Ruijuan Li's Homepage

Ruijuan Li

I am a Bioinformatics Scientist at Inari Agriculture. My work in Inari focuses on using advanced genomics, statistical, and computational methods to accelerate plant breeding. Before joning Inari, I worked as a postdoctoral Researcher in University of California, Davis, working with Julin Maloof and Richard Michelmore. I did my PhD in Auburn University using system biology method to understand how cotton gene regulatory networks involving RNA and small RNA were modified under the attack of nematode.

My research passion lies in population genetics, quantitative genetics, and genomics. Using data analytics to help understand and ultimately engineer biological systems is always one of my career goals.

Publications

Integrated QTL and eQTL mapping provides insights and candidate genes for fatty acid composition, flowering time, and growth traits in a F2 population of a novel synthetic allopolyploid Brassica napus
Ruijuan Li, Kwangju Jeong, John T. Davis, Seungmo Kim, Soonbong Lee, Richard W. Michelmore, Shinje Kim, Julin N. Maloof Frontiers in Plant Science 2018 Github Paper

Genome-wide association study of Gossypium arboreum resistance to reniform nematode
Ruijuan Li, John E. Erpelding, Salliana R. Stetina BMC genetics 2018 Paper

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

Education

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

Experiences

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, Nozue K, Devisetty UK, Maloof JN. “An atlas of gene expression changes in response to shade in two Brassica rapa genotypes” (in preparation)

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