Wikipedia

Jian Ma (computer scientist)

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.

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/

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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