Guangchuang Yu


School of Public Health, The University of Hong Kong (852)-62269693
L5-14, 5/F, Laboratory Block, Faculty of Medicine Building guangchuangyu@gmail.com
22 Sassoon Road, Pokfulam, Hong Kong https://guangchuangyu.github.io

Education

2013-2017
PhD; The University of Hong Kong; Evolution Study of Influenza A Virus
2006-2009
MSc; Anhui Medical University; Biochemistry and Molecular Biology
2001-2005
BSc; South China Agricultural University; Biotechnology
2015
Institut Pasteur, Paris; Train the Trainers 2015

CERTIFICATE

2015
Certificate of Teaching and Learning in Higher Education, Centre for Enhancement of Teaching and Learning, The University of Hong Kong

EMPLOYMENT

2017
Post-doctoral Fellow, State Key Laboratory of Infectious Diseases, School of Public Health, The University of Hong Kong:
2009-2013
Bioinformatician, College of Life Science and Technology, Jinan University:

Teaching

2013-2014
Student Helper; BIOL6001 Presentation Skills and Research Seminars in Biological Sciences (postgraduate course), The University of Hong Kong
2011-2012
Lecturer; Functional Proteomics (postgraduate course), Jinan University

Awards

2013-2017
Postgraduate Studentships (for PhD students at The University of Hong Kong)
2012
Best paper of the year 2010, Journal of Integrated OMICS.

Grants

2013
(completed) PI, Investigate functions of hnRNPK in regulating cytokinesis of human lung cancer cell, Fundamental Research Funds for the Central Universities (21613414), ¥100,000
2011
(completed) PI, Dynamic proteomic analysis of HeLa cell cycle, Fundamental Research Funds for the Central Universities (21611303), ¥20,000

Publications

Citation = 1476, H-index = 14, I10-index = 18

(data from Google Scholar, Apr 2018)

         ESI Hot Paper (X1)

         ESI Highly Cited Paper (X4)

         Methods in Ecology and Evolution (X1, rank 11 in Environment Ecology, IF = 5.708)

         Bioinformatics (X3, rank 4 in Computer Science, IF = 7.307)

         ( indicates equal contribution, * indicates corresponding)

Journal Articles

  1. G Yu. clusterProfiler: universal enrichment tool for functional and comparative study. bioRxiv. 2018, https://doi.org/10.1101/256784
  2. G Yu, DK Smith, H Zhu, Y Guan, TTY Lam*. 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. citation
  3. G Yu, QY He*. ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization. Molecular BioSystems. 2016, 12(2):477-479. citation
  4. G Yu*, LG Wang, QY He*. ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparision and visualization. Bioinformatics. 2015, 31(14):2382-2383. citation
  5. G Yu*, LG Wang, GR Yan, QY He*. DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis. Bioinformatics. 2015, 31(4):608-609. citation
  6. G Yu, LG Wang, XH Meng, QY He*. LXtoo: an integrated live Linux distribution for the bioinformatics community. BMC Research Notes. 2012, 5(1):360.
  7. G Yu, LG Wang, Y Han, QY He*. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287. citation
  8. G Yu, QY He*. Functional similarity analysis of human virus-encoded miRNAs. Journal of Clinical Bioinformatics. 2011, 1(1):15.
  9. G Yu, CL Xiao, X Bo, CH Lu, Y Qin, S Zhan, QY He*. A new method for measuring functional similarity of microRNAs. Journal of Integrated OMICS. 2011, 1(1):49-54.
  10. G Yu, CL Xiao, CH Lu, HT Jia, F Ge, W Wang, XF Yin, HL Jia, JX He*, QY He*. Phosphoproteome profile of human lung cancer cell line A549. Molecular BioSystems. 2011, 7(2):472-479.
  11. G Yu, F Li, Y Qin, X Bo*, Y Wu, S Wang*. GOSemSim: an R package for measuring semantic similarity among GO terms and gene products. Bioinformatics. 2010, 26(7):976-978. citation
  12. X Sun, G Yu, Q Xu, N Li, C Xiao, X Yin, K Cao, J Han, QY He*. Putative cobalt- and nickel-binding proteins and motifs in Streptococcus pneumonia. Metallomics. 2013, 5(7):928-935.
  13. YY Zhu, G Yu, Y Zhang, Z Xu, YQ Huang, GR Yan*, 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.
  14. XY Yang, K He, G Du, X Wu, G Yu, Y Pan, G Zhang*, X Sun*, QY He*. Integrated Translatomics with Proteomics to Identify Novel Iron–Transporting Proteins in Streptococcus pneumoniae. Frontiers in Microbiology. 2016, 7:78.
  15. PY Huang, CCD Lee, CH Yip, CL Cheung, G Yu, TTY Lam, DK Smith, H Zhu*, Y Guan*. Genetic characterization of highly pathogenic H5 influenza viruses from poultry in Taiwan, 2015. Infection, Genetics and Evolution. 2016, 38:96-100.
  16. SH Xu, JZ Huang, ML Xu, G Yu, XF Yin, D Chen*, GR Yan*. ACK1 Promotes Gastric Cancer Epithelial-Mesenchymal Transition and Metastasis through AKT-POU2F1-ECD Signaling. The Journal of Pathology. 2015, 236(2):175-185.
  17. 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 copper resistance of Streptococcus pneumonia. Metallomics. 2015, 7(3):448-454.
  18. XY Yang, L Zhang, J Liu, N Li, G Yu, K Cao, J Han, G Zeng, Y Pan, X Sun*, QY He*. Proteomic analysis on the antibacterial activity of a Ru(II) complex against Strepococcus pneumonia. Journal of Proteomics. 2015, 115:107-116.
  19. N Wang, J Zhang, L Zhang, XY Yang, N Li, G Yu, J Han, K Cao, Z Guo, X Sun*, QY He*. Proteomic analysis of putative heme-binding proteins in Streptococcus pyogenes. Metallomics. 2014, 6(8):1451-1459.
  20. H Sun*, J Weng, G Yu, RH Massawe. A DNA-Based Semantic Fusion Model for Remote Sensing Data. PLoS One. 2013, 8(10):e77090.
  21. GR Yan, Z Tan, Y Wang, ML Xu, G Yu, Y Li*, QY He*. Quantitative Proteomics Characterization on the Anti-tumor Effects of Isodexyelephantopin against Nasopharyngeal Carcinoma. Proteomics. 2013, 13(21):3222-3232.
  22. J Li, X Lu, Q Wu, G Yu, Z Xu, L Qiu, Z Pei, Y Lin, J Pang*. Design, SAR, angiogenic activities evaluation and pro-angiogenic mechanism of new marine cyclopeptide analogs. Current Medicinal Chemistry. 2013, 20(9):1183-1194.
  23. Y Han, G Yu, H Sarioglu, A Caballero-Martinez, F Schlott, M Ueffing, H Haase, C Peschel, AM Krackhardt*. 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.
  24. 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*. 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.
  25. GR Yan, FY Zhou, BL Dang, Y Zhang, G Yu, X Liu, QY He*. Genistein-induced mitotic arrest of gastric cancer cells by downregulating KIF20A, a proteomics study. Proteomics. 2012, 12(14):2391-2399.
  26. X Sun, XY Yang, XF Yin, G Yu, CL Xiao, X 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.

Books

  1. G Yu, "Bioinformatics II", in "Functional Protein Research", 385-425, Qing-Yu He (Eds), Science Press, 2012. (China’s Twelfth Five-Year National Important Books Project, in Chinese)

Conference Proceedings

Presentations

  1. ggtree for tree visualization & annotation (invited), Phylogenetic tree visualization workshop/hackathon, The Field Museum of Natural History, Chicago, May. 2017
  2. Computational Methods in Ecology and Evolution, The Second International Workshop on Environmental Microbiomes, Sun Yat-sen University, Guangzhou, April. 2017
  3. ggtree for visualization and annotation of phylogenetic trees (invited), The 9th China-R Conference, Renmin University of China, Beijing, May. 2016

Posters

  1. ggtree: a programming package for complex data integration and analysis in phylogeny to identify potential genetic markers of influenza a virus that determine interspecies transmission, Scientific Advisory Board (SAB) Meeting for the Theme-based Research Scheme on Viral, Host and Environmental Determinants of Influenza Virus Transmission and Pathogenesis, The University of Hong Kong, Hong Kong, Jun. 2017
  2. Phylogeny-guided genome assembly method for short read nucleotide sequences from co-infecting influenza A viruses, Options IX for the control of influenza, International Society for Influenza and other Respiratory Virus Disease, Chicago, Aug. 2016
  3. ggtree: an R package for visualization and annotation of phylogenetic tree with different types of meta-data, The 20th Research Postgraduate Symposium, The University of Hong Kong, Hong Kong, Dec. 2015

Public Media

"Plotting trees + data" lecture by Guangchuang Yu. https://youtu.be/tqspAXM0UQE

Professional Affiliations

2016
Member; International Society for Influenza and other Respiratory Virus Diseases
2015
Steering Committee; International Network for Data Analysis, Institut Pasteur
2005-2009
Visiting Student; Beijing Institute of Radiation Medicine

Professional Services

Associate Editor
Journal of Integrated OMICS, 2011-
Reviewer

Bioinformatics

BMC Bioinformatics

Computational Biology and Chemistry

Current Bioinformatics

Gastroenterology Research and Practice

Molecular BioSystems

R Journal

Software Development

R ranking: ranked 49/72201 worldwide by Git Awards

badger
Badge for R Package
dlstats
Download Stats of R Packages
emojifont
Emoji and Font Awesome in Graphics
ggplotify
Convert Plot to 'grob' or 'ggplot' Object
ggimage
Use Image in 'ggplot2'
meme
Create Meme
rvcheck
R/Package Version Check
scatterpie
Scatter Pie Plot
shadowtext
Shadow Text Grob and Layer
ChIPseeker
ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
clusterProfiler
statistical analysis and visualization of functional profiles for genes and gene clusters
DOSE
Disease Ontology Semantic and Enrichment analysis
ggtree
an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
GOSemSim
GO-terms Semantic Similarity Measures
meshes
MeSH Enrichment and Semantic analyses
ReactomePA
Reactome Pathway Analysis
seqcombo
Visualization Tool for Sequence Recombination and Reassortment
tidytree
A Tidy Tool for Phylogenetic Tree Data Manipulation
TIPars
Taxa Insertion by Parsimony
treeio
Base Classes and Functions for Phylogenetic Tree Input and Output

Contributions to open source libraries

basicTrendline
Add Trendline of Basic Regression Models to Plot
cowsay
Messages, Warnings, Strings with Ascii Animals
kableExtra
Construct Complex Table with 'kable' and Pipe Syntax
microbiomeViz
Visualizing Microbiome Data
MSnbase
Base Functions and Classes for Mass Spectrometry and Proteomics
scholar
Analyse Citation Data from Google Scholar