Carnegie Mellon University

jianma_082017.jpeg Jian Ma

Ray and Stephanie Lane Professor of Computational Biology,  Ray and Stephanie Lane Computational Biology Department


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



The main focus of Dr. Ma's ongoing research is the development of machine learning algorithms to reveal fundamental connections between human genome structure and function and their implications in human diseases. We also work on machine learning methods for cohesive integration of multimodal biomedical data and for enhancing model interpretability and generalizability. Recent interests include nuclear genome organization, single-cell epigenomics, spatial omics, comparative genomics, and complex molecular interactions. Our lab is currently leading a UM1 Center in the Phase 2 of NIH 4D Nucleome Program.

Lab Members

 Shahul Alam

Ph.D Student

 Xue Er Ding

Ph.D. Student

 Nicholas Ho

Ph.D. Student

Spencer Krieger

Lane Fellow

 Shaoheng Liang

Lane Fellow

 Xinyue Lu

Ph.D. Student

 Shike Wang

Ph.D. Student

 Muyu Yang

Ph.D. Student

 Yang Zhang

Project Scientist/Engineer

 Tianming Zhou

Ph.D. Student

Highlighted Publications

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, doi:, 2022.

Yang Y, Wang Y, Zhang Y, and Ma J. CONCERT: Genome-wide prediction of sequence elements that modulate DNA replication timing. RECOMB, 2022.

Zhang R†,*, Zhou T, and Ma J*. Ultrafast and interpretable single-cell 3D genome analysis with Fast-Higashi. RECOMB, 2022.

Reilly A, Creamer JP, Stewart S, Stolla MC, Wang Y, Du J, Wellington R, Busch S, Estey EH, Becker PS, Fang M, Keel SB, Abkowitz JL, Soma LA, Ma J, Duan Z, and Doulatov S. Lamin B1 deletion in myeloid neoplasms causes nuclear anomaly and altered hematopoietic stem cell function. Cell Stem Cell, 29(4):577-592.e8, 2022.

Melamed A, Fitzgerald TW, Wang Y, Ma J, Birney E, and Bangham CRM. Selective clonal persistence of human retroviruses in vivo: radial chromatin organization, integration site and host transcription. Science Advances, 8(17):eabm6210, 2022.

Yang M and Ma J. Machine learning methods for exploring sequence determinants of 3D genome organization. Journal of Molecular Biology, doi: 10.1016/j.jmb.2022.167666, 2022.


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