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BMC Bioinformatics|September 16, 2018
Using controls to limit false discovery in the era of big dataMatthew M Parks, Benjamin J Raphael, Charles E LawrenceBioinformatics (Oxford, England)|September 9, 2010
Parsimony and likelihood reconstruction of human segmental duplicationsCrystal L Kahn, Borislav H Hristov, Benjamin J RaphaelBioinformatics (Oxford, England)|October 10, 2003
Reconstructing tumor genome architecturesBenjamin J Raphael, Stanislav Volik, Colin Collins, et al.Bioinformatics (Oxford, England)|July 15, 2025
Fast tumor phylogeny regression via tree-structured dual dynamic programmingHenri Schmidt, Yuanyuan Qi, Benjamin J Raphael, et al.Bioinformatics (Oxford, England)|November 11, 2008
Discovery of phosphorylation motif mixtures in phosphoproteomics dataAnna Ritz, Gregory Shakhnarovich, Arthur R Salomon, et al.Genome Research|January 30, 2020
netNMF-sc: leveraging gene-gene interactions for imputation and dimensionality reduction in single-cell expression analysisRebecca Elyanow, Bianca Dumitrascu, Barbara E Engelhardt, et al.Genome Medicine|February 1, 2014
Identifying driver mutations in sequenced cancer genomes: computational approaches to enable precision medicineBenjamin J Raphael, Jason R Dobson, Layla Oesper, et al.Journal of Computational Biology : a Journal of Computational Molecular Cell Biology|January 5, 2021
NetMix: A Network-Structured Mixture Model for Reduced-Bias Estimation of Altered SubnetworksMatthew A Reyna, Uthsav Chitra, Rebecca Elyanow, et al.Bioinformatics (Oxford, England)|November 14, 2018
Hierarchical HotNet: identifying hierarchies of altered subnetworksMatthew A Reyna, Mark D M Leiserson, Benjamin J RaphaelCancer Letters|January 29, 2013
Advances for studying clonal evolution in cancerLi Ding, Benjamin J Raphael, Feng Chen, et al.Pageof 19