About

I am a Lane Fellow in Carnegie Mellon University’s Ray and Stephanie Lane Computational Biology Department, working with Jian Ma.

I received my Ph.D. in Computer Science from Rice University, advised by Ken Chen and Luay Nakhleh, and conducted my doctoral research at MD Anderson Cancer Center. Before joining CMU, I worked as a bioinformatics research scientist at NuProbe. I earned my B.Eng. from Tsinghua University.

My research experience encompasses machine learning and computational biology. Right now, I focus on generative and interpretable models for single-cell and spatial omics. I aim to connect accurate prediction with biological insight by identifying molecular programs and cell–cell interactions that explain changes in cellular state. My work addresses questions in cancer, immunity, and development, with the goal of generating testable hypotheses that guide experiments.

Selected publications

^* Co-first author; ^† co-corresponding author. · Full publication list (Google Scholar)

STEAMBOAT: Attention-based multiscale delineation of cellular interactions in tissues

RECOMB 2025; extended manuscript accepted in principle by Nature Methods. Paper Code
Shaoheng Liang, Junjie Tang, Guanghan Wang, Jian Ma.

TissueNarrator: Generative Modeling of Spatial Transcriptomics with Large Language Models

bioRxiv preprint, 2025; under review at Nature Biomedical Engineering. Paper Code
Sizhe Liu, Junjie Tang, Jian Ma^†, Shaoheng Liang^†.

Single-cell manifold-preserving feature selection for detecting rare cell populations

Nature Computational Science 1(5), 374–384, 2021. Paper Code
Shaoheng Liang, Vakul Mohanty, Jinzhuang Dou, Qi Miao, Yuefan Huang, Muharrem Müftüoğlu, Li Ding, Weiyi Peng, Ken Chen.

Latent periodic process inference from single-cell RNA-seq data

Nature Communications 11(1), 1441, 2020. Paper Code
Shaoheng Liang, Fang Wang, Jincheng Han, Ken Chen.

Bi-order multimodal integration of single-cell data

Genome Biology 23, 112, 2022. Paper Code
Jinzhuang Dou^*, Shaoheng Liang^*, Vakul Mohanty, Qi Miao, Yuefan Huang, Qingnan Liang, Xuesen Cheng, Sangbae Kim, Jongsu Choi, Yumei Li, et al.

In-depth analysis of SARS-CoV-2–specific T cells reveals diverse differentiation hierarchies in vaccinated individuals

JCI Insight 7(7), e156559, 2022. Paper
Li Li^*, Muharrem Muftuoglu^*, Shaoheng Liang^*, Mahesh Basyal, Jiangxing Lv, Mehmet Emin Akdogan, Ken Chen, Michael Andreeff, Christopher R. Flowers, Simrit Parmar.

Single-cell CRISPR immune screens reveal immunological roles of tumor intrinsic factors

NAR Cancer 4(4), zcac038, 2022. Paper
Jiakai Hou^*, Shaoheng Liang^*, Chunyu Xu, Yanjun Wei, Yunfei Wang, Yukun Tan, Nidhi Sahni, Daniel J. McGrail, Chantale Bernatchez, Michael Davies, et al.

Mentees