Cong Ma, PhD
Assistant Professor of Computational Medicine and Bioinformatics
Medical School
[email protected]

Available to mentor
Cong Ma, PhD
Assistant Professor
  • About
  • Links
  • Qualifications
  • Research Overview
  • Recent Publications
    • Manage Your Profile
    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
    • Postdoctoral Research Associate
      Princeton University, Department of Computer Science, 2024
    • PhD
      Carnegie Mellon University, 2020
    • BS
      Zhejiang University, 2015
    Research Overview

    Spatial transcriptomics

    Recent Publications See All Publications
    • Journal Article
      Mapping the topography of spatial gene expression with interpretable deep learning.
      Chitra U, Arnold BJ, Sarkar H, Sanno K, Ma C, Lopez-Darwin S, Raphael BJ. Nat Methods, 2025 Feb; 22 (2): 298 - 309. DOI:10.1038/s41592-024-02503-3
      PMID: 39849132
    • Journal Article
      Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics.
      Ma C, Balaban M, Liu J, Chen S, Wilson MJ, Sun CH, Ding L, Raphael BJ. Nat Methods, 2024 Dec; 21 (12): 2239 - 2247. DOI:10.1038/s41592-024-02438-9
      PMID: PMC11621028
    • Journal Article
      Tumour evolution and microenvironment interactions in 2D and 3D space.
      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. DOI:10.1038/s41586-024-08087-4
      PMID: PMC11525187
    • Journal Article
      Epigenetic regulation during cancer transitions across 11 tumour types.
      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. DOI:10.1038/s41586-023-06682-5
      PMID: PMC10632147
    • Journal Article
      Spatial epigenome-transcriptome co-profiling of mammalian tissues.
      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. DOI:10.1038/s41586-023-05795-1
      PMID: PMC10076218
    • Journal Article
      Belayer: Modeling discrete and continuous spatial variation in gene expression from spatially resolved transcriptomics.
      Ma C, Chitra U, Zhang S, Raphael BJ. Cell Syst, 2022 Oct 19; 13 (10): 786 - 797.e13. DOI:10.1016/j.cels.2022.09.002
      PMID: PMC9814896
    • Journal Article
      Deriving Ranges of Optimal Estimated Transcript Expression due to Nonidentifiability.
      Zheng H, Ma C, Kingsford C. J Comput Biol, 2022 Feb; 29 (2): 121 - 139. DOI:10.1089/cmb.2021.0444
      PMID: PMC8892959
    • Journal Article
      Exact transcript quantification over splice graphs.
      Ma C, Zheng H, Kingsford C. Algorithms Mol Biol, 2021 May 10; 16 (1): 5 DOI:10.1186/s13015-021-00184-7
      PMID: PMC8112020