Available to mentor
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.
https://sites.google.com/view/congmalab/home
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Postdoctoral Research AssociatePrinceton University, Department of Computer Science, 2024
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PhDCarnegie Mellon University, Pittsburgh, 2020
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BSZhejiang University of Science and Technology, Hangzhou, 2015
Spatial transcriptomics
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Terekhanova NV, Karpova A, Liang W-W, Strzalkowski A, Chen S, Li Y, Southard-Smith AN, Iglesia MD, Wendl MC, Jayasinghe RG, Liu J, Song Y, Cao S, Houston A, Liu X, Wyczalkowski MA, Lu RJ-H, Caravan W, Shinkle A, Naser Al Deen N, Herndon JM, Mudd J, Ma C, Sarkar H, Sato K, Ibrahim OM, Mo C-K, Chasnoff SE, Porta-Pardo E, Held JM, Pachynski R, Schwarz JK, Gillanders WE, Kim AH, Vij R, DiPersio JF, Puram SV, Chheda MG, Fuh KC, DeNardo DG, Fields RC, Chen F, Raphael BJ, Ding L. Nature, 2023 Nov; 623 (7986): 432 - 441.Journal ArticleEpigenetic regulation during cancer transitions across 11 tumour types.
DOI:10.1038/s41586-023-06682-5 PMID: 37914932 -
Zhang D, Deng Y, Kukanja P, Agirre E, Bartosovic M, Dong M, Ma C, Ma S, Su G, Bao S, Liu Y, Xiao Y, Rosoklija GB, Dwork AJ, Mann JJ, Leong KW, Boldrini M, Wang L, Haeussler M, Raphael BJ, Kluger Y, Castelo-Branco G, Fan R. Nature, 2023 Apr; 616 (7955): 113 - 122.Journal ArticleSpatial epigenome-transcriptome co-profiling of mammalian tissues.
DOI:10.1038/s41586-023-05795-1 PMID: 36922587 -
Ma C, Chitra U, Zhang S, Raphael BJ. Cell Syst, 2022 Oct 19; 13 (10): 786 - 797.e13.Journal ArticleBelayer: Modeling discrete and continuous spatial variation in gene expression from spatially resolved transcriptomics.
DOI:10.1016/j.cels.2022.09.002 PMID: 36265465 -
Zheng H, Ma C, Kingsford C. J Comput Biol, 2022 Feb; 29 (2): 121 - 139.Journal ArticleDeriving Ranges of Optimal Estimated Transcript Expression due to Nonidentifiability.
DOI:10.1089/cmb.2021.0444 PMID: 35041494 -
Ma C, Zheng H, Kingsford C. Algorithms Mol Biol, 2021 May 10; 16 (1): 5Journal ArticleExact transcript quantification over splice graphs.
DOI:10.1186/s13015-021-00184-7 PMID: 33971903 -
Qiu Y, Ma C, Xie H, Kingsford C. Algorithms Mol Biol, 2020 15: 9Journal ArticleDetecting transcriptomic structural variants in heterogeneous contexts via the Multiple Compatible Arrangements Problem.
DOI:10.1186/s13015-020-00170-5 PMID: 32467720 -
Ma C, Kingsford C. Cell Syst, 2019 Dec 18; 9 (6): 589 - 599.e7.Journal ArticleDetecting, Categorizing, and Correcting Coverage Anomalies of RNA-Seq Quantification.
DOI:10.1016/j.cels.2019.10.005 PMID: 31786209 -
Ma C, Shao M, Kingsford C. Genome Biol, 2018 Apr 12; 19 (1): 52Journal ArticleSQUID: transcriptomic structural variation detection from RNA-seq.
DOI:10.1186/s13059-018-1421-5 PMID: 29650026
