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 evolution, 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 epigenomics, comparative genomics, spatial genomics, and single-cell analysis. 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] He leads an NIH 4D Nucleome Center to develop machine learning algorithms to better understand the cell nucleus.[5][12] He is the Program Chair for RECOMB 2024.[13]

Recent Publications[edit]

  • Zhang Y, Boninsegna L, Yang M, Misteli T, Alber F, and Ma J. Computational methods for analysing multiscale 3D genome organization. Nature Reviews Genetics, https://doi.org/10.1038/s41576-023-00638-1, 2023.
  • 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.
  • Zhang R and Ma J. MATCHA: Probing multi-way chromatin interaction with hypergraph representation learning. Cell Systems, 10(5):397-407.E5, 2020.
  • Tian D, Zhang R, Zhang Y, Zhu X, and Ma J. MOCHI enables discovery of heterogeneous interactome modules in 3D nucleome. Genome Research, 30(2):227-238, 2020. [Cover Article]
  • Yang Y, Zhang Y, Ren B, Dixon J, and Ma J. Comparing 3D genome organization in multiple species using Phylo-HMRF. Cell Systems, 8(6):494-505.e14, 2019.
  • Ma J and Duan Z. Replication timing becomes intertwined with 3D genome organization. Cell, 176(4):681-684, 2019
  • Yang Y, Gu Q, Zhang Y, Sasaki T, Crivello J, O'Neill R, Gilbert DM, and Ma J. Continuous-trait probabilistic model for comparing multi-species functional genomic data. Cell Systems, 7(2):208-218.e11, 2018.

References[edit]

  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. ^ "CMU tapped to lead NIH research center building 3D map of cell nuclei". Pittsburgh Post-Gazette. Retrieved 2021-06-19.
  13. ^ "RECOMB 2024 | HOME". recomb.org. Retrieved 2023-09-23.

External links[edit]

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