[Last updated on 2024.12.05]

Curriculum Vitae

Jia-Xing Yue (岳家兴)

State Key Laboratory of Oncology in South China
Guangdong Provincial Clinical Research Center for Cancer
Sun Yat-sen University Cancer Center (SYSUCC)

Email: yuejiaxing[at]gmail[dot]com; yuejx[at]sysucc[dot]org[dot]cn
Lab website: https://www.evomicslab.org

Education and Experiences

  • 2019.11-present  Principal Investigator (PI), Sun Yat-Sen University Cancer Center (SYSUCC).
  • 2015.06-2019.09  Postdoctoral fellow, Institute for Research on Cancer and Aging, Nice (IRCAN), CNRS. Advisor: Dr. Gianni Liti.
  • 2014.08-2015.03    Visiting student, Institute for Research on Cancer and Aging, Nice (IRCAN), CNRS. Host: Dr. Gianni Liti.
  • 2013.08-2014.05    Visiting student researcher, Department of Molecular and Cell Biology, UC Berkeley. Host: Dr. Daniel S. Rokhsar.
  • 2010.08-2015.05    Ph. D. in Evolutionary Biology, BioSciences at Rice, Rice University. Advisor: Dr. Nicholas H. Putnam & Dr. Michael H. Kohn.
  • 2007.09-2010.06    M. Sc. in Botany, School of Life Sciences, Nanjing University. Advisor: Dr. Dacheng Tian.
  • 2003.09-2007.06    B. Sc. in Biological Science, School of Life Sciences, Nanjing University.

Honors and Awards

  • 2019   The Pearl River Talents Program of Guangdong Province, China (2019QN01Y183)
  • 2018    EMBO Travel Grant (EUR €500)
  • 2018    Lindau Nobel Laureate Meeting Alumni (Nominated by CNRS)
  • 2015    Postdoctoral fellowship from Fondation ARC pour la Recherche sur le Cancer (3-year salary)
  • 2012    Edgar O’Rear graduate student travel award from Institute of Biosciences and Bioengineering (IBB), Rice University (USD $500)
  • 2011    Excellent master thesis award in Jiangsu Province, China

Awarded Research Supports

  • 2025.1-2028.12 National Natural Science Foundation of China (NSFC)
    General Program, 32470663
    The development and application of a bioinformatics method for structural variation detection based on pangenome graph.
    PI. [CNY ¥500,000]
  • 2024.1-2024.12    Fundamental Research Funds for the Central Universities, Sun Yat-sen University, 24qnpy293
    The identification, detection, and screen application for risk-associated variants of Human papillomavirus virus.
    PI. [CNY ¥50,000]
  • 2022.1-2024.12    Guangdong Basic and Applied Basic Research Foundation
    General Program, 2022A1515010717
    The development of integrated virus genome analysis framework and its application on nasopharyngeal cancer associated EB virus.
    PI. [CNY ¥100,000]
  • 2021.1-2024.12    National Natural Science Foundation of China (NSFC)
    General Program, 32070592
    The evolutionary impacts of aneuploidy on genome instability and phenotypic adaptivity.
    PI. [CNY ¥580,000]
  • 2020.1-2022.12    Guangdong Basic and Applied Basic Research Foundation
    Youth Program, 2019A1515110762
    The development and application of bioinformatic software for detecting genomic variants with full spectrum
    PI. [CNY ¥100,000]
  • 2019.11-2024.10    Sun Yat-sen University
    Young Talents Program of Sun Yat-sen University Cancer Center, YTP-SYSUCC-0042
    PI. [CNY ¥2,000,000]
  • 2017.09.02-2018.09.02    Microsoft Corporation
    Microsoft Azure Research Award, CRM:0740871
    Assessing the impact of structural variation on meiotic recombination
    PI. [USD $20,000 credit for using Microsoft Azure cloud computing service]
  • 2017.08.06-2018.08.06    XSEDE
    Startup allocation, TG-BIO170065
    Decoding the Genome of the Bahamas amphioxus, Asymmetron lucayanum
    co-PI. (PI: Linda Z. Holland, University of California, San Diego). [1,000 large memory service units and 500 GB storage on the PSC Bridges supercomputer with an estimated value of USD $705]
  • 2012.06.08-2013.06.08    XSEDE
    Startup allocation, TG-MCB120138
    Decoding the Asymmetron Genome
    co-PI. (PI: Nicholas H. Putnam, Rice University). [50,000 service units on the PSU Blacklight supercomputer]

Selected Publications

[ORCID] [Google Scholar] [Web of Science] [ResearchGate]
Total papers: 44; Total citations: 3880; h-index: 23; i10-index: 30.
(based on the Google Scholar statistics; last accessed on 2024/12/05)

corresponding author: *,  co-1st author: ^

  • Zepu Miao^, Yifan Ren^, Andrea Tarabini^, Ludong Yang, Huihui Li, Chang Ye, Gianni Liti, Gilles Fischer, Jing Li*, Jia-Xing Yue*. (2024) ScRAPdb, an integrated pan-omics database for the Saccharomyces cerevisiae reference assembly panel. Nucleic Acids Research, online advance (doi: 10.1093/nar/gkae955)
  • Zegeng Chen^, He Huang^, Huangming Hong^, Huageng Huang, Huawei Weng, Le Yu, Jian Xiao, Zhao Wang, Xiaojie Fang, Yuyi Yao, Jia-Xing Yue*, Tongyu Lin*. (2024) Full-spectral genome analysis of natural killer/T cell lymphoma highlights impacts of genome instability in driving its progression. Genome Medicine, 16(1):48.
  • Samuel O’Donnell^, Jia-Xing Yue^, Omar Abou Saada, Nicolas Agier, Claudia Caradec, Thomas Cokelaer, Matteo De Chiara, Stephane Delmas, Fabien Dutreux, Teo Fournier, Anne Friedrich, Etienne Kornobis, Jing Li, Zepu Miao, Lorenzo Tattini, Joseph Schacherer*, Gianni Liti*, Gilles Fischer*. (2023) Telomere-to-telomere assemblies of 142 strains characterize the genome structural landscape in Saccharomyces cerevisiae. Nature Genetics, 55(8):1390-1399.
  • Jing Li, Bertrand Llorente, Gianni Liti*, Jia-Xing Yue*. (2022) RecombineX: a generalized computational framework for automatic high-throughput gamete genotyping and tetrad-based recombination analysis. PLoS Genetics, 18(5):e1010047.
  • Jia-Xing Yue*, Gianni Liti*. (2019) simuG: a general-purpose genome simulator.  Bioinformatics, 35(21):4442-4444.
  • Jia-Xing Yue*, Gianni Liti*. (2018) Long-read sequencing data analysis for yeasts. Nature Protocols, 13(6):1213–1231.
  • Jia-Xing Yue, Jing Li, Louise Aigrain, Johan Hallin, Karl Persson, Karen Oliver, Anders Bergström, Paul Coupland, Jonas Warringer, Marco Cosentino Lagomarsino, Gilles Fischer, Richard Durbin, Gianni Liti*. (2017) Contrasting evolutionary genome dynamics between domesticated and wild yeasts. Nature Genetics, 49(6):913-924.
  • Jia-Xing Yue, Iryna Kozmikova, Hiroki Ono, Carlos W. Nossa, Zbynek Kozmik, Nicholas H. Putnam, Jr-Kai Yu, Linda Z. Holland*. (2016) Conserved noncoding elements in the most distant genera of cephalochordates: the Goldilocks principle. Genome Biology and Evolution, 8(8):2387-2405.
  • Jia-Xing Yue, Jr-Kai Yu, Nicholas H. Putnam, Linda Z. Holland*. (2014) The transcriptome of an amphioxus, Asymmetron lucayanum, from the Bahamas: a window into chordate evolution. Genome Biology and Evolution, 6(10):2681-2696.
  • Jia-Xing Yue, Blake C. Meyers, Jian-Qun Chen, Dacheng Tian*, Sihai Yang*. (2012) Tracing the origin and evolutionary history of plant NBS-LRR genes. New Phytologist, 193(4):1049–1063.
  • Jia-Xing Yue, Jinpeng Li, Dan Wang, Hitoshi Araki, Dacheng Tian, Sihai Yang*. (2010) Genome-wide investigation reveals high evolutionary rates in annual model plants. BMC Plant Biology, 10:242.

Software Development

Database Development

Conference Presentations

  • 2024.11.03-2024.11.06
    The 2024 Annual Conference of the Genetics Society of China, Changsha, Hunan, China.
    Oral presentation:​ ​Towards a pangenome and multi-omics understanding of genome and trait evolution via the classic model organism Saccharomyces cerevisiae.
  • 2024.08.16-2024.08.18
    The GPB Omics & Bioinformatics Frontiers Symposium 2024 (GFS2024), Chengdu, China.
    Oral presentation:​ ​Towards a pangenome and multi-omics understanding of genome and trait evolution via the lens of the Saccharomyces cerevisiae Reference Assembly Panel (ScRAP).
  • 2023.12.26-2023.12.18
    The 3rd AsiaEvo Conference, Singapore, Singapore.
    Oral presentation:​ ​The pathogenicity evolution of papillomavirus revealed by a compendium of 3,562 human and animal papillomavirus genomes.
  • 2023.11.27-2023.11.30
    The 11th National Assembly of the Genetics Society of China, Wuhan, Hubei, China.
    Oral presentation:​ ​Comparative genomics in the telomere-to-telomere (T2T) era: insights from the budding yeast Saccharomyces cerevisiae.
  • 2023.10.20-2023.10.22
    Society of Molecular Biology and Evolution (SMBE) Regional Evolutionary Genetics Meeting, Shanghai, China.
    Oral presentation:​ ​The pathogenicity evolution of papillomavirus revealed by a compendium of 3,562 human and animal papillomavirus genomes.
  • 2023.08.11-2023.08.14
    The 10th National Academic Conference on Microbial Genetics, Qingdao, Shandong, China.
    Oral presentation:​ ​The establishment of the global Saccharomyces cerevisiae T2T Reference Assembly Panel and and its comparative genomics study .
  • 2023.05.12-2023.05.15
    The 14th Chinese Model Fungi Conference, Shenyang, Liaoning, China.
    Oral presentation:​ ​Towards a pangenome understanding of structural genome dynamics via the lens of the Saccharomyces cerevisiae Reference Assembly Panel (ScRAP).
  • 2021.05.14-2021.05.17
    The 13th Chinese Model Fungi Conference, Wuhan, Hubei, China.
    Oral presentation:​ ​High-throughput tetrad genotyping & meiotic recombination profiling.
  • 2018.10.17-2018.10.20
    EMBO Workshop: Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems, Heidelberg, Baden-Württemberg, Germany.
    Oral presentation: Towards high resolution yeast meiotic recombination landscape and its genomic modulators.
  • 2017.11.27-2017.11.29
    iGenolevures Meeting 2017: The present and future of yeast genomics, Paris, France.
    Oral presentation:​ ​Parental​ ​genomic​ ​variation​ ​and​ ​its​ ​impacts​ ​on​ ​the​ ​meiotic​ ​offspring.
  • 2017.07.10-2017.07.12
    XXe Congrès National sur les Elements Transposables (CNET), Nice, PACA, France.
    Oral presentation: Evolutionary genome dynamics in domesticated and wild yeasts.
  • 2016.07.26-2016.07.29
    The amphioxus satellite meeting associated with the 6th meeting of the European Society for Evolutionary Developmental Biology (EED), Uppsala, Sweden.
    Oral presentation: Comparative transcriptomics and genomics of the Bahamas amphioxus, Asymmetron lucayanum.
  • 2016.10.10-2016.10.14
    Conférences Jacques Monod: Evolutionary genomics and systems biology: bringing together theoretical and experimental approaches, Roscoff, Brittany, France
    Poster presentation: Contrasting genome dynamics between domesticated and wild yeasts.
  • 2014.05.06-2014.05.10
    CSHL Conference: The Biology of Genomes (BOG), Cold Spring Harbor, New York, USA
    Poster presentation: Insight into cephalochordate evolution from a genomic study of the Bahama amphioxus, Asymmetron lucayanum.
  • 2013.01.03-2013.03.07
    Society for Integrative and Comparative Biology (SICB) Annual Meeting, San Francisco, California, USA
    Poster presentation: Functional characterization of the Asymmetron lucayanum genome.

Academic Responsibilities

  • 2024.06-present Editorial Board Member of Yeast

Academic and Professional Trainings

  • 2017-2018 GENETICS Peer Review Training Program (the first cohort)
  • 2012 Rice Teaching Workshop for Future and Current Teachers, Houston, Texas, USA
  • 2011 Workshop on Molecular Evolution at Marine Biological Laboratory (MBL), Woods Hole, Massachusetts, USA
  • 2011 Workshop on Comparative Genomics in North America, Fort Collins, Colorado, USA

Teaching Experiences

  • 2024 Spring co-Lecturer for “EC3032: Seminars in Evolutionary Biology”, Sun Yat-sen University
  • 2023-2024 Spring/Fall co-Lecturer for “AH2134: Introduction to basic and clinical research techniques”, Sun Yat-sen University
  • 2013 Spring TA for “EBIO372: Coral Reef Ecosystems”, Rice University
  • 2012 Spring TA for “EBIO328: Evolution of Genes and Genomes”, Rice University

Society Membership

  • The Genetics Society of China (GSC)
  • The Genetics Society of America (GSA)
  • The Society for Molecular Biology and Evolution (SMBE)

Journal Referee

Total=77.

* The number in parentheses denotes the number of versions of manuscripts that I reviewed for the corresponding journal (verified by Web of Science).

Aging and Cancer (2), Bioinformatics (8), BMC Bioinformatics (2), BMC Genomics (1), BMC Methods (2), Cell Insights (1), Computational and Structural Biotechnology Journal (1), Database (2), eLife (1), Evolution & Development (2), Frontiers in Plant Science (1), Frontiers in Microbiology (1), G3 (6), GENETICS (5), Genome Biology and Evolution (1), Genomics (2), Genomics Proteomics & Bioinformatics (1), Heliyon (2), Hereditas (Beijing) (2), Journal of Genetics and Genomics (2), Molecular Genetics and Genomics (9), NAR Genomics and Bioinformatics (2), Nature Communications (3), New Phytologist (1), Plant Molecular Biology (2), Plant Science (1), PLoS Genetics (3), PLoS One (5), SoftwareX (1), Yeast (6).