Journal Article Local rules simulation of the kinetics of virus capsid self-assembly 1998 • Biophysical Journal • 75(6):2626-2636 Schwartz R, Shor PW, Prevelige PE, Berger B
Preprint A Simulator for Somatic Evolution Study Design 2022.05.01.487551 Srivatsa A, Lei H, Schwartz R
Preprint CITEgeist: Cellular Indexing of Transcriptomes and Epitopes for Guided Exploration of Intrinsic Spatial Trends 2025.02.15.638331 Chang AC-C, Schlegel BT, Carleton N, McAuliffe PF, Oesterreich S, Schwartz R, Lee AV
Preprint Computationally reconstructing the evolution of cancer progression risk 2024.12.23.629914 Cao K, Schwartz R
Preprint ConTreeDP: A consensus method of tumor trees based on maximum directed partition support problem 2021.10.13.463978 Fu X, Schwartz R
Preprint Deconvolution and Phylogeny Inference of Diverse Variant Types Integrating Bulk DNA-seq with Single-cell RNA-seq 2025.01.24.634791 Bristy NA, Schwartz R
Preprint Deconvolution and phylogeny inference of structural variations in tumor genomic samples 257014 Eaton J, Wang J, Schwartz R
Preprint Determining Optimal Placement of Copy Number Aberration Impacted Single Nucleotide Variants in a Tumor Progression History 2024.03.10.584318 Wu CH, Joshi S, Robinson W, Robbins PF, Schwartz R, Sahinalp SC, Malikić S
Journal Article Improving personalized prediction of cancer prognoses with clonal evolution models 761510 Tao Y, Rajaraman A, Cui X, Cui Z, Eaton J, Kim H, Ma J, Schwartz R
Preprint Interpretable deep learning for chromatin-informed inference of transcriptional programs driven by somatic alterations across cancers 2021.09.07.459263 Tao Y, Ma X, Palmer D, Schwartz R, Lu X, Osmanbeyoglu HU
Preprint Marker selection strategies for circulating tumor DNA guided by phylogenetic inference 2024.03.21.585352 Fu X, Luo Z, Deng Y, LaFramboise W, Bartlett D, Schwartz R
Preprint Modeling the effect of spatial structure on solid tumor evolution and ctDNA composition 2023.11.10.566658 Rachman T, Bartlett D, Laframboise W, Wagner P, Schwartz R, Carja O
Preprint Optimizing Design of Genomics Studies for Clonal Evolution Analysis 2024.03.14.585055 Srivatsa A, Schwartz R
Preprint Sc-TUSV-ext: Single-cell clonal lineage inference from single nucleotide variants (SNV), copy number alterations (CNA) and structural variants (SV) 2023.12.07.570724 Bristy NA, Fu X, Schwartz R
Preprint Tumor Copy Number Deconvolution Integrating Bulk and Single-Cell Sequencing Data 519892 Lei H, Lyu B, Gertz EM, Schäffer AA, Shi X, Wu K, Li G, Xu L, Hou Y, Dean M, Schwartz R
Preprint Tumor heterogeneity assessed by sequencing and fluorescence in situ hybridization (FISH) data 2020.02.29.970392 Lei H, Gertz EM, Schäffer AA, Fu X, Tao Y, Heselmeyer-Haddad K, Torres I, Shi X, Wu K, Li G, Xu L, Hou Y, Dean M, Ried T, Schwartz R
