Journal Article 3D Collagen Vascular Tumor-on-a-Chip Mimetics for Dynamic Combinatorial Drug Screening 2021 • Molecular Cancer Therapeutics • 20(6):1210-1219 Wan L, Yin J, Skoko J, Schwartz R, Zhang M, LeDuc PR, Neumann CA
Journal Article Assessing the contribution of tumor mutational phenotypes to cancer progression risk 2021 • PLoS Computational Biology • 17(3): Tao Y, Rajaraman A, Cui X, Cui Z, Chen H, Zhao Y, Eaton J, Kim H, Ma J, Schwartz R
Conference ConTreeDP: A consensus method of tumor trees based on maximum directed partition support problem 2021 • 2021 IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE, BIBM • 125-130 Fu X, Schwartz R
Journal Article Joint Clustering of Single-Cell Sequencing and Fluorescence In Situ Hybridization Data for Reconstructing Clonal Heterogeneity in Cancers 2021 • Journal of Computational Biology • 28(11):1035-1051 Fu X, Lei H, Tao Y, Heselmeyer-Haddad K, Torres I, Dean M, Ried T, Schwartz R
Journal Article RECOMB 2020 Special Issue 2021 • Journal of Computational Biology • 28(4):345-345 Schwartz R
Journal Article RECOMB 2020 Special Issue 2021 • Journal of Computational Biology • 28(5):433-434 Schwartz R
Journal Article Tumor heterogeneity assessed by sequencing and fluorescence <i>in situ</i> hybridization (FISH) data 2021 • Bioinformatics • 37(24):4704-4711 Lei H, Gertz EM, Schaffer AA, Fu X, Tao Y, Heselmeyer-Haddad K, Torres I, Li G, Xu L, Hou Y, Wu K, Shi X, Dean M, Ried T, Schwartz R
Conference A Diffusion Based Embedding of the Stochastic Simulation Algorithm in Continuous Space 2020 • Biophysical Journal • 118(3):302A-302A Thomas M, Schwartz RS
Journal Article Modelling cancer progression using Mutual Hazard Networks 2020 • Bioinformatics • 36(1):241-249 Schill R, Solbrig S, Wettig T, Spang R
Journal Article Mycorrhiza: genotype assignment using phylogenetic networks 2020 • Bioinformatics • 36(1):212-220 Georges-Filteau J, Hamelin RC, Blanchette M
Journal Article Neural Network Deconvolution Method for Resolving Pathway-Level Progression of Tumor Clonal Expression Programs With Application to Breast Cancer Brain Metastases 2020 • Frontiers in Physiology • 11: Tao Y, Lei H, Lee AV, Ma J, Schwartz R
Conference Predicting Drug Sensitivity of Cancer Cell Lines via Collaborative Filtering with Contextual Attention 2020 • MACHINE LEARNING FOR HEALTHCARE CONFERENCE, VOL 126 • 126:660-683 Taoy Y, Ren S, Ding MQ, Schwartz R, Lu X
Journal Article Preface 2020 • Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) • 12074 LNBI:v-vi Schwartz R
Journal Article Robust and accurate deconvolution of tumor populations uncovers evolutionary mechanisms of breast cancer metastasis 2020 • Bioinformatics • 36:407-416 Tao Y, Lei H, Fu X, Lee AV, Ma J, Schwartz R
Journal Article Soft windowing application to improve analysis of high-throughput phenotyping data 2020 • Bioinformatics • 36(5):1492-1500 Schwartz R, and others
Journal Article tugHall: a simulator of cancer-cell evolution based on the hallmarks of cancer and tumor-related genes 2020 • Bioinformatics • 36(11):3597-3599 Nagornov IS, Kato M
Journal Article Tumor Copy Number Deconvolution Integrating Bulk and Single-Cell Sequencing Data 2020 • Journal of Computational Biology • 27(4):565-598 Lei H, Lyu B, Gertz EM, Schaffer AA, Shi X, Wu K, Li G, Xu L, Hou Y, Dean M, Schwartz R
Conference A Stochastic Spatial Simulation Method for Self-Assembly Reactions 2019 • Biophysical Journal • 116(3):290A-290A Thomas M, Schwartz RS
Conference Abstract 1650: Deconvolution of copy number alterations combining bulk and single-cell genomic data 2019 1650-1650 Lei H, Lyu B, Gertz EM, Schaeffer AA, Shi X, Wu K, Li G, Xu L, Hou Y, Dean M, Schwartz R
Journal Article CaPSSA: visual evaluation of cancer biomarker genes for patient stratification and survival analysis using mutation and expression data 2019 • Bioinformatics • 35(24):5341-5343 Jang Y, Seo J, Jang I, Lee B, Kim S, Lee S
Journal Article ClinOmicsTrailbc: a visual analytics tool for breast cancer treatment stratification 2019 • Bioinformatics • 35(24):5171-5181 Schneider L, Kehl T, Thedinga K, Grammes NL, Backes C, Mohr C, Schubert B, Lenhof K, Gerstner N, Hartkopf AD, Wallwiener M, Kohlbacher O, Keller A, Meese E, Graf N, Lenhof H-P
Journal Article Comparison of six breast cancer classifiers using qPCR 2019 • Bioinformatics • 35(18):3412-3420 Berchtold E, Vetter M, Gündert M, Csaba G, Fathke C, Ulbrich SE, Thomssen C, Zimmer R, Kantelhardt EJ
Chapter Computational Models for Cancer Phylogenetics 2019 • Computational Biology • 29:243-275 Schwartz R
Conference Deconvolution of copy number alterations combining bulk and single-cell genomic data 2019 • Cancer Research • 79(13): Lei H, Lyu B, Gertz EM, Schaeffer AA, Shi X, Wu K, Li G, Xu L, Hou Y, Dean M, Schwartz R
Journal Article DiscoverSL: an R package for multi-omic data driven prediction of synthetic lethality in cancers 2019 • Bioinformatics • 35(4):701-702 Das S, Deng X, Camphausen K, Shankavaram U
