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
Journal Article The development and application of bioinformatics core competencies to improve bioinformatics training and education 2018 • PLoS Computational Biology • 14(2): Mulder N, Schwartz R, Brazas MD, Brooksbank C, Gaeta B, Morgan SL, Pauley MA, Rosenwald A, Rustici G, Sierk M, Warnow T, Welch L
Journal Article The evolution of single cell-derived colorectal cancer cell lines is dominated by the continued selection of tumor-specific genomic imbalances, despite random chromosomal instability 2018 • Carcinogenesis • 39(8):993-1157 Wangsa D, Braun R, Schiefer M, Gertz EM, Bronder D, Quintanilla I, Padilla-Nash HM, Torres I, Hunn C, Warner L, Buishand FO, Hu Y, Hirsch D, Gaiser T, Camps J, Schwartz R, Schaffer AA, Heselmeyer-Haddad K, Ried T
Conference Tumor Copy Number Data Deconvolution Integrating Bulk and Single-cell Sequencing Data 2018 • IEEE ... International Conference on Computational Advances in Bio and Medical Sciences : [proceedings]. IEEE International Conference on Computational Advances in Bio and Medical Sciences Lei H, Lyu B, Gertz EM, Schaffer AA, Schwartz R
Conference Tumor Copy Number Data Deconvolution Integrating Bulk and Single-cell Sequencing Data 2018 1-1 Lei H, Lyu B, Gertz EM, Schaffer AA, Schwartz R
Conference Abstract 2908: Single-cell genetic analysis of ductal carcinoma in situ with and without synchronous invasive breast cancer by multiplex FISH delineates specific patterns of tumor clonality and heterogeneity 2017 • Cancer Research • 77(13_Supplement):2908-2908 Torres IM, Hernandez L, Tzeng J, Schwartz R, Schaffer A, Gertz E, Brower S, Sanchez M, Auer G, Heselmeyer-Haddad K, Thomas R
Conference Abstract 4387: The clonal composition of colorectal cancer cell lines is defined by the maintenance of specific genomic imbalances, not by ongoing chromosomal instability 2017 • Cancer Research • 77(13_Supplement):4387-4387 Wangsa D, Schiefer M, Bronder D, Padilla-Nash H, Torres I, Warner L, Hu Y, Gertz EM, Schwartz R, Schäffer AA, Hirsch D, Gaiser T, Meyer R, Camps J, Heselmeyer-Haddad K, Ried T
Journal Article Abstract 974: Automating deconvolution of heterogeneous bulk tumor genomic data 2017 • Cancer Research • 77(13_Supplement):974-974 Roman T, Xiao B, Schwartz R
Journal Article Automated deconvolution of structured mixtures from heterogeneous tumor genomic data 2017 • PLoS Computational Biology • 13(10): Roman T, Xie L, Schwartz R
Journal Article Derivative-Free Optimization of Rate Parameters of Capsid Assembly Models from Bulk in Vitro Data 2017 • IEEE/ACM Transactions on Computational Biology and Bioinformatics • 14(4):844-855 Xie L, Smith GR, Schwartz R
Journal Article Quantitative computational models of molecular self-assembly in systems biology 2017 • Physical Biology • 14(3): Thomas M, Schwartz R
Journal Article The evolution of tumour phylogenetics: principles and practice 2017 • Nature Reviews Genetics • 18(4):213-229 Schwartz R, Schaffer AA
Journal Article Abstract 849: Improved geometric deconvolution of bulk tumor genomic data 2016 • Cancer Research • 76(14_Supplement):849-849 Roman T, Xie L, Schwartz R
Journal Article Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB's Education Committee) 2016 • PLoS Computational Biology • 12(5): Welch L, Brooksbank C, Schwartz R, Morgan SL, Gaeta B, Kilpatrick AM, Mietchen D, Moore BL, Mulder N, Pauley M, Pearson W, Radivojac P, Rosenberg N, Rosenwald A, Rustici G, Warnow T
Preprint Automated deconvolution of structured mixtures from bulk tumor genomic data 2016 Roman T, Xie L, Schwartz R
Journal Article Classifying the Progression of Ductal Carcinoma from Single-Cell Sampled Data via Integer Linear Programming: A Case Study 2016 • IEEE/ACM Transactions on Computational Biology and Bioinformatics • 13(4):643-655 Catanzaro D, Shackney SE, Schaffer AA, Schwartz R
Conference Computationally resolving heterogeneity in mixed genomic samples 2016 • IEEE ... International Conference on Computational Advances in Bio and Medical Sciences : [proceedings]. IEEE International Conference on Computational Advances in Bio and Medical Sciences Schwartz R
Journal Article FISHtrees 3.0: Tumor Phylogenetics Using a Ploidy Probe 2016 • PLoS ONE • 11(6): Gertz EM, Chowdhury SA, Lee W-J, Wangsa D, Heselmeyer-Haddad K, Ried T, Schwartz R, Schaffer AA
Journal Article Medoidshift clustering applied to genomic bulk tumor data 2016 • BMC Genomics • 17: Roman T, Xie L, Schwartz R
Journal Article Modeling Effects of RNA on Capsid Assembly Pathways via Coarse-Grained Stochastic Simulation 2016 • PLoS ONE • 11(5): Smith GR, Xie L, Schwartz R
Journal Article Phylogenetic analysis of multiple FISH markers in oral tongue squamous cell carcinoma suggests that a diverse distribution of copy number changes is associated with poor prognosis 2016 • International Journal of Cancer • 138(1):98-109 Wangsa D, Chowdhury SA, Ryott M, Gertz EM, Elmberger G, Auer G, Lundqvist EA, Kueffer S, Stroebel P, Schaeffer AA, Schwartz R, Munck-Wikland E, Ried T, Heselmeyer-Haddad K