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.

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

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

TissueNarrator: Generative Modeling of Spatial Transcriptomics with Large Language Models

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

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

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

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

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

Bi-order multimodal integration of single-cell data

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

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

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

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

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

Teaching experience

Guest lecture: Local sequence alignment and the Burrows–Wheeler transform

Carnegie Mellon University, 2026.

Guest lecture: Introduction to spatial omics

Carnegie Mellon University, 2025.

Workshop instruction: Multiomics integration and feature selection

Gulf Coast Consortia Single-Cell Omics Workshop, 2026.

Teaching assistant: Statistical Machine Learning

Rice University, 2018–2020.

Teaching assistant: Statistical Models and Algorithms for Data Science

Rice University, 2018–2019.