2026
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, In press 2026 (ISMB oral presentation)
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, In press 2026 (ISMB oral presentation)
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
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
2025
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
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
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
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
Energy-Regularized Graph Learning for Multiscale Spatial Representation
Qiyu Gong, Kai Cao, Jackson A. Weir, Qitian Wu, Dongshunyi Li, Fei Chen
bioRxiv 2025
Energy-Regularized Graph Learning for Multiscale Spatial Representation
Qiyu Gong, Kai Cao, Jackson A. Weir, Qitian Wu, Dongshunyi Li, Fei Chen
bioRxiv 2025
Securing diagonal integration of multimodal single-cell data against ambiguous mapping
Han Zhou, Kai Cao, Yang Lu
Bioinformatics 2025
Securing diagonal integration of multimodal single-cell data against ambiguous mapping
Han Zhou, Kai Cao, Yang Lu
Bioinformatics 2025
2024
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)
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)
2022
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
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
2021
Manifold alignment for heterogeneous single-cell multi-omics data integration using Pamona
Kai Cao, Yiguang Hong, Lin Wan
Bioinformatics 2021
Manifold alignment for heterogeneous single-cell multi-omics data integration using Pamona
Kai Cao, Yiguang Hong, Lin Wan
Bioinformatics 2021
2020
Learning implicit information in Bayesian games with knowledge transfer
Guangpu Chen, Kai Cao, Yiguang Hong
Control Theory and Technology 2020
Learning implicit information in Bayesian games with knowledge transfer
Guangpu Chen, Kai Cao, Yiguang Hong
Control Theory and Technology 2020
Unsupervised Topological Alignment for Single-Cell Multi-Omics Integration
Kai Cao, Xiangqi Bai, Yiguang Hong, Lin Wan
Bioinformatics 2020 (ISMB oral presentation)
Unsupervised Topological Alignment for Single-Cell Multi-Omics Integration
Kai Cao, Xiangqi Bai, Yiguang Hong, Lin Wan
Bioinformatics 2020 (ISMB oral presentation)
Class conditional distribution alignment for domain adaptation
Kai Cao, Zhipeng Tu, Yang Ming
Control Theory and Technology 2020
Class conditional distribution alignment for domain adaptation
Kai Cao, Zhipeng Tu, Yang Ming
Control Theory and Technology 2020
2017
Continuous-time distributed algorithms for solving linear algebraic equation
Kai Cao, Xianlin Zeng, Yiguang Hong
Chinese Control Conference 2017
Continuous-time distributed algorithms for solving linear algebraic equation
Kai Cao, Xianlin Zeng, Yiguang Hong
Chinese Control Conference 2017
Computation of linear algebraic equations with solvability verification over multi-agent networks
X. Zeng, K. Cao
Kybernetika 2017
Computation of linear algebraic equations with solvability verification over multi-agent networks
X. Zeng, K. Cao
Kybernetika 2017