Research

My research is focused on the design and application of computational methods to analyze large-scale biological data. My group uses diverse computatational approaches including combinatorial optimization, graph algorithms, machine learning, and statistical methods. Recent areas of emphasis include cancer evolution, network/pathway analysis of genetic variants, and structural variation in human and cancer genomes. Our algorithms have been used in multiple projects from The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC). I co-led the TCGA Pancreatic Adenocarcinoma project and the network analysis in the ICGC Pan-Cancer Analysis of Whole Genomes (PCAWG).

Further information about my research is on my research group webpage. and a full list of publications is on Google Scholar.

I joined Princeton University in 2016, after a decade on the faculty in the Computer Science Department and Center for Computational Molecular Biology (CCMB) at Brown University, and directed the CCMB from 2013-2016. I am Associated Faculty in the Lewis-Sigler Institute for Integrative Genomics, the Omenn-Darling Bioengineering Institute, and the Center for Statistics and Machine Learning at Princeton University. I am also a Affiliate Faculty at the Rutgers Cancer Institute of New Jersey, the Irving Institute for Cancer Dynamics at Columbia University, and the New York Genome Center.

Awards

  • Fellow, Association for Computing Machinery (ACM), 2024
  • Test of Time Award, RECOMB Conference, 2023
  • Test of Time, Runner Up, RECOMB Conference, 2022
  • Innovator Award, International Society for Computational Biology (ISCB), 2021
  • Best Paper, Runner Up, RECOMB Conference, 2021
  • Fellow, International Society for Computational Biology (ISCB), 2020
  • AACR Team Science Award, 2020
  • NSF Career Award, 2011
  • Best Paper, RECOMB Conference, 2013
  • Sloan Research Fellowship, Computational & Evolutionary Molecular Biology, 2010-2012

    • Current Graduate Students and Postdoctoral Fellows

    Ph.D. Students

    • Gillian Chu (Computer Science). 2022-present
    • Peter Halmos (Computer Science). 2023-present
    • William Howard-Synder (Computer Science), 2024-present
    • Gary Hu (Computer Science). 2022-present
    • Akhil Jakatdar (Computer Science). 2022-present
    • Xinhao Liu (Computer Science). 2021-present
    • Runpeng (John) Luo (Computer Science). 2024-present
    • Sereno Lopez-Darwin (Quantitative and Computational Biology, Co-advised with Yibin Kang), 2022-present
    • Henri Schmidt (Computer Science). 2021-present
    • Richard Zhang (Quantitative and Computational Biology, Co-advised with Michelle Chan), 2022-present
    • Clover Zheng (Computer Science). 2022-present

    Postdoctoral Fellows

    • Yihang Shen (Postdoctoral Research Associate, September 2024 - present)
    • Hongyu Zheng (Postdoctoral Research Associate, September 2023 - present)

    Former Graduate Students and Postdoctoral Fellows

    Ph.D. Students (Princeton University)

    1. Uthsav Chitra (Ph.D. Computer Science. 2018-2024) → Schmidt Fellow, Broad Institute → Assistant Professor, Johns Hopkins University
    2. Ahmed Shuaibi(Ph.D. Quantitative and Computational Biology. 2021-2025) → ML Research Scientist, Meta
    3. Alexander Strzalkowski (Ph.D. Computer Science. 2020-2024)
    4. Tyler Park (Ph.D. Quantitative and Computational Biology, 2018-2023) → Postdoctoral Fellow, Memorial Sloan Kettering Cancer Center
    5. Matthew Myers (Ph.D. Computer Science, 2017-2022) → Computational Biologist, Memorial Sloan Kettering Cancer Center

    Ph.D. Students (Brown University)

    1. Gryte Satas (Ph.D. Computer Science, 2020) → Postdoctoral Fellow, Memorial Sloan Kettering Cancer Center
    2. Rebecca Elyanow (Ph.D. Computational Biology and Computer Science, 2020)→ Adaptive Biotechnologies
    3. Max Leiserson (Ph.D. Computational Biology and Computer Science, 2016) [NSF Graduate Research Fellowship, 2012-2015] → Postdoctoral Fellow, Microsoft Research New England → Assistant Professor, University of Maryland (Starting Fall 2017)
    4. Hsin-Ta Wu (Ph.D. Computational Biology and Computer Science, 2016) → Senior Bioinformatician, Natera
    5. Layla Oesper (Ph.D. Computer Science 2015) [NSF Graduate Research Fellowship, 2011-2014, Google Anita Borg Scholarship 2014] → Assistant Professor, Carleton College
    6. Matthew Parks (Ph.D. Applied Mathematics 2014) [Co-advised with Chip Lawrence] → Postdoctoral Fellow, Weil Cornell Medical School
    7. Anna Ritz (Ph.D. Computer Science 2012) [NSF Graduate Research Fellowship, 2008-2011] → Postdoc at Virginia Tech → Assistant Professor, Reed College
    8. Crystal Kahn (Ph.D. Computer Science 2010) [NSF Graduate Research Fellowship, 2005-2008] → Ab Initio → Assistant Professor, Amherst College

    Postdoctoral Fellows and Research Faculty (Princeton University)

    1. Hirak Sarkar(Ludwig Scholar, February 2023 - July 2025) → Assistant Professor, Vanderbilt University
    2. Uyen Mai (Princeton Presidential Postdoctoral Research Fellow, August 2022 - November 2024)
    3. Metin Balaban (Postdoctoral Research Associate, August 2022 - August 2024) → Computational Scientist at Myriad Genetics
    4. Palash Sashittal (Postdoctoral Research Associate, September 2021 - July 2024) → Assistant Professor, Virgina Tech
    5. Cong Ma (Postdoctoral Research Associate, October 2020 - July 2024) → Assistant Professor, University of Michigan
    6. Pijus Simonaitis (Postdoctoral Research Associate, January 2021 - March 2022)
    7. Ron Zeira (Postdoctoral Research Associate, January 2019-February 2022) → Verily, Israel
    8. Simone Zaccaria (Postdoctoral Research Associate, April 2017-August 2020) → Group Leader at University College London
    9. Sergey Aganezov (Postdoctoral Research Associate, July 2017-July 2018) → Postdoctoral Fellow, Johns Hopkins University
    10. Mohammed El-Kebir (Postdoctoral Research Associate, October 2014-January 2018) → Assistant Professor, Computer Science, University of Illinois Urbana-Champaign
    11. Matthew Reyna (Postdoctoral Research Associate, August 2014-November 2018) → Postdoctoral Fellow → Assistant Professor, Emory University

    Postdoctoral Fellows and Research Faculty (Brown University)

    1. Dora Erdos (Postdoctoral Research Associate, September 2015-August 2016) → Lecturer, Boston University
    2. Jason Dobson (Postdoctoral Fellow, 2013-2014) → Novartis
    3. Iman Hajirasouliha (Postdoctoral Fellow, 2013-2014) → Postdoctoral Fellow, Stanford University → Assistant Professor, Weil Cornell Medical School
    4. Fabio Vandin (Visiting Ph.D. Student and Postdoctoral Fellow, 2008-2013) → Assistant Professor, University of Southern Denmark → Associate Professor, University of Padova
    5. Suzanne Sindi (Postdoctoral Fellow 2006-2012) → Assistant Professor, UC Merced