Manuel Garber
2011-present
Principal investigator
Systems immunology, regulatory genomics, and computational models of human inflammatory disease.
People
A cross-disciplinary lab
We are a group of scientists with diverse backgrounds spanning biology, math, and computer science, devoted to tackling key problems in immunity through a data-driven approach.
Current members
Principal investigator
Lab administration
Heidi Beberman
2013-present
Department Financial Administrator
Heidi is the department's financial administrator, and the person who keeps this lab running. She manages our finances and grants, listens to everyone, and always finds a way to help.
Graduate students
Shuo Shan
2020-present
Graduate Student
I map expression and response QTLs (reQTLs) in human skin cells to understand how genetic variants shape cytokine responses. My work combines eQTL and reQTL mapping with chromatin accessibility data and sequence-based deep learning models to identify variants that alter regulatory DNA elements and transcription factor binding.
Wei-Che Ko
2022-present
Millennium Program PhD Student
I am a board-certified dermatologist with subspecialty expertise in allergic contact dermatitis. In the clinic, I perform patch testing to identify the specific allergens driving a patient's skin disease. In my research, I combine clinical sampling with single-cell approaches and computational methods to define allergen-specific molecular signatures and dissect the immune mechanisms underlying contact allergy.
Computational scientists and research staff
Carolina Salomao Lopes
2019-present
Senior Scientist
I systematically stimulate skin stromal, mesenchymal, and immune cells with defined cytokines to map their precise responses. I use these response maps to identify the key signaling forces driving inflammation in autoimmune skin disease.
Thomas Jacob
2023-present
Bioinformatician
I am the bioinformatician and data scientist for the VIGOR study, a longitudinal vitiligo family study aimed at identifying the genetic and environmental causes of the disease. I build and maintain computational workflows to harmonize study data, derive insights from complex genomic datasets, integrate wearable biometrics (e.g., Fitbit data), and manage the cohort across platforms. My current focus is developing pipelines to evaluate genomic risk scores in the VIGOR cohort to better understand how a person's genome influences vitiligo onset.
Sandhiya Ravi
2026-present
Computational Biologist
I apply computational and AI/ML approaches to analyze single-cell and spatial transcriptomic data. My current work includes developing gene-expression scoring methods and studying cellular responses and states in inflammatory skin diseases.
Clinical and experimental collaborators
Alumni and past members
Graduate students
Yuqing Wang
March 2019 - June 2026
Graduate Student and Postdoctoral Fellow
Investigating the molecular mechanisms of photosensitivity in autoimmune skin diseases, including dermatomyositis and cutaneous lupus erythematosus (CLE), through integrated multi-omics analyses encompassing single-cell RNA sequencing (scRNA-seq), proteomics, and spatial transcriptomics.
Now: Bioinformatics Scientist, New England Biolabs, Inc.
Working on: Enzyme characterization using NGS, pipeline development and automation.
Yuming Cao
Sept 2018 - May 2025
Graduate Student and Postdoctoral Fellow
Investigated host-virus dynamics at single cell resolution in primary human cells.
Now: Computational Scientist, Broad Institute of MIT and Harvard
Working on: Computational tool development for large-scale single cell Perturb-seq screens
Jake Gellatly
March 2016 - May 2021
Graduate Student
With Patrick and Alan, I set up the lab's in-house inDrop system, and I developed the first single-cell analysis pipeline the lab used. During my PhD I focused on leveraging early single-cell blister biopsy data to identify the cell circuits underlying disease, leading the lab's first single-cell study of human vitiligo. That work laid the basis for all of the lab's skin autoimmunity projects since.
Now: Director of Product, FoxyAI, an AI real estate company
Working on: Applying vision-language models to solve problems for FoxyAI's customers
Pranitha Vangala
Sept 2014 - May 2020
Graduate Student and Postdoctoral Fellow
Role of cis-regulatory elements in transcriptional regulation integrating evolutionary approaches, 4D interaction data and chromatin activity maps
Now: Computational Biologist, Takeda Pharmaceuticals
Working on: Biomarkers and translational data science for gastro-intestinal and inflammatory diseases
Shaked Afik
2012-2013
Visiting Graduate Student
I worked on type 1 diabetes, analyzing RNA-seq of highly purified human adult and fetal islet alpha and beta cells with the Harlan and Greiner labs as part of the Human Islet Research Network (HIRN) effort. I also developed methods for 3' end RNA-seq analysis, defining transcription start and polyadenylation sites genome-wide. I went on to Nir Yosef's lab at UC Berkeley as a PhD student.
Postdoctoral fellows
Khashayar Afshari
May 2020 - June 2025
Joint Postdoctoral Fellow with Mehdi Rashighi
Immunology of autoimmune and inflammatory skin diseases, with a focus on disease mechanisms and the interplay between innate and adaptive immunity, particularly the role of myeloid cells. Studied the molecular mechanisms of photosensitivity in dermatomyositis and cutaneous lupus erythematosus (CLE), through integrated multi-omics analyses encompassing single-cell RNA sequencing (scRNA-seq), proteomics, and spatial transcriptomics, using mechanistic clinical trials as well as in vitro and ex vivo mechanistic studies in human cells and tissue.
Now: Scientist, Dr. Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine
Working on: Developing and applying multi-omic approaches to advance precision medicine in translational dermatology.
Artür Manukyan
August 2020 - Sept 2022
Postdoctoral Fellow
Development of bioinformatics analysis platforms and studying how skin diseases such as vitiligo and Stevens-Johnson syndrome arise at the molecular level using single-cell multi-omics integration
Now: Bioinformatics Scientist, Max Delbrück Center for Molecular Medicine
Working on: Multi-omics integration and software development for single-cell and spatial omics
Elisa Donnard
2014-2020
Postdoctoral Fellow
Single-cell and comparative genomics approaches to dissect transcriptional and post-transcriptional regulatory programs across diverse tissues. A particular focus was Fragile X syndrome, showing how loss of the FMRP protein leads to cell-type-specific transcriptional changes in mouse brain, and is linked to mRNA stability.
Now: Group Leader / Principal Investigator, Broad Institute / Novo Nordisk Foundation Center for Genomic Mechanisms of Disease
Working on: Functional genomics and gene regulation in metabolic disease-relevant cell models, using cell villages and large-scale Perturb-seq screens
Xiaopeng Zhu
Postdoctoral Fellow
Now: Jian Ma Lab, University of Pittsburgh
Computational scientists and research staff
Alan Derr
Computational Biologist
I developed the End Sequence Analysis Toolkit (ESAT), which extracts additional information from single-cell RNA-seq data through 3' end sequencing, and built it into the core of the lab's single-cell analysis pipeline.
Now: Retired
Working on: Traveling the world, biking, cooking, and designing jewelry, and combining traveling and biking as much as possible
Narayan Sadagopan
Bioinformatician
Rachel Murphy
Research Technician
Joined the lab as a technician right after graduating from WPI.
In memoriam
Patrick McDonel
1977–2023
Patrick passed away on November 19, 2023. The Garber lab owes much of the things we do to him. He established our molecular biology operation and instilled its philosophy.
It was not only in science that Patrick knew what was important. He kept everyone in touch — whether it was his Christmas gathering for non-Christians, an overnight smoking affair, or just cocktails, it was always at Patrick's house that we'd end up seeing people the rest of us hadn't made the time to seek out ourselves. He is sorely missed, and we keep his memory with us.