publications

2026

1. NeurIPS

   

   TransMap: Image-Native Representations for Single-Cell Genomics

   Sijie Chen and others

   NeurIPS (under review), 2026

   Abs

   Single-cell RNA-seq profiles are sparse, high-dimensional gene-expression vectors whose gene order carries no biological geometry. We introduce TransMap, a representation framework that converts each cell into a 2D transcriptomic image by arranging genes on a fixed grid via Gromov–Wasserstein optimal transport, so that nearby pixels correspond to genes with similar relational profiles. On five scRNA-seq benchmarks, CNN encoders on TransMap images match or outperform parameter-matched MLPs on scIB embedding metrics. A shared pixel grid further aligns cell states on a human–mouse pancreas benchmark without explicit ortholog conversion.

2025

1. Gen. Res.

   TFcomb Identifies Transcription Factor Combinations for Cellular Reprogramming Based on Single-Cell Multi-Omics Data

   Chen Li, Sijie Chen, Yixin Chen, and 4 more authors

   Genome Research, 2025
2. Nature

   Erythropoietin Receptor on cDC1s Dictates Immune Tolerance

   Xiangyue Zhang, Christopher S. McGinnis, Guotao Yu, and 3 more authors

   Nature, 2025

   Accepted
3. Nature

   MorPhiC Consortium: Towards Functional Characterization of All Human Genes

   The MorPhiC Consortium

   Nature, 2025

2024

1. RECOMB

   Velocity-Informed Integration of Single-Cell RNA Sequencing Data

   Sijie Chen, Lei Wei, and Xuegong Zhang

   RECOMB, 2024

   Conference abstract
2. RECOMB/ISMB

   

   scMulan: A Multitask Generative Pre-trained Language Model for Single-Cell Analysis

   Haiyang Bian, Yixin Chen, Xiaomin Dong, and 7 more authors

   In RECOMB / ISMB, 2024
3. Nat. Imm.

   Reciprocal Regulation of T Follicular Helper Cells and Dendritic Cells Drives Chronic Colitis Development

   Xue Bai, Sijie Chen, Xinxin Chi, and 9 more authors

   Nature Immunology, 2024
4. Comms Bio

   STEM Enables Mapping of Single-Cell and Spatial Transcriptomics Data with Transfer Learning

   Minsheng Hao, Erpai Luo, Yixin Chen, and 8 more authors

   Communications Biology, 2024
5. Nature

   Molecular Convergence of Risk Variants for Congenital Heart Defects Leveraging a Regulatory Map of the Human Fetal Heart

   X. Rosa Ma, Stephanie D. Conley, others, and 3 more authors

   Nature, 2024

   2nd-round review
6. Allergy

   Single-Cell Profiling Highlights Pathogenic Myeloid Features in House-Dust-Mite-Induced Murine Airway Inflammation

   Jiachen Liu, Jiaoyan Lv, Sijie Chen, and 8 more authors

   Allergy, 2024

2023

1. Mucosal Imm.

   Dynamic Regulation of Innate Lymphoid Cell Development During Ontogeny

   Tao* Wu, Sijie* Chen, Jie Ma, and 8 more authors

   Mucosal Immunology, 2023
2. Comms Bio

   Building a Learnable Universal Coordinate System for Single-Cell Atlas with a Joint-VAE Model

   Haoxiang Gao, Kui Hua, Lei Wei, and 5 more authors

   Communications Biology, 2023
3. Eur. Rad.

   ITHscore: Comprehensive Quantification of Intra-Tumor Heterogeneity in NSCLC by Multi-Scale Radiomic Features

   Jiaqi Li, Zhenbin Qiu, Chao Zhang, and 8 more authors

   European Radiology, 2023
4. DMS

   Colonic L-Cell Impairment in Aged Subjects with Type 2 Diabetes Leads to Diminished GLP-1 Production

   Qing-Yu Wang, Wei Zhang, Yue Zhao, and 9 more authors

   Diabetes & Metabolic Syndrome: Clinical Research & Reviews, 2023

2022

1. iScience

   

   hECA: The Cell-Centric Assembly of a Cell Atlas

   Sijie* Chen, Yanting* Luo, Haoxiang* Gao, and 8 more authors

   iScience, 2022

   HTML
2. NSR

   Toward a Unified Information Framework for Cell Atlas Assembly

   Sijie* Chen, Yanting* Luo, Haoxiang* Gao, and 8 more authors

   National Science Review, 2022
3. eLife

   Cellular Features of Localized Microenvironments in Human Meniscal Degeneration: A Single-Cell Transcriptomic Study

   Weili* Fu, Sijie* Chen, Runze Yang, and 4 more authors

   eLife, 2022
4. JEM

   Intestinal Toxicity to CTLA-4 Blockade Driven by IL-6 and Myeloid Infiltration

   Yifan Zhou, Yusra B. Medik, Bhakti Patel, and 4 more authors

   Journal of Experimental Medicine, 2022

2020

1. BMCG

   Using DenseFly Algorithm for Cell Searching on Massive scRNA-seq Datasets

   Yixin* Chen, Sijie* Chen, and Xuegong Zhang

   BMC Genomics, 2020
2. Patterns

   An Experiment on ab initio Discovery of Biological Knowledge from scRNA-seq Data Using Machine Learning

   Najeebullah Shah, Jiaqi Li, Fanhong Li, and 5 more authors

   Patterns, 2020

2019

1. Bioinformatics

   

   A New Statistic for Efficient Detection of Repetitive Sequences

   Sijie Chen, Yixin Chen, Fengzhu Sun, and 2 more authors

   Bioinformatics, 2019

   HTML
2. IEEE BIBM

   Pixel-Level Clustering Reveals Intra-Tumor Heterogeneity in Non-Small-Cell Lung Cancer

   Jiaqi Li, Haiming Lu, Xiang Fang, and 2 more authors

   In 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2019

2018

1. Quant. Bio.

   Comprehensive Simulation of Metagenomic Sequencing Data with Non-Uniform Sampling Distribution

   Shansong Liu, Kui Hua, Sijie Chen, and 1 more author

   Quantitative Biology, 2018