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 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 ClinOmicsTrail<sup>bc</sup>: 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 HP
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, Schwartz R
Journal Article Genome-wide identification of the essential protein-coding genes and long non-coding RNAs for human pan-cancer 2019 • Bioinformatics • 35(21):4344-4349 Zhang Y, Tao Y, Ji H, Li W, Guo X, Ng DM, Haleem M, Xi Y, Dong C, Zhao J, Zhang L, Zhang X, Xie Y, Dai X, Liao Q, Schwartz R
Journal Article Gsmodutils: A python based framework for test-driven genome scale metabolic model development 2019 • Bioinformatics • 35(18):3397-3403 Gilbert J, Pearcy N, Norman R, Millat T, Winzer K, King J, Hodgman C, Minton N, Twycross J
Journal Article MEpurity: Estimating tumor purity using DNA methylation data 2019 • Bioinformatics • 35(24):5298-5300 Liu B, Yang X, Wang T, Lin J, Kang Y, Jia P, Ye K
Journal Article NEMO: Cancer subtyping by integration of partial multi-omic data 2019 • Bioinformatics • 35(18):3348-3356 Rappoport N, Shamir R
Journal Article OncodriveCLUSTL: A sequence-based clustering method to identify cancer drivers 2019 • Bioinformatics • 35(22):4788-4790 Arnedo-Pac C, Mularoni L, Muiños F, Gonzalez-Perez A, Lopez-Bigas N
Conference Phylogenies Derived from Matched Transcriptome Reveal the Evolution of Cell Populations and Temporal Order of Perturbed Pathways in Breast Cancer Brain Metastases 2019 • Lecture Notes in Computer Science • 11826:3-28 Tao Y, Lei H, Lee AV, Ma J, Schwartz R
Journal Article A method for efficient Bayesian optimization of self-assembly systems from scattering data 2018 • BMC Systems Biology • 12: Thomas M, Schwartz R
Journal Article Aneuploidy, <i>TP53</i> mutation, and amplification of <i>MYC</i> correlate with increased intratumor heterogeneity and poor prognosis of breast cancer patients 2018 • Genes Chromosomes and Cancer • 57(4):165-175 Oltmann J, Heselmeyer-Haddad K, Hernandez LS, Meyer R, Torres I, Hu Y, Doberstein N, Killian JK, Petersen D, Zhu YJ, Edelman DC, Meltzer PS, Schwartz R, Gertz EM, Schaffer AA, Auer G, Habermann JK, Ried T
Journal Article Deconvolution and phylogeny inference of structural variations in tumor genomic samples 2018 • Bioinformatics • 34(13):357-365 Eaton J, Wang J, Schwartz R
Conference Genomic dynamics in breast cancer progression analyzed by miFISH analysis 2018 • Cancer Research • 78(13): Torres IM, Hernandez L, Tzeng J, Schwartz R, Schaffer A, Gertz EM, Hirsch D, Brower S, Sanchez M, Auer G, Heselmeyer-Haddad K, Ried T
Journal Article Machine Learning and Radiogenomics: Lessons Learned and Future Directions 2018 • Frontiers in Oncology • 8: Kang J, Rancati T, Lee S, Oh JH, Kerns SL, Scott JG, Schwartz R, Kim S, Rosenstein BS