Curriculum Vitae

Ashir Borah

PhD candidate · UCSF / Arc Institute · functional genomics, virology, and AI-enabled research systems

ashiraseesh@gmail.com · Google Scholar · GitHub · LinkedIn

Summary

PhD candidate in the Biological and Medical Informatics program at UCSF, jointly mentored by Luke Gilbert and Brian Hie at the Arc Institute. Research at the intersection of functional genomics, virology, and computational biology — combining CRISPR-based screening, assay development, and high-dimensional data analysis to study gene regulation, host–virus interactions, and disease mechanisms.

In parallel, building AI-enabled research systems — LLM-based councils, research agents, APIs, and multi-agent workflows for literature synthesis, hypothesis generation, experimental planning, and scientific reasoning.

Before UCSF, nearly three years at the Broad Institute on the Cancer Dependency Map, using statistical modeling and machine learning on genome-scale perturbation data to discover and validate cancer targets. B.S. Mathematics & Computer Science from Dickinson College, Magna Cum Laude, Phi Beta Kappa.

Education & positions

  1. Arc Institute

    Jun 2023 — Present
    PhD Researcher · Palo Alto, CA
    • Designing experimental and computational methods for functional genomics and virology.
    • Building CRISPR-based screening and perturbation systems to study gene regulation, host–virus biology, and disease mechanisms.
    • Developing assay platforms and analysis workflows for high-dimensional genomic datasets.
    • Building AI-enabled scientific tooling — LLM councils, APIs, and multi-agent workflows for literature synthesis, hypothesis generation, and experimental planning.

  2. University of California, San Francisco

    Sep 2022 — Present
    PhD Candidate · Biological and Medical Informatics · San Francisco, CA
    • PhD research in functional genomics, virology, and computational biology, in collaboration with the Arc Institute.
    • Developing computational and experimental approaches for studying gene regulation, perturbation biology, and disease mechanisms.
    • Analyzing large-scale biological datasets with statistical, machine learning, and high-dimensional methods.
    • Led an R bootcamp for postdocs and clinicians — 100+ trainees.

  3. Broad Institute of MIT and Harvard

    Jul 2019 — Apr 2022
    Computational Associate I & II · Cancer Data Science · Dependency Map Project · Cambridge, MA
    • Validated candidate cancer targets identified through genome-scale CRISPR knockout screens.
    • Applied machine learning and statistical methods to identify vulnerabilities in cancer cell lines, with a focus on GI cancers.
    • Prioritized candidate dependencies for downstream therapeutic investigation.
    • Contributed to an open-source ML platform modeling genetic-knockout dependency profiles across >100,000 genomic features.

  4. Uliza

    Sep — Dec 2017
    Machine Learning Developer
    • Built ML-driven systems to support crowdsourced workflow automation.
    • Set up core technical infrastructure — server management, database optimization, and disaster recovery.

  5. Dickinson College

    2015 — 2019
    B.S. Mathematics & Computer Science · Magna Cum Laude · Phi Beta Kappa · Carlisle, PA
    • Student research project on secure CoAP-DTLS systems for resource-constrained devices.
    • Best Poster, All-College Science Symposium (2019).
    • Teaching assistant for Introduction to Java and Data Structures; tutoring and residential leadership roles.

Publications

1,125 citations · h-index 10 · i10-index 10 View on Scholar →

  1. SKI complex loss renders 9p21.3-deleted or MSI-H cancers dependent on PELO
    P.C. Borck, I. Boyle, K. Jankovic, N. Bick, K. Foster, A.C. Lau, L.I. Parker-Burns, …, A.A. Borah, et al.
    Nature2025Cited by 22
  2. Integrated epigenetic and genetic programming of primary human T cells
    L. Goudy, A. Ha, A.A. Borah, J.M. Umhoefer, L. Chow, C. Tran, A. Winters, et al.
    Nature Biotechnology2025Cited by 17
  3. A systematic search for RNA structural switches across the human transcriptome
    M. Khoroshkin, D. Asarnow, S. Zhou, A. Navickas, A. Winters, J. Goudreau, …, A.A. Borah, et al.
    Nature Methods2024Cited by 18
  4. In vivo Perturb-seq of cancer and microenvironment cells dissects oncologic drivers and radiotherapy responses in glioblastoma
    S.J. Liu, C. Zou, J. Pak, A. Morse, D. Pang, T. Casey-Clyde, A.A. Borah, D. Wu, et al.
    Genome Biology2024Cited by 18
  5. Lineage-specific canonical and non-canonical activity of EZH2 in advanced prostate cancer subtypes
    V.B. Venkadakrishnan, A.G. Presser, R. Singh, M.A. Booker, N.A. Traphagen, …, A.A. Borah, et al.
    Nature Communications2024Cited by 66
  6. A ubiquitination cascade regulating the integrated stress response and survival in carcinomas
    L.D. Cervia, T. Shibue, A.A. Borah, B. Gaeta, L. He, L. Leung, N. Li, et al.
    Cancer Discovery2023Cited by 66
  7. Partial gene suppression improves identification of cancer vulnerabilities when CRISPR-Cas9 knockout is pan-lethal
    J.M. Krill-Burger, J.M. Dempster, A.A. Borah, B.R. Paolella, D.E. Root, T.R. Golub, et al.
    Genome Biology2023Cited by 39
  8. Sparse dictionary learning recovers pleiotropy from human cell fitness screens
    J. Pan, J.J. Kwon, J.A. Talamas, A.A. Borah, F. Vazquez, J.S. Boehm, et al.
    Cell Systems2022Cited by 43
  9. Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer
    S. Raghavan, P.S. Winter, A.W. Navia, H.L. Williams, A. DenAdel, K.E. Lowder, …, A.A. Borah, et al.
    Cell2021Cited by 611
  10. Repeat expansions confer WRN dependence in microsatellite-unstable cancers
    N. van Wietmarschen, S. Sridharan, W.J. Nathan, A. Tubbs, E.M. Chan, …, A.A. Borah, et al.
    Nature2020Cited by 204

See the full list on Google Scholar →

Selected honors

  • Spot Award (×2), Broad Institute · 2020, 2021
  • Phi Beta Kappa Honor Society · 2019
  • Best Poster, All-College Science Symposium · 2019
  • Richard Howland Memorial Scholarship · sole CS recipient · 2018
  • Pi Mu Epsilon (Mathematics) & Upsilon Pi Epsilon (CS) · 2018
  • Jane Hill Prize in Computer Science · 2016
  • Torchbearer Award, Bhumi · 6 of 8,000 volunteers · 2015

Languages

English (native) · Hindi (professional) · Assamese (conversational)