Jian Ma
Ray and Stephanie Lane Professor of Computational Biology, Ray and Stephanie Lane Computational Biology Department
Address:
Ray and Stephanie Lane Computational Biology Department, SCS
Carnegie Mellon University
5000 Forbes Avenue
Pittsburgh, PA 15213
Gates Hillman Center Room 7705
Work Phone: 412-268-2776
Administrative Assistant: Ally Ricarte
Lab Members
Shahul Alam
Ph.D Student
Xue Er Ding
Ph.D. Student
Nicholas Ho
Ph.D. Student (co-advised by Eric Xing)
Ellie Huber
Ph.D. Student (Machine Learning Department)
Spencer Krieger
Lane Fellow
Shaoheng Liang
Lane Fellow
Reming Liu
Postdoctoral Fellow
Xinyue Lu
Ph.D. Student
Junjie Tang
Postdoctoral Fellow
Shike Wang
Ph.D. Student
Muyu Yang
Ph.D. Student
Yang Zhang
Project Scientist/Engineer
Highlighted 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]
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.