| 2025 | ICML | Hierarchical Refinement: Optimal Transport to Infinity and Beyond. | Peter Halmos, Julian Gold, Xinhao Liu, Benjamin J. Raphael |
| 2025 | RECOMB | Learning Latent Trajectories in Developmental Time Series with Hidden-Markov Optimal Transport. | Peter Halmos, Julian Gold, Xinhao Liu, Benjamin J. Raphael |
| 2025 | RECOMB | Inferring Cell Differentiation Maps from Lineage Tracing Data. | Palash Sashittal, Richard Y. Zhang, Benjamin K. Law, Henri Schmidt, Alexander Strzalkowski, Adriano Bolondi, Michelle M. Chan, Benjamin J. Raphael |
| 2025 | RECOMB | The Tree Labeling Polytope: A Unified Approach to Ancestral Reconstruction Problems. | Henri Schmidt, Benjamin J. Raphael |
| 2025 | RECOMB | Joint Imputation and Deconvolution of Gene Expression Across Spatial Transcriptomics Platforms. | Hongyu Zheng, Hirak Sarkar, Benjamin J. Raphael |
| 2024 | RECOMB | Mapping the Topography of Spatial Gene Expression with Interpretable Deep Learning. | Uthsav Chitra, Brian J. Arnold, Hirak Sarkar, Cong Ma, Sereno Lopez-Darwin, Kohei Sanno, Benjamin J. Raphael |
| 2024 | RECOMB | DeST-OT: Alignment of Spatiotemporal Transcriptomics Data. | Peter Halmos, Xinhao Liu, Julian Gold, Feng Chen, Li Ding, Benjamin J. Raphael |
| 2024 | RECOMB | Inferring Allele-Specific Copy Number Aberrations and Tumor Phylogeography from Spatially Resolved Transcriptomics. | Cong Ma, Metin Balaban, Jingxian Liu, Siqi Chen, Li Ding, Benjamin J. Raphael |
| 2024 | RECOMB | Maximum Likelihood Inference of Time-Scaled Cell Lineage Trees with Mixed-Type Missing Data. | Uyen Mai, Gillian Chu, Benjamin J. Raphael |
| 2022 | RECOMB | NetMix2: Unifying Network Propagation and Altered Subnetworks. | Uthsav Chitra, Tae Yoon Park, Benjamin J. Raphael |
| 2022 | RECOMB | Belayer: Modeling Discrete and Continuous Spatial Variation in Gene Expression from Spatially Resolved Transcriptomics. | Cong Ma, Uthsav Chitra, Shirley Zhang, Benjamin J. Raphael |
| 2022 | WABI | A Maximum Parsimony Principle for Multichromosomal Complex Genome Rearrangements. | Pijus Simonaitis, Benjamin J. Raphael |
| 2021 | ICML | Quantifying and Reducing Bias in Maximum Likelihood Estimation of Structured Anomalies. | Uthsav Chitra, Kimberly Ding, Jasper C. H. Lee, Benjamin J. Raphael |
| 2021 | WABI | Genome Halving and Aliquoting Under the Copy Number Distance. | Ron Zeira, Geoffrey Mon, Benjamin J. Raphael |
| 2020 | RECOMB | NetMix: A Network-Structured Mixture Model for Reduced-Bias Estimation of Altered Subnetworks. | Matthew A. Reyna, Uthsav Chitra, Rebecca Elyanow, Benjamin J. Raphael |
| 2020 | RECOMB | Single-Cell Tumor Phylogeny Inference with Copy-Number Constrained Mutation Losses. | Gryte Satas, Simone Zaccaria, Geoffrey Mon, Benjamin J. Raphael |
| 2019 | ICML | Random Walks on Hypergraphs with Edge-Dependent Vertex Weights. | Uthsav Chitra, Benjamin J. Raphael |
| 2019 | RECOMB | netNMF-sc: A Network Regularization Algorithm for Dimensionality Reduction and Imputation of Single-Cell Expression Data. | Rebecca Elyanow, Bianca Dumitrascu, Barbara E. Engelhardt, Benjamin J. Raphael |
| 2019 | RECOMB | Inferring Tumor Evolution from Longitudinal Samples. | Matthew A. Myers, Gryte Satas, Benjamin J. Raphael |
| 2017 | RECOMB | The Copy-Number Tree Mixture Deconvolution Problem and Applications to Multi-sample Bulk Sequencing Tumor Data. | Simone Zaccaria, Mohammed El-Kebir, Gunnar W. Klau, Benjamin J. Raphael |
| 2016 | RECOMB | Multi-state Perfect Phylogeny Mixture Deconvolution and Applications to Cancer Sequencing. | Mohammed El-Kebir, Gryte Satas, Layla Oesper, Benjamin J. Raphael |
| 2016 | WABI | Copy-Number Evolution Problems: Complexity and Algorithms. | Mohammed El-Kebir, Benjamin J. Raphael, Ron Shamir, Roded Sharan, Simone Zaccaria, Meirav Zehavi, Ron Zeira |
| 2015 | PSB | Session Introduction. | Sren Brunak, Francisco M. de la Vega, Adam A. Margolin, Benjamin J. Raphael, Gunnar Rtsch, Joshua M. Stuart |
| 2015 | RECOMB | CoMEt: A Statistical Approach to Identify Combinations of Mutually Exclusive Alterations in Cancer. | Mark D. M. Leiserson, Hsin-Ta Wu, Fabio Vandin, Benjamin J. Raphael |
| 2015 | RECOMB | On the Sample Complexity of Cancer Pathways Identification. | Fabio Vandin, Benjamin J. Raphael, Eli Upfal |
| 2014 | RECOMB | Simultaneous Inference of Cancer Pathways and Tumor Progression from Cross-Sectional Mutation Data. | Benjamin J. Raphael, Fabio Vandin |
| 2014 | WABI | Reconstructing Mutational History in Multiply Sampled Tumors Using Perfect Phylogeny Mixtures. | Iman Hajirasouliha, Benjamin J. Raphael |
| 2013 | PSB | Modeling cell heterogeneity: from single-cell variations to mixed cells populations. | Eric Batchelor, Maricel G. Kann, Teresa M. Przytycka, Benjamin J. Raphael, Damian Wjtowicz |
| 2013 | PSB | Session introduction. | Grkan Bebek, Mehmet Koyutrk, Thomas LaFramboise, Benjamin J. Raphael, Mark R. Chance |
| 2013 | RECOMB | Inferring Intra-tumor Heterogeneity from High-Throughput DNA Sequencing Data. | Layla Oesper, Ahmad Mahmoody, Benjamin J. Raphael |
| 2013 | RECOMB | Genome-Wide Survival Analysis of Somatic Mutations in Cancer. | Fabio Vandin, Alexandra Papoutsaki, Benjamin J. Raphael, Eli Upfal |
| 2012 | PSB | Discovery of Mutated Subnetworks Associated with Clinical Data in Cancer. | Fabio Vandin, Patrick Clay, Eli Upfal, Benjamin J. Raphael |
| 2011 | RECOMB | Untitled record | Fabio Vandin, Eli Upfal, Benjamin J. Raphael |
| 2011 | WABI | Finding Driver Pathways in Cancer: Models and Algorithms. | Fabio Vandin, Eli Upfal, Benjamin J. Raphael |
| 2010 | RECOMB | Algorithms for Detecting Significantly Mutated Pathways in Cancer. | Fabio Vandin, Eli Upfal, Benjamin J. Raphael |
| 2009 | PSB | A Parsimony Approach to Analysis of Human Segmental Duplications. | Crystal L. Kahn, Benjamin J. Raphael |
| 2009 | RECOMB | Optimizing PCR Assays for DNA Based Cancer Diagnostics. | Ali Bashir, Qing Lu, Dennis Carson, Benjamin J. Raphael, Yu-Tsueng Liu, Vineet Bafna |
| 2009 | RECOMB | Identification and Frequency Estimation of Inversion Polymorphisms from Haplotype Data. | Suzanne S. Sindi, Benjamin J. Raphael |
| 2009 | WABI | Efficient Algorithms for Analyzing Segmental Duplications, Deletions, and Inversions in Genomes. | Crystal L. Kahn, Shay Mozes, Benjamin J. Raphael |
| 2008 | ECCB | Analysis of segmental duplications via duplication distance. | Crystal L. Kahn, Benjamin J. Raphael |
| 2007 | RECOMB | Identification of Deletion Polymorphisms from Haplotypes. | Erik Corona, Benjamin J. Raphael, Eleazar Eskin |
| 2004 | ISMB | Reconstructing tumor amplisomes. | Benjamin J. Raphael, Pavel A. Pevzner |
| 2003 | ECCB | Reconstructing tumor genome architectures. | Benjamin J. Raphael, Stanislav Volik, Colin C. Collins, Pavel A. Pevzner |