Current Group Members


Ben Raphael (PI). Curriculum Vitae: PDF

Postdoctoral Fellows

  • Metin Balaban (Postdoctoral Research Associate, August 2022 - present)
  • Cong Ma (Postdoctoral Research Associate, October 2020 - present)
  • Uyen Mai (Princeton Presidential Postdoctoral Research Fellow, August 2022 - present)
  • Hirak Sarkar (Ludwig Scholar, February 2023 - present)
  • Palash Sashittal (Postdoctoral Research Associate, September 2021 - present)
  • Hongyu Zheng (Postdoctoral Research Associate, September 2023 - present

Ph.D. Students

  • Uthsav Chitra (Computer Science). 2018-present
  • Gillian Chu (Computer Science). 2022-present
  • Maya Gupta (Computer Science). 2022-present
  • Peter Halmos (Computer Science). 2023-present
  • Gary Hu (Computer Science). 2022-present
  • Akhil Jakatdar (Computer Science). 2022-present
  • Xinhao Liu (Computer Science). 2021-present
  • Sereno Lopez-Darwin (Quantitative and Computational Biology, Co-advised with Yibin Kang), 2022-present
  • Henri Schmidt (Computer Science). 2021-present
  • Ahmed Shuaibi (Quantitative and Computational Biology). 2021-present
  • Alexander Strzalkowski (Computer Science). 2020-present
  • Richard Zhang (Quantitative and Computational Biology, Co-advised with Michelle Chan), 2022-present


  • Rishabh Rout (Summer 2021 - present)


  • Ph.D. students. We recruit students primarily through the Princeton Computer Science Ph.D. program and the Quantitative and Computational Biology Ph.D. program. Please consult the program websites for further details.
  • Postdoctoral fellows and staff programmers, or undergraduate students. Contact Professor Raphael for further information about current positions. Please include in your email your CV and, if you are a student, a list of courses you are taking this year.


Ph.D. Students

  • Tyler Park (Ph.D. Quantitative and Computational Biology, 2018-2023) → Postdoctoral Fellow, Memorial Sloan Kettering Cancer Center
  • Matthew Myers (Ph.D. Computer Science, 2017-2022) → Computational Biologist, Memorial Sloan Kettering Cancer Center
  • Gryte Satas (Ph.D. Computer Science, 2020) → Postdoctoral Fellow, Memorial Sloan Kettering Cancer Center
  • Rebecca Elyanow (Ph.D. Computational Biology and Computer Science, 2020)→ Adaptive Biotechnologies
  • 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)
  • Hsin-Ta Wu (Ph.D. Computational Biology and Computer Science, 2016) → Senior Bioinformatician, Natera
  • Layla Oesper (Ph.D. Computer Science 2015) [NSF Graduate Research Fellowship, 2011-2014, Google Anita Borg Scholarship 2014] → Assistant Professor, Carleton College
  • Matthew Parks (Ph.D. Applied Mathematics 2014) [Co-advised with Chip Lawrence] → Postdoctoral Fellow, Weil Cornell Medical School
  • Anna Ritz (Ph.D. Computer Science 2012) [NSF Graduate Research Fellowship, 2008-2011] → Postdoc at Virginia Tech → Assistant Professor, Reed College
  • Crystal Kahn (Ph.D. Computer Science 2010) [NSF Graduate Research Fellowship, 2005-2008] → Ab Initio → Assistant Professor, Amherst College

Postdoctoral Fellows and Research Faculty

  • Pijus Simonaitis (Postdoctoral Research Associate, January 2021 - March 2022)
  • Ron Zeira (Postdoctoral Research Associate, January 2019-February 2022) → Verily, Israel
  • Simone Zaccaria (Postdoctoral Research Associate, April 2017-August 2020) → Group Leader at University College London
  • Sergey Aganezov (Postdoctoral Research Associate, July 2017-July 2018) → Postdoctoral Fellow, Johns Hopkins University
  • Mohammed El-Kebir (Postdoctoral Research Associate, October 2014-January 2018) → Assistant Professor, Computer Science, University of Illinois Urbana-Champaign
  • Matthew Reyna (Postdoctoral Research Associate, August 2014-November 2018) → Postdoctoral Fellow → Assistant Professor, Emory University
  • Dora Erdos (Postdoctoral Research Associate, September 2015-August 2016) → Lecturer, Boston University
  • Jason Dobson (Postdoctoral Fellow, 2013-2014) → Novartis
  • Iman Hajirasouliha (Postdoctoral Fellow, 2013-2014) → Postdoctoral Fellow, Stanford University → Assistant Professor, Weil Cornell Medical School
  • Fabio Vandin (Visiting Ph.D. Student and Postdoctoral Fellow, 2008-2013) → Assistant Professor, University of Southern Denmark → Associate Professor, University of Padova
  • Suzanne Sindi (Postdoctoral Fellow 2006-2012) → Assistant Professor, UC Merced

Master’s Students

  • Ashley Conard (Sc.M. Computational Biology and Computer Science 2018) → Ph.D. student, Brown University
  • Jeremy Watson (Sc.M. 2016)
  • John Shen (Sc.M. 2015) → IBM Watson
  • Jonathan Eldridge (Sc.M. 2014) → Redfin
  • Ahmad Mahmoody (Sc.M. Computer Science, 2013) → Brown Computer Science Ph.D. (Advisor: Eli Upfal)
  • Alexandra Papoutsaki (Sc.M. Computer Science 2013) → Brown Computer Science Ph.D. (Advisor: Jeff Huang)
  • Borislav Hristov (Sc.B./Sc.M. 2010) → Oracle → Princeton Computer Science Ph.D. Program
  • Selim Onal (Sc.M. 2010) → Oracle → Google
  • Brendan Hickey (Sc.M. 2009) → Google
  • Eric Lim (Sc.M. 2007) → Ph.D. Biology, Brown University 2011

Undergraduate and Visiting Students

  • Kimberly Ding (Thesis, 2021)
  • Yaw Asante (Thesis, 2021)
  • Ellen Su (Summer 2021)
  • Shirley Zhang (2020)
  • Max Land (2020)
  • Chandler Ault (Summer 2020)
  • Claire Du (Honors Thesis, 2020)
  • Geoffrey Mon (Summer 2018, 2019)
  • Devina Singh (Honors Thesis, 2018)
  • Alexandra Wong (UTRA Summer 2015 and 2016 → Yelp → M.D. student, Brown University
  • Jonathan Chang (UTRA, Summer 2016)
  • Zheng Shi (UTRA, Summer 2016) → Ph.D. student, Computer Science, Princeton University
  • Uthsav Chitra (Honors Thesis, Sc.B. Computer Science, 2017; UTRA, Summer 2015)
  • David Liu (Honors Thesis, Sc.B. Computer Science, 2017; UTRA Summer, 2014 and 2016)
  • Eddie Williams (UTRA, Summer 2016)
  • Michael Mueller (UTRA, Summer 2016)
  • Alex Asherly (UTRA, Summer 2015)
  • Isaac Kim (UTRA, Summer 2015)
  • David Liu (UTRA, Summer 2014) → M.D. Student, Brown University
  • Younhun Kim (UTRA, Summer 2014) → Ph.D.Student, MIT
  • Jacob Thomas (UTRA, Summer 2014)
  • Hannah Acheson-Field (Honors Thesis, Sc.B. Computational Biology, 2015) →
  • Caleb Weinreb → Ph.D. Student, Harvard Systems Biology
  • Vivian Hsiao (Honors Thesis, Sc.B. Computer Science, 2014) → M.D. student, Brown University
  • Vishesh Jain (Honors Thesis, Sc.B. Computational Biology, 2014)
  • Jovian Yu (Honors Thesis, Sc.B. Statistics, 2012) → M.D. student, Brown University
  • Tony Cannistra (Computer Science, Tufts University)
  • Adrien Deschamps (Applied Mathematics)
  • Stephanie DeMane (Sc.B. Computational Biology)
  • Sarah Aerni (Visting from Stanford BMI)
  • Ali Bashir (Visiting from UCSD Bioinformatics) → Assistant Professor, Mount Sinai School of Medicine
  • Ryan Drebin (Sc.B. Computational Biology, 2012) → Yelp
  • Jonathan Eldridge (Sc.B. 2011) → Microsoft
  • Elena Helman (Honors Thesis, Sc.B. Computational Biology 2008) → Ph.D., MIT HST 2013 → Personalis
  • Edward Rice (A.B. Computer Science 2012) → NIH → UCSC Biomolecular Engineering Ph.D. Program
  • Erik Corona (undergraduate) → Ph.D., Stanford Biomedical Informatics →

High School Students

Funded through NSF CAREER award Summer outreach program

  • Christina Wong (Summer 2018) →
  • Isabella Millard (Summer 2015) →
  • Anthony Rolland (Summer 2014) → MIT, undergraduate
  • Ava Brignol (Summer 2013, 2014) → Harvard University, undergraduate
  • Methany Eltigani (Summer 2013) → University of Pennsylvania, undergraduate
  • Nadiva Brown (Summer 2011) → Providence College, undergraduate

Ben Raphael Scientific Biography

Ben Raphael joined Brown University in September 2006 as an Assistant Professor in the Department of Computer Science and Center for Computational Molecular Biology. His research focuses on the design of combinatorial and statistical algorithms for the interpretation of genomes. Current research interests include next-generation DNA sequencing, structural variation, genome rearrangements in cancer and evolution, and network analysis of somatic mutations in cancer. Earlier research included topics in comparative genomics, multiple sequence alignment, and motif finding. He is the recipient of a National Science Foundation CAREER Award and an Alfred P. Sloan Research Fellowship.

From 2002-2006, he was a postdoctoral fellow in the Bioinformatics Group at the University of California, San Diego led by Professor Pavel Pevzner, supported by a postdoctoral fellowship in Computational Molecular Biology from the Alfred P. Sloan Foundation, and by a Career Award at the Scientific Interface from the Burroughs Wellcome Fund.

He received his Ph.D. in Mathematics from the University of California, San Diego in 2002 under the supervision of Jim Agler. His doctoral research was in operator theory, specifically on certain problems related to functional calculus of linear operators on Hilbert space. Many of the results from his Ph.D. thesis “A Computational Investigation of Spectral Sets and Rational Dilations Over Multiply-Connected Domains” appear in this monograph.

He received an S.B. in Mathematics with a minor in Biology from the Massachusetts Institute of Technology in 1996. As an undergraduate, he worked with Jim Propp on problems in combinatorics, and worked in the laboratory of David Page at the Whitehead Institute for Biomedical Research.

Curriculum Vitae: PDF

Group Photos:

Welcome dinner for Iman
January 2013 - Welcome dinner for Iman

Group Retreat 2012
Group Retreat 2012 - Lake Winnipesaukee, NH

Group Retreat 2011
Group Retreat 2011 - Ludlow, VT

View More Photos in Interactive Gallery