Cong Ma, PhD
Assistant Professor of Computational Medicine and Bioinformatics
Medical School
[email protected]
Available to mentor
Cong Ma, PhD
Assistant Professor
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About
Professor Cong Ma develops mathematical, statistical, and machine learning models to study the spatial heterogeneity and organization of cell types including genetic and epigenetic states, in a variety of tissues, particularly in cancer tissues. Ma’s computational models can be applied to different types of tissues, either for foundational biology investigation or clinical research.
Her work includes accurately identifying the tissue geometries and the associated gradient of epigenetic variation. These computational models bring insights into disease mechanisms and could lead to the discovery of diagnostic biomarkers. For example, in cancers, her computational analysis shows how tumorous tissues organization evolves in space and behavior, which can inform potential treatments.
Links
https://sites.google.com/view/congmalab/home
Qualifications
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Postdoctoral Research AssociatePrinceton University, Department of Computer Science, Princeton, United States
2020 - 2024
Postdoctoral Research
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PhDCarnegie Mellon University, Pittsburgh, United States
2015 - 2020
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BSZhejiang University, Hangzhou, China
2011 - 2015
Research Overview
Spatial transcriptomics
Recent Publications
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Park J, Zhang T, Ma C. Cancer Research, 2026 Apr 3; 86 (7_Supplement): 6837 - 6837.Journal ArticleAbstract 6837: Scalable cell type and spatial domain modeling using spatially informed topic inference of cancer niches.
DOI:10.1158/1538-7445.am2026-6837 -
Hara T, Ma C. Cancer Cell, 2025 Dec 8; 43 (12): 2189 - 2190.Journal ArticleSpatial patterns of glioblastoma
DOI:10.1016/j.ccell.2025.10.013 PMID: 41270754 -
Samarah LZ, Zheng C, Xing X, Lee WD, Afriat A, Chitra U, MacArthur MR, Lu W, Jankowski CSR, Ma C, Hunter CJ, Neinast M, Weilandt DR, Raphael BJ, Rabinowitz JD. Nature, 2025 Dec 8; 648 (8092): 182 - 190.Journal ArticleSpatial metabolic gradients in the liver and small intestine
DOI:10.1038/s41586-025-09616-5 -
Zhang D, Rubio Rodríguez-Kirby LA, Lin Y, Wang W, Song M, Wang L, Wang L, Kanatani S, Jimenez-Beristain T, Dang Y, Zhong M, Kukanja P, Bao S, Wang S, Chen XL, Gao F, Wang D, Xu H, Ma C, Lou X, Liu Y, Chen J, Sestan N, Uhlén P, Kriegstein A, Zhao H, Castelo-Branco G, Fan R. Nature, 2025 Nov 6; 647 (8088): 213 - 227.Journal ArticleSpatial dynamics of brain development and neuroinflammation
DOI:10.1038/s41586-025-09663-y PMID: 41193846 -
Ma C, Najarian K. 2025 Sep 6; arXiv,PreprintRethinking the long-range dependency in Mamba/SSM and transformer models
DOI:10.48550/arxiv.2509.04226 -
Chitra U, Arnold BJ, Sarkar H, Sanno K, Ma C, Lopez-Darwin S, Raphael BJ. Nat Methods, 2025 Feb; 22 (2): 298 - 309.Journal ArticleMapping the topography of spatial gene expression with interpretable deep learning.
DOI:10.1038/s41592-024-02503-3 PMID: PMC12370209 -
Ma C, Balaban M, Liu J, Chen S, Wilson MJ, Sun CH, Ding L, Raphael BJ. Nat Methods, 2024 Dec; 21 (12): 2239 - 2247.Journal ArticleInferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics.
DOI:10.1038/s41592-024-02438-9 PMID: PMC11621028 -
Mo C-K, Liu J, Chen S, Storrs E, Targino da Costa ALN, Houston A, Wendl MC, Jayasinghe RG, Iglesia MD, Ma C, Herndon JM, Southard-Smith AN, Liu X, Mudd J, Karpova A, Shinkle A, Goedegebuure SP, Abdelzaher ATMA, Bo P, Fulghum L, Livingston S, Balaban M, Hill A, Ippolito JE, Thorsson V, Held JM, Hagemann IS, Kim EH, Bayguinov PO, Kim AH, Mullen MM, Shoghi KI, Ju T, Reimers MA, Weimholt C, Kang L-I, Puram SV, Veis DJ, Pachynski R, Fuh KC, Chheda MG, Gillanders WE, Fields RC, Raphael BJ, Chen F, Ding L. Nature, 2024 Oct; 634 (8036): 1178 - 1186.Journal ArticleTumour evolution and microenvironment interactions in 2D and 3D space.
DOI:10.1038/s41586-024-08087-4 PMID: PMC11525187
Featured News & Stories
Department News
Announcing CCMB/DCMB Winter 2026 seminar series
DCMB/CCMB seminar series features outstanding scientists in the field of computational medicine and bioinformatics, machine learning and AI. From prestigious universities from across the country and U-M, they will present their latest research.
