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Cell Systems|June 24, 2019
CALDER: Inferring Phylogenetic Trees from Longitudinal Tumor SamplesMatthew A Myers, Gryte Satas, Benjamin J RaphaelBiorxiv : the Preprint Server for Biology|July 29, 2024
Quantifying higher-order epistasis: beware the chimeraUthsav Chitra, Brian J Arnold, Benjamin J RaphaelBioinformatics (Oxford, England)|June 17, 2014
Detecting independent and recurrent copy number aberrations using interval graphsHsin-Ta Wu, Iman Hajirasouliha, Benjamin J RaphaelBioinformatics (Oxford, England)|August 29, 2015
HapCol: accurate and memory-efficient haplotype assembly from long readsYuri Pirola, Simone Zaccaria, Riccardo Dondi, et al.Journal of Computational Biology : a Journal of Computational Molecular Cell Biology|June 10, 2016
On the Minimum Error Correction Problem for Haplotype Assembly in Diploid and Polyploid GenomesPaola Bonizzoni, Riccardo Dondi, Gunnar W Klau, et al.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing|December 17, 2011
Discovery of mutated subnetworks associated with clinical data in cancerFabio Vandin, Patrick Clay, Eli Upfal, et al.Bioinformatics (Oxford, England)|May 30, 2009
A geometric approach for classification and comparison of structural variantsSuzanne Sindi, Elena Helman, Ali Bashir, et al.Bioinformatics (Oxford, England)|June 28, 2024
A count-based model for delineating cell-cell interactions in spatial transcriptomics dataHirak Sarkar, Uthsav Chitra, Julian Gold, et al.Cell Systems|October 20, 2022
Belayer: Modeling discrete and continuous spatial variation in gene expression from spatially resolved transcriptomicsCong Ma, Uthsav Chitra, Shirley Zhang, et al.Genome Biology|July 3, 2025
Maximum likelihood inference of time-scaled cell lineage trees with mixed-type missing data using LAMLGillian Chu, Uyen Mai, Henri Schmidt, et al.Pageof 19