Journal Article Abstract 3695: A mechanistic model of ctDNA shedding and its relevance for clinical interpretation 2025 • Cancer Research • 85(8_Supplement_1):3695-3695 Rachman T, Wagner P, LaFramboise W, Bartlett D, Schwartz R, Carja O
Journal Article Biological databases in the age of generative artificial intelligence 2025 • Bioinformatics Advances • 5(1): Pop M, Attwood TK, Blake JA, Bourne PE, Conesa A, Gaasterland T, Hunter L, Kingsford C, Kohlbacher O, Lengauer T, Markel S, Moreau Y, Noble WS, Orengo C, Ouellette BFF, Parida L, Przulj N, Przytycka TM, Ranganathan S, Schwartz R, Valencia A, Warnow T
Journal Article Cell-Free DNA, Tumor Molecular Concordance, and Clinical Correlates of Patients with Cancer Treated in a Large Community Health Care Network 2025 • Journal of Molecular Diagnostics • 27(9):882-898 LaFramboise WA, Petrosko P, Gallo PH, Gil L, Lam TL, Barr RM, Schumacher PE, Kharoud HK, Taylor KM, Dalton E, Bapat B, Patel S, Nakayama J, Hilton CJ, Ercolano LB, Zaidi AH, Allen CJ, Rachman T, Carja O, Schwartz R, Wagner PL, Bartlett DL
Journal Article Marker selection strategies for circulating tumor DNA guided by phylogenetic inference 2025 • Bioinformatics • 41(4): Fu X, Luo Z, Deng Y, LaFramboise W, Bartlett D, Schwartz R
Journal Article Multicenter phase I/II study of abemaciclib and ramucirumab in metastatic gastroesophageal adenocarcinoma (GEA): CDK4/6 and cyclin D1 alterations as a predictor of response and survival. 2025 • Journal of Clinical Oncology • 43(16_suppl):4063-4063 Kelly RJ, Lam VK, Paulson AS, McCollum AD, Kitchens BL, Abushahin LI, Sherry C, Anees M, LaFramboise W, Schwartz RS, Goel A, Zheng P, Wagner P, Bartlett DL, Raj MS, Anagnostou V, Zaidi AH
Journal Article Sc-TUSV-Ext: Single-Cell Clonal Lineage Inference from Single Nucleotide Variants, Copy Number Alterations, and Structural Variants 2025 • Journal of Computational Biology • 32(8):723-737 Bristy NA, Fu X, Schwartz R
Journal Article Abstract 2326: Integrating single nucleotide variants (SNVs), copy number alterations (CNAs), and structural variants (SVs) into single-cell clonal lineage inference 2024 • Cancer Research • 84(6_Supplement):2326-2326 Bristy N, Fu X, Schwartz R
Journal Article Abstract 2334: Computational methods for optimizing marker selection, clonal lineage reconstruction, and longitudinal tracking of clonal dynamics via circulating tumor DNA (ctDNA) 2024 • Cancer Research • 84(6_Supplement):2334-2334 Fu X, Deng Y, Luo Z, Laframboise W, Bartlett D, Schwartz R
Chapter Chapter 3 Machine learning applications in cancer genomics 2024 41-72 El-Charif O, Schwartz R, Yuan Y, Tao Y
Chapter Determining Optimal Placement of Copy Number Aberration Impacted Single Nucleotide Variants in a Tumor Progression History 2024 • Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) • 14758:438-443 Wu CH, Joshi S, Robinson W, Robbins PF, Schwartz R, Sahinalp SC, Malikic S
Journal Article Modeling the Effect of Spatial Structure on Solid Tumor Evolution and Circulating Tumor DNA Composition 2024 • Cancers • 16(5): Rachman T, Bartlett D, Laframboise W, Wagner P, Schwartz R, Carja O
Journal Article Optimizing design of genomics studies for clonal evolution analysis 2024 • Bioinformatics Advances • 4(1): Srivatsa A, Schwartz R
Journal Article The ISCB competency framework v. 3: a revised and extended standard for bioinformatics education and training 2024 • Bioinformatics Advances • 4(1): Brooksbank C, Brazas MD, Mulder N, Schwartz R, Ras V, Morgan SL, Llinares ML, Lopez PC, Larcombe L, Ghouila A, Hancocks T, Satagopam V, de las Rivas J, Mazandu G, Gaeta B
Journal Article A Clonal Evolution Simulator for Planning Somatic Evolution Studies 2023 • Journal of Computational Biology • 30(8):831-847 Srivatsa A, Lei H, Schwartz R
Journal Article Abstract 6621: Simulating the distortion of clonal fractions in ctDNA due to spatially heterogenous selection 2023 • Cancer Research • 83(7_Supplement):6621-6621 Rachman TW, Carja O, Schwartz R
Journal Article Grand challenges in bioinformatics education and training 2023 • Nature Biotechnology • 41(8):1171-1174 Isik EB, Brazas MD, Schwartz R, Gaeta B, Palagi PM, van Gelder CWG, Suravajhala P, Singh H, Morgan SL, Zahroh H, Ling M, Satagopam VP, McGrath A, Nakai K, Tan TW, Gao G, Mulder N, Schonbach C, Zheng Y, De Las Rivas J, Khan AM
Journal Article Ten simple rules for writing a <i>PLOS Computational Biology</i> quick tips article 2023 • PLoS Computational Biology • 19(12): Palagi PM, Schwartz R, Markel S, Ouellette BFF
Conference <i>De novo</i> Prediction of Cell-Drug Sensitivities Using Deep Learning-based Graph Regularized Matrix Factorization 2022 • Pacific Symposium on Biocomputing • 278-289 Ren S, Tao Y, Yu K, Xue Y, Schwartz R, Lu X
Chapter A Clonal Evolution Simulator for Planning Somatic Evolution Studies 2022 • Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) • 13760:229-242 Srivatsa A, Lei H, Schwartz R
Journal Article Abstract 5031: Improved deconvolution of combined bulk and single-cell RNA-sequencing data 2022 • Cancer Research • 82(12_Supplement):5031-5031 Lei H, Guo XA, Tao Y, Ding K, Fu X, Oesterreich S, Lee AV, Schwartz R
Conference Improved deconvolution of combined bulk and single-cell RNA-sequencing data 2022 • Cancer Research • 82(12): Lei H, Guo XA, Tao Y, Ding K, Fu X, Oesterreich S, Lee AV, Schwartz R
Conference Improved deconvolution of combined bulk and single-cell RNA-sequencing data. 2022 • Cancer Research • 82(12): Lei H, Guo XA, Tao Y, Ding K, Fu X, Oesterreich S, Lee AV, Schwartz R
Journal Article Interpretable deep learning for chromatin-informed inference of transcriptional programs driven by somatic alterations across cancers 2022 • Nucleic Acids Research (NAR) • 50(19):10869-10881 Tao Y, Ma X, Palmer D, Schwartz R, Lu X, Osmanbeyoglu HU
Journal Article Reconstructing tumor clonal lineage trees incorporating single-nucleotide variants, copy number alterations and structural variations 2022 • Bioinformatics • 38(SUPPL 1):125-133 Fu X, Lei H, Tao Y, Schwartz R
Journal Article Semi-deconvolution of bulk and single-cell RNA-seq data with application to metastatic progression in breast cancer 2022 • Bioinformatics • 38(SUPPL 1):386-394 Lei H, Guo XA, Tao Y, Ding K, Fu X, Oesterreich S, Lee AV, Schwartz R
