Tianming's photo 
Ph.D. student in Computer Science
     

About me

I am a 6th year Ph.D. student in Prof. Jian Ma's lab in the School of Computer Science at Carnegie Mellon University. I earned a Master in Machine Learning during my Ph.D. and hold a B.E. in Computer Science and Technology from Yao Class, Institute for Interdisciplinary Information Sciences at Tsinghua University. During undergraduate, I worked with Prof. Jianyang Zeng at Tsinghua University and Prof. Jinbo Xu at Toyota Technological Institute at Chicago.

My research passion resides at the intersection of multimodal representation learning and biology. I am dedicated to advancing the field through the development of explainable artificial intelligence (XAI) methodologies, including probabilistic graphical models, graph neural networks, large language models, and tensor decomposition algorithms. Furthermore, I specialize in interpreting model outcomes and exploring cross-modality relationships. I apply these methodologies to tackle real-world challenges in various biological areas, including spatial transcriptomics, 3D genome structures, single-cell multiome, and protein-protein interactions.

Publications

Note: denotes equal contribution.

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GAGE-seq concurrently profiles multiscale 3D genome organization and gene expression in single cells
Zhou T, Zhang R, Jia D, Doty RT, Munday AD, Gao D, Xin L, Abkowitz JL, Duan Z, Ma J
Nature Genetics. 2024. Impact Factor=41.38
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SPICEMIX enables integrative single-cell spatial modeling of cell identity
Chidester B, Zhou T, Alam S, Ma J
Nature Genetics. 2023. Impact Factor=41.38
Early version in Proceedings of the 25th Annual Conference on Research in Computational Molecular Biology (RECOMB), 2021.
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Ultrafast and interpretable single-cell 3D genome analysis with Fast-Higashi
Zhang R, Zhou T, Ma J
Cell System. 2022. Impact Factor=11.09
Early version in Proceedings of the 26th Annual Conference on Research in Computational Molecular Biology (RECOMB), 2022.
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Multiscale and integrative single-cell Hi-C analysis with Higashi
Zhang R, Zhou T, Ma J
Nature Biotechnology. 2022. Impact Factor=68.16
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The 3D Genome Structure of Single Cells
Zhou T, Zhang R, Ma J
Annual Review of Biomedical Data Science. 2021.
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Rotation equivariant and invariant neural networks for microscopy image analysis
Chidester B, Zhou T, Do MN, Ma J
Bioinformatics. 2019. Impact Factor=6.937
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ComplexContact: a web server for inter-protein contact prediction using deep learning
Zeng H, Wang S, Zhou T, Zhao F, Li X, Wu Q, Xu J
Nucleic Acids Research. 2018. Impact Factor=19.16
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Deep learning reveals many more inter-protein residue-residue contacts than direct coupling analysis
Zhou TM, Wang S, Xu J
Proceedings of the 22th Annual Conference on Research in Computational Molecular Biology (RECOMB), 2018.

Awards

  • Outstanding Research Accomplishment Award, CBD, CMU, 2023
  • Honorable Mention for the Outstanding Research Accomplishment Award, CBD, CMU, 2021 and 2022
  • Tsinghua Xuetang Scholarship, 2014-2017
  • Silver Medal in National Olympiad in Informatics (NOI), 2013
  • Gold Medal in National Olympiad in Informatics in Provinces (NOIP), 2014

Presentations

  • Concurrent profiling of multiscale 3D genome organization and gene expression in single mammalian cells. 12/10/2023
    Talk presentation & poster. 2023 4DN Annual Meeting, Boston, US.
  • Integrative machine learning solutions for single-cell 3D genome analysis. 12/08/2022
    Poster. 2022 4DN Annual Meeting, San Diego, US.
  • Integrative analysis of single-cell 3D genome variation and gene transcription. 10/06/2022
    Talk presentation. 4DNsc4ALL, Virtual Meeting.
  • SpiceMix: Integrative single-cell spatial modeling for inferring cell identity. 03/25/2022
    Talk presentation. Spatial Omics Seminar 2022, Virtual Meeting.
    YouTube
  • Efficient and interpretable single-cell 3D genome analysis. 02/01/2022
    Talk presentation. 4DN Neuro IG, Virtual Meeting.
  • Deep learning reveals many more inter-protein residue-residue contacts than direct coupling analysis. 04/22/2018
    Talk presentation. RECOMB 2018, Paris, France.