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

2013–2014

2011– 2013
​ 

​2008–2013

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

Research Interest

​I am interested in a wide range of topics in plant evolution, especially crop evolution under the human-altered environment. 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)

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
Chenlu Di 
Hong An
Tara Hall

Daniel Cui
 Undergraduate student, University of Arizona 2017
 Graduate student. University of Arizona 2016
 Graduate student. Huazhong Agriculture University 2014-2016
 Undergraduate student, University of Arizona 2015- 2016
 (now graduate student at Cornell University)
 Undergraduate student, Washington University in St. Louis 2013-2014
​(now graduate student at Washington University)

Field Work

2015
2013
2010
2010
2009
​2008
Specimen and DNA collection, Selaginella, CA and AZ, USA
Specimen and DNA collection, Echinochloa weeds, MO, USA
Field survey, specimen and DNA collection, Ginkgo biloba, Tianmu Mt, China
Ecological flora survey, Thousand-island lake, China
Specimen and DNA collection, Neolitsea sericea, Zhoushan islands, China
Specimen and DNA collection, Kirengeshoma palmate, Cercidiphyllum japonicum, Platycrater arguta, Davidia involucrata, China.

Outreach

2013
2013
2014
​2017​
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