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

I am a Postdoctoral 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 focuses on understanding and engineering cells at scale — developing computational methods to characterize cellular identity from multimodal data, map cells in their spatial context, and model or redesign their molecular programs. I am particularly interested in applications to immune recognition and programmable gene regulation.

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
Our work "A structure-informed deep learning framework for modeling TCR-peptide-HLA interactions" was accepted by Nature Communications. Featured
Aug 11
Our work "CPS Mapping Physical Coordinates to High-Fidelity Spatial Transcriptomics via Privileged Multi-Scale Context Distillation" was published in Bioinformatics and presented at ISMB Conference 2026.
Jul 15
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
Our work "Graspot A graph attention network for spatial transcriptomics data integration with optimal transport" was accepted to ECCB Conference 2024.
May 31
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
2021
I was honored with the China National Scholarship for doctoral students.
Oct 31
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

Nature Communications 2026 (accepted)

[Paper] [Code]

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

Nature Communications 2026 (accepted)

[Paper] [Code]

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] [Code]

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] [Code]

Graspot: A graph attention network for spatial transcriptomics data integration with optimal transport
Graspot: A graph attention network for spatial transcriptomics data integration with optimal transport

Zizhan Gao, Kai Cao#, Lin Wan# (# corresponding author)

Bioinformatics 2024 (ECCB oral presentation)

[Paper] [Code]

Graspot: A graph attention network for spatial transcriptomics data integration with optimal transport

Zizhan Gao, Kai Cao#, Lin Wan# (# corresponding author)

Bioinformatics 2024 (ECCB oral presentation)

[Paper] [Code]

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] [Code]

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] [Code]

Manifold alignment for heterogeneous single-cell multi-omics data integration using Pamona
Manifold alignment for heterogeneous single-cell multi-omics data integration using Pamona

Kai Cao, Yiguang Hong, Lin Wan

Bioinformatics 2021

[Paper] [Code]

Manifold alignment for heterogeneous single-cell multi-omics data integration using Pamona

Kai Cao, Yiguang Hong, Lin Wan

Bioinformatics 2021

[Paper] [Code]

Unsupervised Topological Alignment for Single-Cell Multi-Omics Integration
Unsupervised Topological Alignment for Single-Cell Multi-Omics Integration

Kai Cao, Xiangqi Bai, Yiguang Hong, Lin Wan

Bioinformatics 2020 (ISMB oral presentation)

[Paper] [Code]

Unsupervised Topological Alignment for Single-Cell Multi-Omics Integration

Kai Cao, Xiangqi Bai, Yiguang Hong, Lin Wan

Bioinformatics 2020 (ISMB oral presentation)

[Paper] [Code]

All publications