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 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.^[12] He is the Program Chair for RECOMB 2024.^[13]

Selected Recent Publications

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, https://doi.org/10.1038/s41588-024-01745-3, 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.