Russell Schwartz

According to our database, Russell Schwartz authored at least 80 papers between 1999 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

Determining Optimal Placement of Copy Number Aberration Impacted Single Nucleotide Variants in a Tumor Progression History.

Chih Hao Wu, Suraj Joshi, Welles Robinson, Paul F. Robbins, Russell Schwartz, Süleyman Cenk Sahinalp, Salem Malikic

Proceedings of the Research in Computational Molecular Biology, 2024

2023

Ten simple rules for writing a PLOS Computational Biology quick tips article.

Patricia M. Palagi, Russell Schwartz, Scott Markel, B. F. Francis Ouellette

PLoS Comput. Biol., December, 2023

A Clonal Evolution Simulator for Planning Somatic Evolution Studies.

Arjun Srivatsa, Haoyun Lei, Russell Schwartz

J. Comput. Biol., August, 2023

2022

Semi-deconvolution of bulk and single-cell RNA-seq data with application to metastatic progression in breast cancer.

Haoyun Lei, Xiaoyan A. Guo, Yifeng Tao, Kai Ding, Xuecong Fu, Steffi Oesterreich, Adrian V. Lee, Russell Schwartz

Bioinform., 2022

Reconstructing tumor clonal lineage trees incorporating single-nucleotide variants, copy number alterations and structural variations.

Xuecong Fu, Haoyun Lei, Yifeng Tao, Russell Schwartz

Bioinform., 2022

2021

Assessing the contribution of tumor mutational phenotypes to cancer progression risk.

Yifeng Tao, Ashok Rajaraman, Xiaoyue Cui, Ziyi Cui, Haoran Chen, Yuanqi Zhao, Jesse Eaton, Hannah Kim, Jian Ma, Russell Schwartz

PLoS Comput. Biol., 2021

RECOMB 2020 Special Issue.

Russell Schwartz

J. Comput. Biol., 2021

Joint Clustering of Single-Cell Sequencing and Fluorescence In Situ Hybridization Data for Reconstructing Clonal Heterogeneity in Cancers.

Xuecong Fu, Haoyun Lei, Yifeng Tao, Kerstin Heselmeyer-Haddad, Irianna Torres, Michael Dean, Thomas Ried, Russell Schwartz

J. Comput. Biol., 2021

Tumor heterogeneity assessed by sequencing and fluorescence in situ hybridization (FISH) data.

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

Bioinform., 2021

ConTreeDP: A consensus method of tumor trees based on maximum directed partition support problem.

Xuecong Fu, Russell Schwartz

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2021

2020

Tumor Copy Number Deconvolution Integrating Bulk and Single-Cell Sequencing Data.

Haoyun Lei, Bochuan Lyu, E. Michael Gertz, Alejandro A. Schäffer, Xulian Shi, Kui Wu, Guibo Li, Liqin Xu, Yong Hou, Michael Dean, Russell Schwartz

J. Comput. Biol., 2020

Robust Multi-Agent Task Assignment in Failure-Prone and Adversarial Environments.

Russell Schwartz, Pratap Tokekar

CoRR, 2020

IBDkin: fast estimation of kinship coefficients from identity by descent segments.

Ying Zhou, Sharon R. Browning, Brian L. Browning, Russell Schwartz

Bioinform., 2020

Predicting target genes of non-coding regulatory variants with IRT.

Zhenqin Wu, Nilah M. Ioannidis, James Zou, Russell Schwartz

Bioinform., 2020

Robust and accurate deconvolution of tumor populations uncovers evolutionary mechanisms of breast cancer metastasis.

Yifeng Tao, Haoyun Lei, Xuecong Fu, Adrian V. Lee, Jian Ma, Russell Schwartz

Bioinform., 2020

Efficient toolkit implementing best practices for principal component analysis of population genetic data.

Florian Privé, Keurcien Luu, Michael G. B. Blum, John J. McGrath, Bjarni J. Vilhjálmsson, Russell Schwartz

Bioinform., 2020

Metasubtract: an R-package to analytically produce leave-one-out meta-analysis GWAS summary statistics.

Ilja M. Nolte, Russell Schwartz

Bioinform., 2020

Predicting Drug Sensitivity of Cancer Cell Lines via Collaborative Filtering with Contextual Attention.

Yifeng Tao, Shuangxia Ren, Michael Q. Ding, Russell Schwartz, Xinghua Lu

Proceedings of the Machine Learning for Healthcare Conference, 2020

2019

Phylogenies Derived from Matched Transcriptome Reveal the Evolution of Cell Populations and Temporal Order of Perturbed Pathways in Breast Cancer Brain Metastases.

Yifeng Tao, Haoyun Lei, Adrian V. Lee, Jian Ma, Russell Schwartz

Proceedings of the Mathematical and Computational Oncology - First International Symposium, 2019

2018

The development and application of bioinformatics core competencies to improve bioinformatics training and education.

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

PLoS Comput. Biol., 2018

A method for efficient Bayesian optimization of self-assembly systems from scattering data.

Marcus Thomas, Russell Schwartz

BMC Syst. Biol., 2018

Deconvolution and phylogeny inference of structural variations in tumor genomic samples.

Jesse Eaton, Jingyi Wang, Russell Schwartz

Bioinform., 2018

Tumor Copy Number Data Deconvolution Integrating Bulk and Single-cell Sequencing Data.

Haoyun Lei, Bochuan Lyu, E. Michael Gertz, Alejandro A. Schäffer, Russell Schwartz

Proceedings of the 8th IEEE International Conference on Computational Advances in Bio and Medical Sciences, 2018

Reconstructing Tumor Evolution and Progression in Structurally Variant Cancer Cells.

Russell Schwartz

Proceedings of the Computing and Combinatorics - 24th International Conference, 2018

2017

Derivative-Free Optimization of Rate Parameters of Capsid Assembly Models from Bulk in Vitro Data.

Lu Xie, Gregory R. Smith, Russell Schwartz

IEEE ACM Trans. Comput. Biol. Bioinform., 2017

Automated deconvolution of structured mixtures from heterogeneous tumor genomic data.

Theodore Roman, Lu Xie, Russell Schwartz

PLoS Comput. Biol., 2017

2016

Classifying the Progression of Ductal Carcinoma from Single-Cell Sampled Data via Integer Linear Programming: A Case Study.

Daniele Catanzaro, Stanley E. Shackney, Alejandro A. Schäffer, Russell Schwartz

IEEE ACM Trans. Comput. Biol. Bioinform., 2016

Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB's Education Committee).

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

PLoS Comput. Biol., 2016

Medoidshift clustering applied to genomic bulk tumor data.

Theodore Roman, Lu Xie, Russell Schwartz

BMC Genom., 2016

Computationally resolving heterogeneity in mixed genomic samples.

Russell Schwartz

Proceedings of the 6th IEEE International Conference on Computational Advances in Bio and Medical Sciences, 2016

2015

A simplicial complex-based approach to unmixing tumor progression data.

Theodore Roman, Amir Nayyeri, Brittany Fasy, Russell Schwartz

BMC Bioinform., 2015

Inferring models of multiscale copy number evolution for single-tumor phylogenetics.

Salim Akhter Chowdhury, E. Michael Gertz, Darawalee Wangsa, Kerstin Heselmeyer-Haddad, Thomas Ried, Alejandro A. Schäffer, Russell Schwartz

Bioinform., 2015

2014

Bioinformatics Curriculum Guidelines: Toward a Definition of Core Competencies.

Lonnie R. Welch, Fran Lewitter, Russell Schwartz, Catherine Brooksbank, Predrag Radivojac, Bruno A. Gaëta, Maria Victoria Schneider

PLoS Comput. Biol., 2014

Phenotypic Signatures Arising from Unbalanced Bacterial Growth.

Cheemeng Tan, Robert Phillip Smith, Ming-Chi Tsai, Russell Schwartz, Lingchong You

PLoS Comput. Biol., 2014

Algorithms to Model Single Gene, Single Chromosome, and Whole Genome Copy Number Changes Jointly in Tumor Phylogenetics.

Salim Akhter Chowdhury, Stanley E. Shackney, Kerstin Heselmeyer-Haddad, Thomas Ried, Alejandro A. Schäffer, Russell Schwartz

PLoS Comput. Biol., 2014

Editorial.

Serafim Batzoglou, Russell Schwartz

Bioinform., 2014

Reference-free inference of tumor phylogenies from single-cell sequencing data.

Ayshwarya Subramanian, Russell Schwartz

Proceedings of the IEEE 4th International Conference on Computational Advances in Bio and Medical Sciences, 2014

2013

Coalescent-Based Method for Learning Parameters of Admixture Events from Large-Scale Genetic Variation Data.

Ming-Chi Tsai, Guy E. Blelloch, R. Ravi, Russell Schwartz

IEEE ACM Trans. Comput. Biol. Bioinform., 2013

Novel Multisample Scheme for Inferring Phylogenetic Markers from Whole Genome Tumor Profiles.

Ayshwarya Subramanian, Stanley Shackney, Russell Schwartz

IEEE ACM Trans. Comput. Biol. Bioinform., 2013

Phylogenetic analysis of multiprobe fluorescence <i>in situ</i> hybridization data from tumor cell populations.

Salim Akhter Chowdhury, Stanley Shackney, Kerstin Heselmeyer-Haddad, Thomas Ried, Alejandro A. Schäffer, Russell Schwartz

Bioinform., 2013

A mixed integer linear programming model to reconstruct phylogenies from single nucleotide polymorphism haplotypes under the maximum parsimony criterion.

Daniele Catanzaro, Ramamoorthi Ravi, Russell Schwartz

Algorithms Mol. Biol., 2013

2012

A Report of the Curriculum Task Force of the ISCB Education Committee.

Lonnie R. Welch, Russell Schwartz, Fran Lewitter

PLoS Comput. Biol., 2012

Novel Multi-sample Scheme for Inferring Phylogenetic Markers from Whole Genome Tumor Profiles.

Ayshwarya Subramanian, Stanley Shackney, Russell Schwartz

Proceedings of the Bioinformatics Research and Applications - 8th International Symposium, 2012

2011

A Consensus Tree Approach for Reconstructing Human Evolutionary History and Detecting Population Substructure.

Ming-Chi Tsai, Guy E. Blelloch, R. Ravi, Russell Schwartz

IEEE ACM Trans. Comput. Biol. Bioinform., 2011

Approximation algorithms for speeding up dynamic programming and denoising aCGH data.

Charalampos E. Tsourakakis, Richard Peng, Maria A. Tsiarli, Gary L. Miller, Russell Schwartz

ACM J. Exp. Algorithmics, 2011

An Optimization-Based Sampling Scheme for Phylogenetic Trees.

Navodit Misra, Guy E. Blelloch, R. Ravi, Russell Schwartz

J. Comput. Biol., 2011

Generalized Buneman Pruning for Inferring the Most Parsimonious Multi-State Phylogeny.

Navodit Misra, Guy E. Blelloch, R. Ravi, Russell Schwartz

J. Comput. Biol., 2011

Approximate Dynamic Programming using Halfspace Queries and Multiscale Monge Decomposition.

Gary L. Miller, Richard Peng, Russell Schwartz, Charalampos E. Tsourakakis

Proceedings of the Twenty-Second Annual ACM-SIAM Symposium on Discrete Algorithms, 2011

Phylogenetics of Heterogeneous Samples - (Keynote Talk).

Russell Schwartz

Proceedings of the Bioinformatics Research and Applications - 7th International Symposium, 2011

Inference of tumor phylogenies from genomic assays on heterogeneous samples.

Ayshwarya Subramanian, Stanley Shackney, Russell Schwartz

Proceedings of the ACM International Conference on Bioinformatics, 2011

2010

Approximate Dynamic Programming for Fast Denoising of aCGH Data

Gary L. Miller, Richard Peng, Russell Schwartz, Charalampos E. Tsourakakis

CoRR, 2010

Theory and Algorithms for the Haplotype Assembly Problem.

Russell Schwartz

Commun. Inf. Syst., 2010

Applying unmixing to gene expression data for tumor phylogeny inference.

Russell Schwartz, Stanley Shackney

BMC Bioinform., 2010

Robust unmixing of tumor states in array comparative genomic hybridization data.

David Tolliver, Charalampos E. Tsourakakis, Ayshwarya Subramanian, Stanley Shackney, Russell Schwartz

Bioinform., 2010

Tiling Binary Matrices in Haplotyping: Complexity, Models and Algorithms.

Giuseppe Lancia, Romeo Rizzi, Russell Schwartz

Proceedings of the Prague Stringology Conference 2010, Prague, Czech Republic, August 30, 2010

2009

Network-Based Inference of Cancer Progression from Microarray Data.

Yongjin Park, Stanley Shackney, Russell Schwartz

IEEE ACM Trans. Comput. Biol. Bioinform., 2009

2008

Mixed Integer Linear Programming for Maximum-Parsimony Phylogeny Inference.

Srinath Sridhar, Fumei Lam, Guy E. Blelloch, R. Ravi, Russell Schwartz

IEEE ACM Trans. Comput. Biol. Bioinform., 2008

Learning with ecosystem models: a tale of two classrooms.

Steven Gray, Cindy E. Hmelo-Silver, Lei Liu, Rebecca Jordan, Heisawn Jeong, Russell Schwartz, Heather Finkelstein, Daniel Wolsten, Marylee Demeter, Suparna Sinha

Proceedings of the Cre8ing a learning world: Proceedings of the 8th International Conference for the Learning Sciences, 2008

2007

Algorithms for Efficient Near-Perfect Phylogenetic Tree Reconstruction in Theory and Practice.

Srinath Sridhar, Kedar Dhamdhere, Guy E. Blelloch, Eran Halperin, R. Ravi, Russell Schwartz

IEEE ACM Trans. Comput. Biol. Bioinform., 2007

Reconstructing Tumor phylogenies from Heterogeneous Single-Cell Data.

Gregory Pennington, Charles A. Smith, Stanley Shackney, Russell Schwartz

J. Bioinform. Comput. Biol., 2007

Direct maximum parsimony phylogeny reconstruction from genotype data.

Srinath Sridhar, Fumei Lam, Guy E. Blelloch, R. Ravi, Russell Schwartz

BMC Bioinform., 2007

Stochastic Modelling for Systems Biology: Darren J. Wilkinson.

Russell Schwartz

Briefings Bioinform., 2007

Efficiently Finding the Most Parsimonious Phylogenetic Tree Via Linear Programming.

Srinath Sridhar, Fumei Lam, Guy E. Blelloch, R. Ravi, Russell Schwartz

Proceedings of the Bioinformatics Research and Applications, Third International Symposium, 2007

2006

Relaxing Haplotype Block Models for Association Testing.

Natalie Castellana, Kedar Dhamdhere, Srinath Sridhar, Russell Schwartz

Proceedings of the Biocomputing 2006, 2006

Simple Reconstruction of Binary Near-Perfect Phylogenetic Trees.

Srinath Sridhar, Kedar Dhamdhere, Guy E. Blelloch, Eran Halperin, R. Ravi, Russell Schwartz

Proceedings of the Computational Science, 2006

Fixed Parameter Tractability of Binary Near-Perfect Phylogenetic Tree Reconstruction.

Guy E. Blelloch, Kedar Dhamdhere, Eran Halperin, R. Ravi, Russell Schwartz, Srinath Sridhar

Proceedings of the Automata, Languages and Programming, 33rd International Colloquium, 2006

2005

Implementation of a discrete event simulator for biological self-assembly systems.

Tiequan Zhang, Rori Rohlfs, Russell Schwartz

Proceedings of the 37th Winter Simulation Conference, Orlando, FL, USA, December 4-7, 2005, 2005

2004

Algorithms for Association Study Design Using a Generalized Model of Haplotype Conservation.

Russell Schwartz

Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004

2003

Robustness of Inference of Haplotype Block Structure.

Russell Schwartz, Bjarni V. Halldórsson, Vineet Bafna, Andrew G. Clark, Sorin Istrail

J. Comput. Biol., 2003

Haplotypes and informative SNP selection algorithms: don't block out information.

Vineet Bafna, Bjarni V. Halldórsson, Russell Schwartz, Andrew G. Clark, Sorin Istrail

Proceedings of the Sventh Annual International Conference on Computational Biology, 2003

Haplotype Motifs: An Algorithmic Approach to Locating Evolutionarily Conserved Patterns in Haploid Sequences.

Russell Schwartz

Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference, 2003

Epitope Prediction Algorithms for Peptide based Vaccine Design.

Liliana Florea, Bjarni V. Halldórsson, Oliver Kohlbacher, Russell Schwartz, Stephen Hoffman, Sorin Istrail

Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference, 2003

2002

Algorithmic strategies for the single nucleotide polymorphism haplotype assembly problem.

Ross Lippert, Russell Schwartz, Giuseppe Lancia, Sorin Istrail

Briefings Bioinform., 2002

Methods for Inferring Block-Wise Ancestral History from Haploid Sequences.

Russell Schwartz, Andrew G. Clark, Sorin Istrail

Proceedings of the Algorithms in Bioinformatics, Second International Workshop, 2002

Inferring Piecewise Ancestral History from Haploid Sequences.

Russell Schwartz, Andrew G. Clark, Sorin Istrail

Proceedings of the Computational Methods for SNPs and Haplotype Inference, 2002

2001

Visualization challenges for a new cyberpharmaceutical computing paradigm.

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

Proceedings of the IEEE 2001 Symposium on Parallel and Large-Data Visualization and Graphics, 2001

SNPs Problems, Complexity, and Algorithms.

Giuseppe Lancia, Vineet Bafna, Sorin Istrail, Ross Lippert, Russell Schwartz

Proceedings of the Algorithms, 2001

2000

The local rules dynamics model for self-assembly simulation.

Russell Schwartz

PhD thesis, 2000

Local rule mechanism for selecting icosahedral shell geometry.

Bonnie Berger, Jonathan A. King, Russell Schwartz, Peter W. Shor

Discret. Appl. Math., 2000

1999

Lattice Simulations of Aggregation Funnels for Protein Folding.

Sorin Istrail, Russell Schwartz, Jonathan A. King

J. Comput. Biol., 1999