shaoxin0801 Goto Github PK

followers: 14.0 following: 30.0 repos: 33.0 gists: 0.0

Name: Shao, Xin

Type: User

Company: Zhejiang University

Bio: Single-cell omics; Cell-cell communication; Spatial omics

Twitter: shaoxin0801

Location: Hangzhou, China

Blog: https://person.zju.edu.cn/shaoxin

Hi there, I am Shao, Xin 👏

and I am mainly engaged in the research of single-cell and spatial omics, cell-cell communication, and liver disease omics with machine learning and deep learning methods.

Study and work experience 🎓

2022-present, Hangzhou First People's Hospital Affiliated to Zhejiang University School of Medicine, Research Associate.
2021-present, Hangzhou First People's Hospital Affiliated to Zhejiang University School of Medicine, Postdoc. (Supervisor: Prof. Xu, Xiao/Prof. Fan, Xiaohui)
2015-2021, Zhejiang University, Ph.D. degree (Supervisor: Prof. Fan, Xiaohui)
2011-2015, Zhejiang University, Bachelor degree

Main research articles 📑

Shao X†, Li C†, Yang H†, Lu X, Liao J, Qian J, Wang K, Cheng J, Yang P, Chen H*, Xu X*, Fan X*. Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data with SpaTalk. Nat. Commun. 2022. 13(1):4429.
Shao X†, Yang H†, Zhuang X, Liao J, Yang P, Cheng J, Lu X, Chen H*, Fan X*. scDeepSort: a pre-trained cell-type annotation method for single-cell transcriptomics using deep learning with a weighted graph neural network. Nucleic Acids Res. 2021. 49(21):e122.
Shao X†, Liao J†, Li C†, Lu X, Cheng J, Fan X*. CellTalkDB: a manually curated database of ligand-receptor interactions in humans and mice. Brief Bioinform. 2021. 22(4):bbaa269.
Shao X†, Lu X†, Liao J, Chen H, Fan X*. New avenues for systematically inferring cell-cell communication: through single-cell transcriptomics data. Protein Cell. 2020;11(12):866-880.
Shao X, Liao J, Lu X, Xue R, Ai N, Fan X*. scCATCH: Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data. iScience. 2020;23(3):100882.
Shao X†, Wang Y†, Lu X†, Hu Y, Liao J, Li J, Chen X, Yu Y, Ai N, Ying M, Fan X*. A Clinical Genomics-Guided Prioritizing Strategy Enables Selecting Proper Cancer Cell Lines for Biomedical Research. iScience. 2020. 23(11):101748.
Shao X, Lv N, Liao J, Long J, Xue R, Ai N, Xu D*, Fan X*. Copy number variation is highly correlated with differential gene expression: a pan-cancer study. BMC Med. Genet. 2019. 20(1):175.
Shao X, Ai N*, Xu D*, Fan X. Exploring the interaction between Salvia miltiorrhiza and human serum albumin: Insights from herb-drug interaction reports, computational analysis and experimental studies. Spectrochim Acta A Mol Biomol Spectrosc. 2016. 161:1-7.

If you are interested in more details, check out my website!

Shao, Xin's Projects

awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

beautiful-visualization-with-r

《R语言数据可视化之美》配套代码

ccl-cgps-1

CCL-cGPS: a clinical genomics-guided prioritizing strategy enables accurately selecting proper cancer cell lines for biomedical research

cell-cell-communication

Collection of computational tools for cell-cell communication inference for single-cell and spatially resolved omics

cellassign

Automated, probabilistic assignment of cell types in scRNA-seq data

cellchat

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data

cellphonedb

celltalkdb

A manually curated database of literature-supported ligand-receptor interactions in human and mouse

clash_for_windows_pkg

A Windows/macOS GUI based on Clash

deepsort

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

garnett

Automated cell type classification

giotto

Single-cell spatial analysis toolbox

listen1_desktop

one for all free music in china (Windows, Mac, Linux desktop)

lx-music-desktop

一个基于 electron 的音乐软件

multinichenetr

nichenetr

NicheNet: predict active ligand-target links between interacting cells

ppms

Pri-miRNA profiling for single-cell RNA-seq data

rsoptsc

Cell-cell communication and lineage inference for scRNA-seq data

sccatch

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

sccatch_performance_comparison

The source code and results of performance comparison on the detail of the process among scCATCH, CellAssign, Garnett, SingleR, scMap and CHETAH, and CellMatch database