Bottom Row: Yu Zhao, Saori Sakaue, Hannah Park, Elizabeth Morrison, Lakshay Sood
Principal Investigator
Soumya Raychaudhuri
Professor of Medicine and Biomedical Informatics, Harvard Medical School
Director, Center for Data Sciences, Brigham and Women’s Hospital
Institute Member, Broad Institute of Harvard and MIT
Harvard New Research Building
Brigham and Women’s Hospital, Division of Genetics
77 Ave. Louis Pasteur, Suite 250D
Boston, MA 02115
Research Scientists
Hyunsun Lee
Investigator, Brigham and Women’s Hospital
Lecturer, Harvard Medical School
Aparna Nathan
Lecturer on Bioinformatics, Department of Biomedical Informatics, Harvard Medical School
I am a lecturer at Harvard, and completed my PhD in Bioinformatics and Integrative Genomics in 2022 in the Raychaudhuri Lab. My dissertation focused on the integration of multimodal T cell data—RNA, surface proteins, genetics—to better understand their roles in infectious and autoimmune diseases. I also designed a single-cell approach to model state-dependent expression quantitative trait loci (eQTL) and I am currently extending this work to scale it to larger datasets without sacrificing statistical robustness. I use these methods to better understand the genetic architecture and state-dependent regulatory impact of immune disease-associated loci. Outside of research, I enjoy teaching and mentoring, writing about science for the public, and exploring Boston on foot.
Saori Sakaue
Instructor
I am an instructor who is excited to work with genetics and functional genomics data generated from novel experimental technologies to understand disease biology, teasing apart causality from consequences. As a rheumatologist, my goal is to contribute to better characterization of a spectrum of autoimmune diseases, individualized prediction of prognostic outcome, and optimized therapeutic intervention.
I joined the Raychaudhuri lab in 2020. Before then, I obtained MD and PhD at the University of Tokyo, where I studied human genetics using biobank-scale genotype data and applying statistical methods to understand biology of complex human traits.
Outside of the lab, I like cooking, reading books, and chatting with friends.
email: ssakaue@broadinstitute.org
Postdoctoral Fellows
Dylan Kotliar
Medical Resident
I’m a Medical Resident at Harvard Medical School in the Health Sciences and Technology track. I did my Ph.D in Pardis Sabeti’s lab at the Broad Institute in the Harvard Systems Biology PhD program. My Ph.D combined computational and experimental biology with field work in Nigeria, Liberia, and Sierra Leone to better understand deadly viral illnesses. I am now working on understanding immune cell states in infection and autoimmunity and how this relates to diversity in HLA genes and immune receptor repertoires.
Yakir Reshef
Clinical Fellow in Rheumatology
I am an MD/PhD computer scientist interested in the immune system. My research focuses on developing quantitative methods to compare immune state across samples in both single-cell and spatial transcriptomics datasets. In 2018, I completed a PhD in computer science at Harvard University working on problems in statistics, machine learning, and statistical genetics. In 2011, I was a Fulbright scholar in the Department of Applied Math and Computer Science at the Weizmann Institute of Science. In 2009, I graduated from Harvard College with a BA in mathematics, where I wrote my undergraduate thesis on pseudorandomness.
Personal website <https://yakirr.github.io/>
GitHub <https://github.com/yakirr>
Cristian Valencia
Postdoctoral Fellow
I’m a postdoctoral fellow that is interested in applying genetics and genomics to understand the interindividual variability on immune-related phenotypes. I joined the Raychaudhuri lab in 2021 and I am working on integrating single cell multi-omic thechnologies to better understand the genetics and the regulatory programs of immune mediated disease like type 1 diabetes. I completed my PhD at Johns Hopkins School of Public Health in 2021 under the supervision of Dr. Priya Duggal and Dr. Ben Larman where I studied the genetics of the antibody response to Epstein-Barr virus and Human Adenovirus at the epitope level. I am originally from Peru where I got my BA in biology from Universidad Nacional Federico Villarreal in 2012. Outside the lab I enjoy exploring the national parks and I am a foodie and black coffee lover.
José Alquicira-Hernández
Postdoctoral Fellow
I’m a postdoctoral fellow interested in understanding the genetic control of gene expression and its role in driving pathological cell states underlying autoimmune disease. I obtained my PhD on statistical genetics and cellular genomics at the University of Queensland and the Garvan Institute of Medical Research in Australia under the supervision of Professor Joseph Powell. During my PhD, I pioneered statistical and computational methods for single-cell genomics and applied statistical genetics approaches to study the genetic architecture of autoimmune disease at single-cell resolution. I am working group leader of the single-cell eQTLgen consortium since 2019, the largest initiative globally to map the genetic effects of gene expression at the single-cell level across multiple human tissues.
Links:
https://twitter.com/josealquicirah
https://joseah.github.io/
https://www.linkedin.com/in/jose-alquicira/
Annelise Mah-Som
Postdoctoral Fellow
Yu Zhao
Postdoctoral Fellow
I joined the Raychaudhuri lab in summer of 2023 as a postdoctoral research fellow. My research interests lie in the intersection of immunology, genetics and computational biology. I am particularly interested in T cell function and how T cell activation is regulated in different immune mediated diseases. I grew up in China and got my BS in biotechnology from Tongji University. Before moving to the US, I spent 7 years in Germany where I did my MS at the International Max Planck Research School for Neuroscience in Goettingen and received my PhD at University Medical Center Hamburg-Eppendorf. My dissertation focused on the computational characterization of T cell heterogeneity and function in different inflammatory diseases (supervisors: Prof. Stefan Bonn and Prof. Ulf Panzer). Outside of research, I enjoy reading, jogging, sightseeing and cooking with friends.
Contact Information:
yzhao44@bwh.harvard.edu
Websites:
Twitter: https://twitter.com/yu48693
LinkedIn: https://www.linkedin.com/in/yu-zhao-630930a8/
Google Scholar: https://scholar.google.com/citations?user=G8ruIu8AAAAJ&hl=en
Zepeng “Phoenix” Mu
Postdoctoral Fellow
I joined the lab as a Postdoctoral Fellow in Janurary 2024. Standing at the intersection of immunology and genetics, I’m passionate about combining the latest genomics technologies with state-of-the-art statistical methods to understand how non-coding genetic variants affect gene regulation and human complex traits, in particular autoimmune diseases. Before moving to Boston, I obtained my Ph.D. in Genetics with Dr. Yang I. Li at the University of Chicago, where I studied the impact of non-coding SNPs on gene expression and chromatin accessibility in immune cells, and how they can be used to understand disease GWAS. In 2018, I received my BS from University of Chinese Academy of Sciences (UCAS). When not thinking about science, I like reading, swimming, and drinking coffee!
Twitter: ZepengMu
Website: https://zepengmu.netlify.app
Students
Kaitlyn Lagattuta
Harvard Medical School MD-PhD Student
I’m an MD/PhD student (MD though the Harvard/MIT HST program and PhD in Bioinformatics & Integrative Genomics). I joined the Raychaudhuri lab in the summer of 2020, and I am currently analyzing covariation between T cell receptor (TCR) sequence features and T cell phenotype. More broadly, I am interested in how the immune receptor repertoire modifies disease risk, and how developmental processes give rise to age- and sex- specific incidences of various autoimmune diseases. In undergrad, I studied Computer Science at Stanford and worked on integrating genetic and epigenetic data to predict metastatic recurrence in kidney cancer. Outside of lab, I enjoy baking, going on hikes, playing softball, and doing anything with kids!
Kathryn Weinand
Harvard BIG PhD Student
I’m a PhD student in the Bioinformatics & Integrative Genomics Program. I joined the Raychaudhuri Lab in January 2020 and am currently working with scATAC-seq and snATAC/snRNA multiome tissue datasets to define the open chromatin landscape of dynamic pathogenic transcriptional cell states in rheumatoid arthritis. Before coming to graduate school, I worked as a computational technician in Dr. Martha Bulyk’s lab developing transcription factor motif enrichment software for TF ChIP-seq and chromatin accessibility datasets. I graduated with a bachelor’s degree in Cheminformatics from Michigan Technological University, where I investigated ab initio modeling of drug-target molecular interactions. Beyond lab, I enjoy reading historical fiction, exploring Boston on long rambles, and traveling both back home to Wisconsin and abroad.
Hannah Park
Undergraduate Student
I am an undergraduate student at Harvard College concentrating in Integrative Biology and Mathematics. I joined the Raychaudhuri Lab in early 2023 and have a keen interest in the T cell receptor (TCR). Specifically, I am focused on predictively quantifying TCR expression and characterizing genetic variants that regulate its expression. Prior to undergrad, I developed my interest in genetics and immunology under the supervision of Dr. Benjamin Tycko at the Hackensack Meridian Health Center for Discovery and Innovation. My 4-year project focused on medullary and cortical thymic epithelial cell differentiation and its influence on thymocyte development in a knockout mouse model of Down syndrome. Outside of the lab, I enjoy playing the violin and being a congressional advocate for Alzheimer’s and dementia research funding.
Sreekar Mantena
Harvard Medical School MD-PhD Student
Hafsa Mire
Harvard Immunology PhD Student
Research Staff
Majd Al Suqri
Technical Research Assistant
I graduated from the University of Colorado Boulder in 2021 with a double major in Neuroscience and Psychology and joined the Raychaudhuri lab shortly after. I’m passionate about understanding human disease in general, and the role of genetics in contributing to autoimmune disease specifically. In my free time, I enjoy being outdoors, listening to music, and reading.
Michelle Curtis
Bioinformatics Analyst
I graduated from Cornell University in 2021 with a Bachelor of Science in Biology, concentration in Computational Biology, and minor in Business. In my undergraduate research, I studied the virology of potatoes and benth in both a wet and dry lab capacity. Since joining the Raychauduri Lab in June 2021, I have focused on bioinformatics as I integrate multimodal methods to study immune-related disease. I enjoy nature, baking, and reading.
Lakshay Sood
Bioinformatics Analyst
Nicholas Sugiarto
Bioinformatics Analyst
I grew up in San Diego, California and Jakarta, Indonesia. Prior to joining the Raychaudhuri lab in 2023, I attend Dartmouth College and graduated in Biomedical Engineering and Computational Biology. I previously researched SWI/SNF and chromatin remodeling under Professor Xiaofeng Wang. I have no hobbies.
Administrative Staff
Cecilia Robinson
Senior Administrative Assistant
Alumni: Instructors
Ilya Korsunsky – Instructor in Medicine, Harvard Medical School
Yang Luo – Senior Research Fellow, Oxford University
Alumni: Research Scientists
Fan Zhang – Assistant Professor, University of Colorado
Alumni: Postdoctoral Fellows
Yuriy Baglaenko – Assistant Professor, University of Cincinnati
Jatin Arora – Postdoctoral Fellow
Kazuyoshi Ishigaki – Group Leader, Riken Center for Integrative Medical Science
Dorothee Diogo – Director of Statistical Genetics, Takeda. Boston, Massachusetts, United States
Yukinori Okada – Professor, University of Osaka, Osaka, Japan
Sherman Jia – Group Medical Director, Biomarker Development, Genentech, San Francisco, CA
Eli Stahl – Director of Statistical Genetics at Regeneron Genetics Center
Tobias Lenz – Professor for Evolutionary Immunogenomics at the University of Hamburg
Buhm Han – Associate Professor, Seoul National University, Seoul, Korea
Gosia Trynka – Group Leader at the Sanger Institute and Experimental Science Director at Open Targets, Welcome Trust Sanger Center, Cambridge, UK
Samira Asgari – Assistant Professor, Icahn School of Medicine, Mount Sinai
Chikashi Terao – Research Scientist, RIKEN Center for Integrative Medical Sciences; Professor, University of Shizuoka
Deepak Rao – Assistant Professor of Medicine, Harvard Medical School, Boston, MA; Co-mentored with Dr. Michael B. Brenner
Rachel Knevel – Assistant Professor, Leiden University Medical Center, Leiden, Netherlands
Maria Gutierrez Arcelus – Instructor in Medicine, Boston Children’s Hospital
Emma Davenport – Group Leader, Wellcome Sanger Institute, Cambridge, UK
Harm-Jan Westra – Postdoctoral Fellow, University of Groningen, Groningen, Netherlands
Alumni: Students
Laurie Rumker
Joyce Kang
Tiffany Amariuta – Postdoctoral Fellow, Harvard T. H. Chan School of Public Health
Aaron Deutsch – Endoccrinology Fellow, Brigham and Women’s Hospital, Boston, MA
Chamith Fonseka – Computational Biologist, Sana Biotechnology, MA
Xinli Hu – Director, Pfizer Inc., Cambridge, MA
Jennie Pouget – Psychiatric Resident, University of Toronto, Toronto, Canada
Amber Shen – PhD Student, Harvard Medical School
Kamil Slowikowski – Postdoctoral Associate, Massachusetts General Hospital, Boston, MA
Sushil Upadhyayula – Associate Consultant at Bain & Company
Gopal Vashishtha – Product Manager, Azure Machine Learning
Alumni: Research Technicians
Siddarth Gurajala – Masters student, University of Washington
Joseph Mears – MD/PhD student, University of Michigan
Qian Xiao – PhD student, Harvard Medical School
Ryan Agnew – PhD student, Washington University
Jessica Beynor – MD/PhD Student, University of Colorado
Susan Hannes – Associate Scientist, Novartis, Cambridge, MA
Hyun Kim – Pharmacist, Children’s Hospital, Boston, MA
Xinyi Li – PhD Student, University of Chicago, Chicago, IL
Dana Macfarlane – Technical Research Assistant
Nikola Teslovich – MD Student, Stanford University School of Medicine, Palo Alto, CA