Publications

  • Zhao T, Zhu G, Dubey H, Flaherty P (2023) Identification of significant gene expression changes in multiple perturbation experiments using knockoffs. Briefings in Bioinformatics 24 (2): https://doi.org/10.1093/bib/bbad084
  • Sarsani V, Aldikacti B, He S, Zeinert R, Chien P, Flaherty P (2022) Model-based identification of conditionally-essential genes from transposon-insertion sequencing data. PLOS Computational Biology 18(3): e1009273. https://doi.org/10.1371/journal.pcbi.1009273
  • He S, Schein A, Sarsani V, Flaherty P. A Bayesian Nonparametric Model for Inferring Subclonal Populations from Structures DNA Sequencing Data. Ann Appl Stat. 2021 Jun;15(2):925-951. doi: 10.1214/20-aoas1434. Epub 2021 Jul 12. PMID: 34262633; PMCID: PMC8277113.
  • Giguere, Collin, Harsh Dubey, Vishal Sarsani, Hachem Saddiki, Shai He, and Patrick Flaherty. “SCSIM: Jointly simulating correlated single-cell and bulk next-generation DNA sequencing data.” BMC Bioinformatics 21, no. 215 (2020): 1–10. https://doi.org/10.1186/s12859-020-03550-1. biorxiv: biorxiv: 10.1101/2020.02.03.930354.