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<!DOCTYPE html>
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<meta name="description" content="Tianming Zhou, Ph.D. student in CS at Carnegie Mellon University" />
<meta name="author" content="Tianming Zhou" />
<meta name="keywords" content="Tianming Zhou, 周天茗, Yao Class, Tsinghua, CMU, Carnegie Mellon University, Machine Learning, Single-Cell, Multi-Modal Learning, 3D Genome Structure">
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<li class="nav-item"><a class="nav-link" href="#about">About</a></li>
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<div class="col-sm-7 col-md-8 col-lg-10 col-xl-9 lead">
<div>Ph.D. student in Computer Science</div>
<div><a href="https://www.cs.cmu.edu/">Carnegie Mellon University</a></div>
<div>Email: <a href="mailto:tianmingzhou1995@gmail.com">tianmingzhou1995@gmail.com</a></div>
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<a href="https://github.com/tianmingzhou" target="_blank" class="icon"><i class="fa-brands fa-github-square fa-2x"></i></a>
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<h2>About me</h2>
<p class="lead">I am a 6th year Ph.D. student in <a href="https://www.cs.cmu.edu/~jianma/">Prof. Jian Ma's lab</a> in the <a href="https://www.cs.cmu.edu/">School of Computer Science</a> at <a href="http://www.cmu.edu/">Carnegie Mellon University</a>. I earned a <a href="https://www.ml.cmu.edu/academics/machine-learning-masters-curriculum.html">Master in Machine Learning</a> during my Ph.D. and hold a B.E. in Computer Science and Technology from <a href="https://iiis.tsinghua.edu.cn/en/yaoclass/">Yao Class, Institute for Interdisciplinary Information Sciences</a> at <a href="https://www.tsinghua.edu.cn/en/index.htm">Tsinghua University</a>. During undergraduate, I worked with <a href="http://group.iiis.tsinghua.edu.cn/~compbio/">Prof. Jianyang Zeng</a> at Tsinghua University and <a href="https://home.ttic.edu/~jinbo/">Prof. Jinbo Xu</a> at <a href="https://www.ttic.edu/">Toyota Technological Institute at Chicago</a>.</p>
<p class="lead">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.
</p>
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<section id="publications">
<div class="container px-4"><div class="row gx-4 justify-content-center"><div class="col-lg-10">
<h2>Publications</h2>
<p>Note: <span>†</span> denotes equal contribution.</p>
<div class="row my-5" id="zhou2023concurrent">
<div class="col-md-5"><img class="mw-100" alt="Paper image" src="./figures/zhou2023concurrent-overview.jpeg"></div>
<div class="col-md-7">
<div class="title">GAGE-seq concurrently profiles multiscale 3D genome organization and gene expression in single cells</div>
<div><b>Zhou T</b>, Zhang R, Jia D, Doty RT, Munday AD, Gao D, Xin L, Abkowitz JL, Duan Z, Ma J</div>
<div><span class="fst-italic text-dark fw-bold">Nature Genetics</span>. 2024. <span class="text-primary">Impact Factor=41.38</span></div>
<div>
<a class="btn btn-outline-primary my-1 mr-1 btn-sm" target="_blank" rel="noopener" href="https://www.nature.com/articles/s41588-024-01745-3">Paper</a>
<a class="btn btn-outline-primary my-1 mr-1 btn-sm" target="_blank" rel="noopener" href="https://github.com/ma-compbio/GAGE-seq">GitHub</a>
</div>
</div>
</div>
<div class="row my-5" id="chidester2023spicemix">
<div class="col-md-5"><img class="mw-100" alt="Paper image" src="./figures/chidester2023spicemix-overview.png"></div>
<div class="col-md-7">
<div class="title">SPICEMIX enables integrative single-cell spatial modeling of cell identity</div>
<div>Chidester B<span>†</span>, <b>Zhou T</b><span>†</span>, Alam S, Ma J</div>
<div><span class="fst-italic text-dark fw-bold">Nature Genetics</span>. 2023. <span class="text-primary">Impact Factor=41.38</span></div>
<div>Early version in Proceedings of the 25th Annual Conference on Research in Computational Molecular Biology (<span class="fst-italic text-dark fw-bold">RECOMB</span>), 2021.</div>
<div>
<a class="btn btn-outline-primary my-1 mr-1 btn-sm" target="_blank" rel="noopener" href="https://www.nature.com/articles/s41588-022-01256-z">Paper</a>
<a class="btn btn-outline-primary my-1 mr-1 btn-sm" target="_blank" rel="noopener" href="https://www.nature.com/ng/volumes/55/issues/1">Cover Article</a>
<a class="btn btn-outline-primary my-1 mr-1 btn-sm" target="_blank" rel="noopener" href="https://www.cs.cmu.edu/news/2023/cell-identity-understanding">SCS News</a>
<a class="btn btn-outline-primary my-1 mr-1 btn-sm" target="_blank" rel="noopener" href="https://cbd.cmu.edu/news/2023/machine-learning-method-improves-cell-identity-understanding.html">CBD News</a>
<a class="btn btn-outline-primary my-1 mr-1 btn-sm" target="_blank" rel="noopener" href="https://github.com/ma-compbio/SpiceMix">GitHub</a>
<a class="btn btn-outline-primary my-1 mr-1 btn-sm" target="_blank" rel="noopener" href="https://www.youtube.com/watch?v=EELkmK56Pn8">Spatial Omics Seminar</a>
</div>
</div>
</div>
<div class="row my-5" id="zhang2022ultrafast">
<div class="col-md-5"><img class="mw-100" alt="Paper image" src="./figures/zhang2022ultrafast-overview.png"></div>
<div class="col-md-7">
<div class="title">Ultrafast and interpretable single-cell 3D genome analysis with Fast-Higashi</div>
<div>Zhang R<sup>†</sup>, <b>Zhou T</b><sup>†</sup>, Ma J</div>
<div><span class="fst-italic text-dark fw-bold">Cell System</span>. 2022. <span class="text-primary">Impact Factor=11.09</span></div>
<div>Early version in Proceedings of the 26th Annual Conference on Research in Computational Molecular Biology (<span class="fst-italic text-dark fw-bold">RECOMB</span>), 2022.</div>
<div>
<a class="btn btn-outline-primary my-1 mr-1 btn-sm" target="_blank" rel="noopener" href="https://doi.org/10.1016/j.cels.2022.09.004">Paper</a>
<a class="btn btn-outline-primary my-1 mr-1 btn-sm" target="_blank" rel="noopener" href="https://www.cell.com/cell-systems/issue?pii=S2405-4712(21)X0011-7#fullCover">Cover Article</a>
<a class="btn btn-outline-primary my-1 mr-1 btn-sm" target="_blank" rel="noopener" href="https://github.com/ma-compbio/Fast-Higashi">GitHub</a>
</div>
</div>
</div>
<div class="row my-5" id="zhang2022multiscale">
<div class="col-md-5"><img class="mw-100" alt="Paper image" src="./figures/zhang2022multiscale-overview.png"></div>
<div class="col-md-7">
<div class="title">Multiscale and integrative single-cell Hi-C analysis with Higashi</div>
<div>Zhang R, <b>Zhou T</b>, Ma J</div>
<div><span class="fst-italic text-dark fw-bold">Nature Biotechnology</span>. 2022. <span class="text-primary">Impact Factor=68.16</span></div>
<div>
<a class="btn btn-outline-primary my-1 mr-1 btn-sm" target="_blank" rel="noopener" href="https://www.nature.com/articles/s41587-021-01034-y">Paper</a>
<a class="btn btn-outline-primary my-1 mr-1 btn-sm" target="_blank" rel="noopener" href="https://github.com/ma-compbio/Higashi">GitHub</a>
<a class="btn btn-outline-primary my-1 mr-1 btn-sm" target="_blank" rel="noopener" href="https://www.cs.cmu.edu/news/2021/higashi-algorithm">SCS News</a>
<a class="btn btn-outline-primary my-1 mr-1 btn-sm" target="_blank" rel="noopener" href="https://cbd.cmu.edu/news/2021/machine-learning-genome-folding.html">CBD News</a>
</div>
</div>
</div>
<div class="row my-5" id="zhou20213d">
<div class="col-md-5"><img class="mw-100" alt="Paper image" src="./figures/zhou20213d-overview.png"></div>
<div class="col-md-7">
<div class="title">The 3D Genome Structure of Single Cells</div>
<div><b>Zhou T</b><sup>†</sup>, Zhang R<sup>†</sup>, Ma J</div>
<div><span class="fst-italic text-dark fw-bold">Annual Review of Biomedical Data Science</span>. 2021.</div>
<div>
<a class="btn btn-outline-primary my-1 mr-1 btn-sm" target="_blank" rel="noopener" href="https://www.annualreviews.org/doi/full/10.1146/annurev-biodatasci-020121-084709">Paper</a>
</div>
</div>
</div>
<div class="row my-5" id="chidester2019rotation">
<div class="col-md-5"><img class="mw-100" alt="Paper image" src="./figures/chidester2019rotation-overview.png"></div>
<div class="col-md-7">
<div class="title">Rotation equivariant and invariant neural networks for microscopy image analysis</div>
<div>Chidester B, <b>Zhou T</b>, Do MN, Ma J</div>
<div><span class="fst-italic text-dark fw-bold">Bioinformatics</span>. 2019. <span class="text-primary">Impact Factor=6.937</span></div>
<div>
<a class="btn btn-outline-primary my-1 mr-1 btn-sm" target="_blank" rel="noopener" href="https://doi.org/10.1093/bioinformatics/btz353">Paper</a>
<a class="btn btn-outline-primary my-1 mr-1 btn-sm" target="_blank" rel="noopener" href="https://github.com/bchidest/CFNet">GitHub</a>
</div>
</div>
</div>
<div class="row my-5" id="zeng2018complexcontact">
<div class="col-md-5"><img class="mw-100" alt="Paper image" src="./figures/zeng2018complexcontact-overview.png"></div>
<div class="col-md-7">
<div class="title">ComplexContact: a web server for inter-protein contact prediction using deep learning</div>
<div>Zeng H<span>†</span>, Wang S<span>†</span>, <b>Zhou T</b><span>†</span>, Zhao F, Li X, Wu Q, Xu J</div>
<div><span class="fst-italic text-dark fw-bold">Nucleic Acids Research</span>. 2018. <span class="text-primary">Impact Factor=19.16</span></div>
<div>
<a class="btn btn-outline-primary my-1 mr-1 btn-sm" target="_blank" rel="noopener" href="https://academic.oup.com/nar/article/46/W1/W432/5001161">Paper</a>
<!-- <a class="btn btn-outline-primary my-1 mr-1 btn-sm" target="_blank" rel="noopener" href="http://raptorx.uchicago.edu/ComplexContact/">Server</a>-->
</div>
</div>
</div>
<div class="row my-5" id="zhou2018deep">
<div class="col-md-5"><img class="mw-100" alt="Paper image" src="./figures/zhou2018deep-overview.png"></div>
<div class="col-md-7">
<div class="title">Deep learning reveals many more inter-protein residue-residue contacts than direct coupling analysis</div>
<div><b>Zhou TM</b><sup>†</sup>, Wang S<sup>†</sup>, Xu J</div>
<div>Proceedings of the 22th Annual Conference on Research in Computational Molecular Biology (<span class="fst-italic text-dark fw-bold">RECOMB</span>), 2018.</div>
<div>
<a class="btn btn-outline-primary my-1 mr-1 btn-sm" target="_blank" rel="noopener" href="https://dblp.org/db/conf/recomb/recomb2018.html">Proceeding</a>
<a class="btn btn-outline-primary my-1 mr-1 btn-sm" target="_blank" rel="noopener" href="https://www.biorxiv.org/content/10.1101/240754v3">BioRxiv</a>
</div>
</div>
</div>
</div></div></div>
</section>
<!-- Awards section-->
<section id="awards" class="bg-light">
<div class="container px-4"><div class="row gx-4 justify-content-center"><div class="col-lg-10">
<h2>Awards</h2>
<ul class="lead">
<li>Outstanding Research Accomplishment Award, CBD, CMU, 2023</li>
<li>Honorable Mention for the Outstanding Research Accomplishment Award, CBD, CMU, 2021 and 2022</li>
<li>Tsinghua Xuetang Scholarship, 2014-2017</li>
<li>Silver Medal in National Olympiad in Informatics (NOI), 2013</li>
<li>Gold Medal in National Olympiad in Informatics in Provinces (NOIP), 2014</li>
</ul>
</div></div></div>
</section>
<!-- Presentations section-->
<section id="presentations">
<div class="container px-4"><div class="row gx-4 justify-content-center"><div class="col-lg-10">
<h2>Presentations</h2>
<ul class="lead">
<li>
<div>Concurrent profiling of multiscale 3D genome organization and gene expression in single mammalian cells. 12/10/2023</div>
<div>Talk presentation & poster. <b>2023 4DN Annual Meeting</b>, Boston, US.</div>
</li>
<li>
<div>Integrative machine learning solutions for single-cell 3D genome analysis. 12/08/2022</div>
<div>Poster. <b>2022 4DN Annual Meeting</b>, San Diego, US.</div>
</li>
<li>
<div>Integrative analysis of single-cell 3D genome variation and gene transcription. 10/06/2022</div>
<div>Talk presentation. <b>4DNsc4ALL</b>, Virtual Meeting.</div>
</li>
<li>
<div>SpiceMix: Integrative single-cell spatial modeling for inferring cell identity. 03/25/2022</div>
<div>Talk presentation. <b>Spatial Omics Seminar</b> 2022, Virtual Meeting.</div>
<a class="btn btn-outline-primary my-1 mr-1 btn-sm" target="_blank" rel="noopener" href="https://www.youtube.com/watch?v=EELkmK56Pn8">YouTube</a>
</li>
<li>
<div>Efficient and interpretable single-cell 3D genome analysis. 02/01/2022</div>
<div>Talk presentation. <b>4DN Neuro IG</b>, Virtual Meeting.</div>
</li>
<li>
<div>Deep learning reveals many more inter-protein residue-residue contacts than direct coupling analysis. 04/22/2018</div>
<div>Talk presentation. <b>RECOMB</b> 2018, Paris, France.</div>
</ul>
</div></div></div>
</section>
<!-- Misc section-->
<section id="misc" class="bg-light">
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<h2>Misc</h2>
<h3>Reviewer</h3>
<ul>
<li>Reviewer for <a href="https://www.nature.com/ncomms/">Nature Communications</a>, 2023</li>
<li>Reviewer for <a href="https://genbio-workshop.github.io/">GenBio NeurIPS Workshop</a>, 2023</li>
<li>Reviewer for <a href="https://www.computer.org/csdl/journal/tb">IEEE/ACM Transactions on Computational Biology and Bioinformatics</a>, 2023</li>
<li>Reviewer for <a href="https://psb.stanford.edu/">Pacific Symposium on Biocomputing (PSB)</a> 2024</li>
<li>Reviewer for <a href="https://journals.plos.org/ploscompbiol/">PLOS Computational Biology</a>, 2023</li>
<li>Reviewer for <a href="https://icml-compbio.github.io/">The ICML Workshop on Computational Biology</a>, 2023</li>
<li>Reviewer for <a href="https://www.frontiersin.org/journals/immunology">Frontiers in Immunology</a>, 2023</li>
<li>Reviewer for <a href="https://academic.oup.com/bioinformatics">Bioinformatics</a>, 2023</li>
<li>Reviewer for <a href="https://www.frontiersin.org/journals/oncology">Frontiers in Oncology</a>, 2023</li>
<li>Secondary reviewer for <a href="https://www.iscb.org/ismbeccb2023">International Conference on Intelligent Systems for Molecular Biology (ISMB)</a> 2023</li>
<li>Secondary reviewer for <a href="https://recomb2022.net/">International Conference on Research in Computational Molecular Biology (RECOMB)</a> 2022</li>
<li>Secondary reviewer for <a href="https://www.iscb.org/ismbeccb2021">International Conference on Intelligent Systems for Molecular Biology (ISMB)</a> 2021</li>
<li>Secondary reviewer for <a href="https://www.iscb.org/ismb2020">International Conference on Intelligent Systems for Molecular Biology (ISMB)</a> 2020</li>
<li>Secondary reviewer for <a href="https://recomb2020.org/">International Conference on Research in Computational Molecular Biology (RECOMB)</a> 2020</li>
<li>Secondary reviewer for <a href="https://www.iscb.org/ismbeccb2019">International Conference on Intelligent Systems for Molecular Biology (ISMB)</a> 2019</li>
</ul>
<h3>Teaching Assistant</h3>
<ul>
<li>15-351/15-650/02-613: Algorithms and Advanced Data Structures, 2020 Fall & 2021 Spring</li>
</ul>
</div></div></div>
</section>
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