Lab Members

Our group consists of graduate students, postdocs, undergraduates, and high school interns from several departments and programs across MIT and Harvard (MIT Electrical Engineering and Computer Science, MIT Computational and Systems Biology, MIT Mathematics, and Harvard Bioinformatics and Integrative Genomics).

Ruochi Zhang

Eric and Wendy Schmidt Postdoctoral Fellow

PhD, MS — Carnegie Mellon University

BE — Tsinghua University

Interests: graph representation learning, single cell genomics, gene regulation

Bowen Jing

(co with Tommi Jaakkola)

EECS PhD

BS — Stanford University

Interests: protein structure, molecular dynamics, diffusion models

Lillian Zhang

EECS PhD

BS — MIT

Interests: computational genomics

Daniel Lazarev

Math PhD + Stony Brook MD

BA — Yeshiva University

Interests: variational principles with applications to optimal representations of data, entropy and information, statistical genetics

Onkar Gujral

Math PhD

BA — Duke University

Interests: machine learning for biology, interpretability

Shuvom Sadhuka

EECS PhD

AB — Harvard University

Interests: uncertainty quantification, fairness, privacy

Anna Sappington

EECS PhD + Harvard MD

MPhil — Cambridge University

MSc — University College London

BS — MIT

Interests: protein evolution, representation learning for biological data

Seokmin Ha

Math PhD

BS — KAIST

Interests: causal inference, mathematical modeling

Megan Le

(co with Heng Li)

EECS PhD

MS, BS, BA — UT Austin

Interests: computational genomics

Daniel Schäffer

CSB PhD

BS — Carnegie Mellon University

Interests: regulatory genomics, evolution, host-pathogen interactions

Helen Kang

(co with Rajat Gupta)

CSB PhD

BA — UC Berkeley

Interests: regulatory genomics, single cell analysis

Mihir Bafna

EECS PhD

BS — Georgia Tech

Interests: generative modeling, structural biology, single-cell

Lab Alumni

Barış Ekim (PhD 2025 –> Postdoc @ Yale)

Sam Sledzieski (PhD 2024 –> Flatiron Research Fellow @ Flatiron Institute)

Derek Yen (MEng 2024 –> PhD in Computer Science @ NYU)

Simon Mendelsohn (Software Engineer –> Software Engineer @ Watershed Bio)

Lena Erlach (visiting student from ETH Zürich)

Alexander Wu (PhD 2023 –> Senior AI Scientist @ Genentech)

Max Sherman (PhD 2023 –> Co-founder and CTO @ Serinus Biosciences)

Adam Yaari (PhD 2023 –> Co-founder and CEO @ Serinus Biosciences)

Younhun Kim (PhD 2023 –> Postdoc @ Harvard Medical School)

Chiho Im (MEng 2023 –> PhD in Computer Science @ Stanford)

Reema Guda (RSI summer intern –> Undergrad @ Harvard)

Bhushan Mohanraj (RSI summer intern –> Undergrad @ Stanford)

Sara Althaqafi (RSI summer intern)

Shorna Alam (UROP)

Peter Pao-Huang (visiting student –> PhD student in Computer Science @ Stanford)

Ben DeMeo (PhD 2022 –> Machine Learning Scientist @ Cellarity)

Ashwin Narayan (PhD 2022 –> VP of Data Science @ MissionWired)

Sarah Nyquist (PhD 2022 –> Postdoc @ Gladstone Institutes)

Ellen Zhong (PhD 2022 –> Assistant Professor @ Princeton Computer Science)

Jeffrey Chen (MEng 2022 –> Software Engineer @ Mosaic ML)

Binwei Yan (UROP)

Anish Mudide (RSI summer intern –> Undergrad @ MIT)

Ariya Shajii (PhD 2021 –> Co-founder and CTO @ Exaloop)

Brian Hie (PhD 2021 –> Stanford Science Fellow, now Assistant Professor @ Stanford Chemical Engineering and Data Science)

Andy Tso (MEng 2021)

Tristan Bepler (PhD 2020 –> Co-founder and CEO @ OpenProtein.AI + Group Leader @ Simons Machine Learning Center)

Shreyan Jain (MEng 2020 –> Machine Learning Engineer @ Robust Intelligence, now Software Engineer @ Ramp)

Timothy Truong (MEng 2020)

Hyunghoon Cho (PhD 2019 –> Schmidt Fellow @ Broad, now Assistant Professor @ Yale Biomedical Data Science)

Ibrahim Numanagic (Postdoc –> Assistant Professor @ University of Victoria Computational Biology and Data Science)

Sumaiya Nazeen (PhD 2019 –> Postdoc @ Harvard Medical School)

Perry Palmedo (PhD 2018 –> VP of Corporate Development and Strategy @ insitro –> Co-founder and CEO @ Conflux)

Ryan Chung (MEng 2018 –> PhD in Computational Biology @ UC Berkeley)

Yun William Yu (PhD 2017 –> Assistant Professor @ University of Toronto Applied Math, now Assistant Professor @ CMU Computational Biology)

Noah Daniels (postdoc –> Associate Professor @ University of Rhode Island)

Larson Hogstrom (SM 2016 –> Computational Associate @ Broad Institute, now Senior Scientist in Computational Biology @ Exact Sciences)

Yuhao Wang (SM 2016 –> PhD in Computer Science @ MIT, now Associate Professor @ Tsinghua University)

Divya Shanmugam (undergrad –> PhD student @ MIT CSAIL)

Deniz Yorukoglu (PhD 2015 –> Senior Software Engineer @ Google)

Sean Simmons (PhD 2015 –> Senior Computational Scientist @ Broad Institute)

Sebastian Will (Postdoc –> Professor of Bioinformatics @ École Polytechnique)

Mark Lipson (PhD 2014 –> Senior Staff Scientist @ Harvard Medical School)

George Tucker (PhD 2014 –> Research Scientist @ Google Brain)

Po-Ru Loh (PhD 2013 –> Associate Professor of Medicine @ Harvard Medical School)

Daniel Park (SM 2013)

Hadar Benyamini (Postdoc –> Bioinformatician @ Hebrew University of Jerusalem)

Alex Levin (PhD 2013 –> Software Engineer @ Yelp)

Patrick Schmid (PhD 2012 –> CTO @ Activate Care, now CTO @ Sharpen.com)

Rohit Singh (PhD 2012 –> Co-founder and CEO @ Tech Square Trading, now Assistant Professor @ Duke Biostatistics and Bioinformatics, Cell Biology, and Electrical and Computer Engineering)

Raghavendra Hosur (PhD 2012 –> Senior Scientist @ Biogen, now Computational Biology and Machine Learning @ Encoded Therapeutics)

Nathan Palmer (PhD 2012 –> Senior Research Scientist and Director of Data Analytics and Platforms @ Harvard Medical School)

Michael Schnall-Levin (PhD 2011 –> Founding Scientist and CTO @ 10x Genomics)

Luke Hutchison (PhD 2011 –> Senior Research Scientist @ Google Accelerated Science, now CEO and Founder, Click Social)

Charles O’Donnell (PhD 2011 –> Vice President of Computational Genomics and Data Sciences @ Omega Therapeutics)

Eric Eisner (MEng 2011 –> Software Engineer @ Google)

Michael Yu (MEng 2011 –> PhD in Bioinformatics and Systems Biology @ UC San Diego, now Senior Applied Scientist @ Amazon)

Leonid Chindelevitch (PhD 2010, Postdoc @ Yale –> Assistant Professor @ Simon Fraser Computer Science, now Assistant Professor @ Imperial College London Epidemiology)

Oaz Nir (PhD 2010 –> Partner @ Hudson River Trading)

Jason Trigg (MEng 2010 –> Quantitative Analyst @ Tech Square Trading, now Co-founder @ Arch)

Michael Baym (PhD 2009 –> Postdoc @ Harvard Medical School, now Associate Professor @ Harvard Medical School Department of Biomedical Informatics)

Allen Bryan (PhD 2009 –> Harvard MD/PhD, now Assistant Professor of Medicine @ UC Davis School of Medicine)

Matthew Menke (PhD 2009 –> Senior Software Engineer @ Google)

Vinay Pulim (PhD 2008 –> Co-founder at CTO @ MileWise, now co-founder and CTO @ Canopy)

Shannon Wieland (PhD 2007 –> MD/PhD @ Harvard Medical School)

Gopal Ramachandran (PhD 2007 –> MD/PhD @ Harvard Medical School, now Head of Machine Learning @ SolveBio)

Brad Friedman (PhD 2006 –> Senior Principal Scientist @ Genentech)

Arthur Dong (PhD 2004 –> Postdoc @ LMU Munich, now Senior Director of AI and Big Data @ OrigiMed)

Eben Scanlon (SM 2004 –> Engagement Manager @ McKinsey & Company, now Chief Commercial Officer @ OneStudyTeam)

Manolis Kellis (PhD 2003 –> Professor of Computer Science @ MIT)

Phil Bradley (PhD 2001 –> Professor @ Fred Hutch Cancer Center Public Health )

Russell Schwartz (PhD 2000 –> Professor @ CMU Computational Biology)

Serafim Batzoglou (PhD 2000 –> Professor @ Stanford Computer Science –> Chief Data Officer @ insitro, now Chief Data Officer @ Seer, Inc.)

Eric Banks (MEng 2000 –> PhD in Computational Biology @ Princeton, now Senior Director of the Data Sciences Platform @ Broad Institute)

Valentin Spitkovsky (MEng 2000 –> PhD in Computer Science @ Stanford)

Lior Pachter (PhD 1999 –> Professor UC Berkeley Math, now Bren Professor @ Caltech Computational Biology and Computing and Mathematical Sciences)

C. Esther Jesurum (PhD 1997 –> Chief Architect @ Zengines)

George Homsy (SM 1997)

Ethan Wolf (PhD 1996)

Mona Singh (PhD 1995 –> Wang Family Professor @ Princeton Computer Science)