People

Lab Head


Manolis Kellis

Manolis Kellis

Professor, MIT Department of
Computer Science Head
MIT Computational Biology group 
Associate Member
Broad Institute of MIT and
 Harvard Member
MIT Computer Science and 
Artificial Intelligence Lab

Staff


Amy Grayson

Amy Grayson

Project Manager 
MIT Computer Science
Broad Institute
Kyriakitsa Galani

Kyriakitsa Galani

Li-Lun Ho

Li-Lun Ho

Staff 
Research Scientist
Maya Sekhar

Maya Sekhar

Technical Associate
Nicola Sykes

Nicola Sykes

Project Manager
Patty Purcell

Patty Purcell

Project Manager 
MIT Computer Science
Broad Institute
Sydney Kelly

Sydney Kelly

Technical Associate
Stuart Fass

Stuart Fass

Computational Biologist
Yena Sung

Yena Sung

Technical Associate

Postdoctoral Researchers


Alec Chapman

Alec Chapman

Postdoctoral Associate
Ben Lengerich

Ben Lengerich

Bo Zhao

Bo Zhao

Elee Shimshoni

Elee Shimshoni

Postdoctoral Associate
Complex in vitro models for 
target validation and drug testing
Fiona Song

Fiona Song

Irwin Jungreis

Irwin Jungreis

Research Scientist
GENCODE, stop codon 
readthrough, SARS-CoV-2
Jackie Yang

Jackie Yang

Kai Kang

Kai Kang

Leandro Agudelo

Leandro Agudelo

Lei Hou

Lei Hou

Postdoctoral Associate /Research Scientist
Disease genetics + epigenomics
Lei Xiong

Lei Xiong

Martin Wohlwend

Martin Wohlwend

Postdoctoral Associate
Functional genomics, iPSCs
Riley Mangan

Riley Mangan

Postdoctoral Associate
Gene Regulation, Evolution
Suvi Linna-Kuosmanen

Suvi Linna-Kuosmanen

Xikun Han

Xikun Han

Xushen Xiong

Xushen Xiong

Yosuke Tanigawa

Yosuke Tanigawa

Postdoctoral Associate
Disease heterogeneity dissection;
 inclusive polygenic scores
Zunpeng Liu

Zunpeng Liu

Postdoctoral Associate
Single-cell epigenomics
Shanshan Zhang

Shanshan Zhang

Postdoctoral Associate
Single-cell genomics and epigenomics
Eman Alnabati

Eman Alnabati

Postdoctoral Associate

PhD Students


Alexander Lenail

Alexander Lenail

PhD
Computational Systems Biology
Benjamin James

Benjamin James

PhD
Single-cell genomics
Eloi Schmauch

Eloi Schmauch

Elvira Kinzina

Elvira Kinzina

Na Sun

Na Sun

Sebastian Pineda

Sebastian Pineda

Meng Students


Alexandra Berg

Alexandra Berg

Meng
Computation and Cognition Research Assistant
Cassia Wang

Cassia Wang

Meng
Computational Biology

Visitors


Liang He

Liang He

Assistant Professor
Human-Computer Interaction
Purdue University
Elektra Manolakos

Elektra Manolakos

William Ruzicka

William Ruzicka

Simon Mack

Simon Mack

Visiting student
Epigenomic imputation
Wendi Liu

Wendi Liu

Xiaohe Tian

Xiaohe Tian

Visiting student
Cell-type Informed PRS Models
Visiting PhD student
AI for Drug Discovery

UROP


Alvin Zheng

Alvin Zheng

Ananth Shyamal

Ananth Shyamal

Andrew Zhang

Andrew Zhang

Archita Khaire

Archita Khaire

Ashley Martin

Ashley Martin

Ashwini Suriyaprakash

Ashwini Suriyaprakash

SuperUROP: Building the 
Gene Regulatory Network 
using Deep Learning
Benson Lin

Benson Lin

Deep Learning VAEs for phenotypic decoupling
 of single-cell expression patterns in Alzheimer's
 Disease
Catherine Li

Catherine Li

Cell Type Inference with Bayesian Models in
 Spatial Transcriptomics
Elaine Jiang

Elaine Jiang

Interactive Idea Navigator Collaborative Space:
 AI-Enhanced Team Interaction and Collaboration
Erin Johnson

Erin Johnson

Ethan Harbaugh

Ethan Harbaugh

Using mutations to gauge the significance 
of structure in protein coding and
 non-coding exons
Evan Bell

Evan Bell

Himani Kamineni

Himani Kamineni

Variational auto-encoders for dissecting 
phenotypic drivers of single-cell 
expression patterns variation in post-
mortem human brain samples across 
427 individuals
Ian Gatlin

Ian Gatlin

HaploReg v5
Isabella Zhu

Isabella Zhu

Jay Bhan

Jay Bhan

Jayashabari Shankar

Jayashabari Shankar

Uncovering Human Evolutionary 
History Through Large Scale Bayesian 
Ancestral Sequence Reconstruction
Katherine Xie

Katherine Xie

Kathleen Zhang

Kathleen Zhang

Kevin Wu

Kevin Wu

Kevin Wen

Kevin Wen

Statistical Inference for Spatial 
Transcriptomics
Kevin Yang

Kevin Yang

Lara Ozkan

Lara Ozkan

LeAnn Tai

LeAnn Tai

Protein Language Models for 
Therapeutics
Mahdi Afshari

Mahdi Afshari

Hierarchical Modeling of Protein Structure for 
Predicting Function
Maya Bose

Maya Bose

Nikitha Thoduguli

Nikitha Thoduguli

Bayesian estimation of ancient DNA error rates and 
diploid variants for hominin genome reconstruction
Olivia Han

Olivia Han

samAssembler: a reference-biased diploid genome 
pseudoassembly for functional modeling of ancient 
DNA
Olivia Tang

Olivia Tang

Pascal Passigan

Pascal Passigan

Interactive Idea Navigator Collaborative Space: 
AI-Enhanced Team Interaction and Collaboration
Remi Kuba

Remi Kuba

Web-based Visualization of Single-Cell 
RNA Sequencing Data
Saniya Karwa

Saniya Karwa

Interactive Idea Navigator Collaborative 
Space
Sarah Dufays

Sarah Dufays

Interactive Idea Navigator Collaborative Space: 
AI-Enhanced Team Interaction and Collaboration
Sarah Zhao

Sarah Zhao

Recent Human Evolution and Disease 
Susceptibility: Brain, Metabolism, Immunity
Serena Pei

Serena Pei

Shagun Singh

Shagun Singh

Shreya Chaudhary

Shreya Chaudhary

Non-Coding Exon Structural Analyses
Spruce Campbell

Spruce Campbell

Launching Mantis - Interactive Idea Navigator
Unyime Usua

Unyime Usua

Vanessa Xiao

Vanessa Xiao

Spatial Transcriptomics and Geometric Deep 
Learning in Cancer
Will Hathaway

Will Hathaway

Academic Text Embeddings Using Citation 
Networks
William Li

William Li

Polygenic dissection of phenotypic heterogeneity 
in Alzheimer's Disease
Yuru Lin

Yuru Lin

Evolutionary Genetic Analysis of Human Aging 
and Longevity
Zach Marinov

Zach Marinov

Alumni


Ferhat Ay

Ferhat Ay

Visiting Ph.D. student
Regulatory Networks
Mukul Bansal

Mukul Bansal

Postdoc Associate
Phylogenetics (with Eric Alm)
Chris Bristow

Chris Bristow

Postdoc Fellow
Drosophila Regulation
Laura Cantini

Laura Cantini

Postdoc Fellow
Cancer
William Chen

William Chen


High-throughput perturbations (with Tim Lu)
Melina Claussnitzer

Melina Claussnitzer

Postdoc / Visiting Scientist Harvard/Germany
Disease mechanism
Jose Davila-Velderrain

Jose Davila-Velderrain

Postdoctoral Associate (from Mexico)
Brain Networks
Luisa Di Stefano

Luisa Di Stefano

Scientific Manager
modEncode
Abdoulaye Diallo

Abdoulaye Diallo

Postdoc Associate (from McGill)
Gene and Species Evolution (with Eric Alm)
Jason Ernst

Jason Ernst

Postdoc Fellow
Epigenomics
Soheil Feizi

Soheil Feizi

Ph.D. student with Muriel Medard
Regulatory Genomics
Loyal Goff

Loyal Goff

Postdoc Fellow
Small RNAs and Chromatin (with John Rinn)
Joshua Grochow

Joshua Grochow

M.Eng. student, Fall 2006-June 2007
Network motifs and evolution
David Hendrix

David Hendrix

Postdoc Associate
RNAs/Regulation
Ah-Ram Kim

Ah-Ram Kim

Postdoc Associate
Transcription Modeling & Regulatory Genomics
Anshul Kundaje

Anshul Kundaje


ENCODE/Epigenomics
Yue Li

Yue Li

Postdoc Associate
Transcriptional networks & Epigenomics in diseases
Erez Lieberman

Erez Lieberman

Ph.D. student (Harvard)
Motif evolution
Yaping Liu

Yaping Liu

Postdoc Associate
Epigenomics
Daniel Marbach

Daniel Marbach

Postdoc Fellow
Biological Networks
Wouter Meuleman

Wouter Meuleman

Postdoctoral Associate
Epigenomics
Patrick E. Meyer

Patrick E. Meyer

Visiting Postdoc
Biological networks
Eva Maria Novoa

Eva Maria Novoa

Postdoc Fellow
RNA modifications Post-transcriptional Regulation
Stephan Ossowski

Stephan Ossowski

Postdoc Associate
Disease Epigenomics
Yongjin Park

Yongjin Park


Statistical Genetics
Leopold Parts

Leopold Parts

UROP student, Summer 2006
microRNA discovery
Andreas Pfenning

Andreas Pfenning

Postdoc Associate
Epigenomics, Neurobiology, Evolution
Aviva Presser

Aviva Presser

Ph.D. student (Harvard)
Network evolution
Gerald Quon

Gerald Quon

Postdoc Associate
Comparative genomics
Sushmita Roy

Sushmita Roy

Postdoc Fellow
Evolution of Regulation (with Aviv Regev)
Alexander Stark

Alexander Stark

PostDoc (EMBL)
2005-2008 Networks in Fly
Jianrong Wang

Jianrong Wang

Postdoc
Epigenomic linking
Robert Waterhouse

Robert Waterhouse

Marie Curie Fellow
Comparative Genomics
Max Wolf

Max Wolf

CSBi Ph.D.
Transcriptomics
Jessica Wu

Jessica Wu

Ph.D. Student Domain evolution
Xiaohui Xie

Xiaohui Xie

Postdoc Fellow (Broad) with Eric Lander Fall 2004-2007
Human motifs
Nezar Abdennur

Nezar Abdennur

Ph.D (with Leonid Mirny)
HiC
Yuri Ahuja

Yuri Ahuja

MD/Ph.D. (HST)
EHR mining
Jieun Jeong

Jieun Jeong

Research Scientist 2019, Visiting Scientist 2016-2018
Gene Regulation
Thrasyvoulos Karydis

Thrasyvoulos Karydis

Media Lab with Joe Jacobson
Deep Learning
Sam Sungil Kim

Sam Sungil Kim

EECS with Alkes Price
Statistical Genetics
Dianbo Liu

Dianbo Liu

Visiting Student UK
Disease Networks
Tobias Madsen

Tobias Madsen

Visiting Student with Jakob Pedersen
Cancer Networks
Khoi Nguyen

Khoi Nguyen

Ph.D. (with Ron Weiss)
Differentiation
Yu-Ping Poh

Yu-Ping Poh

Postdoctoral Associate (from Harvard)
Population Genetics
Malene Rasmussen

Malene Rasmussen

Visiting Student with Jakob Pedersen
Cancer Networks
Abhishek Sarkar

Abhishek Sarkar

Ph.D.
Disease Genomics
Rachel Sealfon

Rachel Sealfon

Ph.D. student with Pardis Sabeti
Microbial Genomics
Andrew Shea

Andrew Shea

EECS
EHRs
Sam Sledziesk

Sam Sledziesk

EECS
Single-cell lineages
Dan Sosa

Dan Sosa

M.Eng. Student
Regulatory Networks
Rohil Verma

Rohil Verma

EECS
Brain genomics
Austin Wang

Austin Wang

EECS with Sasha Gusev
Statistical Genetics
Xinchen Wang

Xinchen Wang

Ph.D. student
Complex Disease Epigenomics (with Laurie Boyer)
Bob Altshuler

Bob Altshuler

Ph.D.
Mammalian Regulation
Luis Barrera

Luis Barrera

HST Ph.D.
Regulatory Genomics (with Martha Bulyk)
Kunal Bhutani

Kunal Bhutani

Visiting Student
Pop Gen With Nick Schork
Florin Chelaru

Florin Chelaru

Postdoctoral Associate
Epigenetic Visualization
Matthew Eaton

Matthew Eaton

Postdoc Associate
Epigenomics
Michael Gutbrod

Michael Gutbrod

Postdoc
Disease Dissection
Pouya Kheradpour

Pouya Kheradpour


Regulatory Motifs
Maria Kousi

Maria Kousi

Research Scientist
Dinesh Kumar

Dinesh Kumar

Postdoctoral (Fellow Swedish Medical Council SSMF)
Brain methylation and memory
Mike Lin

Mike Lin

Ph.D. student
Protein-coding genes and selection
Shahin Mohammadi

Shahin Mohammadi

Postdoctoral Associate
Single-cell analysis, Systems biology
Karthik Murugadoss

Karthik Murugadoss

S.M. Student
Cancer
Peter Nguyen

Peter Nguyen

M.Eng. Student
Epigenomics
Matt Rasmussen

Matt Rasmussen

Grad Student/Postdoc
Phylogenomics
Richard Sallari

Richard Sallari

Postdoctoral Associate
Cancer Genomics
Alvin Shi

Alvin Shi

CSBi
Cancer/immune
Luke Ward

Luke Ward

Postdoc associate
Population (epi)genomics (with Pardis Sabeti)
Stefan Washietl

Stefan Washietl

Postdoc Fellow
Long ncRNAs and structure
Thomas Willems

Thomas Willems

CSBi Ph.D. with Yaniv Erlich
Pop Gen
Vinod Yadav

Vinod Yadav

Postdoctoral Associate
Cancer
Angela Yen

Angela Yen

Ph.D. (EECS)
Epigenomics
Zhizhuo Zhang

Zhizhuo Zhang

Postdoctoral Associate
Regulatory Grammars
Ikechukwu Adebi

Ikechukwu Adebi

MEng student
Aurora Alvarez-Buylla

Aurora Alvarez-Buylla

Super UROP
Naeimeh Atabaki Pasdar

Naeimeh Atabaki Pasdar

Visitng PostDoc
metabolism
Anna Ayuso

Anna Ayuso

M.Eng. student
Drosophila Image Analysis
Neil Band

Neil Band

Grad student
single cell, AD
Carles Boix

Carles Boix

PhD '22
Genomic Circuitry
Wes Brown

Wes Brown

6.UAP/MEng
Phylogenomics
Rogerio Candeias

Rogerio Candeias

Ph.D. (Portugal)
Regulatory Networks
Stephanie Chang

Stephanie Chang

UROP student, Fall 2011
Hem N Chaudhary

Hem N Chaudhary

UROP student
Contextualized Machine Learning(CML) to understand obesity-related metabolism disorders at the individual patient level
Isabel Chien

Isabel Chien

MEng student
Hoon Cho

Hoon Cho

Ph.D. (EECS)
Regulatory models
Adrian Dalca

Adrian Dalca

EECS Rotation student Fall 2009
Azim Dehghani Amirabad

Azim Dehghani Amirabad

PostDoc
Single cell, epigenomics
Ameya Deoras

Ameya Deoras

MS student, Fall 2006-June 2007
Spectral analyses of genomes
Antoine Despinasse

Antoine Despinasse

Visitng student
Matt Edwards

Matt Edwards

EECS Rotation student Fall 2009
Aria R Eppinger

Aria R Eppinger

UROP student
Investigating Inflammatory Components Across Multiple Diseases
Lilia Evgeniou

Lilia Evgeniou

Undergrad intern
Doris Fu

Doris Fu

MEng student
Melanoma
Issao Fujiwara

Issao Fujiwara

M.Eng. student
Evolutionary Signatures
Will Gibson

Will Gibson

HST Ph.D. rotation
Disease Epigenomics
Rushil Goel

Rushil Goel

Ph.D. student
Regulatory Networks
Michal Grzadkowski

Michal Grzadkowski

Ph.D.
Networks
Nathan Han

Nathan Han

UROP student
Liang He

Liang He

PostDoc
Ben Holmes

Ben Holmes

Ph.D.
Regulatory Networks (with Feng Zhang)
Christian Hwa

Christian Hwa

MEng student
Benjamin Iriarte

Benjamin Iriarte

Ph.D. (Math)
Expression Variation
Assel Ismoldayeva

Assel Ismoldayeva

MEng student
Olivier Jaillon

Olivier Jaillon

Research Scientist
Genome Evolution
Roger Jin

Roger Jin

MEng student
TCR alpha-beta pairing
Hyun Kim

Hyun Kim

UROP student
Computational Biology Database/Dataset Search Optimization and Cross-Connection
Yuliya Kodysh

Yuliya Kodysh

UROP student, Fall 2006
Motif conservation in distant species
Johnny Li

Johnny Li

Grad student
Haozhi Lin

Haozhi Lin

UROP student, Summer 2012
Sabrina Liu

Sabrina Liu

Grad student
Amber Luo

Amber Luo

UROP student
Single-cell Dissection of the Obesity-Exercise Axis in the Brain
Hanna Mendes

Hanna Mendes


Research Compute Infrastructure
Mariana Mendoza

Mariana Mendoza

Visiting student
Network inference
Hayden Metsky

Hayden Metsky

M.Eng. student; UROP student, Summer 2012
Epigenomics and regulatory elements
Joseph Min

Joseph Min

Grad student
Maria Moran

Maria Moran

Research scientist
Tom Morgan

Tom Morgan

UROP student
Embryo Development With Tommi Poggio
Johannes Ojanen

Johannes Ojanen

Visiting student
Heart
Matthew Pandelakis

Matthew Pandelakis

Technical associate
Ashley Renfro

Ashley Renfro

Technical associate
Maha Shady

Maha Shady

MEng student
Max Shen

Max Shen

Grad student
Miriam Shiffman

Miriam Shiffman

Grad student
Josephine Simmons

Josephine Simmons

Summer intern
Nick Sinnott-Armstrong

Nick Sinnott-Armstrong

Visitng grad student
Eric Soderstrom

Eric Soderstrom

UROP student, Summer/Fall 2011
Ava Soleimany

Ava Soleimany

Rotation Student
Schizophrenia Networks
Teodora Stan

Teodora Stan

UROP student
single-cell
Longzhi Tan

Longzhi Tan

UROP student, Summer/Fall 2011
Remy Tuyeras

Remy Tuyeras

PostDoc
Petr Volkov

Petr Volkov

Visiting Student
Diabetes Epigenomics
Maggie Walker

Maggie Walker

Super UROP
Jennifer Wang

Jennifer Wang

UROP student, Summer/Fall 2011
Tom Watkins

Tom Watkins

Visitng PostDoc
Xushen Xiong

Xushen Xiong

PostDoc
eGTEX/single-cell AD
Iris Xu

Iris Xu

UROP student, Summer 2011
Deniz Yorukoglu

Deniz Yorukoglu

Ph.D.
Population Genomics
Xinyi Zhang

Xinyi Zhang

Rotation
Jemmie Chang

Jemmie Chang

Experimental With Li-Huei Tsai Lab
Sarah Goggin

Sarah Goggin

Research Associate; Experimental
GWAS dissection
Julio Mantero

Julio Mantero

Research Associate
Single-cell Genomics
Benoit Molinie

Benoit Molinie

Research Associate; Experimental
GWAS dissection
Alham Saadat

Alham Saadat

Experimental
Debora Sobreira

Debora Sobreira

Experimental; Visiting
Sophie Strobel

Sophie Strobel

Visiting Student With Melina Claussnitzer and Ron Weiss
Adipocytes
Nicholas Van Wittenberghe

Nicholas Van Wittenberghe

Experimental
Li Wang

Li Wang

Postdoc; Experimental
GWAS dissection
Yixin Zhang

Yixin Zhang

Experimental
Ran Liebeskind-Hadas

Ran Liebeskind-Hadas

Visiting Professor
Phylogenomics
Je-Yoel Cho

Je-Yoel Cho

Visiting Professor; Dean, College of Veterinary Medicine
Epigenomics
Winston Hide

Winston Hide

Visiting Professor; Department of Neuroscience
AD
Batula Zaidi

Batula Zaidi

Project Manager
GWAS, GTEx
Gerri McGowan

Gerri McGowan

Admin Assistant
Cindy Gibbs

Cindy Gibbs

Admin Assistant
Debbi Goodwin

Debbi Goodwin

Admin Assistant
Jeff Taft

Jeff Taft

Admin