Computational & Systems Biology Program

The Dana Pe'er Lab

Dana Pe'er, PhD

Chair, Computational and Systems Biology Program, SKI; Investigator, Howard Hughes Medical Institute; Alan and Sandra Gerry Endowed Chair

Professor

The Pe’er lab is an interdisciplinary group that combines advanced genomics approaches with machine learning to address fundamental questions in biomedical science. Empowered by potent technologies such as single-cell genomics and imaging-based molecular profiling, we analyze complex data to understand basic biology and disease. Our group is interested in how organisms develop from a single cell to generate a vast diversity of cell types, how epigenetic control over these processes rewires over the course of development, and how cells communicate to execute multicellular responses. We have a longstanding interest in cellular plasticity, the consequences of intra-tumor heterogeneity, the evolution and metastasis of cancer cells, and the mechanisms by which regulatory circuits go awry in disease. By understanding the mechanisms that different cancers use to initiate, progress, spread and interact with the immune system, we can spur the development of personalized therapies and immunotherapies.

Featured News

Researchers Russell Kunes, Thomas Walle, and Dana Pe'er

MSK Researchers Develop New Open-Source Method To Improve Decoding of Single-Cell Data

MSK researchers have developed a new open-source computational method, dubbed Spectra, which improves the analysis of single-cell transcriptomic data — and made it freely available to researchers around the world.

In the Lab

Fluorescent image of mouse prostate gland

New Discovery Explains How the Prostate Gland Regenerates Itself

Androgen-deprivation therapy, a mainstay of prostate cancer treatment, may give prostate cells new growth abilities, scientists at Memorial Sloan Kettering have found.

“Beautiful Patterns in Biology”: How SKI’s Dana Pe’er Earned a Top Honor and Advocates for Women Scientists

Dana Pe’er was recently named a Howard Hughes Medical Institute Investigator — one of the highest honors in biomedical science. As part of that designation, she will receive approximately $9 million over a seven-year term, with opportunity for renewal.

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Publications Highlights

Supervised discovery of interpretable gene programs from single-cell data. Kunes RZ*, Walle T*, Land M, Nawy T, Pe’er D. Nat Biotechnol. 2023 Sep 21. PMID: 37735262.

Epigenetic plasticity cooperates with cell-cell interactions to direct pancreatic tumorigenesis. Burdziak C*, Alonso-Curbelo D*, Walle T, Reyes J, Barriga FM, Haviv D, Xie Y, Zhao Z, Zhao CJ, Chen HA, Chaudhary O, Masilionis I, Choo ZN, Gao V, Luan W, Wuest A, Ho YJ, Wei Y, Quail DF, Koche R, Mazutis L, Chaligné R, Nawy T, Lowe SW†, Pe’er D†. Science. 2023 May 12;380(6645):eadd5327. PMID: 37167403.

The emergent landscape of the mouse gut endoderm at single-cell resolution. Nowotschin S*, Setty M*, Kuo YY, Liu V, Garg V, Sharma R, Simon CS, Saiz N, Gardner R, Boutet SC, Church DM, Hoodless PA, Hadjantonakis AK†, Pe’er D†. Nature. 2019 May;569(7756):361-367. PMID: 30959515

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People

Dana Pe'er, PhD

Chair, Computational and Systems Biology Program, SKI; Investigator, Howard Hughes Medical Institute; Alan and Sandra Gerry Endowed Chair

Professor

Computational biologist Dana Pe’er combines single-cell and spatial profiling technologies with machine learning approaches to address fundamental questions in gene regulation, cellular plasticity and cell-cell communication in the contexts of cancer, immunity and development.
PhD, Hebrew University, Jerusalem Israel

[email protected]: Email Address

Members

Cassandra Burdziak
Postdoctoral Researcher

Ronan Chaligné
Assistant Lab Member and Director of SAIL

Alejandro Jiménez-Sánchez
Postdoctoral Researcher

Andrew Moorman
Computational Biologist II, SAIL

Jo Adams — Josephine Adams
Computational Biologist, SAIL

Sydney Blattman

Postdoctoral Researcher

Tobias Krause

Bioinformatics Engineer I, SAIL

Rahul Saha
Computational Biologist, SAIL

Lab Alumni

Jaeyoung Chun
Manager, Computational Biologist, SAIL

Noor Sohail
Computational Biologist, SAIL

Ambrose Carr

PhD Student

Kristy Choi

Undergraduate Student

Herman Gudjonson
Postdoctoral Researcher

Simon Joost, PhD — Simon Joost
Postdoctoral Researcher

Pooja Kathail

Undergraduate Student

Vaidotas Kiseliovas
Postdoctoral Researcher

Sanjay Kottapalli
Computational Biologist, SAIL

Ashley Laughney
Postdoctoral Research Fellow

Jacob Levine

PhD Student

Awni Mousa
Senior Bioinformatics Engineer

Sandhya Prabhakaran
Postdoctoral Researcher

Deena Shefter
Computational Biologist, SAIL

Lisa Sikkema
Computational Biologist, SAIL

David van Dijk

Postdoctoral Researcher

Lab Affiliations

Achievements

2023 Class of 2023 Inductee - American Academy of Cancer Research (AACR) Academy
2023 Innovator Award - International Society for Computational Biology (ISCB)
2021 Fellow - International Society for Computational Biology (ISCB)
2019 Ernst W. Bertner Memorial Award - University of Texas MD Anderson Cancer Center
2016 Lenfest Distinguished Faculty Award - Columbia University

2014 Director’s Pioneer Award - National Institutes of Health
2014 Overton Prize - International Society for Computational Biology (ISCB)
2012 Test of Time Award - Research in Computational Molecular Biology (RECOMB)
2010 Innovator Award - Stand Up 2 Cancer/American Academy of Cancer Research (AACR)
2009 Packard Fellowship in Science and Engineering - The David and Lucile Packard Foundation
2007 NIH Director's New Innovator Award - National Institutes of Health
2005 Breakthrough of the Year Runner-up - Science Magazine
2005 Career Award at the Scientific Interface - Burroughs Wellcome Fund

Open Positions

To learn more about available postdoctoral opportunities, please visit our Career Center

To learn more about compensation and benefits for postdoctoral researchers at MSK, please visit Resources for Postdocs

Bioinformatics Engineer II - Genomics Algorithm Development

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PhD student and postdoctoral positions

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Get in Touch

[email protected]

Lab Head Email
646-888-3486

Dry Lab Phone
646-888-2319

Wet Lab Phone

Disclosures

Doctors and faculty members often work with pharmaceutical, device, biotechnology, and life sciences companies, and other organizations outside of MSK, to find safe and effective cancer treatments, to improve patient care, and to educate the health care community.

MSK requires doctors and faculty members to report (“disclose”) the relationships and financial interests they have with external entities. As a commitment to transparency with our community, we make that information available to the public.

Dana Pe'er discloses the following relationships and financial interests:

Insitro, Inc.
Equity; Professional Services and Activities

The information published here is a complement to other publicly reported data and is for a specific annual disclosure period. There may be differences between information on this and other public sites as a result of different reporting periods and/or the various ways relationships and financial interests are categorized by organizations that publish such data.

This page and data include information for a specific MSK annual disclosure period (January 1, 2023 through disclosure submission in spring 2024). This data reflects interests that may or may not still exist. This data is updated annually.

Learn more about MSK’s COI policies here. For questions regarding MSK’s COI-related policies and procedures, email MSK’s Compliance Office at [email protected].

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