Genomes are organized in a non-random way with strong architecture at different genomic scales (e.g. local genomic regions, subchromosomal domains, and whole chromosomes). A multi-scale understanding of such genome architecture is critical to dissect how genome functions and evolves. Therefore, the core mission of our lab is to investigate the evolutionary dynamics of genome architecture and its functional implications, especially in the context of cancer biology. Specifically, we want to understand how different scales of genome architecture variation (e.g. polyploidy, aneuploidy, subtelomere, structural variation, repetitive elements, etc.) may contribute to evolutionary adaptation and genome instability. To achieve this goal, we combine both in silico genomic analysis and experimental evolution approaches in our projects. On one hand, we can directly introduce various genome architecture variation to the cell and to monitor evolution in action through experimental variation; on the other hand, we can also dig into the genomic data generated by both basic and clinical research to retrospectively reconstruct the tempo and mode of genome architecture evolution.

2003.09-2007.06    B. Sc. in Biological Science, School of Life Sciences, Nanjing University.

2007.09-2010.06    M. Sc. in Botany, School of Life Sciences, Nanjing University.

2010.08-2015.05    Ph. D. in Evolutionary Biology, BioSciences at Rice, Rice University.

2013.08-2014.05    Visiting student researcher, Department of Molecular and Cell Biology, UC Berkeley.

2014.08-2015.03    Visiting student, Institute for Research on Cancer and Aging, Nice (IRCAN), CNRS.

2015.06-2019.10    Postdoctoral fellow, Institute for Research on Cancer and Aging, Nice (IRCAN), CNRS.

* corresponding author; ^ co-first author.

1. Oleg Simakov^, Ferdinand Marlétaz^, Jia-Xing Yue, Brendan O’Connell, Jerry Jenkins, Alexander Brandt, Robert Calef, Che-Huang Tung, Tzu-Kai Huang, Jeremy Schmutz, Nori Satoh, Jr-Kai Yu, Nicholas H. Putnam, Richard E. Green, Daniel S. Rokhsar. (2020) Deeply conserved synteny resolves early events in vertebrate evolution. Nature Ecology and Evolution, (doi: 10.1038/s41559-020-1156-z) 

2. Benjamin P Barré, Johan Hallin, Jia-Xing Yue, Karl Persson, Ekaterina Mikhalev, Agurtzane Irizar, Dawn Thompson, Mikael Molin, Jonas Warringer, Gianni Liti*. (2020) Intragenic repeat expansions control yeast chronological aging. Genome Research, (doi: 10.1101/gr.253351.119)

3. Liudmyla Lototska, Jia-Xing Yue, Jing Li, Marie-Josèphe Giraud-Panis, Zhou Songyang, Nicola J Royle, Gianni Liti, Jing Ye*, Eric Gilson*, Aaron Mendez-Bermudez*. (2020) Human RAP1 specifically protects telomeres of senescent cells from DNA damage. EMBO Reports, e49076. (doi: 10.15252/embr.201949076)

4. Jia-Xing Yue*, Gianni Liti*. (2019) simuG: a general-purpose genome simulator. Bioinformatics, 35(21):4442–4444. (doi:10.1093/bioinformatics/btz424; software available at https://github.com/yjx1217/simuG) 

5. Jia-Xing Yue*, Gianni Liti*. (2018) Long-read sequencing data analysis for yeasts. Nature Protocols, 13(6):1213–1231. (doi:10.1038/nprot.2018.025; software available at https://github.com/yjx1217/LRSDAY) 

6. Jackson Peter^, Matteo De Chiara^, Anne Friedrich, Jia-Xing Yue, David Pflieger, Anders Bergström, Anastasie Sigwalt, Benjamin Barré, Kelle Freel, Agnès Llored, Corinne Cruaud, Karine Labadie, Jean Marc Aury, Benjamin Istace, Kevin Lebrigand, Pascal Barbry, Stefan Engelen, Arnaud Lemainque, Gianni Liti*, Joseph Schacherer*. (2018) Genome evolution across 1,011 Saccharomyces cerevisiae isolates. Nature, 556(7701):339–344. (doi:10.1038/s41586-018-0030-5) 

7. 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 genome dynamics between domesticated and wild yeasts. Nature Genetics, 49(6):913-924. (doi:10.1038/ng.3847) 

8. Chun-Min Shan^, Jiyong Wang^, Ke Xu^, Huijie Chen, Jia-Xing Yue, Stuart Andrews, James J. Moresco, John R. Yates III, Peter L. Nagy, Liang Tong*, Songtao Jia*.  (2016) A histone H3K9M mutation traps histone methyltransferase Clr4 to prevent heterochromatin spreading. eLife, 5:e17903. (doi:10.7554/eLife.17903) 

9. 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. (doi:10.1093/gbe/evw158) 

10. 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. (doi:10.1093/gbe/evu212) 

11. 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. (doi:10.1111/j.1469-8137.2011.04006.x) 

12. 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. (doi:10.1186/1471-2229-10-242) 

Updated by International Office, Sun Yat-sen University Cancer Center