Portrait
Kai Cao
Postdoctoral Researcher
Broad Institute of MIT and Harvard
About Me

I am a Postdoc Researcher at the Eric and Wendy Schmidt Center, Broad Institute of MIT and Harvard, working with Prof. Caroline Uhler and Prof. Ramnik Xavier. My research aims to bridge machine learning and biology, focusing on developing computational methods to tackle unresolved biological problems. Actively contributing to the academic community, I serve as a reviewer for journals such as Genome Research, Advanced Science and PLOS Computational Biology, as well as top conferences such as ISMB and RECOMB.

Education
  • Chinese Academy of Sciences
    Chinese Academy of Sciences
    Ph.D. in System Science, Academy of Mathematics and Systems Science
    Sep. 2017 - 2022
  • University of Science and Technology of China
    University of Science and Technology of China
    B.E. in Automation, School of Information Science and Technology
    Sep. 2013 - Jul. 2017
Experience
  • Broad Institute of MIT and Harvard
    Broad Institute of MIT and Harvard
    Postdoctoral Researcher, Eric and Wendy Schmidt Center
    Nov. 2022 - Present
  • University of Newcastle, Australia
    University of Newcastle, Australia
    Visiting Student, Department of Electrical and Computer Engineering
    June 2016 - Sep. 2016
News
2026
I gave a talk at the EWSC Symposium 2026. Watch video
Apr 27
Our work "CPS Mapping Physical Coordinates to High-Fidelity Spatial Transcriptomics via Privileged Multi-Scale Context Distillation" was accepted by ISMB Conference 2026, and will be published on Bioinformatics.
Apr 01
2025
Our work "scCausalVI disentangles single-cell perturbation responses with causality-aware generative model" was accepted by Cell Systems.
Jul 17
Our work "Securing diagonal integration of multimodal single-cell data against ambiguous mapping" was accepted by Bioinformatics.
Jun 01
2024
I gave a talk about "Learning to navigate the two-way street of AI and biology" at Broad Institute.
Dec 15
I gave a talk at "Models, Inference & Algorithms (MIA)" at Broad Institute. Watch video
Mar 05
2022
Our work "A unified framework for single-cell data integration with optimal transport" was accepted by Nature Communications and selected as Editor's Highlight.
Nov 17
I joined Caroline Uhler lab at MIT as a Postdoctoral Researcher. Featured
Nov 13
I passed the PhD thesis defense.
May 21
I gave a talk at the 1st Chinese Intelligent Health & Bioinformatics Conference.
Mar 23
Selected Publications (view all )
A structure-informed deep learning framework for modeling TCR-peptide-HLA interactions
A structure-informed deep learning framework for modeling TCR-peptide-HLA interactions

Kai Cao, Rui Li, Martin Strazar, Eric M. Brown, Phuong N. U. Nguyen, Marie-Madlen Pust, Jihye Park, Daniel B. Graham, Orr Ashenberg, Caroline Uhler, Ramnik Xavier

bioRxiv 2026

[Paper]

A structure-informed deep learning framework for modeling TCR-peptide-HLA interactions

Kai Cao, Rui Li, Martin Strazar, Eric M. Brown, Phuong N. U. Nguyen, Marie-Madlen Pust, Jihye Park, Daniel B. Graham, Orr Ashenberg, Caroline Uhler, Ramnik Xavier

bioRxiv 2026

[Paper]

Generative Design of Cell Type-Specific RNA Splicing Elements for Programmable Gene Regulation
Generative Design of Cell Type-Specific RNA Splicing Elements for Programmable Gene Regulation

Xi Dawn Chen*, Maile Jim*, Mounica Vallurupalli*, Kai Cao*, Andrea Navarro Torres, Jing Wesley Leong, Yifan Zhang, David Wollensak, Qiyu Gong, Jing Sun, Mehdi Borji, Gail Schor, Sofia Mrowka, Margaret Hu, Anisha Laumas, Jennifer A. Roth, Todd Golub, Fei Chen (* equal contribution)

bioRxiv 2025

[Paper]

Generative Design of Cell Type-Specific RNA Splicing Elements for Programmable Gene Regulation

Xi Dawn Chen*, Maile Jim*, Mounica Vallurupalli*, Kai Cao*, Andrea Navarro Torres, Jing Wesley Leong, Yifan Zhang, David Wollensak, Qiyu Gong, Jing Sun, Mehdi Borji, Gail Schor, Sofia Mrowka, Margaret Hu, Anisha Laumas, Jennifer A. Roth, Todd Golub, Fei Chen (* equal contribution)

bioRxiv 2025

[Paper]

A unified framework for single-cell data integration with optimal transport
A unified framework for single-cell data integration with optimal transport

Kai Cao*, Qiyu Gong*, Yiguang Hong, Lin Wan (* equal contribution)

Nature Communications 2022 Editors’ Highlights

[Paper]

A unified framework for single-cell data integration with optimal transport

Kai Cao*, Qiyu Gong*, Yiguang Hong, Lin Wan (* equal contribution)

Nature Communications 2022 Editors’ Highlights

[Paper]

All publications