Reconstructing tumor genome architectures. - Benjamin J. Raphael; Stanislav Volik; Colin C. Collins; Pavel A. Pevzner (ECCB, 2003)

Reconstructing tumor amplisomes. - Benjamin J. Raphael; Pavel A. Pevzner (ISMB/ECCB (Supplement of Bioinformatics), 2004)

A Uniform Projection Method for Motif Discovery in DNA Sequences. - Benjamin J. Raphael; Lung-Tien Liu; George Varghese (IEEE ACM Trans. Comput. Biol. Bioinform., 2004)

AliWABA: alignment on the web through an A-Bruijn approach. - Neil Christopher Jones; Degui Zhi; Benjamin J. Raphael (Nucleic Acids Res., 2006)

Microinversions in mammalian evolution. - Mark Chaisson; Benjamin J. Raphael; Pavel A. Pevzner (Proc. Natl. Acad. Sci. USA, 2006)

Identification of Deletion Polymorphisms from Haplotypes. - Erik Corona; Benjamin J. Raphael; Eleazar Eskin (RECOMB, 2007)

Optimization of primer design for the detection of variable genomic lesions in cancer. - Ali Bashir; Yu-Tsueng Liu; Benjamin J. Raphael; Dennis Carson; Vineet Bafna (Bioinform., 2007)

Analysis of segmental duplications via duplication distance. - Crystal L. Kahn; Benjamin J. Raphael (ECCB, 2008)

Evaluation of Paired-End Sequencing Strategies for Detection of Genome Rearrangements in Cancer. - Ali Bashir; Stanislav Volik; Colin C. Collins; Vineet Bafna; Benjamin J. Raphael (PLoS Comput. Biol., 2008)

A Parsimony Approach to Analysis of Human Segmental Duplications. - Crystal L. Kahn; Benjamin J. Raphael (Pacific Symposium on Biocomputing, 2009)

Discovery of phosphorylation motif mixtures in phosphoproteomics data. - Anna M. Ritz; Gregory Shakhnarovich; Arthur R. Salomon; Benjamin J. Raphael (Bioinform., 2009)

A geometric approach for classification and comparison of structural variants. - Suzanne S. Sindi; Elena Helman; Ali Bashir; Benjamin J. Raphael (Bioinform., 2009)

Efficient algorithms for analyzing segmental duplications with deletions and inversions in genomes. - Crystal L. Kahn; Shay Mozes; Benjamin J. Raphael (Algorithms Mol. Biol., 2010)

Parsimony and likelihood reconstruction of human segmental duplications. - Crystal L. Kahn; Borislav H. Hristov; Benjamin J. Raphael (Bioinform., 2010)

Structural variation analysis with strobe reads. - Anna M. Ritz; Ali Bashir; Benjamin J. Raphael (Bioinform., 2010)

Optimizing PCR Assays for DNA-Based Cancer Diagnostics. - Ali Bashir; Qing Lu; Dennis Carson; Benjamin J. Raphael; Yu-Tsueng Liu; Vineet Bafna (J. Comput. Biol., 2010)

Identification and Frequency Estimation of Inversion Polymorphisms from Haplotype Data. - Suzanne S. Sindi; Benjamin J. Raphael (J. Comput. Biol., 2010)

Gremlin: An Interactive Visualization Model for Analyzing Genomic Rearrangements. - Trevor M. O'Brien; Anna M. Ritz; Benjamin J. Raphael; David H. Laidlaw (IEEE Trans. Vis. Comput. Graph., 2010)

Workshop: Characterization of structural variants with next generation DNA sequencing. - Benjamin J. Raphael; Suzanne S. Sindi; Anna M. Ritz; Ali Bashir (ICCABS, 2011)

De Novo Discovery of Mutated Driver Pathways in Cancer. - Fabio Vandin; Eli Upfal; Benjamin J. Raphael (RECOMB, 2011)

Detection of recurrent rearrangement breakpoints from copy number data. - Anna M. Ritz; Pamela L. Paris; Michael Ittmann; Colin C. Collins; Benjamin J. Raphael (BMC Bioinform., 2011)

Algorithms for Detecting Significantly Mutated Pathways in Cancer. - Fabio Vandin; Eli Upfal; Benjamin J. Raphael (J. Comput. Biol., 2011)

Workshop: Algorithms for discovery of mutated pathways in cancer. - Fabio Vandin; Eli Upfal; Benjamin J. Raphael (ICCABS, 2012)

Discovery of Mutated Subnetworks Associated with Clinical Data in Cancer. - Fabio Vandin; Patrick Clay; Eli Upfal; Benjamin J. Raphael (Pacific Symposium on Biocomputing, 2012)

Finding Driver Pathways in Cancer: Models and Algorithms. - Fabio Vandin; Eli Upfal; Benjamin J. Raphael (Algorithms Mol. Biol., 2012)

Identification of polymorphic inversions from genotypes. - Alejandro Cáceres; Suzanne S. Sindi; Benjamin J. Raphael; Mario Cáceres; Juan R. González (BMC Bioinform., 2012)

Reconstructing genome mixtures from partial adjacencies. - Ahmad Mahmoody; Crystal L. Kahn; Benjamin J. Raphael (BMC Bioinform., 2012)

Reconstructing cancer genomes from paired-end sequencing data. - Layla Oesper; Anna M. Ritz; Sarah J. Aerni; Ryan Drebin; Benjamin J. Raphael (BMC Bioinform., 2012)

Algorithms and Genome Sequencing: Identifying Driver Pathways in Cancer. - Fabio Vandin; Eli Upfal; Benjamin J. Raphael (Computer, 2012)

Chapter 6: Structural Variation and Medical Genomics. - Benjamin J. Raphael (PLoS Comput. Biol., 2012)

Workshop: Reconstructing the organization of cancer genomes. - Layla Oesper; Benjamin J. Raphael (ICCABS, 2013)

Identifying significant mutations in large cohorts of cancer genomes. - Fabio Vandin; Eli Upfal; Benjamin J. Raphael (ICCABS, 2013)

Modeling cell heterogeneity: from single-cell variations to mixed cells populations. - Eric Batchelor; Maricel G. Kann; Teresa M. Przytycka; Benjamin J. Raphael; Damian Wójtowicz (Pacific Symposium on Biocomputing, 2013)

Session introduction. - Gürkan Bebek; Mehmet Koyutürk; Thomas LaFramboise; Benjamin J. Raphael; Mark R. Chance (Pacific Symposium on Biocomputing, 2013)

Inferring Intra-tumor Heterogeneity from High-Throughput DNA Sequencing Data. - Layla Oesper; Ahmad Mahmoody; Benjamin J. Raphael (RECOMB, 2013)

Genome-Wide Survival Analysis of Somatic Mutations in Cancer. - Fabio Vandin; Alexandra Papoutsaki; Benjamin J. Raphael; Eli Upfal (RECOMB, 2013)

Simultaneous Identification of Multiple Driver Pathways in Cancer. - Mark D. M. Leiserson; Dima Blokh; Roded Sharan; Benjamin J. Raphael (PLoS Comput. Biol., 2013)

A combinatorial algorithm to identify independent and recurrent copy number aberrations across cancer types. - Hsin-Ta Wu; Iman Hajirasouliha; Benjamin J. Raphael (ICCABS, 2014)

Reconstructing Mutational History in Multiply Sampled Tumors Using Perfect Phylogeny Mixtures. - Iman Hajirasouliha; Benjamin J. Raphael (WABI, 2014)

A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data. - Iman Hajirasouliha; Ahmad Mahmoody; Benjamin J. Raphael (Bioinform., 2014)

Quantifying tumor heterogeneity in whole-genome and whole-exome sequencing data. - Layla Oesper; Gryte Satas; Benjamin J. Raphael (Bioinform., 2014)

Characterization of structural variants with single molecule and hybrid sequencing approaches. - Anna M. Ritz; Ali Bashir; Suzanne S. Sindi; David Hsu; Iman Hajirasouliha; Benjamin J. Raphael (Bioinform., 2014)

Detecting independent and recurrent copy number aberrations using interval graphs. - Hsin-Ta Wu; Iman Hajirasouliha; Benjamin J. Raphael (Bioinform., 2014)

Session Introduction. - Søren Brunak; Francisco M. de la Vega; Adam A. Margolin; Benjamin J. Raphael; Gunnar Rätsch; Joshua M. Stuart (Pacific Symposium on Biocomputing, 2015)

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 (RECOMB, 2015)

Reconstruction of clonal trees and tumor composition from multi-sample sequencing data. - Mohammed El-Kebir; Layla Oesper; Hannah Acheson-Field; Benjamin J. Raphael (Bioinform., 2015)

Simultaneous Inference of Cancer Pathways and Tumor Progression from Cross-Sectional Mutation Data. - Benjamin J. Raphael; Fabio Vandin (J. Comput. Biol., 2015)

Accurate Computation of Survival Statistics in Genome-Wide Studies. - Fabio Vandin; Alexandra Papoutsaki; Benjamin J. Raphael; Eli Upfal (PLoS Comput. Biol., 2015)

Multi-state Perfect Phylogeny Mixture Deconvolution and Applications to Cancer Sequencing. - Mohammed El-Kebir; Gryte Satas; Layla Oesper; Benjamin J. Raphael (RECOMB, 2016)

Copy-Number Evolution Problems: Complexity and Algorithms. - Mohammed El-Kebir; Benjamin J. Raphael; Ron Shamir; Roded Sharan; Simone Zaccaria; Meirav Zehavi; Ron Zeira (WABI, 2016)

A weighted exact test for mutually exclusive mutations in cancer. - Mark D. M. Leiserson; Matthew A. Reyna; Benjamin J. Raphael (Bioinform., 2016)

Identification of hierarchical chromatin domains. - Caleb Weinreb; Benjamin J. Raphael (Bioinform., 2016)

On the Sample Complexity of Cancer Pathways Identification. - Fabio Vandin; Benjamin J. Raphael; Eli Upfal (J. Comput. Biol., 2016)

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 (RECOMB, 2017)

Complexity and algorithms for copy-number evolution problems. - Mohammed El-Kebir; Benjamin J. Raphael; Ron Shamir; Roded Sharan; Simone Zaccaria; Meirav Zehavi; Ron Zeira (Algorithms Mol. Biol., 2017)

Tumor phylogeny inference using tree-constrained importance sampling. - Gryte Satas; Benjamin J. Raphael (Bioinform., 2017)

Identifying structural variants using linked-read sequencing data. - Rebecca Elyanow; Hsin-Ta Wu; Benjamin J. Raphael (Bioinform., 2018)

Identifying simultaneous rearrangements in cancer genomes. - Layla Oesper; Simone Dantas; Benjamin J. Raphael (Bioinform., 2018)

Hierarchical HotNet: identifying hierarchies of altered subnetworks. - Matthew A. Reyna; Mark D. M. Leiserson; Benjamin J. Raphael (Bioinform., 2018)

Haplotype phasing in single-cell DNA-sequencing data. - Gryte Satas; Benjamin J. Raphael (Bioinform., 2018)

Using controls to limit false discovery in the era of big data. - Matthew M. Parks; Benjamin J. Raphael; Charles E. Lawrence (BMC Bioinform., 2018)

Phylogenetic Copy-Number Factorization of Multiple Tumor Samples. - Simone Zaccaria; Mohammed El-Kebir; Gunnar W. Klau; Benjamin J. Raphael (J. Comput. Biol., 2018)

Random Walks on Hypergraphs with Edge-Dependent Vertex Weights. - Uthsav Chitra; Benjamin J. Raphael (ICML, 2019)

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 (RECOMB, 2019)

Inferring Tumor Evolution from Longitudinal Samples. - Matthew A. Myers; Gryte Satas; Benjamin J. Raphael (RECOMB, 2019)

12 Grand Challenges in Single-Cell Data Science. - David Laehnemann; Johannes Köster; Ewa Szczurek; Davis J. McCarthy; Stephanie C. Hicks; Mark D. Robinson; Catalina A. Vallejos; Niko Beerenwinkel; Kieran R. Campbell; Ahmed Mahfouz; Luca Pinello; Pavel Skums; et al. (PeerJ Prepr., 2019)

Single-Cell Tumor Phylogeny Inference with Copy-Number Constrained Mutation Losses. - Gryte Satas; Simone Zaccaria; Geoffrey Mon; Benjamin J. Raphael (RECOMB, 2020)

Identifying tumor clones in sparse single-cell mutation data. - Matthew A. Myers; Simone Zaccaria; Benjamin J. Raphael (Bioinform., 2020)

Copy number evolution with weighted aberrations in cancer. - Ron Zeira; Benjamin J. Raphael (Bioinform., 2020)

Quantifying and Reducing Bias in Maximum Likelihood Estimation of Structured Anomalies. - Uthsav Chitra; Kimberly Ding; Benjamin J. Raphael (CoRR, 2020)

The evolutionary history of 2,658 cancers. - Moritz Gerstung; Clemency Jolly; Ignaty Leshchiner; Stefan C. Dentro; Santiago Gonzalez; Thomas J. Mitchell; Yulia Rubanova; Pavana Anur; Kaixian Yu; Maxime Tarabichi; Amit G. Deshwar; Jeff Wintersinger; et al. (Nat., 2020)

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. - Esther Rheinbay; Morten Muhlig Nielsen; Federico Abascal; Jeremiah Wala; Ofer Shapira; Grace Tiao; Henrik Hornshøj; Julian M. Hess; Randi Istrup Juul; Ziao Lin; Lars Feuerbach; Radhakrishnan Sabarinathan; et al. (Nat., 2020)

Quantifying and Reducing Bias in Maximum Likelihood Estimation of Structured Anomalies. - Uthsav Chitra; Kimberly Ding; Jasper C. H. Lee; Benjamin J. Raphael (ICML, 2021)

Genome Halving and Aliquoting Under the Copy Number Distance. - Ron Zeira; Geoffrey Mon; Benjamin J. Raphael (WABI, 2021)

NetMix: A Network-Structured Mixture Model for Reduced-Bias Estimation of Altered Subnetworks. - Matthew A. Reyna; Uthsav Chitra; Rebecca Elyanow; Benjamin J. Raphael (J. Comput. Biol., 2021)

NetMix2: Unifying Network Propagation and Altered Subnetworks. - Uthsav Chitra; Tae Yoon Park; Benjamin J. Raphael (RECOMB, 2022)

Belayer: Modeling Discrete and Continuous Spatial Variation in Gene Expression from Spatially Resolved Transcriptomics. - Cong Ma 008; Uthsav Chitra; Shirley Zhang 001; Benjamin J. Raphael (RECOMB, 2022)

A Maximum Parsimony Principle for Multichromosomal Complex Genome Rearrangements. - Pijus Simonaitis; Benjamin J. Raphael (WABI, 2022)

NetMix2: A Principled Network Propagation Algorithm for Identifying Altered Subnetworks. - Uthsav Chitra; Tae Yoon Park; Benjamin J. Raphael (J. Comput. Biol., 2022)

A zero-agnostic model for copy number evolution in cancer. - Henri Schmidt; Palash Sashittal; Benjamin J. Raphael (PLoS Comput. Biol., 2023)

Low-Rank Optimal Transport through Factor Relaxation with Latent Coupling. - Peter Halmos; Xinhao Liu 009; Julian Gold; Benjamin J. Raphael (NeurIPS, 2024)

Mapping the Topography of Spatial Gene Expression with Interpretable Deep Learning. - Uthsav Chitra; Brian J. Arnold; Hirak Sarkar; Cong Ma 008; Sereno Lopez-Darwin; Kohei Sanno; Benjamin J. Raphael (RECOMB, 2024)

DeST-OT: Alignment of Spatiotemporal Transcriptomics Data. - Peter Halmos; Xinhao Liu 009; Julian Gold; Feng Chen; Li Ding; Benjamin J. Raphael (RECOMB, 2024)

Inferring Allele-Specific Copy Number Aberrations and Tumor Phylogeography from Spatially Resolved Transcriptomics. - Cong Ma 008; Metin Balaban; Jingxian Liu; Siqi Chen; Li Ding; Benjamin J. Raphael (RECOMB, 2024)

Maximum Likelihood Inference of Time-Scaled Cell Lineage Trees with Mixed-Type Missing Data. - Uyen Mai; Gillian Chu; Benjamin J. Raphael (RECOMB, 2024)

Maximum likelihood phylogeographic inference of cell motility and cell division from spatial lineage tracing data. - Uyen Mai; Gary Hu; Benjamin J. Raphael (Bioinform., 2024)

A count-based model for delineating cell-cell interactions in spatial transcriptomics data. - Hirak Sarkar; Uthsav Chitra; Julian Gold; Benjamin J. Raphael (Bioinform., 2024)

Joint inference of cell lineage and mitochondrial evolution from single-cell sequencing data. - Palash Sashittal; Viola Chen; Amey Pasarkar; Benjamin J. Raphael (Bioinform., 2024)

A regression based approach to phylogenetic reconstruction from multi-sample bulk DNA sequencing of tumors. - Henri Schmidt; Benjamin J. Raphael (PLoS Comput. Biol., 2024)

Learning Latent Trajectories in Developmental Time Series with Hidden-Markov Optimal Transport. - Peter Halmos; Julian Gold; Xinhao Liu 009; Benjamin J. Raphael (RECOMB, 2025)

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 (RECOMB, 2025)

The Tree Labeling Polytope: A Unified Approach to Ancestral Reconstruction Problems. - Henri Schmidt; Benjamin J. Raphael (RECOMB, 2025)

Joint Imputation and Deconvolution of Gene Expression Across Spatial Transcriptomics Platforms. - Hongyu Zheng; Hirak Sarkar; Benjamin J. Raphael (RECOMB, 2025)

Hierarchical Refinement: Optimal Transport to Infinity and Beyond. - Peter Halmos; Julian Gold; Xinhao Liu 009; Benjamin J. Raphael (CoRR, 2025)