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Biorxiv : the Preprint Server for Biology|December 22, 2025
Riemannian Metric Learning for Alignment of Spatial MultiomicsPeter Halmos, Yufan Xia, Benjamin J RaphaelBioinformatics (Oxford, England)|July 7, 2026
Riemannian metric learning for alignment of spatial multiomicsPeter Halmos, Yufan Xia, Benjamin J RaphaelTrends in Cancer|April 14, 2023
Insights into the metastatic cascade through research autopsiesSonya Hessey, Petros Fessas, Simone Zaccaria, et al.BMC Bioinformatics|July 5, 2018
HapCHAT: adaptive haplotype assembly for efficiently leveraging high coverage in long readsStefano Beretta, Murray D Patterson, Simone Zaccaria, et al.Journal of Computational Biology : a Journal of Computational Molecular Cell Biology|December 16, 2022
NetMix2: A Principled Network Propagation Algorithm for Identifying Altered SubnetworksUthsav Chitra, Tae Yoon Park, Benjamin J RaphaelNucleic Acids Research|July 18, 2006
AliWABA: alignment on the web through an A-Bruijn approachNeil C Jones, Degui Zhi, Benjamin J RaphaelNature Genetics|April 28, 2018
Inferring parsimonious migration histories for metastatic cancersMohammed El-Kebir, Gryte Satas, Benjamin J RaphaelBMC Bioinformatics|January 4, 2013
Reconstructing genome mixtures from partial adjacenciesAhmad Mahmoody, Crystal L Kahn, Benjamin J RaphaelAlgorithms for Molecular Biology : AMB|January 6, 2010
Efficient algorithms for analyzing segmental duplications with deletions and inversions in genomesCrystal L Kahn, Shay Mozes, Benjamin J RaphaelBioinformatics (Oxford, England)|November 8, 2017
Identifying structural variants using linked-read sequencing dataRebecca Elyanow, Hsin-Ta Wu, Benjamin J RaphaelPageof 19