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Bioinformatics (Oxford, England)|June 17, 2014
A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing dataIman Hajirasouliha, Ahmad Mahmoody, Benjamin J RaphaelAlgorithms for Molecular Biology : AMB|September 8, 2012
Finding driver pathways in cancer: models and algorithmsFabio Vandin, Eli Upfal, Benjamin J RaphaelNature Communications|February 17, 2025
Resolving discrepancies between chimeric and multiplicative measures of higher-order epistasisUthsav Chitra, Brian Arnold, Benjamin J RaphaelBioinformatics (Oxford, England)|July 7, 2026
LAML-Pro: joint maximum likelihood inference of cell genotypes and cell lineage treesGillian Chu, Henri Schmidt, Benjamin J RaphaelGenome Research|August 8, 2023
Partial alignment of multislice spatially resolved transcriptomics dataXinhao Liu, Ron Zeira, Benjamin J RaphaelJournal of Computational Biology : a Journal of Computational Molecular Cell Biology|March 10, 2011
Algorithms for detecting significantly mutated pathways in cancerFabio Vandin, Eli Upfal, Benjamin J RaphaelGenome Research|June 10, 2011
De novo discovery of mutated driver pathways in cancerFabio Vandin, Eli Upfal, Benjamin J RaphaelBioinformatics (Oxford, England)|October 10, 2014
Quantifying tumor heterogeneity in whole-genome and whole-exome sequencing dataLayla Oesper, Gryte Satas, Benjamin J RaphaelBiorxiv : the Preprint Server for Biology|April 10, 2026
LAML-Pro: Joint Maximum Likelihood Inference of Cell Genotypes and Cell Lineage TreesGillian Chu, Henri Schmidt, Benjamin J RaphaelGenome Research|November 17, 2025
Joint imputation and deconvolution of gene expression across spatial transcriptomics platformsHongyu Zheng, Hirak Sarkar, Benjamin J RaphaelPageof 19