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Jian Ma

Associate Professor, Computational Biology
( Affiliated Faculty, Machine Learning )
School of Computer Science
Carnegie Mellon University

Office: GHC 7705
Phone: (412) 268-2776
Admin Assistant: Janet Garrand


Welcome to our Computational Genomics Laboratory! I am an Associate Professor (with tenure) in the Computational Biology Department (with an Affiliated Faculty appointment in the Machine Learning Department) within the School of Computer Science at Carnegie Mellon University. Our group started at the University of Illinois at Urbana-Champaign in August 2009 and we moved to Carnegie Mellon in January 2016. I have been fortunate to receive a few awards, including, among others, being named "Tomorrow's PI" by Genome Technology (2011), a National Science Foundation CAREER award (2011), and a Guggenheim Fellowship (2020).

Our main focus is to develop algorithms to better understand the organization and function of the human genome and the molecular mechanisms of human disease. We also work on methods for integrating biomedical data from multiple modalities. Recent interests include nuclear genome organization, comparative genomics, complex molecular interactions, cancer genomics, and single cell biology.

Selected Publications ▮ By topic: 3D genome ∣ comparative genomics ∣ cancer genomics ∣ machine learning

Recent News ▮ all updates
12/18/2020.
Two papers accepted to RECOMB 2021.
12/18/2020.
Yuchuan's SPIN paper accepted by Genome Biology.
11/19/2020.
Yang Yang defended her PhD dissertation and will join the lab of Dana Pe'er as a postdoc.
10/15/2020.
Our lab will lead a UM1 Center in the next phase of NIH 4D Nucleome [CMU News].
09/18/2020.
Ruochi received the Outstanding Research Accomplishment Award from the department.
06/25/2020.
Try our Nucleome Browser: a multimodal, interactive data visualization platform to integrate genomic, imaging, and 3D structure data to study 4D Nucleome. Watch an earlier talk.
06/25/2020.
Jian joined the Advisory Board of Cell Systems and the Editorial Board of Genome Biology.
05/20/2020.
MATCHA paper published in Cell Systems.
04/13/2020.
Yang Zhang's MutSpace paper accepted to ISMB 2020.
04/09/2020.
Jian Ma received Guggenheim Fellowship (in Computer Science) [CMU News].
02/20/2020.
MOCHI paper published in Genome Research as a Cover Article [CMU News].
12/23/2019.
Ruochi's paper accepted to RECOMB 2020.
12/20/2019.
Jian Ma promoted to Deputy Editor of PLOS Computational Biology.
12/19/2019.
Ruochi's Hyper-SAGNN paper accepted to ICLR 2020.
11/19/2019.
We received an ASPIRE Award from the Mark Foundation.
11/08/2019.
Yang Yang's Phylo-HMGP among the RECOMB/ISCB RSG Reading List 2018.
11/07/2019.
Kyle's SNIPER paper published in Nature Communications [CMU News].
07/27/2019.
Yang Yang is selected to attend the EECS Rising Stars 2019 workshop.
06/19/2019.
Phylo-HMRF published in Cell Systems.
06/18/2019.
We received renewal of our comparative genomics R01 (for 5 more years) from NHGRI/NIH.

Mailing Address
School of Computer Science, Carnegie Mellon University
5000 Forbes Avenue, Pittsburgh, PA 15213, USA