Jian Ma (

Chinese Chinese can refer to: * Something related to China * Chinese people, people of Chinese nationality, citizenship, and/or ethnicity **''Zhonghua minzu'', the supra-ethnic concept of the Chinese nation ** List of ethnic groups in China, people of va ...

: 马坚) is an American

computer scientist A computer scientist is a person who is trained in the academic study of computer science. Computer scientists typically work on the theoretical side of computation, as opposed to the hardware side on which computer engineers mainly focus (al ...

and

computational biologist Computational biology refers to the use of data analysis, mathematical modeling and computational simulations to understand biological systems and relationships. An intersection of computer science, biology, and big data, the field also has fo ...

. He is the Ray and Stephanie Lane Professor of Computational Biology in the School of Computer Science at

Carnegie Mellon University Carnegie Mellon University (CMU) is a private research university in Pittsburgh, Pennsylvania. One of its predecessors was established in 1900 by Andrew Carnegie as the Carnegie Technical Schools; it became the Carnegie Institute of Technology ...

. He is a faculty member in the

Computational Biology Department The Computational Biology Department (CBD) is a division within the School of Computer Science at Carnegie Mellon University in Pittsburgh, Pennsylvania, United States. It is located in the Gates-Hillman Center. Established in 2007 by Robert F ...

. His lab develops machine learning algorithms to study the structure and function of the

human genome The human genome is a complete set of nucleic acid sequences for humans, encoded as DNA within the 23 chromosome pairs in cell nuclei and in a small DNA molecule found within individual mitochondria. These are usually treated separately as the n ...

. During his Ph.D. and postdoc training, he developed algorithms to reconstruct the ancestral mammalian genome. His research group has recently pioneered a series of new machine learning methods for 3D epigenomics and spatial genomics. He received an

NSF CAREER NSF may stand for: Political organizations *National Socialist Front, a Swedish National Socialist party *NS-Frauenschaft, the women's wing of the former German Nazi party *National Students Federation, a leftist Pakistani students' political gr ...

award in 2011. In 2020, he was awarded a

Guggenheim Fellowship Guggenheim Fellowships are grants that have been awarded annually since by the John Simon Guggenheim Memorial Foundation to those "who have demonstrated exceptional capacity for productive scholarship or exceptional creative ability in the ar ...

in Computer Science. He is an elected Fellow of the

American Association for the Advancement of Science The American Association for the Advancement of Science (AAAS) is an American international non-profit organization with the stated goals of promoting cooperation among scientists, defending scientific freedom, encouraging scientific respons ...

. He leads an NIH 4D Nucleome Center to develop machine learning algorithms to better understand the cell nucleus.

Recent Publications

* 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. over 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. over 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. *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. over Article*Zhang R, Zou Y, and Ma J. Hyper-SAGNN: a self-attention based graph neural network for hypergraphs. ''ICLR'', 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 *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

External links

Jian Ma's publications
indexed by Google Scholar {{DEFAULTSORT:Ma, Jian computer scientist Carnegie Mellon University faculty University of Illinois faculty American computer scientists Machine learning researchers Computational biologists Living people Fellows of the American Association for the Advancement of Science Year of birth missing (living people)