Indika Rajapakse, PhD

 Indika Rajapakse
Professor of Computational Medicine and Bioinformatics, Medical School
Professor of Mathematics, College of Literature, Science, and the Arts
Professor of Biomedical Engineering, Medical School and College of Engineering
[email protected]
Available to mentor
Indika Rajapakse, PhD
Indika Rajapakse
Professor
  • Qualifications
  • Center Memberships
  • Research Overview
  • Links
  • Recent Publications

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    • Qualifications
    • Postdoctoral Fellow
      Fred Hutchinson Cancer Research Center, Genome Cell Biology, Seattle, United States
      2009 - 2012

    Center Memberships
    • Center Member
      Center for Global Health Equity
    • Center Member
      Rogel Cancer Center
    • Center Member
      Biosciences Initiative

    Research Overview

    Biology: Cell Reprogramming and Digital Biology. Mathematics: Data-guided Learning and Control of Higher Order Structures and Mathematics of Synchronization.

    Links
    • Rajapakse Lab

    Recent Publications

     See All Publications
    • Preprint
      ARCH3D: A foundation model for global genome architecture
      Galioto N, Stansbury C, Gorodetsky AA, Rajapakse I. 2026 Feb 27; bioRxiv, DOI:10.64898/2026.02.23.707580
    • Journal Article
      Dynamic sensor selection for biomarker discovery.
      Pickard J, Stansbury C, Surana A, Muir L, Bloch A, Rajapakse I. Proc Natl Acad Sci U S A, 2025 Oct 14; 122 (41): e2501324122 DOI:10.1073/pnas.2501324122
      PMID: PMC12541339
    • Journal Article
      Apropos the long-lost letter from Levinson to Smale, now found!
      Rajapakse I, Koiller J. Notices of the American Mathematical Society, 2025 Jun 3;
    • Presentation
      Kuramoto Problem and Smale Institute
      2026 Jan 21;
    • Journal Article
      Automatic biomarker discovery and enrichment with BRAD
      Pickard J, Prakash R, Choi MA, Oliven N, Stansbury C, Cwycyshyn J, Galioto N, Gorodetsky A, Velasquez A, Rajapakse I. Bioinformatics, 2025 May 1; 41 (5): DOI:10.1093/bioinformatics/btaf159
      PMID: 40323323
    • Presentation
      Cell Reprogramming and Digital Biology
      2025 Jun 3;
    • Journal Article
      A Hands-On Introduction to Data Analytics for Biomedical Research
      Pickard J, Sturgess VE, Mcdonald KO, Rossiter N, Arnold KB, Shah YM, Rajapakse I, Beard DA. Function, 2025 Jan 1; 6 (2): DOI:10.1093/function/zqaf015
      PMID: 40199731
    • Journal Article
      Scalable hypergraph algorithms for observability of gene regulation
      Pickard J, Bloch A, Rajapakse I. Proceedings of the 2025 23rd European Control Conference (ECC), 2025 Jun 3;

    Featured News & Stories

         human body blue purple computerized
    Health Lab

    Applying engineering principles to biological studies could identify disease biomarkers more quickly

    In a new paper published in PNAS, a research team proposes that the fundamental principles of control theory and observability can be applied to study biological processes that change over time.
         Joshua Pickard, PhD, thesis committee
    Department News

    Joshua Pickard, Ph.D., developed computational methods and tools for biomarker discovery

    On June 13, 2025, he defended his thesis titled “Observability and higher-order methods for biomarker discovery,” and his mentor was professor Indika Rajapakse.
         AI-generated fantasist illustration with two identical cells in a blueprint style
    Department News

    A new grant for the Rajapakse lab

    The Rajapakse lab receives a new grant from the Defense Advanced Research Projects Agency (DARPA) to develop an AI assisted foundation model for direct cell reprogramming.
    Department News

    2023 Faculty Promotions and Accolades

    2023 Faculty Promotions and Accolades at the U-M Department of Computational Medicine and Bioinformatics (DCMB).
    Department News

    BAB in the Lab

    BAB is a tall, quiet, and infatigable robot. BAB lives at the University of Michigan North Campus Research Complex, in Dr. Indika Rajapakse’s lab.