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 • 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 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. 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 • 13760:229-242 Srivatsa A, Lei H, 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
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 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(5):433-434 Schwartz R
Journal Article RECOMB 2020 Special Issue 2021 • Journal of Computational Biology • 28(4):345-345 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
