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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 machine learning algorithms for the study of the structure and function of the human genome and cellular organization, as well as their implications for evolution, health, and disease. We also explore machine learning methods for the cohesive integration of multimodal biomedical data, as well as methods for enhancing model interpretability and generalizability. Recent interests include nuclear organization, single-cell epigenomics, spatial omics, comparative genomics, and complex molecular interactions.

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 epigenomicscomparative genomicscancer genomicsmachine learning

Recent News ▮ all updates
GAGE-seq paper accepted in principle in Nature Genetics.
scGHOST paper accepted in principle in Nature Methods.
Xinyue, Nick, Xue Er, and Shike join our lab as new PhD students.
Shaoheng gave a talk on LLMs for comp bio in a Generative AI Workshop at DTI.
Shahul selected as CPCB NIH T32 Trainee.
Our review on methods for 3D genome analysis published in Nature Reviews Genetics.
Tianming received the Outstanding Research Accomplishment Award from the department.
Jian gave a talk with the title "LLMs in Computational Biology: A Primer" at CGSI in UCLA.
Jian gave a talk at the Human Cell Atlas 2023 meeting.
Jian will serve as the Program Chair for RECOMB 2024.
In collab. w/ Su-In Lee at UW, we received a Single-cell Data Insights grant from CZI.
Jian is elected 2022 AAAS Fellow [CMU News].
Jian represented the 4DN Program and gave a presentation to the NIH Council of Councils.
SPICEMIX published in Nature Genetics as a Cover Story [CMU News].
We received an award from Google Research to work on ML methods for genomics.
Fast-Higashi published in Cell Systems and featured on the Cover.
CMU School of Computer Science celebrates three chair professorships, including the Ray and Stephanie Lane Professorship that Jian received. [Photo]
We received an R01 to develop ML methods for single-cell 3D epigenomics from NHGRI/NIH.
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].
Our lab will lead a UM1 Center in the next phase of NIH 4D Nucleome [CMU News].
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