CURRICULUM VITAE

Xinshuai Qi
Ph.D.
Postdoctoral Fellow

(Updated Jul, 2017)

Email:
qxs@email.arizona.edu

Links:
The Barker lab @UA
The Pires lab @UM
The Olsen lab @WUSTL
The Soltis lab @UF
The Fu and Qiu lab @ZJU
CGM
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Education and Employment:

2014 – present          Postdoctoral Researcher. Lab Affiliation: Michael S. Barker. University of Arizona, Tucson, AZ, USA
2013 -  2014              Postdoctoral Researcher. Lab Affiliation: Kenneth M. Olsen. Washington University in St. Louis, MO, USA
2011 -  2013              Visiting Graduate Student (part of my Ph.D. program). Advisor:                                  
                                  Douglas E. Soltis, Pamela S. Soltis. University of Florida, Gainesville, FL, USA
2008 - 2013               Ph.D. Botany. Advisor: Yingxiong Qiu, Chengxin Fu. Zhejiang University, Hangzhou, China
2004 – 2008              B.S. Biotech. Northwest Agriculture & Forest University, Yangling, China
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Current Research:

I am interested in a wide range of topics in plant evolution. My research has involved in wild and crop plant population genetics, genomics, QTL mapping, phylogeography and plant gene family evolution. I am also interested in topics like comparative genomics, transcriptomics, local adaptation, crop domestication, weed and invasive species evolution, bioinformatics, hybridization, phylogeny and ecological niche modeling.

Skills:
Bioinformatics and Comparative Genomics NGS data (GBS, RNASeq), De novo and Reference based Reads Assembly, SNP Variation Calling (Tophat, VCFTools, BCFTools, SamTools, PLink), Selective Sweep Scan (SweeD, H12 test), Gene Expression Analysis (Cufflinks, CummeRbund, DESeq), Gene Annotation (SnpEff), Gene Ontology, CIRCOS plot, LeafJ
 
Computer and Data Science Linux/Unix, Python (Pandas, Numpy, Scipy, Scikit-learn), R (R/qtl, ggplot2, RMarkdown), SQL, LaTex, GitHub.
 
Population and Quantitative Genetics STRUCTURE, PCA, DIY-ABC, ∂a∂i, PAML, fastSimCoal, SLiM, WGCNA, QTL mapping, GWAS, Marker Assistant Selection.
 
Biogeography TCS, Ecological Niche Modeling, Phylogeny Construction (RAxML, BEAST, TreeMix)

Research projects:
  • The influence of domestication and polyploidy on Brassica rapa crops (NSF #1339156)
  • Origin and genetic basis of weediness traits in the US weedy rice (NSF #1032023, NSF #0638820)
  • Evolution and phylogeny of GSK3 gene family (NSF #0922742, CSC-Joint training program 2011)
  • Phylogeography of East Asia endemic plants – role of land bridges in East Asia (LSEB lab open funding, CAS)

Selected Publications:
       I have a total of 14 publications with ~ 400 citations. Below is a list of my selected publications:
  1. Qi X-S, An H, Ragsdale A et al. (2017) Genomic inferences of domestication events are corroborated by written records in Brassica rapa. Molecular ecology, 26, 3373-3388.
  2. Qi X-S, Liu Y, Vigueira CC et al. (2015) More than one way to evolve a weed: parallel evolution of US weedy rice through independent genetic mechanisms. Molecular ecology, 24, 3329–3344.
  3. Qi X-S, Chanderbali AS, Wong GK-S, Soltis DE, Soltis PS (2013) Phylogeny and evolutionary history of glycogen synthase kinase 3/SHAGGY-like kinase genes in land plants. BMC evolutionary biology, 13, 143.
  4. Albert VA, Barbazuk WB, dePamphilis CW et al. (2013) The Amborella Genome and the Evolution of Flowering Plants. Science, 342, 1241089.
  5. Qi X-S, Chen C, Comes HP et al. (2012) Molecular data and ecological niche modelling reveal a highly dynamic evolutionary history of the East Asian Tertiary relict Cercidiphyllum (Cercidiphyllaceae). New Phytologist, 196, 617–630.
  6. Qi X-S, Yuan N, Comes HP, Sakaguchi S, Qiu Y-X (2014) A strong “filter”effect of the East China Sea land bridge for East Asia’s temperate plant species: inferences from molecular phylogeography and ecological niche modelling of Platycrater arguta (Hydrangeaceae). BMC evolutionary biology, 14, 41.

        More details about my publication is available on Google scholar

Symposium Participation and Presentations:
  1. “Genomic inferences of domestication events are corroborated by written records in Brassica rapa”, June 24-28, 2017 Fort Worth, TX, USA.
  2. “Identifying the origin and history of candidate genes during domestication of multiple Brassica rapa crops”, June 4-8, 2017, Huntsville, AL, USA.
  3. “Understanding the evolutionary genetics of crop domestication”, March 21, 2017, University of Vermont, VT, USA.
  4. “Triplication, domestication and diversification of Brassica rapa” Evolution 2016, June 17-21th, 2016, Austin, TX, USA.
  5. “Genomics of domestication of Brassica rapa” Plant & Animal Genome (PAG) meeting 2016, Jan 9th, 2016, San Diego, CA, USA.
  6. “Brassica evolution influenced by polyploidization and domestication” Sep 29th, 2015. Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA.
  7. “Higher substitution rates and more deleterious loci in polyploid plants” Botany 2015. July 25-29th, 2015. Edmonton, Alberta, Canada.
  8. “Relaxed purifying selection leads to more deleterious loci in polyploid plants”. Comparative Genomics and Transcriptomics Meeting and Workshops, May 10-12, 2015. New Mexico State University, Las Cruces. NM.
  9. “Evopipes – identifying orthologous genes from transcriptome data”. Comparative Genomics and Transcriptomics Meeting and Workshops, May 10-12, 2015. New Mexico State University, Las Cruces. NM.
  10. “NGS and its application in plant evolution research”. ECOL-346 Bioinformatics, April 14th, 2015. University of Arizona, Tucson, AZ
  11.  “Comparative QTL mapping, population genetics and the parallel evolution of weedy rice”. St. Louis Ecology, Evolution and Conservation (SLEEC) retreat, September 27th, 2014. Saint Louis Zoo, St. Louis, MO.
  12. Invited talk on my previous research. Sep 10th, 2014. University of Missouri, Columbia, MO.
  13. “QTL mapping using Genotyping-by-Sequencing shed light on the parallel evolution of weedy rice: more than one way to evolve a weed”. 10th Annual Postdoc Scientific Symposium, April 3, 2014. Washington University School of Medicine, St. Louis, MO.
  14. “Comparative QTL mapping, population genetics, and the parallel evolution of weedy rice”. Evolution 2014, July 23, 2014. Raleigh, NC.
  15. “De-domestication and the evolutionary genomics of weedy red rice”. Poster presented at SMBE 2014, June 8-12, 2014. San Juan, Puerto Rico.
  16. St. Louis Ecology, Evolution and Conservation (SLEEC) retreat, September 28, 2012, Saint Louis Zoo, St. Louis, MO.
  17. “What do thousands of SNPs reveal about the origin of Asian weedy rice v.s. U.S. weedy rice” WUSTL Plant & Microbial Biosciences annual retreat, October 18, 2013, Tyson Research Center, Eureka, MO.
  18. “Evolutionary history of the East Asian Tertiary relict Cercidiphyllum (Cercidiphyllaceae)”. Botany 2012, July 4-7, 2012 Columbus, Ohio.
  19. “Phylogeography of East Asia endemic disjunctive plant Platycrater arguta based on multiple molecular markers”. Symposium of plant systematics and evolution, Oct. 26-27, 2011, Kunming, China.
 
Peer Review Experience:
Molecular Ecology, BMC Genetics, BMC Evolutionary Biology, PLOS One, Taxon, American Journal of Botany, Journal of Heredity, Scientific Report, Pest Management, Annals of Applied Biology, Journal of Systematics and Evolution, Plant Molecular Biology Reporter, Computational and Structural Biotechnology Journal.
 
Mentoring Experience:
Daniel Oliver             Undergraduate student, University of Arizona 2017
Chenlu Di                  Graduate student. University of Arizona 2016
Hong An                    Graduate student. Huazhong Agriculture University 2014-2016
Tara Hall                    Undergraduate student, University of Arizona 2015- 2016
                                  (now graduate student at Cornell University)
Daniel Cui                 Undergraduate student, Washington University in St. Louis 2013-                                         2014 (now graduate student at Washington University)

Field Work:
2015              Specimen and DNA collection, Selaginella, CA and AZ, USA
2013              Specimen and DNA collection, Echinochloa weeds, MO, USA
2010              Field survey, specimen and DNA collection, Ginkgo biloba, Tianmu Mt, China
2010              Ecological flora survey, Thousand-island lake, China
2009              Specimen and DNA collection, Neolitsea sericea, Zhoushan islands, China
2008 -2009    Specimen and DNA collection, Kirengeshoma palmate, Cercidiphyllum                                  japonicum, Platycrater arguta, Davidia involucrata, China.
 
Outreach:
Earth Day                           FLMNH, University of Florida, FL, 2013
Rice Day                            Stuttgart, AR, 2013
Co-found and organize      Chinese St. Louis evolution discussion group, 2014
Co-found and organize      Chinese Genomics Online Meet-up                                                                                          (chinesegenomics.weebly.com), 2017
 
Honors and Awards:
  • Natural Science Award (II), Outstanding Science Research Achievements in Higher Institution, China,  2016
  • Songdu scholarship, Zhejiang University, China. 2013. ~$2,000
  • Outstanding Graduate Students of Zhejiang Province, China. 2013. $500
  • Joint-training Ph.D. program, China Scholarship Council. 2011-2013. $28,800
  • Meritorious Winner of Excellent Graduate Student, Zhejiang University, China. 2011