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Jian Ma

Ray and Stephanie Lane Professor of Computational Biology
School of Computer Science
Carnegie Mellon University

Office: GHC 7705
Phone: (412) 268-2776
Admin Assistant: Ally Ricarte

🌈 We are looking for new Postdocs and PhD students (CBD or MLD) to work on Comp Bio + ML.

I am the Ray and Stephanie Lane Professor of Computational Biology in the School of Computer Science at Carnegie Mellon University. I also have an Affiliated Faculty appointment in Machine Learning. Our group started at the University of Illinois at Urbana-Champaign in August 2009. 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).

The main focus of our ongoing research is the development of machine learning algorithms to reveal fundamental connections between human genome structure and function and their implications in human diseases. We also work on machine learning methods for cohesive integration of multimodal biomedical data and for enhancing model interpretability and generalizability. Recent interests include nuclear genome organization, single-cell epigenomics, spatial omics, comparative genomics, and complex molecular interactions. Our lab is currently leading a UM1 Center in the Phase 2 of NIH 4D Nucleome Program [CMU News].

Selected Publications ▮ By topic: 3D genomecomparative genomicscancer genomicsmachine learning

Recent News ▮ all updates
Our manuscript describing Nucleome Browser is on bioRxiv. Also see our Tweetorial.
College of Fellows of the American Institute for Medical and Biological Engineering [CMU News].
We received an R01 to develop ML methods for single-cell 3D epigenomics from NHGRI/NIH.
Two papers accepted to RECOMB 2022.
Yang Yang received CMU SCS Dissertation Award Honorable Mention.
We received a Multi-PI grant from the NIH SenNet Program [CMU News].
Higashi published in Nature Biotechnology [CMU News].
Jian is named the Ray and Stephanie Lane Professor of Computational Biology [CMU News].
Tianming received Honorable Mention for the CBD Outstanding Research Accomplishment Award.
We are part of a Data and Admin Coordinating Center of the NHGRI IGVF [WashU News].
Jian has been promoted to Full Professor, effective on July 1, 2021.
Yuchuan's SPIN paper published in Genome Biology.
Two papers accepted to RECOMB 2021.
Our lab will lead a UM1 Center in the next phase of NIH 4D Nucleome [CMU News].
Ruochi received the Outstanding Research Accomplishment Award from the department.
MATCHA published in Cell Systems.
Jian received Guggenheim Fellowship (in Computer Science) [CMU News].
MOCHI published in Genome Research as a Cover Article [CMU News].
We received an ASPIRE Award from the Mark Foundation.
SNIPER published in Nature Communications [CMU News].
Yang Yang is selected to attend the EECS Rising Stars 2019 workshop.
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