 J jnl
Predicting target genes of non-coding regulatory variants with IRT.
Bioinform.
Zhenqin Wu, Nilah M. Ioannidis, James Zou, Russell Schwartz
2020 B ed.
Research in Computational Molecular Biology - 24th Annual International Conference, RECOMB 2020, Padua, Italy, May 10-13, 2020, Proceedings
RECOMB
Russell Schwartz
2020 J jnl
Robust Multi-Agent Task Assignment in Failure-Prone and Adversarial Environments.
CoRR
Russell Schwartz, Pratap Tokekar
2020 J jnl
Robust and accurate deconvolution of tumor populations uncovers evolutionary mechanisms of breast cancer metastasis.
Bioinform.
Yifeng Tao, Haoyun Lei, Xuecong Fu, Adrian V. Lee, Jian Ma, Russell Schwartz
2020 J jnl
Tumor Copy Number Deconvolution Integrating Bulk and Single-Cell Sequencing Data.
J. Comput. Biol.
Haoyun Lei, Bochuan Lyu, E. Michael Gertz, Alejandro A. Schäffer, Xulian Shi, Kui Wu, Guibo Li, Liqin Xu, Yong Hou, Michael Dean, Russell Schwartz
2019 — conf
Phylogenies Derived from Matched Transcriptome Reveal the Evolution of Cell Populations and Temporal Order of Perturbed Pathways in Breast Cancer Brain Metastases.
ISMCO
Yifeng Tao, Haoyun Lei, Adrian V. Lee, Jian Ma, Russell Schwartz
2019 B conf
Tumor Copy Number Deconvolution Integrating Bulk and Single-Cell Sequencing Data.
RECOMB
Haoyun Lei, Bochuan Lyu, E. Michael Gertz, Alejandro A. Schäffer, Xulian Shi, Kui Wu, Guibo Li, Liqin Xu, Yong Hou, Michael Dean, Russell Schwartz
2018 J jnl
A method for efficient Bayesian optimization of self-assembly systems from scattering data.
BMC Syst. Biol.
Marcus Thomas, Russell Schwartz
2018 J jnl
Deconvolution and phylogeny inference of structural variations in tumor genomic samples.
Bioinform.
Jesse Eaton, Jingyi Wang, Russell Schwartz
2018 Misc conf
Reconstructing Tumor Evolution and Progression in Structurally Variant Cancer Cells.
COCOON
Russell Schwartz
2018 J jnl
The development and application of bioinformatics core competencies to improve bioinformatics training and education.
PLoS Comput. Biol.
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
2018 — conf
Tumor Copy Number Data Deconvolution Integrating Bulk and Single-cell Sequencing Data.
ICCABS
Haoyun Lei, Bochuan Lyu, E. Michael Gertz, Alejandro A. Schäffer, Russell Schwartz
2017 C ed.
17th International Workshop on Algorithms in Bioinformatics, WABI 2017, Boston, MA, USA, August 21-23, 2017
WABI
Russell Schwartz, Knut Reinert
2017 J jnl
Automated deconvolution of structured mixtures from heterogeneous tumor genomic data.
PLoS Comput. Biol.
Theodore Roman, Lu Xie, Russell Schwartz
2017 J jnl
Derivative-Free Optimization of Rate Parameters of Capsid Assembly Models from Bulk in Vitro Data.
IEEE ACM Trans. Comput. Biol. Bioinform.
Lu Xie, Gregory R. Smith, Russell Schwartz
2016 J jnl
Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB's Education Committee).
PLoS Comput. Biol.
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
2016 J jnl
Classifying the Progression of Ductal Carcinoma from Single-Cell Sampled Data via Integer Linear Programming: A Case Study.
IEEE ACM Trans. Comput. Biol. Bioinform.
Daniele Catanzaro, Stanley E. Shackney, Alejandro A. Schäffer, Russell Schwartz
2016 — conf
Computationally resolving heterogeneity in mixed genomic samples.
ICCABS
Russell Schwartz
2016 J jnl
Medoidshift clustering applied to genomic bulk tumor data.
BMC Genom.
Theodore Roman, Lu Xie, Russell Schwartz
2015 J jnl
A simplicial complex-based approach to unmixing tumor progression data.
BMC Bioinform.
Theodore Roman, Amir Nayyeri, Brittany Terese Fasy, Russell Schwartz
2015 J jnl
Inferring models of multiscale copy number evolution for single-tumor phylogenetics.
Bioinform.
Salim Akhter Chowdhury, E. Michael Gertz, Darawalee Wangsa, Kerstin Heselmeyer-Haddad, Thomas Ried, Alejandro A. Schäffer, Russell Schwartz
2014 J jnl
Algorithms to Model Single Gene, Single Chromosome, and Whole Genome Copy Number Changes Jointly in Tumor Phylogenetics.
PLoS Comput. Biol.
Salim Akhter Chowdhury, Stanley E. Shackney, Kerstin Heselmeyer-Haddad, Thomas Ried, Alejandro A. Schäffer, Russell Schwartz
2014 J jnl
Bioinformatics Curriculum Guidelines: Toward a Definition of Core Competencies.
PLoS Comput. Biol.
Lonnie R. Welch, Fran Lewitter, Russell Schwartz, Catherine Brooksbank, Predrag Radivojac, Bruno A. Gaëta, Maria Victoria Schneider
2014 J jnl
Editorial.
Bioinform.
Serafim Batzoglou, Russell Schwartz
2014 J jnl
Phenotypic Signatures Arising from Unbalanced Bacterial Growth.
PLoS Comput. Biol.
Cheemeng Tan, Robert Phillip Smith, Ming-Chi Tsai, Russell Schwartz, Lingchong You
2014 — conf
Reference-free inference of tumor phylogenies from single-cell sequencing data.
ICCABS
Ayshwarya Subramanian, Russell Schwartz
2013 J jnl
A mixed integer linear programming model to reconstruct phylogenies from single nucleotide polymorphism haplotypes under the maximum parsimony criterion.
Algorithms Mol. Biol.
Daniele Catanzaro, Ramamoorthi Ravi, Russell Schwartz
2013 J jnl
Coalescent-Based Method for Learning Parameters of Admixture Events from Large-Scale Genetic Variation Data.
IEEE ACM Trans. Comput. Biol. Bioinform.
Ming-Chi Tsai, Guy E. Blelloch, R. Ravi, Russell Schwartz
2013 J jnl
Novel Multisample Scheme for Inferring Phylogenetic Markers from Whole Genome Tumor Profiles.
IEEE ACM Trans. Comput. Biol. Bioinform.
Ayshwarya Subramanian, Stanley Shackney, Russell Schwartz
2013 J jnl
Phylogenetic analysis of multiprobe fluorescence
Bioinform.
Salim Akhter Chowdhury, Stanley Shackney, Kerstin Heselmeyer-Haddad, Thomas Ried, Alejandro A. Schäffer, Russell Schwartz
2012 J jnl
A Report of the Curriculum Task Force of the ISCB Education Committee.
PLoS Comput. Biol.
Lonnie R. Welch, Russell Schwartz, Fran Lewitter
2012 — ed.
Bioinformatics Research and Applications - 8th International Symposium, ISBRA 2012, Dallas, TX, USA, May 21-23, 2012. Proceedings
ISBRA
Leonidas G. Bleris, Ion I. Mandoiu, Russell Schwartz, Jianxin Wang
2012 — conf
Coalescent-based method for learning parameters of admixture events from large-scale genetic variation data.
BCB
Ming-Chi Tsai, Guy E. Blelloch, Russell Schwartz, R. Ravi
2012 — conf
Novel Multi-sample Scheme for Inferring Phylogenetic Markers from Whole Genome Tumor Profiles.
ISBRA
Ayshwarya Subramanian, Stanley Shackney, Russell Schwartz
2011 J jnl
A Consensus Tree Approach for Reconstructing Human Evolutionary History and Detecting Population Substructure.
IEEE ACM Trans. Comput. Biol. Bioinform.
Ming-Chi Tsai, Guy E. Blelloch, R. Ravi, Russell Schwartz
2011 B conf
An Optimization-Based Sampling Scheme for Phylogenetic Trees.
RECOMB
Navodit Misra, Guy E. Blelloch, R. Ravi, Russell Schwartz
2011 J jnl
An Optimization-Based Sampling Scheme for Phylogenetic Trees.
J. Comput. Biol.
Navodit Misra, Guy E. Blelloch, R. Ravi, Russell Schwartz
2011 A* conf
Approximate Dynamic Programming using Halfspace Queries and Multiscale Monge Decomposition.
SODA
Gary L. Miller, Richard Peng, Russell Schwartz, Charalampos E. Tsourakakis
2011 J jnl
Approximation algorithms for speeding up dynamic programming and denoising aCGH data.
ACM J. Exp. Algorithmics
Charalampos E. Tsourakakis, Richard Peng, Maria A. Tsiarli, Gary L. Miller, Russell Schwartz
2011 J jnl
Generalized Buneman Pruning for Inferring the Most Parsimonious Multi-State Phylogeny.
J. Comput. Biol.
Navodit Misra, Guy E. Blelloch, R. Ravi, Russell Schwartz
2011 — conf
Inference of tumor phylogenies from genomic assays on heterogeneous samples.
BCB
Ayshwarya Subramanian, Stanley Shackney, Russell Schwartz
2011 — conf
Phylogenetics of Heterogeneous Samples - (Keynote Talk).
ISBRA
Russell Schwartz
2010 — conf
A Consensus Tree Approach for Reconstructing Human Evolutionary History and Detecting Population Substructure.
ISBRA
Ming-Chi Tsai, Guy E. Blelloch, R. Ravi, Russell Schwartz
2010 J jnl
Applying unmixing to gene expression data for tumor phylogeny inference.
BMC Bioinform.
Russell Schwartz, Stanley Shackney
2010 J jnl
Approximate Dynamic Programming for Fast Denoising of aCGH Data
CoRR
Gary L. Miller, Richard Peng, Russell Schwartz, Charalampos E. Tsourakakis
2010 B conf
Generalized Buneman Pruning for Inferring the Most Parsimonious Multi-state Phylogeny.
RECOMB
Navodit Misra, Guy E. Blelloch, R. Ravi, Russell Schwartz
2010 J jnl
Robust unmixing of tumor states in array comparative genomic hybridization data.
Bioinform.
David Tolliver, Charalampos E. Tsourakakis, Ayshwarya Subramanian, Stanley Shackney, Russell Schwartz
2010 J jnl
Theory and Algorithms for the Haplotype Assembly Problem.
Commun. Inf. Syst.
Russell Schwartz
2010 Misc conf
Tiling Binary Matrices in Haplotyping: Complexity, Models and Algorithms.
PSC
Giuseppe Lancia, Romeo Rizzi, Russell Schwartz
2009 J jnl
Network-Based Inference of Cancer Progression from Microarray Data.
IEEE ACM Trans. Comput. Biol. Bioinform.
Yongjin Park, Stanley Shackney, Russell Schwartz
2008 — conf
Learning with ecosystem models: a tale of two classrooms.
ICLS (1)
Steven Gray, Cindy E. Hmelo-Silver, Lei Liu, Rebecca Jordan, Heisawn Jeong, Russell Schwartz, Heather Finkelstein, Daniel Wolsten, Marylee Demeter, Suparna Sinha
2008 J jnl
Mixed Integer Linear Programming for Maximum-Parsimony Phylogeny Inference.
IEEE ACM Trans. Comput. Biol. Bioinform.
Srinath Sridhar, Fumei Lam, Guy E. Blelloch, R. Ravi, Russell Schwartz
2008 — conf
Network-Based Inference of Cancer Progression from Microarray Data.
ISBRA
Yongjin Park, Stanley Shackney, Russell Schwartz
2007 J jnl
Algorithms for Efficient Near-Perfect Phylogenetic Tree Reconstruction in Theory and Practice.
IEEE ACM Trans. Comput. Biol. Bioinform.
Srinath Sridhar, Kedar Dhamdhere, Guy E. Blelloch, Eran Halperin, R. Ravi, Russell Schwartz
2007 J jnl
Direct maximum parsimony phylogeny reconstruction from genotype data.
BMC Bioinform.
Srinath Sridhar, Fumei Lam, Guy E. Blelloch, R. Ravi, Russell Schwartz
2007 — conf
Efficiently Finding the Most Parsimonious Phylogenetic Tree Via Linear Programming.
ISBRA
Srinath Sridhar, Fumei Lam, Guy E. Blelloch, R. Ravi, Russell Schwartz
2007 J jnl
Reconstructing Tumor phylogenies from Heterogeneous Single-Cell Data.
J. Bioinform. Comput. Biol.
Gregory Pennington, Charles A. Smith, Stanley Shackney, Russell Schwartz
2007 J jnl
Stochastic Modelling for Systems Biology: Darren J. Wilkinson.
Briefings Bioinform.
Russell Schwartz
2006 — conf
Fixed Parameter Tractability of Binary Near-Perfect Phylogenetic Tree Reconstruction.
ICALP (1)
Guy E. Blelloch, Kedar Dhamdhere, Eran Halperin, R. Ravi, Russell Schwartz, Srinath Sridhar
2006 Misc conf
Relaxing Haplotype Block Models for Association Testing.
Pacific Symposium on Biocomputing
Natalie Castellana, Kedar Dhamdhere, Srinath Sridhar, Russell Schwartz
2006 Misc conf
Simple Reconstruction of Binary Near-Perfect Phylogenetic Trees.
International Conference on Computational Science (2)
Srinath Sridhar, Kedar Dhamdhere, Guy E. Blelloch, Eran Halperin, R. Ravi, Russell Schwartz
2005 Misc conf
Implementation of a discrete event simulator for biological self-assembly systems.
WSC
Tiequan Zhang, Rori Rohlfs, Russell Schwartz
2004 — conf
Algorithms for Association Study Design Using a Generalized Model of Haplotype Conservation.
CSB
Russell Schwartz
2003 — conf
Epitope Prediction Algorithms for Peptide based Vaccine Design.
CSB
Liliana Florea, Bjarni V. Halldórsson, Oliver Kohlbacher, Russell Schwartz, Stephen Hoffman, Sorin Istrail
2003 — conf
Haplotype Motifs: An Algorithmic Approach to Locating Evolutionarily Conserved Patterns in Haploid Sequences.
CSB
Russell Schwartz
2003 B conf
Haplotypes and informative SNP selection algorithms: don't block out information.
RECOMB
Vineet Bafna, Bjarni V. Halldórsson, Russell Schwartz, Andrew G. Clark, Sorin Istrail
2003 J jnl
Robustness of Inference of Haplotype Block Structure.
J. Comput. Biol.
Russell Schwartz, Bjarni V. Halldórsson, Vineet Bafna, Andrew G. Clark, Sorin Istrail
2002 J jnl
Algorithmic strategies for the single nucleotide polymorphism haplotype assembly problem.
Briefings Bioinform.
Ross Lippert, Russell Schwartz, Giuseppe Lancia, Sorin Istrail
2002 — conf
Inferring Piecewise Ancestral History from Haploid Sequences.
Computational Methods for SNPs and Haplotype Inference
Russell Schwartz, Andrew G. Clark, Sorin Istrail
2002 C conf
Methods for Inferring Block-Wise Ancestral History from Haploid Sequences.
WABI
Russell Schwartz, Andrew G. Clark, Sorin Istrail
2001 A conf
SNPs Problems, Complexity, and Algorithms.
ESA
Giuseppe Lancia, Vineet Bafna, Sorin Istrail, Ross Lippert, Russell Schwartz
2001 — conf
Visualization challenges for a new cyberpharmaceutical computing paradigm.
IEEE Symposium on Parallel and Large-Data Visualization and Graphics
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
2000 J jnl
Local rule mechanism for selecting icosahedral shell geometry.
Discret. Appl. Math.
Bonnie Berger, Jonathan A. King, Russell Schwartz, Peter W. Shor
2000 — —
The local rules dynamics model for self-assembly simulation.
Russell Schwartz
1999 J jnl
Lattice Simulations of Aggregation Funnels for Protein Folding.
J. Comput. Biol.
Sorin Istrail, Russell Schwartz, Jonathan A. King