Shixiang Wang
王诗翔


github.com/ShixiangWang
ORCID Scholar

Research summary

I am a computational biologist working on cancer genomics. I use bioinformatics skills to decode the unfound patterns in cancer, and explore biomarkers for explaining the cancer heterogeneity and predicting the efficacy of cancer treatments, mainly in immunotherapy.

I am passionate about open science and developing open-source analysis toolkits. Because of this, currently I am a community member of Openbiox1, rOpenSci2 and Bioconductor3. My long-term goal in academic field is being a master in a subfield of cancer bioinformatics and trying my best to continually boost the open-source bioinformatics ecosystem in China.

Research positions

year what
2021 — present Postdoctoral Researcher, Experiment Research Department, Sun Yat-sen University Cancer Center4
Supervisor: Prof. Rui-Hua Xu5; Cooperate with Prof. Qi Zhao6

Education

year what
2016 — 2021 PhD in Cancer Biology, ShanghaiTech University7 & Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences8
Supervisor: Prof. Xue-Song Liu9
2012 — 2016 B.E. in Biomedical Engineering, University of Electronic Science and Technology of China
Supervisor: Prof. Yang Xia

Major grants and funding

year what
2022 — 2023 China Postdoctoral Science Foundation10 (¥ 80k), General Project
2024 — 2026 National Natural Science Foundation of China11 (¥ 300k), Young Scientists Fund

Awards & honours

year what
2021 2021 Outstanding Graduate Award, ShanghaiTech University
2020 National Scholarship for Doctoral Students, ShanghaiTech University
ShanghaiTech University Class A Postgraduate Academic Scholarship, ShanghaiTech University

Publications

Journal articles (fully reviewed, † for co-first, * for corresponding)

year number citation
2024 J21 Machine learning-based extrachromosomal DNA identification in large-scale cohorts reveals its clinical implications in cancer
S. Wang†, C. Wu†, M. He†, J. Yong†, Y. Chen, L. Qian, J. Zhang, Z. Zeng, R. Xu, F. Wang, Q. Zhao
Nature Communications (accepted) (JCR Q1, CAS Q1, IF: 16.6)
J20 TCCIA: A Comprehensive Resource for Exploring CircRNA in Cancer Immunotherapy
S. Wang†, Y. Xiong†, Y. Zhang†, H. Wang, M. Chen, J. Li, P. Luo, Y. Luo, M. Hecht, B. Frey, U. S Gaipl, X. Li, Q. Zhao, H. Ma, J. Zhou
Journal for ImmunoTherapy of Cancer (accepted) (JCR Q1, CAS Q2, IF: 10.9)
2023 J19 Unveiling the interplay between mutational signatures and tumor microenvironment: a pan-cancer analysis
L. Luo, S. Li, C. Wei, J. Ma, L. Qian, Y. Chen, S. Wang*, Q. Zhao*
Frontiers in Immunology (JCR Q1, CAS Q2, IF: 8.8)
J18 Accurate prediction of pan-cancer types using machine learning with minimal number of DNA methylation sites
W. Ning, T. Wu, C. Wu, S. Wang, Z. Tao, G. Wang, X. Zhao, K. Diao, J. Wang, J. Chen, F. Chen, X. Liu
Journal of Molecular Cell Biology (JCR Q1, CAS Q2, IF: 8.4)
J17 The repertoire of copy number alteration signatures in human cancer
Z. Tao†, S. Wang†, C. Wu†, T. Wu, X. Zhao, W. Ning, G. Wang, J. Wang, J. Chen, K. Diao, F. Chen, X. Liu
Briefings in Bioinformatics (JCR Q1, CAS Q2, IF: 14.0)
2022 J16 Hiplot: a comprehensive and easy-to-use web service for boosting publication-ready biomedical data visualization
J. Li†, B. Miao†, S. Wang†, W. Dong†, H. Xu†, C. Si†, W. Wang, S. Duan, J. Lou, Z. Bao, H. Zeng, Z. Yang, W. Cheng, F. Zhao, J. Zeng, X. Liu, R. Wu, Y. Shen, Z. Chen, S. Chen, M. Wang, H. Consortium
Briefings in Bioinformatics (JCR Q1, CAS Q2, IF: 14.0)
J15 Deciphering clonal dynamics and metastatic routines in a rare patient of synchronous triple-primary tumors and multiple metastases with MPTevol
Q. Chen, Q. Wu, Y. Rong, S. Wang, Z. Zuo, L. Bai, B. Zhang, S. Yuan, Q. Zhao
Briefings in Bioinformatics (JCR Q1, CAS Q2, IF: 14.0)
J14 Quantification of neoantigen-mediated immunoediting in cancer evolution
T. Wu, G. Wang, X. Wang, S. Wang, X. Zhao, C. Wu, W. Ning, Z. Tao, F. Chen, X. Liu
Cancer Research (JCR Q1, CAS Q1, IF: 13.3)
J13 UCSCXenaShiny: an R/CRAN package for interactive analysis of UCSC Xena data
S. Wang†, Y. Xiong†, L. Zhao†, K. Gu†, Y. Li, F. Zhao, J. Li, M. Wang, H. Wang, Z. Tao, T. Wu, Y. Zheng, X. Li, X. Liu
Bioinformatics (JCR Q1, CAS Q3,, IF: 7.3)
2021 J12 Ggct (γ‐glutamyl cyclotransferase) plays an important role in erythrocyte antioxidant defense and red blood cell survival
Z. He, X. Sun, S. Wang, D. Bai, X. Zhao, Y. Han, P. Hao, X. Liu
British Journal of Haematology (JCR Q1, CAS Q2, IF: 8.6)
J11 Copy number signature analysis tool and its application in prostate cancer reveals distinct mutational processes and clinical outcomes
S. Wang, H. Li, M. Song, Z. Tao, T. Wu, Z. He, X. Zhao, K. Wu, X. Liu
PLoS Genetics (JCR Q1, CAS Q2, IF: 8.2)
J10 Pan-cancer noncoding genomic analysis identifies functional CDC20 promoter mutation hotspots
Z. He†, T. Wu†, S. Wang†, J. Zhang†, X. Sun, Z. Tao, X. Zhao, H. Li, K. Wu, X. Liu
iScience (JCR Q1, CAS Q2, IF: 6.1)
J09 Association of CSMD1 with Tumor Mutation Burden and Other Clinical Outcomes in Gastric Cancer
X. Wang†, S. Wang†, Y. Han, M. Xu, P. Li, M. Ke, Z. Teng, P. Huang, Z. Diao, Y. Yan, Q. Meng, Y. Kuang, W. Zheng, H. Liu, X. Liu, B. Jia
International Journal of General Medicine (JCR Q2, CAS Q4, IF: 2.5)
2020 J08 Sigflow: an automated and comprehensive pipeline for cancer genome mutational signature analysis
S. Wang, Z. Tao, T. Wu, X. Liu
Bioinformatics (JCR Q1, CAS Q3, IF: 7.3)
2019 J07 Can tumor mutational burden determine the most effective treatment for lung cancer patients?
S. Wang, Z. He, X. Wang, H. Li, T. Wu, X. Sun, K. Wu, X. Liu
Lung Cancer Management (IF: 2.8)
J06 Antigen presentation and tumor immunogenicity in cancer immunotherapy response prediction
S. Wang, Z. He, X. Wang, H. Li, X. Liu
eLife (JCR Q1, CAS Q1, IF: 9.3)
J05 The predictive power of tumor mutational burden in lung cancer immunotherapy response is influenced by patients’ sex
S. Wang, J. Zhang, Z. He, K. Wu, X. Liu
International Journal of Cancer (JCR Q1, CAS Q1, IF: 7.4)
J04 Ras downstream effector GGCT alleviates oncogenic stress
Z. He†, S. Wang†, Y. Shao†, J. Zhang†, X. Wu, Y. Chen, J. Hu, F. Zhang, X. Liu
iScience (JCR Q1, CAS Q2 IF: 6.1)
J03 Sex Differences in Cancer Immunotherapy Efficacy, Biomarkers, and Therapeutic Strategy
S. Wang†, L. An Cowley†, X. Liu
Molecules (JCR Q2, CAS Q2 IF: 4.9)
J02 The UCSCXenaTools R package: a toolkit for accessing genomics data from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq
S. Wang, X. Liu
Journal of Open Source Software
2018 J01 APOBEC3B and APOBEC mutational signature as potential predictive markers for immunotherapy response in non-small cell lung cancer
S. Wang†, M. Jia†, Z. He, X. Liu
Oncogene (JCR Q1, CAS Q1, IF: 9.9)

The journal impact factors mentioned above are derived from the maximum values in the history of journal impact factors. Journal impact factors, Chinese Academy of Sciences (CAS) categorization, and JCR categorization were all uniformly updated on 2023.11.02. For future publications that are included, I will update them selectively and will no longer perform uniform updates on all publications.

Preprints (not reviewed, † for co-first, * for corresponding)

year number citation
2023 P5 TCCIA: A Comprehensive Resource for Exploring CircRNA in Cancer Immunotherapy
S. Wang†, Y. Xiong†, Y. Zhang†, H. Wang, M. Chen, J. Li, P. Luo, Y. Luo, M. Hecht, B. Frey, U. S Gaipl, X. Li, Q. Zhao, H. Ma, J. Zhou
bioRxiv
2022 P4 The repertoire of copy number alteration signatures in human cancer
Z. Tao†, S. Wang†, C. Wu†, T. Wu, X. Zhao, W. Ning, G. Wang, J. Wang, J. Chen, K. Diao, F. Chen, X. Liu
bioRxiv
P3 Onlinemeta: A Web Server For Meta-Analysis Based On R-shiny
Y. Yi, A. Lin, C. Zhou, J. Zhang*, S. Wang*, P. Luo*
bioRxiv
2021 P2 ezcox: An R/CRAN Package for Cox Model Batch Processing and Visualization
S. Wang, X. Liu, J. Li, Q. Zhao
arXiv
2020 P1 Revisiting neoantigen depletion signal in the untreated cancer genome
S. Wang†, X. Wang†, T. Wu†, Z. He, H. Li, X. Sun, X. Liu
bioRxiv

Cited by

Talks

year number what
2020 T1 BioC Asia 202012, Online
Sigflow: an automated and comprehensive pipeline for cancer genome mutational signature analysis13
2023 T2 中南大学, 湘雅 中德学术研讨会, Online
Machine learning-based extrachromosomal DNA identification in large-scale cohorts reveals its clinical implications in cancer

Poster presentations

year number what
2019 P1 ShanghaiTech University, BioForum 2019, Shanghai, China
Antigen presentation and tumor immunogenicity in cancer immunotherapy response prediction
2020 P2 BioC Asia 202014
Sigflow: an automated and comprehensive pipeline for cancer genome mutational signature analysis15

Teaching experience

year what
2019 Teaching assistant, Cancer Biology, ShanghaiTech University
Teacher: Xue-Song Liu
2023 Supervisor, Open Source Promotion Plan 202316
Student: Shensuo Li

Service

year what
2021 — present Review Editor in in Cancer Immunity and Immunotherapy Frontiers17
2021 — present Director of Bioinformatics Weekly Project18 Openbiox, for curation and sharing of bioinformatics knowledge and news
2019 — present Reviewer Briefings in Bioinformatics19, Journal of Translational Medicine20, STAR Protocols21, Frontiers in Immunology22, Frontiers in Oncology23, Frontiers in Cell and Developmental Biology24

  1. https://github.com/openbiox↩︎

  2. https://ropensci.org/↩︎

  3. https://www.bioconductor.org/↩︎

  4. http://english.sysucc.org.cn/↩︎

  5. http://english.sysucc.org.cn/info_19.aspx?itemid=154↩︎

  6. https://seqworld.com/↩︎

  7. https://www.shanghaitech.edu.cn/↩︎

  8. http://cemcs.cas.cn/↩︎

  9. https://slst.shanghaitech.edu.cn/lxs_en/main.htm↩︎

  10. https://jj.chinapostdoctor.org.cn/website/index.html↩︎

  11. https://www.nsfc.gov.cn/↩︎

  12. https://biocasia2020.bioconductor.org/↩︎

  13. https://www.youtube.com/watch?v=nzAxPDTznm4↩︎

  14. https://biocasia2020.bioconductor.org/↩︎

  15. https://f1000research.com/posters/9-1217↩︎

  16. https://summer-ospp.ac.cn/org/prodetail/2351d0245?lang=zh&list=pro↩︎

  17. https://www.frontiersin.org/↩︎

  18. https://openbiox.github.io/weekly/↩︎

  19. https://academic.oup.com/bib↩︎

  20. https://translational-medicine.biomedcentral.com/↩︎

  21. https://www.cell.com/star-protocols/home↩︎

  22. https://www.frontiersin.org/journals/immunology↩︎

  23. https://www.frontiersin.org/journals/oncology↩︎

  24. https://www.frontiersin.org/journals/cell-and-developmental-biology↩︎