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] He is a faculty member in the Computational Biology Department. His lab develops machine learning algorithms to study the structure and function of the human genome.[4] During his Ph.D. and postdoc training, he developed algorithms to reconstruct the ancestral mammalian genome.[5] He received an NSF CAREER award in 2011.[6] In 2020, he was awarded a Guggenheim Fellowship[7][8][9] in Computer Science. He leads an NIH 4D Nucleome Center to develop machine learning algorithms to better understand the cell nucleus.[4][10]

Jian Ma
马坚
CitizenshipUnited States
AwardsGuggenheim Fellowship (2020)
Scientific career
Fields
Institutions
Academic advisorsDavid Haussler (postdoc advisor), Webb Miller (PhD advisor)
Websitewww.cs.cmu.edu/~jianma/

Publications

His recent representative papers:

  • Zhang R, Zhou T, and Ma J. Multiscale and integrative single-cell Hi-C analysis with Higashi. Nature Biotechnology, https://doi.org/10.1038/s41587-021-01034-y, 2021
  • Wang Y, Zhang Y, Zhang R, van Schaik T, Zhang L, Sasaki T, Peric-Hupkes D, Chen Y, Gilbert DM, van Steensel B, Belmont AS, and Ma J. SPIN reveals genome-wide landscape of nuclear compartmentalization. Genome Biology, 22:36, 2021.
  • 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.
  • Zhang R, Zou Y, and Ma J. Hyper-SAGNN: a self-attention based graph neural network for hypergraphs. ICLR, 2020.
  • Lazzarotto CR, Malinin NL, Li Y, Zhang R, Yang Y, Lee G, Cowley E, He Y, Lan X, Jividen K, Katta V, Kolmakova NG, Petersen CT, Qi Q, Strelcov E, Maragh S, Krenciute G, Ma J, Cheng Y, and Tsai SQ. CHANGE-seq reveals genetic and epigenetic effects on CRISPR–Cas9 genome-wide activity. Nature Biotechnology, 38(11):1317-1327, 2020.
  • Xiong K and Ma J. Revealing Hi-C subcompartments by imputing inter-chromosomal chromatin interactions. Nature Communications, 10, 5069, 2019.
  • 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
  • Singh S, Poczos B, and Ma J. Minimax reconstruction risk of convolutional sparse dictionary learning. AISTATS, 2018.
  • 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
  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. Carnegie Mellon. "Carnegie Mellon Heads New Center for Studying Structure of Cell Nucleus - News - Carnegie Mellon University". www.cmu.edu. Retrieved 2021-06-19.
  5. 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.
  6. "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.
  7. "John Simon Guggenheim Foundation | Jian Ma". Retrieved 2020-05-22.
  8. "John Simon Guggenheim Foundation | 2020 Guggenheim Fellowship winners announced". Retrieved 2020-05-22.
  9. Carnegie Mellon (2020-04-10). "Jian Ma Wins Guggenheim Fellowship - News - Carnegie Mellon University". www.cmu.edu. Retrieved 2020-05-22.
  10. "CMU tapped to lead NIH research center building 3D map of cell nuclei". Pittsburgh Post-Gazette. Retrieved 2021-06-19.
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