CV

Updated in December, 2017.

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Curriculum Vitae

Jia-Xing Yue (岳家兴)

 Population Genomics and Complex Traits Group
Institute for Research on Cancer and Aging, Nice (IRCAN)
CNRS UMR 7284 – Inserm U 1081 – Université Côte d’Azur (UCA)
Nice 06107, France
Email: yuejiaxing[at]gmail[dot]com
Website: http://www.iamphioxus.org

Education and Experiences

2015.6-present    Postdoctoral fellow, Institute for Research on Cancer and Aging, Nice (IRCAN), CNRS. Advised by Dr. Gianni Liti.
2014.8-2015.3    Visiting student, Institute for Research on Cancer and Aging, Nice (IRCAN), CNRS. Hosted by Dr. Gianni Liti.
2013.8-2014.5    Visiting student researcher, Department of Molecular and Cell Biology, UC Berkeley. Hosted by Dr. Daniel S. Rokhsar.
2010.8-2015.5    Ph. D. in Evolutionary Biology, BioSciences at Rice, Rice University. Advised by Dr. Nicholas H. Putnam & Dr. Michael H. Kohn.
2007.9-2010.6    M. Sc. in Botany, School of Life Sciences, Nanjing University. Advised by Dr. Dacheng Tian.
2003.9-2007.6    B. Sc. in Biological Science, School of Life Sciences, Nanjing University.

Honors and Awards

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

  • 2017.9.2-2018.9.2    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]
  • 2017.8.6-2018.8.6    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]
  • 2012.6.8-2013.6.8    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]

Submitted Manuscripts

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

  • Jing Li, Ignacio Vázquez-García, Karl Persson, Asier González, Jia-Xing Yue, Benjamin Barré, Michael N. Hall, Anthony D. Long, Jonas Warringer, Ville Mustonen, Gianni Liti. Patterns of selection reveal shared molecular targets over short and long evolutionary timescales. (under review; preprint available at https://www.biorxiv.org/content/early/2017/12/06/229419)
  • Oleg Simakov^, Ferdinand Marlétaz^, Jia-Xing Yue, Brendan O’Connell, Jerry Jenkins, Alex Brandt, Robert Calef, Che-Huang Tung, Tzu-Kai Huang, Jeremy Schmutz, Nori Satoh, Jr-Sky Yu, Nicholas H. Putnam, Richard E. Green, Daniel S. Rokhsar*. (2017) Deeply conserved synteny and the origins of vertebrate chromosomes. (under evaluation)
  • Jia-Xing Yue*, Gianni Liti*. (2017) LRSDAY: long-read sequencing data analysis for yeasts. (under review; preprint available at http://www.biorxiv.org/content/early/2017/09/05/184572; software available at https://github.com/yjx1217/LRSDAY)
  • Jackson Peter^, Matteo De Chiara^, Anne Friedrich, Jia-Xing Yue, David Pflieger, Anders Bergstrom, Anastasie Sigwalt, Benjamin Barré, Kelle Freel, Agnes Llored, Corinne Cruaud, Karine Labadie, Jean Marc Aury, Benjamin Istace, Kevin Lebrigand, Pascal Barbry, Stefan Engelen, Arnaud Lemainque, Gianni Liti*, Joseph Schacherer*. (2017) Yeast evolutionary history and natural variation revealed by 1,011 genomes. (accepted in Nature).

Publications

[ORCID] [Google Scholar] [ResearchGate]
Total citations: 536, h-index: 8, i10-index: 8. (based on the Google Scholar statistics; last accessed on 2017/12/07)
corresponding author: *,  co-1st author: ^

  • Francesca Giordano*, Louise Aigrain, Michael A. Quail, Paul Coupland, James K. Bonfield, Robert M. Davies, German Tischler, David K. Jackson, Thomas M. Keane, Jing Li, Jia-Xing Yue, Gianni Liti, Richard Durbin, Zemin Nin. (2017) De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms. Scientific Reports, 7:3935.
  • 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, 49:913-924. (project website: Yeast Population Reference Panel)
  • 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.
  • Jia-Xing Yue, Iryna Kozmikova, Hiroki Ono, Carlos W. Nossa, Zbynek Kozmik, Nicholas H. Putnam, Jr-Kai Yu, Linda Z. Holland*. (2016) Conserved non-coding elements in the most distant genera of cephalochordates: the Goldilocks principle. Genome Biology and Evolution, 8(8):2387-2405.
  • Jia-Xing Yue*, Nicholas D. Holland, Linda Z. Holland, Dimitri D. Deheyn*. (2016) The evolution of genes encoding for green fluorescent proteins: insights from cephalochordates (amphioxus). Scientific Reports, 6:28350. (co-corresponding author)
  • Kristoffer Krogerus*, Mikko Arvas, Matteo De Chiara, Frederico Magalhães, Laura Mattinen, Merja Oja, Virve Vidgren, Jia-Xing Yue, Gianni Liti, Brian Gibson. (2016) Ploidy influences the functional attributes of de novo lager yeast hybrids. Applied Microbiology and Biotechnology, 100:7203.
  • Oleg Simakov*^, Takeshi Kawashima^, Ferdinand Marletaz, Jerry Jenkins, Ryo Koyanagi, Therese Mitros, Kanako Hisata, Jessen Bredeson, Eiichi Shoguchi, Fuki Gyoja, Jia-Xing Yue, …(42 others)…, Nori Satoh*, Daniel Rokhsar*, John Gerhart*. (2015) Two hemichordate genomes illuminate the ancestry and diversification of deuterostomes. Nature, 527:459-465.
  • Roser Buscà, Richard Christen, Matthew Lovern, Alexander M. Clifford, Jia-Xing Yue, Greg G. Goss, Jacques Pouysségur, Philippe Lenormand*. (2015) ERK1 and ERK2 present functional redundancy in tetrapods despite higher evolution rate of ERK1. BMC Evolutionary Biology, 15(1):179.
  • Jia-Xing Yue, Kun-Lung Li, Jr-Kai Yu*. (2015) Discovery of germline-related genes in Cephalochordate amphioxus: A genome wide survey using genome annotation and transcriptome data. Marine Genomics, 24:147-157.
  • 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.
  • Carlos W. Nossa, Paul Havlak, Jia-Xing Yue, Jie Lv, Kimberly Y. Vincent, H. Jane Brockmann, Nicholas H. Putnam*. (2014) Joint assembly and genetic mapping of the Atlantic horseshoe crab genome reveals ancient whole genome duplication. GigaScience, 3:9.
  • Jia-Xing Yue, Blake Meyers, Dacheng Tian, Sihai Yang*. (2012) Tracing the origin and evolutionary history of plant NBS-LRR genes. New Phytologist 193:1049–1063.
  • 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.
  • Sihai Yang^, Xiaohui Zhang^, Jia-Xing Yue, Dacheng Tian*, Jian-Qun Chen*. (2008) Recent duplication dominates the expansion of the NBS-encoding genes in two woody species. Molecular Genetics and Genomics, 280:187-198.

Invited Conference Presentations

  • 2017.11  iGenolevures Meeting 2017 “The present and future of yeast genomics”, Paris, France.
    Title:​ ​Parental​ ​genomic​ ​variation​ ​and​ ​its​ ​impacts​ ​on​ ​the​ ​meiotic​ ​offspring.
  • 2017.7  XXe Congrès National sur les Elements Transposables (CNET), Nice, France.
    Title: Evolutionary genome dynamics in domesticated and wild yeasts.
  • 2016.7  The amphioxus satellite meeting associated with the 6th meeting of the European Society for Evolutionary Developmental Biology (EED), Uppsala, Sweden.
    Title: Comparative transcriptomics and genomics of the Bahamas amphioxus, Asymmetron lucayanum.

Invited Seminars

  • 2017.10.19  Institut Curie, Paris, France.
  • 2014.11.06  Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), Villefranche-sur-mer, France

Other Conferences Presentations

  • 2016  Conférences Jacques Monod:  Evolutionary genomics and systems biology: bringing together theoretical and experimental approaches, Roscoff, Brittany, France
    Poster presentation:
    Title: Contrasting genome dynamics between domesticated and wild yeasts.
  • 2014  CSHL Conference: The Biology of Genomes (BOG), Cold Spring Harbor, NY, USA
    Poster presentation:
    Title: Insight into cephalochordate evolution from a genomic study of the Bahama amphioxus, Asymmetron lucayanum.
  • 2013  Society for Integrative and Comparative Biology (SICB) Annual Meeting, San Francisco, CA, USA
    Poster presentation:
    Title: Functional characterization of the Asymmetron lucayanum genome.

Academic and Professional Trainings

2017-present GENETICS Peer Review Training Program (the first cohort)
2012 Rice Teaching Workshop for Future and Current Teachers, Houston, TX, USA
2011 Workshop on Molecular Evolution at MBL, Woods Hole, MA, USA
2011 Workshop on Comparative Genomics in North America, Fort Collins, CO, USA

Teaching Experiences

2013 Spring TA for “EBIO372: Coral Reef Ecosystems” (lecturing, grading), Rice University
2012 Spring TA for “EBIO328: Evolution of Genes and Genomes” (lecturing, grading), Rice University

Society Membership

The Society for Integrative and Comparative Biology (SICB)
European Society for Evolutionary Developmental Biology (EED)
The Genetics Society of America (GSA)

Journal Referee

* The number in parenthesis denotes the number of manuscripts that I reviewed for the corresponding journal. (verified by Publon)

GENETICS (1), Frontiers in Plant Science (1), Molecular Genetics and Genomics (7), Plant Science (1), PLoS One (2)

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