Russell Schwartz

Russell Schwartz, Sorin Istrail, Bjarni V. Halldórsson, 2003, Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003.

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

Russell Schwartz, Ying Zhou, Brian L. Browning, 2020, Bioinform..

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

Russell Schwartz, Ayshwarya Subramanian, Stanley Shackney, 2012, ISBRA.

Medoidshift clustering applied to genomic bulk tumor data

Russell Schwartz, Lu Xie, Theodore Roman, 2015, BMC Genomics.

A Diffusion Based Embedding of the Stochastic Simulation Algorithm in Continuous Space

Russell Schwartz, Marcus Thomas, R. Schwartz, 2020, Biophysical Journal.

Investigation of virus capsid self-assembly kinetics using discrete-event stochastic simulation

Russell Schwartz, Tiequan Zhang, 2007 .

Local rule mechanism for selecting icosahedral shell geometry

Russell Schwartz, Bonnie Berger, Peter W. Shor, 2000, Discret. Appl. Math..

Stochastic Modelling for Systems Biology: Darren J. Wilkinson

Russell Schwartz, 2007, Briefings Bioinform..

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

Russell Schwartz, Ayshwarya Subramanian, 2014, ICCABS.

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

Russell Schwartz, Ilja M. Nolte, R. Schwartz, 2020, Bioinform..

Network-Based Inference of Cancer Progression from Microarray Data

Russell Schwartz, Stanley Shackney, Yongjin Park, 2008, ISBRA.

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

Russell Schwartz, Marcus Thomas, 2018, BMC Systems Biology.

Approximate Dynamic Programming for Fast Denoising of aCGH Data pdf

Russell Schwartz, Gary L. Miller, Richard Peng, 2010, ArXiv.

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

Russell Schwartz, Alejandro A. Schäffer, Stanley Shackney, 2016, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Creating Teams for Bioinformatics: The Educational Challenge for Biology and Computer Science at the Undergraduate and Graduate Level Four Case Studies from the Great Lakes Area

Russell Schwartz, Sorin Draghici, Robert Blumenthal, 2011 .

Algorithmic strategies for the single nucleotide polymorphism haplotype assembly problem

Russell Schwartz, Giuseppe Lancia, Sorin Istrail, 2002, Briefings Bioinform..

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

Russell Schwartz, Ayshwarya Subramanian, Stanley Shackney, 2012, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

An Optimization-Based Sampling Scheme for Phylogenetic Trees

Navodit Misra, Guy E. Blelloch, R. Ravi, 2011, RECOMB.

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

Russell Schwartz, Daniele Catanzaro, Ramamoorthi Ravi, 2013, Algorithms for Molecular Biology.

Research in Computational Molecular Biology: 24th Annual International Conference, RECOMB 2020, Padua, Italy, May 10–13, 2020, Proceedings

Russell Schwartz, R. Schwartz, Russell Schwartz, 2020, RECOMB.

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

Russell Schwartz, Alejandro A. Schäffer, Stanley Shackney, 2014, PLoS Comput. Biol..

Front Matter, Table of Contents, Preface, List of Authors

Russell Schwartz, Knut Reinert, 2017, WABI.

Applying Derivative-Free Optimization to Fit Kinetic Parameters of Viral Capsid Self-Assembly Models from Multi-Source Bulk in vitro Data

Russell Schwartz, Lu Xie, Gregory D. Smith, 2015 .

Computational biology and bioinformatics.

Russell Schwartz, Serafim Batzoglou, 2014, Bioinformatics.

Predicting target genes of non-coding regulatory variants with IRT

Russell Schwartz, James Zou, Zhenqin Wu, 2020, Bioinform..

Multiscale Simulation of Nucleation-limited Viral Capsid Assembly

Navodit Misra, Russell Schwartz, 2009 .

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

Russell Schwartz, Lonnie R. Welch, Fran Lewitter, 2012, PLoS Comput. Biol..

Visualization challenges for a new cyber-pharmaceutical computing paradigm

Russell Schwartz, Daniel H. Huson, Shibu Yooseph, 2001, Proceedings IEEE 2001 Symposium on Parallel and Large-Data Visualization and Graphics (Cat. No.01EX520).

Efficient stochastic sampling of first passage times for multi-scale simulations

Navodit Misra, Russell Schwartz, 2009 .

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

Russell Schwartz, Lonnie R. Welch, Predrag Radivojac, 2016, PLoS Comput. Biol..

A simplicial complex-based approach to unmixing tumor progression data

Russell Schwartz, Amir Nayyeri, Brittany Terese Fasy, 2015, BMC Bioinformatics.

Tiling Binary Matrices in Haplotyping: Complexity, Models and Algorithms

Russell Schwartz, Giuseppe Lancia, Romeo Rizzi, 2010, Stringology.

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

Russell Schwartz, Lonnie R. Welch, Tandy J. Warnow, 2018, PLoS Comput. Biol..

Deconvolution and phylogeny inference of structural variations in tumor genomic samples

Russell Schwartz, Jingyi Wang, Jesse Eaton, 2018 .

Learning with ecosystem models: a tale of two classrooms

Russell Schwartz, Cindy E. Hmelo-Silver, Lei Liu, 2008, ICLS.

A Computational Pipeline for High-Throughput T-Cell Epitope Prediction

Russell Schwartz, Sorin Istrail, Bjarni V. Halldórsson, 2003 .

Simple Reconstruction of Binary Near-Perfect Phylogenetic Trees

Guy E. Blelloch, R. Ravi, Russell Schwartz, 2006, International Conference on Computational Science.

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

Russell Schwartz, Liqin Xu, Yong Hou, 2020, Journal of computational biology : a journal of computational molecular cell biology.

Robustness of Inference of Haplotype Block Structure

Russell Schwartz, Andrew G. Clark, Sorin Istrail, 2003, J. Comput. Biol..

Relaxing Haplotype Block Models for Association Testing

Russell Schwartz, Kedar Dhamdhere, Srinath Sridhar, 2006, Pacific Symposium on Biocomputing.

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

Navodit Misra, Guy E. Blelloch, R. Ravi, 2011, J. Comput. Biol..

Automated deconvolution of structured mixtures from heterogeneous tumor genomic data

Russell Schwartz, Lu Xie, Theodore Roman, 2016, PLoS Comput. Biol..

Network-Based Inference of Cancer Progression from Microarray Data

Russell Schwartz, Stanley Shackney, Yongjin Park, 2009, IEEE ACM Trans. Comput. Biol. Bioinform..

Abstract 3964: Inference of robust tumor phylogenetic markers from multi-sample data

Russell Schwartz, Ayshwarya Subramanian, Stanley E. Shackney, 2012 .

Fixed Parameter Tractability of Binary Near-Perfect Phylogenetic Tree Reconstruction

Guy E. Blelloch, R. Ravi, Russell Schwartz, 2006, ICALP.

Phenotypic Signatures Arising from Unbalanced Bacterial Growth

Russell Schwartz, Ming-Chi Tsai, Cheemeng Tan, 2014, PLoS Comput. Biol..

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

Guy E. Blelloch, R. Ravi, Russell Schwartz, 2007, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

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

Russell Schwartz, Yong Hou, Alejandro A. Schäffer, 2019, RECOMB.

Approximation algorithms for speeding up dynamic programming and denoising aCGH data

Russell Schwartz, Gary L. Miller, Richard Peng, 2011, JEAL.

Applying unmixing to gene expression data for tumor phylogeny inference

Russell Schwartz, Stanley Shackney, R. Schwartz, 2010, BMC Bioinformatics.

Algorithms for association study design using a generalized model of haplotype conservation

Russell Schwartz, 2004, Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004..

Computationally resolving heterogeneity in mixed genomic samples

Russell Schwartz, 2016, ICCABS.

An Optimization-Based Sampling Scheme for Phylogenetic Trees

Navodit Misra, Guy E. Blelloch, R. Ravi, 2011, J. Comput. Biol..

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

Russell Schwartz, Pratap Tokekar, R. Schwartz, 2020, ArXiv.

The local rules dynamics model for self-assembly simulation

Russell Schwartz, 2000 .

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

Guy E. Blelloch, R. Ravi, Russell Schwartz, 2010, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

17th International Workshop on Algorithms in Bioinformatics (WABI 2017)

Russell Schwartz, Knut Reinert, 2017 .

Direct maximum parsimony phylogeny reconstruction from genotype data

Guy E. Blelloch, R. Ravi, Russell Schwartz, 2007, BMC Bioinformatics.

Phylogenetic analysis of multiprobe fluorescence in situ hybridization data from tumor cell populations

Russell Schwartz, Alejandro A. Schäffer, Stanley Shackney, 2013, Bioinform..

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

Guy E. Blelloch, R. Ravi, Russell Schwartz, 2010, ISBRA.

Queue-based method for efficient simulation of biological self-assembly systems

Russell Schwartz, Rori Rohlfs, Farokh Jamalyaria, 2005 .

Deconvolution and phylogeny inference of structural variations in tumor genomic samples

Russell Schwartz, Jingyi Wang, Jesse Eaton, 2018, bioRxiv.

Mixed Integer Linear Programming for Maximum-Parsimony Phylogeny Inference

Guy E. Blelloch, R. Ravi, Russell Schwartz, 2008, IEEE ACM Trans. Comput. Biol. Bioinform..

Stochastic off-lattice modeling of molecular self-assembly in crowded environments by Green's function reaction dynamics.

Russell Schwartz, Byoungkoo Lee, Philip R Leduc, 2008, Physical review. E, Statistical, nonlinear, and soft matter physics.

Robust unmixing of tumor states in array comparative genomic hybridization data

Russell Schwartz, Charalampos E. Tsourakakis, Ayshwarya Subramanian, 2010, Bioinform..

A multi-threaded simulator for the kinetics of virus shell assembly

Russell Schwartz, 1996 .

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

Jian Ma, Russell Schwartz, Yifeng Tao, 2020, Bioinform..

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

Russell Schwartz, Haoyun Lei, Adrian V. Lee, 2019, ISMCO.

Bridging Mechanical Stimulation of Cellular and Molecular Structure Through Lattice Based Computational Simulations

Russell Schwartz, Philip R. LeDuc, Shlomo Ta'asan, 2004 .

Quantitative computational models of molecular self-assembly in systems biology

Russell Schwartz, Marcus Thomas, R. Schwartz, 2017, Physical biology.

Approximate dynamic programming using halfspace queries and multiscale Monge decomposition

Russell Schwartz, Gary L. Miller, Richard Peng, 2010, SODA '11.

Haplotype motifs: an algorithmic approach to locating evolutionarily conserved patterns in haploid sequences

Russell Schwartz, 2003, Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003.

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

Russell Schwartz, Haoyun Lei, Kerstin Heselmeyer-Haddad, 2021, J. Comput. Biol..

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

Russell Schwartz, Xuecong Fu, 2021, 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

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

Russell Schwartz, Alejandro A. Schäffer, Liqin Xu, 2021, Bioinform..

De novo prediction of Cell-Drug sensitivities using deep learning-based graph regularized matrix factorization

Russell Schwartz, Yifan Xue, Ke Yu, 2021 .

3D Collagen Vascular Tumor-on-a-Chip Mimetics for Dynamic Combinatorial Drug Screening

Russell Schwartz, Philip R. LeDuc, Li Wan, 2021, Molecular Cancer Therapeutics.

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

Russell Schwartz, Alejandro A. Schäffer, Liqin Xu, 2020, bioRxiv.

Evaluating spatial constraints in cellular assembly processes using a Monte Carlo approach

Russell Schwartz, Philip R. LeDuc, Shlomo Ta'asan, 2007, Cell Biochemistry and Biophysics.

Discrete, continuous, and stochastic models of protein sorting in the Golgi apparatus.

Russell Schwartz, Haijun Gong, Yusong Guo, 2010, Physical review. E, Statistical, nonlinear, and soft matter physics.

Cancer Phylogenetics from Single-Cell Assays

Russell Schwartz, Stanley Shackney, Gregory Pennington, 2006 .

A human genome-wide library of local phylogeny predictions for whole-genome inference problems

Russell Schwartz, S. Sridhar, R. Schwartz, 2008, BMC Genomics.

Visualization Challenges for a New Cyberpharmaceutical Computing

Russell Schwartz, Daniel H. Huson, Shibu Yooseph, 2001 .

Optimal imperfect phylogeny reconstruction and haplotyping (IPPH).

Russell Schwartz, Srinath Sridhar, Guy E Blelloch, 2006, Computational systems bioinformatics. Computational Systems Bioinformatics Conference.

Inference of Tumor Phylogenies from Genomic Assays on Heterogeneous Samples

Russell Schwartz, Ayshwarya Subramanian, Stanley Shackney, 2012, Journal of biomedicine & biotechnology.

CGHTRIMMER: Discretizing noisy Array CGH Data

Russell Schwartz, Charalampos E. Tsourakakis, Stanley Shackney, 2010, 1002.4438.

Exploring the parameter space of complex self-assembly through virus capsid models.

Russell Schwartz, Tiequan Zhang, Blake Sweeney, 2008, Biophysical journal.

Surveying capsid assembly pathways through simulation-based data fitting.

Russell Schwartz, Gregory R. Smith, Xian Feng, 2012, Biophysical journal.

Pathway Complexity of Model Virus Capsid Assembly Systems

Navodit Misra, Russell Schwartz, Tiequan Zhang, 2009 .

Stochastic steady state gain in a gene expression process with mRNA degradation control

Russell Schwartz, Hiroyuki Kuwahara, R. Schwartz, 2012, Journal of The Royal Society Interface.

A parameter estimation technique for stochastic self-assembly systems and its application to human papillomavirus self-assembly.

Russell Schwartz, R. Schwartz, M. S. Kumar, 2010, Physical biology.

Computational models of molecular self-organization in cellular environments

Russell Schwartz, Philip LeDuc, R. Schwartz, 2007, Cell Biochemistry and Biophysics.

Haplotype Parsing

Russell Schwartz, 2004, Applied bioinformatics.

A comparative genomics approach to identifying the plasticity transcriptome

Russell Schwartz, Andreas R. Pfenning, Alison L. Barth, 2007, BMC Neuroscience.

Simulated de novo assembly of golgi compartments by selective cargo capture during vesicle budding and targeted vesicle fusion.

Russell Schwartz, Haijun Gong, Adam D. Linstedt, 2008, Biophysical journal.

Local Rule Simulations of Capsid Assembly

Russell Schwartz, Bonnie Berger, Peter W. Shor, 2005 .

Algorithms for association study design using a generalized model of haplotype conservation

Russell Schwartz, 2004 .

Identification of novel mutations by exome sequencing in African American colorectal cancer patients

Russell Schwartz, Edward L. Lee, Sudhir Varma, 2015, Cancer.

Simulation study of the contribution of oligomer/oligomer binding to capsid assembly kinetics.

Russell Schwartz, Tiequan Zhang, R. Schwartz, 2006, Biophysical journal.

Modeling Effects of RNA on Capsid Assembly Pathways via Coarse-Grained Stochastic Simulation

Russell Schwartz, Gregory R. Smith, R. Schwartz, 2016, PloS one.

Optimal Haplotype Block-free Selection of Tagging Snps for Genome-wide Association Studies

Russell Schwartz, Sorin Istrail, Vineet Bafna, 2022 .

Abstract 2895: Phylogenetic models of tumor progression from fluorescence in situ hybridization (FISH) data on many single cells of a solid tumor.

Russell Schwartz, Alejandro A. Schäffer, Darawalee Wangsa, 2013 .

Genome-Wide Association Studies Optimal Haplotype Block-Free Selection of Tagging SNPs for Material Supplemental

Russell Schwartz, Andrew G. Clark, Sorin Istrail, 2004 .