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Bioinformatics (Oxford, England)|September 9, 2017
Tumor phylogeny inference using tree-constrained importance samplingGryte Satas, Benjamin J RaphaelGenome Research|September 5, 2020
Reconstruction of clone- and haplotype-specific cancer genome karyotypes from bulk tumor samplesSergey Aganezov, Benjamin J RaphaelCell Systems|June 1, 2026
The tree labeling polytope: A unified approach to ancestral reconstruction problemsHenri Schmidt, Benjamin J RaphaelJournal of Computational Biology : a Journal of Computational Molecular Cell Biology|March 19, 2015
Simultaneous inference of cancer pathways and tumor progression from cross-sectional mutation dataBenjamin J Raphael, Fabio VandinBiorxiv : the Preprint Server for Biology|March 3, 2025
The tree labeling polytope: a unified approach to ancestral reconstruction problemsHenri Schmidt, Benjamin J RaphaelNucleic Acids Research|December 5, 2003
A statistical sampling algorithm for RNA secondary structure predictionYe Ding, Charles E LawrenceBioinformatics (Oxford, England)|August 12, 2008
Analysis of segmental duplications via duplication distanceCrystal L Kahn, Benjamin J RaphaelJournal of Computational Biology : a Journal of Computational Molecular Cell Biology|April 10, 2010
Identification and frequency estimation of inversion polymorphisms from haplotype dataSuzanne S Sindi, Benjamin J RaphaelBioinformatics (Oxford, England)|July 21, 2004
Reconstructing tumor amplisomesBenjamin J Raphael, Pavel A PevznerPacific Symposium on Biocomputing. Pacific Symposium on Biocomputing|February 13, 2009
A parsimony approach to analysis of human segmental duplicationsCrystal L Kahn, Benjamin J RaphaelPageof 21