Genetic diversity analysis of Gossypium arboreum germplasm accessions using genotyping-by-sequencing
Ruijuan Li, John Erpelding Genetica 2016 Paper

Transcriptome Analysis of Cotton (Gossypium hirsutum L.) Genotypes That Are Susceptible, Resistant, and Hypersensitive to Reniform Nematode (Rotylenchulus reniformis)
Ruijuan Li, Aaron M. Rashotte, Narendra K. Singh, Kathy S. Lawrence, David B. Weaver, Robert D. Locy Plos ONE 2015 Paper

Integrated signaling networks in plant responses to sedentary endoparasitic nematodes: a perspective
Ruijuan Li, Aaron M. Rashotte, Narendra K. Singh, Kathy S. Lawrence, David B. Weaver, Robert D. Locy Plant Cell Reports 2015 Paper 


Auburn University, USA: Ph.D in Plant genomics and Bioinformatics (2014.12)

Department of Biological Science.
Thesis: Small RNA and Transcriptome Analysis of Cotton (Gossypium hirsutum L.) Susceptibility, Resistance, and Hypersensitivity to Reniform Nematodes (Rotylenchulus reniformis)
Advisor: Prof. Robert D. Locy

Hebei Normal University, China: BS in Biotechnology (2009.7)

Department of Life Science.
Thesis: Cloning and characterization of NAC transcription factor from wheat


Postdoctoral Researcher (2016/01 ~ present), UC Davis

Development of novel plant prediction pipeline integrating genomic, transcriptomic, and phenotypic data for Brassica napus breeding (supervised by Julin Maloof and Richard Michelmore).

Postdoctoral Researcher (2015/04 ~ 2015/12), USDA-ARS

Analysis of genotyping-by-sequencing data with the aim of identifying population structure and associating QTL/SNPs with reniform nematode resistance trait of Gossypium arboreum (supervised by John Erpelding).

Graduate Research Assistant (2009/08 ~ 2015/4), Auburn Univeristy

Small RNA and transcriptome analysis of Gossypium hirsutum susceptibility, resistance, and hypersensitivity to reniform nematode using molecular, genomic, and bioinformatics tools (supervised by Robert Locy).

Publications under review or in preparation

  • Li R, Davis J, Jeong K, S Kim, Lee S, Kim S, Michelmore R, Maloof JN. “integrated QTL and eQTL mapping provides insights and promising candidates for fatty acid composition, flowering time, and growth traits in a F2 population of synthetic allopolyploid Brassica napus” (under review in Theoretical and Applied Genetics)
  • Li R, Nozue K, Devisetty UK, Maloof JN. “An atlas of gene expression changes in response to shade in two Brassica rapa genotypes” (in preparation)
  • Li R, Erpelding JE. “Genome-wide association study of Gossypium arboreum resistance to reniform nematode” (under review in BMC genetics)
  • Statistics and bioinformatics resources

    R for Data science: A good intro level R book built on top of tidyverse covering various aspects of data science including data visualization, transformation, import, relational data, manipulation of different data types, etc.
    my code for practice in this book

    Statistical Rethinking: An introduction to applied Bayesian data analysis accompanied by an R package, rethinking, built on top of Stan.
    my code for practice in this book

    An Introduction to Statistical Learning: An introduction to applied machine learning with application in R
    my code for practice in this book