Jian Ma (computer scientist) explained

Jian Ma
Academic Advisors:	David Haussler (postdoc advisor), Webb Miller (PhD advisor)
Citizenship:	United States
Native Name:	马坚

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.^[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

• 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

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

External links

• Jian Ma's publications indexed by Google Scholar