Guangchuang Yu

Professor and dean of the Department of Bioinformatics, School of Basic Medicine, Southern Medical University.

My research group is committed to developing bioinformatics analysis algorithms and software through multidisciplinary integration, providing tools for exploring and analyzing data to solve complex issues in the field of biomedicine. At the same time, through the integration of multi-omics data, we systematically study the pathogenic mechanisms of reproduction and mental diseases.

教授、博导，现任南方医科大学基础医学院生物信息学系系主任。

课题组致力于通过多学科交叉融合，开发生物大数据分析算法和软件，为解决生物医学领域复杂问题提供探索和分析数据的工具；同时通过多组学数据融合，系统性地研究生育与精神类疾病的致病机理

Research Experience

Professor

School of Basic Medical Sciences

Southern Medical University

present - 2018

2021-present, Director, Department of Bioinformatics

2019-2021, Associate director, Department of Bioinformatics

Post-doctoral Fellow

State Key Laboratory of Infectious Diseases

The University of Hong Kong

2018 - 2017

Bioinformatician

Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes

Jinan University

2013 - 2009

Education

PhD., Bioinformaitcs

The University of Hong Kong

Hong Kong, CN

2017 - 2013

Thesis: Big-data computational methods for studying molecular evolution: from accurate genome assembly to phylogenetic analysis and data integration

M.S., Biochemistry and Molecular Biology

Anhui Medical University

Hefei, CN

2009 - 2006

Thesis: miRNA靶基因计算分析新方法及其应用研究

B.S., Biotechnology

South China Agricultural University

Guangzhou, CN

2005 - 2001

Antigenic cartography and antibody landscapes course

University of Cambridge

Cambridge, UK

南方医科大学高层次人才“不忘初心 牢记使命”学习教育

延安干部培训学院

Yan’an, CN

Train the Trainers

Institut Pasteur

Paris, FR

Visiting student

Beijing Institute of Radiation Medicine

Beijing, CN

2009 - 2007

Certificate

高等学校教师资格

广东省教育厅

Certificate of Teaching and Learning in Higher Education

Centre for Enhancement of Teaching and Learning

The University of Hong Kong

Scholarships & Awards

Data Integration, Manipulation and Visualization of Phylogenetic Trees

ISBN: 9781032233574, DOI: 10.1201/9781003279242

Chapman and Hall/CRC

Biomedical Data Visualization: Methods and Applications

ISBN: 9782889761906, DOI: 10.3389/978-2-88976-190-6

G Yu , TTY Lam, CL Xiao, M Zhou (eds.)

Lausanne: Frontiers Media SA

Gene Ontology Semantic Similarity Analysis Using GOSemSim

ISBN: 9781071603000, DOI: 10.1007/978-1-0716-0301-7_11

In: Kidder B. (eds) Stem Cell Transcriptional Networks , Methods in Molecular Biology , 2117:207-215.

Humana, New York, NY

BMB209: Workshops in Applied Bioinformatics

Department of Biochemistry and Molecular Biology

University of Southern Denmark

PhD level class, invited lecture

功能蛋白质研究

College of Life Science and Technology

Jinan University

2012 - 2011

Graduate level class

Publications

The impact of pre-existing influenza antibodies and inflammatory status on the influenza vaccine responses in older adults

Influenza and Other Respiratory Viruses . 2023, 17(7):e13172.

M Kang, F Lin, Z Jiang, X Tan, X Lin, Z Liang, C Xiao, Y Xia, W Guan, Z Yang, G Yu , M Zanin, S Tang ^* , SS Wong ^*

MMINP: A computational framework of microbe-Metabolite interactions-based metabolic profiles predictor based on the O2-PLS algorithm

Gut Microbes . 2023, 15(1):2223349.

W Tang, H Zheng, S Xu, P Li, L Zhan, X Luo, Z Dai, Q Wang, G Yu ^*

MicrobiotaProcess: A comprehensive R package for deep mining microbiome

The Innovation . 2023, 4(2):100388.

S Xu, L Zhan, W Tang, Q Wang, Z Dai, L Zhou, T Feng, M Chen, T Wu, E Hu, G Yu ^*

Editorial: Computational and Systematic Analysis of Multi-omics Data for Drug Discovery and Development

Frontiers in Medicine . 2023, 10:1146896.

S Guo ^* , D Zhang, H Wang, Q An, G Yu , J Han, C Jiang, J Huang

Ggtree: A serialized data object for visualization of a phylogenetic tree and annotation data

iMeta , 2022, 1(4):e56.

S Xu, L Li, X Luo, M Chen, W Tang, L Zhan, Z Dai, TT. Lam, Y Guan, G Yu ^*

Exploring epigenomic datasets by ChIPseeker

Current Protocols in Bioinformatics , 2022, 2(10):e585.

Q Wang ^# , M Li ^# , T Wu, L Zhan, L Li, M Chen, W Xie, Z Xie, E Hu, S Xu, G Yu ^*

Characterization of toxin-antitoxin systems from public sequencing data: a case study in Pseudomonas aeruginosa

Frontiers in Microbiology . 2022, 13:951774.

Z Dai, T Wu, S Xu, L Zhou, W Tang, E Hu, L Zhan M Chen, G Yu ^*

Stemness Analysis Uncovers That The Peroxisome Proliferator-Activated Receptor Signaling Pathway Can Mediate Fatty Acid Homeostasis In Sorafenib-Resistant Hepatocellular Carcinoma Cells

Frontiers in Oncology . 2022, 12:912694.

T Feng ^# , T Wu ^# , Y Zhang ^# , L Zhou ^# , S Liu, L Li, M Li, E Hu, Q Wang, X Fu, L Zhan, Z Xie, W Xie, X Huang ^* , X Shang ^* , G Yu ^*

ggmsa: a visual exploration tool for multiple sequence alignment and associated data

Briefings in Bioinformatics . 2022, 23(4):bbac222.

L Zhou ^# , T Feng ^# , S Xu, F Gao, TT Lam, Q Wang, T Wu, H Huang, L Zhan, L Li, Y Guan, Z Dai ^* , G Yu ^*

CBNplot: Bayesian network plots for enrichment analysis

Bioinformatics . 2022, 38(10):2959-2960.

N Sato, Y Tamada, G Yu , Y Okuno ^*

Editorial: Biomedical Data Visualization: Methods and Applications

Frontiers in Genetics . 2022, 13:890775.

T Wu, CL Xiao, TT Lam, G Yu ^*

Altered gut microbiota as an auxiliary diagnostic indicator for patients with fracture-related infection

Frontiers in Microbiology . 2022, 13:723791.

X Zhao ^# , W Tang ^# , H Wan ^# , Z Lan H Qin, Q Lin, Y Hu, G Yu ^* , N Jiang ^* , B Yu ^*

Use ggbreak to effectively utilize plotting space to deal with large datasets and outliers

Frontiers in Genetics . 2021, 12:774846.

S Xu ^# , M Chen ^# , T Feng, L Zhan, L Zhou, G Yu ^*

clusterProfiler (Wu et al. 2021) , the featured article in 2021-08-24’s website banner of Cell Press

clusterProfiler 4.0: A universal enrichment tool for interpreting omics data

The Innovation . 2021, 2(3):100141.

T Wu ^# , E Hu ^# , S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan, X Fu, S Liu, X Bo ^* , G Yu ^*

ggtreeExtra: Compact visualization of richly annotated phylogenetic data

Molecular Biology and Evolution . 2021, 38(9):4039-4042.

S Xu, Z Dai, P Guo, X Fu, S Liu, L Zhou, W Tang, T Feng, M Chen, L Zhan, T Wu, E Hu, Y Jiang ^* , X Bo ^* , G Yu ^*

ggVennDiagram: An intuitive, easy-to-use, and highly customizable R package to generate Venn diagram

Frontiers in Genetics . 2021, 12:706907.

CH Gao, G Yu , P Cai ^*

IOBR: Multi-Omics Immuno-Oncology Biological Research to Decode Tumor Microenvironment and Signatures

Frontiers in Immunology . 2021, 12:687975.

D Zeng ^# , Z Ye ^# , R Shen, G Yu, J Wu, Y Xiong, R Zhou, W Qiu, N Huang, L Sun, X Li, J Bin, Y Liao, M Shi, W Liao ^*

nCov2019: an R package for studying the COVID-19 coronavirus pandemic

PeerJ . 2021, 9:e11421.

T Wu, E Hu, X Ge ^* , G Yu** ^*

TreeSummarizedExperiment: a S4 class for data with hierarchical structure

F1000Research . 2021, 9:1246.

R Huang, C Soneson, FGM Ernst, KC Rue-Albrecht, G Yu , SC Hicks, MD Robinson ^*

Identification of prognostic Stromal-Immune Score-Based Genes in Hepatocellular Carcinoma microenvironment

Frontiers in Genetics . 2021, 12: 625236.

S Liu, G Yu ^* , L Liu ^* , X Zou, L Zhou, E Hu, Y Song

Gut microbiota and metabolite alterations associated with reduced bone mineral density or bone metabolic indexes in postmenopausal osteoporosis

Aging (Albany NY) . 2020, 12(9):8583-8604.

J He ^# , S Xu ^# , B Zhang, C Xiao, Z Chen, F Si, J Fu, X Lin, G Zheng ^* , G Yu ^* , J Chen ^*

Using ggtree to Visualize Data on Tree-Like Structure

Current Protocols in Bioinformatics, 69(1):e96

G Yu ^*

treeio: an R package for phylogenetic tree input and output with richly annotated and associated data

Molecular Biology and Evolution . 2020, 37(2):599-603.

LG Wang, TTY Lam, S Xu, Z Dai, L Zhou, T Feng, P Guo, CW Dunn, BR Jones, T Bradley, H Zhu, Y Guan, Y Jiang, G Yu ^*

Impact Factor = 16.24

ESI Highly Cited Paper

RIdeogram: drawing SVG graphics to visualize and map genome-wide data on the idiograms

PeerJ Computer Science . 2020, 6:e251.

Z Hao, D Lv, Y Ge, J Shi, D Weijers, G Yu ^* , J Chen ^*

ESI Highly Cited Paper

Two methods for mapping and visualizing associated data on phylogeny using ggtree

Molecular Biology and Evolution . 2018, 35(12):3041-3043.

G Yu ^* , TTY Lam, H Zhu, Y Guan ^*

Impact Factor = 14.797

Using meshes for MeSH term enrichment and semantic analyses

Bioinformatics . 2018, 34(21):3766–3767.

G Yu ^*

ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data

Methods in Ecology and Evolution . 2017, 8(1):28-36

G Yu , DK Smith, H Zhu, Y Guan, TTY Lam ^*

ESI Highly Cited Paper

The ggtree (Yu et al. 2017) paper was selected as a feature article to celebrate the 10 ^th anniversary of the launch of Methods in Ecology and Evolution .

ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization

Molecular BioSystems . 2016, 12(2):477-479

G Yu , QY He ^*

ESI Highly Cited Paper

Integrated Translatomics with Proteomics to Identify Novel Iron–Transporting Proteins in Streptococcus pneumoniae

Frontiers in Microbiology . 2016, 7:78

XY Yang, K He, G Du, X Wu, G Yu , Y Pan, G Zhang ^* , X Sun ^* , QY He ^*

Genetic characterization of highly pathogenic H5 influenza viruses from poultry in Taiwan, 2015

Infection, Genetics and Evolution . 2016, 38:96-100

PY Huang, CCD Lee, CH Yip, CL Cheung, G Yu , TTY Lam, DK Smith, H Zhu ^* , Y Guan ^*

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparision and visualization

Bioinformatics . 2015, 31(14):2382-2383

G Yu ^* , LG Wang, QY He ^*

ESI Highly Cited Paper

DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis

Bioinformatics . 2015, 31(4):608-609

G Yu ^* , LG Wang, GR Yan, QY He ^*

ESI Highly Cited Paper

ACK1 Promotes Gastric Cancer Epithelial-Mesenchymal Transition and Metastasis through AKT-POU2F1-ECD Signaling

Journal of Pathology . 2015, 236(2):175-185

SH Xu, JZ Huang, ML Xu, G Yu , XF Yin, D Chen ^* , GR Yan ^*

Proteomic analysis on the copper resistance of Streptococcus pneumonia

Metallomics . 2015, 7(3):448-454

Z Guo, J Han, XY Yang, K Cao, K He, G Du, G Zeng, L Zhang, G Yu , Z Sun, QY He ^* , X Sun ^*

Proteomic analysis on the antibacterial activity of a Ru(II) complex against Strepococcus pneumonia

Journal of Proteomics . 2015, 115:107-116

XY Yang, L Zhang, J Liu, N Li, G Yu , K Cao, J Han, G Zeng, Y Pan, X Sun ^* , QY He ^*

Proteomic analysis of putative heme-binding proteins in Streptococcus pyogenes

Metallomics . 2014, 6(8):1451-1459

N Wang ^# , J Zhang ^# , L Zhang, XY Yang, N Li, G Yu , J Han, K Cao, Z Guo, X Sun ^* , QY He ^*

Putative cobalt- and nickel-binding proteins and motifs in Streptococcus pneumonia

Metallomics . 2013, 5(7):928-935

X Sun ^# , G Yu ^# , Q Xu, N Li, C Xiao, X Yin, K Cao, J Han, QY He ^*

A novel andrographolide derivative AL-1 exerts its cytotoxicity on K562 cells through a ROS-dependent mechanism

Proteomics , 2013, 13(1):169-178

YY Zhu ^# , G Yu ^# , Y Zhang, Z Xu, YQ Huang, GR Yan ^* , QY He ^*

A DNA-Based Semantic Fusion Model for Remote Sensing Data

PLoS One . 2013, 8(10):e77090

H Sun ^* , J Weng, G Yu , RH Massawe

Quantitative Proteomics Characterization on the Anti-tumor Effects of Isodexyelephantopin against Nasopharyngeal Carcinoma

Proteomics . 2013, 13(21):3222-3232

GR Yan ^# , Z Tan ^# , Y Wang, ML Xu, G Yu , Y Li ^* , QY He ^*

Design, SAR, angiogenic activities evaluation and pro-angiogenic mechanism of new marine cyclopeptide analogs

Current Medicinal Chemistry . 2013, 20(9):1183-1194

J Li, X Lu, Q Wu, G Yu , Z Xu, L Qiu, Z Pei, Y Lin, J Pang ^*

Proteomic investigation of the interactome of FMNL1 in hematopoietic cells unveils a role in calcium-dependent membrane plasticity

Journal of Proteomics . 2013, 78:72-82

Y Han, G Yu , H Sarioglu, A Caballero-Martinez, F Schlott, M Ueffing, H Haase, C Peschel, AM Krackhardt ^*

LXtoo: an integrated live Linux distribution for the bioinformatics community

BMC Research Notes . 2012, 5(1):360

G Yu ^# , LG Wang ^# , XH Meng, QY He ^*

clusterProfiler (Yu et al. 2012) 被中国科学技术信息研究所列为“2011-2021我国高被引论文中被引次数最高的10篇国际论文”（2021年中国科技论文统计报告）

clusterProfiler: an R package for comparing biological themes among gene clusters

OMICS: A Journal of Integrative Biology . 2012, 16(5):284-287

G Yu , LG Wang, Y Han, QY He ^*

ESI Highly Cited Paper

Cellular MicroRNA let-7c Inhibits M1 Protein Expression of the H1N1 Influenza A Virus in Infected Human Lung Epithelial Cells

Journal of Cellular and Molecular Medicine . 2012, 16(10):2539-2546

Y Ma ^# , J Yang ^# , X Fan ^# , H Zhao, W Hu, Z Li, G Yu , X Ding, J Wang, X Bo, X Zheng, Z Zhou ^* , S Wang ^*

Genistein-induced mitotic arrest of gastric cancer cells by downregulating KIF20A, a proteomics study

Proteomics . 2012, 12(14):2391-2399

GR Yan ^# , FY Zhou ^# , BL Dang, Y Zhang, G Yu , X Liu, QY He ^*

Functional similarity analysis of human virus-encoded miRNAs

Journal of Clinical Bioinformatics . 2011, 1(1):15

G Yu , QY He ^*

A new method for measuring functional similarity of microRNAs

Journal of Integrated OMICS . 2011, 1(1):49-54

G Yu ^# , CL Xiao ^# , X Bo, CH Lu, Y Qin, S Zhan, QY He ^*

Phosphoproteome profile of human lung cancer cell line A549

Molecular BioSystems . 2011, 7(2):472-479

G Yu ^# , CL Xiao ^# , CH Lu ^# , HT Jia, F Ge, W Wang, XF Yin, HL Jia, JX He ^* , QY He ^*

Proteomic Analysis of Membrane Proteins from Streptococcus pneumoniae with Multiple Separation Methods plus High Accuracy Mass Spectrometry

OMICS: A Journal of Integrative Biology . 2011, 15(10):683-694

X Sun ^# , XY Yang ^# , XF Yin, G Yu , CL Xiao, X He, QY He ^*

GOSemSim: an R package for measuring semantic similarity among GO terms and gene products

Bioinformatics . 2010, 26(7):976-978

G Yu ^# , F Li ^# , Y Qin, X Bo ^* , Y Wu, S Wang ^*

结合基因组分析预测炎症相关miRNA及其靶标

军事医学科学院院刊 . 2009, 33(3):245-247

余光创 ，王超，许尹，伯晓晨，王升启 ^* ，秦宜德 ^*

依赖于5’端非编码区高级结构的真核生物mRNA翻译调控

中国生物化学与分子生物学报 . 2007, 23(11):881-887

余光创 ，秦宜德，伯晓晨，王升启 ^*

clusterProfiler 4.0: A universal enrichment tool for interpreting omics data

The 7 ^th National Conference on Computational Biology and Bioinformatics

Yantai, CN

Data integration and visualization of phylogenetic trees

BioC Asia, Oct 2020

Virtual Conference

R语言在生物信息学数据可视化中的应用

第八届南方医院博士论坛 - 研而有信之修“生”养“信”, Oct 2019

Southern Medical University

Data integration and visualization of phylogenetic trees

Managing Zoonotic Infections in the era of One Health, Oct 2019

Guangzhou Medical University

R包开发十条建议

第一届生信人才发展论坛

Zhuhai, CN

Two methods for mapping and visualizing associated data on phylogeny using ggtree

第一届南方医科大学基础医学学术年会, Jan 2019

Southern Medical University

ggtree for tree visualization & annotation

Phylogenetic tree visualization workshop/hackathon, May 2017

The Field Museum of Natural History

Computational Methods in Ecology and Evolution

The Second International Workshop on Environmental Microbiomes, Apr 2017

Sun Yat-sen University

R语言与生物信息学

Guangzhou, CN

ggtree for visualization and annotation of phylogenetic trees

The 9 ^th China-R Conference, May 2016

Renmin University of China

Professional affliations

iMeta

Associate Editor

present - 2022

The Innovation

Youth Editor

南方医科大学基础医学院第二届学术分委员会

中国生物工程学会

计算生物学与生物信息学专业委员会委员

present - 2021

广东省精准医学应用学会

微生态医学分会常务委员

Guangdong, CN

present - 2020

广东省医学会

医学遗传学分会青年委员会副主任委员

Guangdong, CN

中国计算机学会

present - 2019

香港大学校友会

present - 2017

广东潮博智库

Guangdong, CN

present - 2014

广东省生物信息学会

2028 - 2023

International Society for Influenza and other Respiratory Virus Disease

Member

International Network for Data Analysis

Steering Committee

Institut Pasteur