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Genome Biology|April 18, 2015
Detecting non-allelic homologous recombination from high-throughput sequencing dataMatthew M Parks, Charles E Lawrence, Benjamin J RaphaelBioinformatics (Oxford, England)|July 15, 2025
GASTON-Mix: a unified model of spatial gradients and domains using spatial mixture-of-expertsUthsav Chitra, Shu Dan, Fenna Krienen, et al.Genome Research|October 15, 2017
Single-cell sequencing data reveal widespread recurrence and loss of mutational hits in the life histories of tumorsJack Kuipers, Katharina Jahn, Benjamin J Raphael, et al.Cell Systems|December 21, 2023
Startle: A star homoplasy approach for CRISPR-Cas9 lineage tracingPalash Sashittal, Henri Schmidt, Michelle Chan, et al.Nature Reviews. Genetics|June 14, 2017
Network propagation: a universal amplifier of genetic associationsLenore Cowen, Trey Ideker, Benjamin J Raphael, et al.Biorxiv : the Preprint Server for Biology|March 3, 2025
Learning Latent Trajectories in Developmental Time Series with Hidden-Markov Optimal TransportPeter Halmos, Julian Gold, Xinhao Liu, et al.Bioinformatics (Oxford, England)|June 28, 2024
Joint inference of cell lineage and mitochondrial evolution from single-cell sequencing dataPalash Sashittal, Viola Chen, Amey Pasarkar, et al.Physical Biology|October 6, 2020
STARCH: copy number and clone inference from spatial transcriptomics dataRebecca Elyanow, Ron Zeira, Max Land, et al.Plos Computational Biology|May 8, 2015
Accurate computation of survival statistics in genome-wide studiesFabio Vandin, Alexandra Papoutsaki, Benjamin J Raphael, et al.Nature Methods|May 16, 2022
Alignment and integration of spatial transcriptomics dataRon Zeira, Max Land, Alexander Strzalkowski, et al.Pageof 19