Journal Article Novel Multisample Scheme for Inferring Phylogenetic Markers from Whole Genome Tumor Profiles 2013 • IEEE/ACM Transactions on Computational Biology and Bioinformatics • 10(6):1422-1431 Subramanian A, Shackney S, Schwartz R
Conference Phylogenetic analysis of multiprobe fluorescence <i>in situ</i> hybridization data from tumor cell populations 2013 • Bioinformatics • 29(13):189-198 Chowdhury SA, Shackney SE, Heselmeyer-Haddad K, Ried T, Schaeffer AA, Schwartz R
Conference Phylogenetic models of tumor progression from fluorescence in situ hybridization (FISH) data on many single cells of a solid tumor. 2013 • Cancer Research • 73(8): Chowdhury SA, Schaeffer AA, Shackney SE, Wangsa D, Heselmeyer-Haddad K, Ried T, Schwartz R
Chapter Tumor phylogenetics in the NGS era: Strategies, challenges, and future prospects 2013 335-357 Subramanian A, Shackney S, Schwartz R
Journal Article A Report of the Curriculum Task Force of the ISCB Education Committee 2012 • PLoS Computational Biology • 8(6): Welch LR, Schwartz R, Lewitter F
Journal Article Biological colloid engineering: Self-assembly of dipolar ferromagnetic chains in a functionalized biogenic ferrofluid 2012 • Applied Physics Letters • 101(6): Ruder WC, Hsu C-PD, Edelman BDJ, Schwartz R, LeDuc PR
Conference Coalescent-based method for learning parameters of admixture events from large-scale genetic variation data 2012 • 2012 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2012 • 90-97 Tsai MC, Blelloch G, Ravi R, Schwartz R
Journal Article Inference of robust tumor phylogenetic markers from multi-sample data 2012 • Cancer Research • 72: Subramanian A, Schwartz R, Shackney S
Journal Article Inference of Tumor Phylogenies from Genomic Assays on Heterogeneous Samples 2012 • Journal of Biomedicine and Biotechnology Subramanian A, Shackney S, Schwartz R
Book Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics): Preface 2012 • Lecture Notes in Computer Science • 7292 LNBI: Bleris L, Mǎndoiu I, Schwartz R, Wang J
Journal Article Modeling Nuclear Blebs in a Nucleoskeleton of Independent Filament Networks 2012 • Cellular and Molecular Bioengineering • 5(1):73-81 Wren NS, Zhong Z, Schwartz RS, Dahl KN
Conference Novel multi-sample scheme for inferring phylogenetic markers from whole genome tumor profiles 2012 • Lecture Notes in Computer Science • 7292 LNBI:250-262 Subramanian A, Shackney S, Schwartz R
Journal Article Single-Cell Genetic Analysis of Ductal Carcinoma <i>in Situ</i> and Invasive Breast Cancer Reveals Enormous Tumor Heterogeneity yet Conserved Genomic Imbalances and Gain of <i>MYC</i> during Progression 2012 • American Journal of Pathology • 181(5):1807-1822 Heselmeyer-Haddad K, Garcia LYB, Bradley A, Ortiz-Melendez C, Lee W-J, Christensen R, Prindiville SA, Calzone KA, Soballe PW, Hu Y, Chowdhury SA, Schwartz R, Schaeffer AA, Ried T
Journal Article Stochastic steady state gain in a gene expression process with mRNA degradation control 2012 • Journal of the Royal Society Interface • 9(72):1589-1598 Kuwahara H, Schwartz R
Journal Article Surveying Capsid Assembly Pathways through Simulation-Based Data Fitting 2012 • Biophysical Journal • 103(7):1545-1554 Xie L, Smith GR, Feng X, Schwartz R
Journal Article Three-Dimensional Stochastic Off-Lattice Model of Binding Chemistry in Crowded Environments 2012 • PLoS ONE • 7(1): Lee B, LeDuc PR, Schwartz R
Conference Translating Bulk Measures of Capsid Assembly Progress into Insights on Fine-Scale Kinetics and Pathways 2012 • Biophysical Journal • 102(3):640A-640A Smith GR, Xie L, Feng X, Lee B, Schwartz R
Conference A coarse-Grained Monte Carlo Model of Cytoskeletal Actin Filament Alignment under Cyclic Stretch 2011 • Biophysical Journal • 100(3):34-34 Kang J, Steward RL, Kim Y, Schwartz RS, LeDuc PR, Puskar KM
Journal Article A Consensus Tree Approach for Reconstructing Human Evolutionary History and Detecting Population Substructure 2011 • IEEE/ACM Transactions on Computational Biology and Bioinformatics • 8(4):918-928 Tsai M-C, Blelloch G, Ravi R, Schwartz R
Journal Article An Optimization-Based Sampling Scheme for Phylogenetic Trees 2011 • Journal of Computational Biology • 18(11):1599-1609 Misra N, Blelloch G, Ravi R, Schwartz R
Conference An Optimization-Based Sampling Scheme for Phylogenetic Trees 2011 • Lecture Notes in Computer Science • 6577:252-+ Misra N, Blelloch G, Ravi R, Schwartz R
Conference Approximate Dynamic Programming using Halfspace Queries and Multiscale Monge Decomposition 2011 • Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms • 1675-1682 Miller GL, Peng R, Schwartz R, Tsourakakis C
Journal Article Approximation algorithms for speeding up dynamic programming and denoising aCGH data 2011 • Journal of Experimental Algorithmics • 16:1.1-1.27 Tsourakakis CE, Peng R, Tsiarli MA, Miller GL, Schwartz R
Journal Article Generalized Buneman Pruning for Inferring the Most Parsimonious Multi-State Phylogeny 2011 • Journal of Computational Biology • 18(3):445-457 Misra N, Blelloch G, Ravi R, Schwartz R
Conference Inference of tumor phylogenies from genomic assays on heterogeneous samples 2011 • 2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011 • 172-181 Subramanian A, Shackney S, Schwartz R
