2026

CPS: Mapping Physical Coordinates to High-Fidelity Spatial Transcriptomics via Privileged Multi-Scale Context Distillation
CPS: Mapping Physical Coordinates to High-Fidelity Spatial Transcriptomics via Privileged Multi-Scale Context Distillation

Lei Zhang, Kai Cao, Shuqiao Zheng, Shu Liang, Lin Wan

Bioinformatics 2026 (ISMB oral presentation)

[Paper] [Code]

CPS: Mapping Physical Coordinates to High-Fidelity Spatial Transcriptomics via Privileged Multi-Scale Context Distillation

Lei Zhang, Kai Cao, Shuqiao Zheng, Shu Liang, Lin Wan

Bioinformatics 2026 (ISMB oral presentation)

[Paper] [Code]

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] [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

bioRxiv 2026

[Paper] [Code]

2025

scCausalVI disentangles single-cell perturbation responses with causality-aware generative model
scCausalVI disentangles single-cell perturbation responses with causality-aware generative model

Shaokun An, Jae-Won Cho, Kai Cao, Jiankang Xiong, Martin Hemberg, Lin Wan

Cell Systems 2025

[Paper] [Code]

scCausalVI disentangles single-cell perturbation responses with causality-aware generative model

Shaokun An, Jae-Won Cho, Kai Cao, Jiankang Xiong, Martin Hemberg, Lin Wan

Cell Systems 2025

[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]

Energy-Regularized Graph Learning for Multiscale Spatial Representation
Energy-Regularized Graph Learning for Multiscale Spatial Representation

Qiyu Gong, Kai Cao, Jackson A. Weir, Qitian Wu, Dongshunyi Li, Fei Chen

bioRxiv 2025

[Paper] [Code]

Energy-Regularized Graph Learning for Multiscale Spatial Representation

Qiyu Gong, Kai Cao, Jackson A. Weir, Qitian Wu, Dongshunyi Li, Fei Chen

bioRxiv 2025

[Paper] [Code]

Securing diagonal integration of multimodal single-cell data against ambiguous mapping
Securing diagonal integration of multimodal single-cell data against ambiguous mapping

Han Zhou, Kai Cao, Yang Lu

Bioinformatics 2025

[Paper] [Code]

Securing diagonal integration of multimodal single-cell data against ambiguous mapping

Han Zhou, Kai Cao, Yang Lu

Bioinformatics 2025

[Paper] [Code]

2024

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]

2022

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]

2021

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]

2020

Learning implicit information in Bayesian games with knowledge transfer

Guangpu Chen, Kai Cao, Yiguang Hong

Control Theory and Technology 2020

[Paper]

Learning implicit information in Bayesian games with knowledge transfer

Guangpu Chen, Kai Cao, Yiguang Hong

Control Theory and Technology 2020

[Paper]

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]

Class conditional distribution alignment for domain adaptation

Kai Cao, Zhipeng Tu, Yang Ming

Control Theory and Technology 2020

[Paper]

Class conditional distribution alignment for domain adaptation

Kai Cao, Zhipeng Tu, Yang Ming

Control Theory and Technology 2020

[Paper]

2017

Continuous-time distributed algorithms for solving linear algebraic equation

Kai Cao, Xianlin Zeng, Yiguang Hong

Chinese Control Conference 2017

[Paper]

Continuous-time distributed algorithms for solving linear algebraic equation

Kai Cao, Xianlin Zeng, Yiguang Hong

Chinese Control Conference 2017

[Paper]

Computation of linear algebraic equations with solvability verification over multi-agent networks

X. Zeng, K. Cao

Kybernetika 2017

[Paper]

Computation of linear algebraic equations with solvability verification over multi-agent networks

X. Zeng, K. Cao

Kybernetika 2017

[Paper]