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Jian Ma (computer scientist)

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Jian Ma
马坚
CitizenshipUnited States
Awards
Scientific career
Fields
Institutions
Academic advisorsDavid Haussler (postdoc advisor), Webb Miller (PhD advisor)
Websitewww.cs.cmu.edu/~jianma/

Jian Ma (Chinese: 马坚) is an American computer scientist and computational biologist.[1] He is the Ray and Stephanie Lane Professor of Computational Biology in the School of Computer Science at Carnegie Mellon University.[2][3][4] He is a faculty member in the Ray and Stephanie Lane Computational Biology Department.

His lab develops machine learning algorithms to study the structure and function of the human genome[5] and cellular organization and their implications for health and disease. During his Ph.D. and postdoc training, he developed algorithms to reconstruct the ancestral mammalian genome.[6] His research group has recently pioneered a series of new machine learning methods for 3D genome organization, single-cell epigenomics, spatial omics, and complex molecular interactions. These methods 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.

He received an NSF CAREER award in 2011.[7] In 2020, he was awarded a Guggenheim Fellowship[8][9][10] in Computer Science. He is an elected Fellow of the American Association for the Advancement of Science[11] and the American Institute for Medical and Biological Engineering.[12] He leads an NIH 4D Nucleome Center to develop machine learning algorithms to better understand the cell nucleus.[5][13] He is the Program Chair for RECOMB 2024.[14]

In 2024, he launched the Center for AI-Driven Biomedical Research (AI4BIO) at CMU, which will be a catalyst for innovations at the intersection of AI and biomedicine across the School of Computer Science and campus.[15][16]

Selected Recent Publications

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  • Chen V#, Yang M#, Cui W, Kim JS, Talwalkar A*, and Ma J*. Applying interpretable machine learning in computational biology - pitfalls, recommendations and opportunities for new developments. Nature Methods, 21(8):1454-1461, 2024.
  • Xiong K#, Zhang R#, and Ma J. scGHOST: Identifying single-cell 3D genome subcompartments. Nature Methods, 21(5):814-822, 2024.
  • Zhou T, Zhang R, Jia D, Doty RT, Munday AD, Gao D, Xin L, Abkowitz JL, Duan Z*, and Ma J*. GAGE-seq concurrently profiles multiscale 3D genome organization and gene expression in single cells. Nature Genetics, 56(8):1701-1711, 2024.
  • Zhang Y, Boninsegna L, Yang M, Misteli T, Alber F, and Ma J. Computational methods for analysing multiscale 3D genome organization. Nature Reviews Genetics, 5(2):123-141, 2024.
  • Chidester B#, Zhou T#, Alam S, and Ma J. SPICEMIX enables integrative single-cell spatial modeling of cell identity. Nature Genetics, 55(1):78-88, 2023. [Cover Article]
  • Zhang R#, Zhou T#, and Ma J. Ultrafast and interpretable single-cell 3D genome analysis with Fast-Higashi. Cell Systems, 13(10):P798-807.E6, 2022. [Cover Article]
  • Zhu X#, Zhang Y#, Wang Y, Tian D, Belmont AS, Swedlow JR, and Ma J. Nucleome Browser: An integrative and multimodal data navigation platform for 4D Nucleome. Nature Methods, 19(8):911-913, 2022.
  • Zhang R, Zhou T, and Ma J. Multiscale and integrative single-cell Hi-C analysis with Higashi. Nature Biotechnology, 40:254–261, 2022.

References

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  1. ^ "Jian Ma - Google Scholar Citations". scholar.google.com. Retrieved 2020-05-22.
  2. ^ "Jian Ma Webpage at Carnegie Mellon".
  3. ^ Carnegie Mellon. "Jian Ma - Computational Biology Department - School of Computer Science - Carnegie Mellon University". cbd.cmu.edu. Retrieved 2021-06-18.
  4. ^ "SCS Faculty Receive Endowed Professorships". Carnegie Mellon School of Computer Science. Retrieved 2021-12-23.
  5. ^ a b Carnegie Mellon. "Carnegie Mellon Heads New Center for Studying Structure of Cell Nucleus - News - Carnegie Mellon University". www.cmu.edu. Retrieved 2021-06-19.
  6. ^ Pennisi, Elizabeth (2005-06-03). "Extinct Genome Under Construction". Science. 308 (5727): 1401–1402. doi:10.1126/science.308.5727.1401b. ISSN 0036-8075. PMID 15933177. S2CID 83068891.
  7. ^ "Jian Ma receives CAREER award for large-scale Genomic Studies | Carl R. Woese Institute for Genomic Biology". www.igb.illinois.edu. Retrieved 2020-05-22.
  8. ^ "John Simon Guggenheim Foundation | Jian Ma". Retrieved 2020-05-22.
  9. ^ "John Simon Guggenheim Foundation | 2020 Guggenheim Fellowship winners announced". Retrieved 2020-05-22.
  10. ^ Carnegie Mellon (2020-04-10). "Jian Ma Wins Guggenheim Fellowship - News - Carnegie Mellon University". www.cmu.edu. Retrieved 2020-05-22.
  11. ^ "Jian Ma Elected 2022 AAAS Fellow". Carnegie Mellon School of Computer Science. Retrieved 2023-02-02.
  12. ^ "CompBio Professor Elected to AIMBE's College of Fellows". Carnegie Mellon School of Computer Science. Retrieved 2024-10-12.
  13. ^ "CMU tapped to lead NIH research center building 3D map of cell nuclei". Pittsburgh Post-Gazette. Retrieved 2021-06-19.
  14. ^ "RECOMB 2024 | HOME". recomb.org. Retrieved 2023-09-23.
  15. ^ "CMU Launches Center for AI-Driven Biomedical Research". Carnegie Mellon School of Computer Science. Retrieved 2024-10-12.
  16. ^ "CMU Launches Center for AI-Driven Biomedical Research - News - Carnegie Mellon University". Carnegie Mellon University. 2024-10-08. Retrieved 2024-10-13.
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