TCM System Biology

 TCM System biology has far advanced our understanding in body-environment dynamics and TCM clinical effectiveness.
 Genes, pathogens, active pharmaceutical ingredients, and the networks between them are critical for homestasis maintenance and disease treatment.

Single-cell Spatiotemperal omics

 Single-cell/spatial omics defines cell states and tissue domains during pathogenesis. Spatial-seq 2.0 is a laser capture microdissection (LCM)-based single-cell resolved spatial transcriptomics that sequences custom selected areas.

AI for Pharmaceutical Sciences

 AI/statistical learning are necessary methods for hypothesis generation and complementary methods when dealing with large amounts of data.

Health Products R&D

 We envision omics-based health products is going to make changes in biological and medical domain, for example, early diagnosis of cancer and local TCM delivery.

Algorithms & Websites
scRank
A computational method to rank and infer drug-responsive cell population towards in-silico drug perturbation using a target-perturbed gene regulatory network (tpGRN) for single-cell transcriptomic data.

scCube
An SRT simulator for simulating multiple spatial variability in spatial resolved transcriptomics and generating unbiased simulated SRT data.

SCOTCH
A Single-Cell multi-modal integration method leveraging the Optimal Transport algorithm and a cell matCHing strategy.

SpaTrio
A computational tool based on optimal transport that can align single-cell multi-omics data in space while preserving the spatial topology of the tissue section and local geometry of modality.

scDeepSort
Cell-type Annotation for Single-cell Transcriptomics using Deep Learning with a Weighted Graph Neural Network.

Spatalk
Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data.

scSpace
An integrative algorithm to distinguish spatially variable cell subclusters by reconstructing cells onto a pseudo space with spatial transcriptome references.

scCrossTalk
Infer and visualize cell-cell communication for single-cell RNA-seq data.

scCATCH
Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data.

bulk2space
A spatial deconvolution method based on deep learning frameworks, which converts bulk transcriptomes into spatially resolved single-cell expression profiles.

CellTalkDB
A manually curated database of literature-supported ligand-receptor interactions in human and mouse.
News & Publications
2024.8.20
Our research group published a review titled "Cellular Chemical Field and Cellular Homostasis", on Engineering (IF=10.1).

2024.7.19
Zhihao Liu and Xiyun Bian uncovered the role of SENP1 in preventing cardiac fibrosis by paracrine signaling. This study was published on Advanced Science (IF=14.3).

2024.6.15
Congradulations! Jingyang Qian and Hudong Bao published scCube, a SRT data simulator that could generate complex tissue structure in an unbiased way, on Nature Communications (IF=14.7).

2024.4.7
Congradulations! Chengyu Li and Xin Shao published scRank, a computational method for discovery of drug-responsive populations using single-cell transcriptomes, on Cell Reports Medicine (IF=14.3).

2023.9
Congradulations! Penghui Yang and Lijun Jin published SpaTrio, which is designed for mapping multi-modal single-cell omics data to spatial locations, on Cell Genomics (IF=8.83).

2022.12
Congradulations! Professor Xiaohui Fan was awarded Baostell Excellent Teacher Award.

2022.9
Professor Xiaohui Fan was invited to serve as an Editor of Journal of Natural Medicines.