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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 was established at the University of Illinois at Urbana-Champaign in August 2009 and later moved to Carnegie Mellon in January 2016. I have been fortunate to receive several 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). I am an elected Fellow of AIMBE and AAAS.

The primary focus of our ongoing research is the development of AI/ML methods to study the structure and function of the human genome and cellular organization, with implications for health and disease. Recent interests include nuclear organization, single-cell epigenomics, spatial omics, and complex molecular interactions. These goals are often pursued through the development of probabilistic models and advanced deep learning techniques, particularly graph-based representation learning, with the aim of driving discovery and guiding experimentation. We are also exploring large language models to uncover gene regulatory mechanisms and the intricate connections among cellular components at various scales in complex tissues. Ultimately, our goal is to learn the language of cells through innovation in AI/ML.

Our lab is leading a UM1 Center in the NIH 4D Nucleome (4DN) Program [CMU News]. I am also serving as Co-Chair of the Steering Committee of the NIH 4DN Program. In addition, our lab is involved in the NIH SenNet Consortium and the IGVF Consortium.

I am the Program Chair for RECOMB 2024.

Selected Publications ▮ By topic: 3D epigenomicssingle cellcomparative genomicsmachine learning

Recent News ▮ all updates
08/30/2024.
We received an MPI NIH R21 with the labs of Guttman (Caltech) and Lomvardas (Columbia).
08/09/2024.
Interpretable ML Perspective article published in Nature Methods [CMU News].
08/07/2024.
News & Views article in Nature Genetics on our GAGE-seq paper.
05/14/2024.
GAGE-seq published in Nature Genetics.
04/20/2024.
Jian joins the External Advisory Board of the NIA ADSP AI/ML Consortium.
04/08/2024.
scGHOST published in Nature Methods [CMU News].
09/06/2023.
Our review on methods for 3D genome analysis published in Nature Reviews Genetics.
04/13/2023.
In collab. w/ Su-In Lee at UW, we received a Single-cell Data Insights grant from CZI.
01/31/2023.
Jian is elected 2022 AAAS Fellow [CMU News].
01/19/2023.
Jian represented the 4DN Program and gave a presentation to the NIH Council of Councils.
01/13/2023.
SPICEMIX published in Nature Genetics as a Cover Story [CMU News].
12/01/2022.
We received an award from Google Research to work on ML methods for genomics.
08/29/2022.
CMU School of Computer Science celebrates three chair professorships, including the Ray and Stephanie Lane Professorship that Jian received. [Photo]
02/11/2022.
We received an R01 to develop ML methods for single-cell 3D epigenomics from NHGRI/NIH.
11/02/2021.
Yang Yang received CMU SCS Dissertation Award Honorable Mention.
10/20/2021.
We received a Multi-PI grant from the NIH SenNet Program [CMU News].
10/11/2021.
Higashi published in Nature Biotechnology [CMU News].
09/29/2021.
Jian is named the Ray and Stephanie Lane Professor of Computational Biology [CMU News].
10/15/2020.
Our lab will lead a UM1 Center in the next phase of NIH 4D Nucleome [CMU News].
04/09/2020.
Jian received Guggenheim Fellowship (in Computer Science) [CMU News].

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