Paul Stothard

About

Degree 

PhD, molecular biology and genetics, University of Alberta

Job/Research Area 

Bioinformatics, genomics, and genetics

Links

Stothard Research Group

Google Scholar

GitHub

Research

Understanding the genetic basis of traits in animals. We are using genomics and bioinformatics to identify DNA sequence differences that explain variation in simply-inherited and polygenic traits in animals. Our findings have been incorporated into DNA tests used in cattle and pig breeding.

Cataloging genome variation in cattle and bison. We are using short- and long-read whole-genome sequencing and custom software to find and visualize genome differences among individuals and species. Through this work we identified functionally important de novo structural variants in cattle, and developed a SNP chip used in bison farming and conservation.

Facilitating metagenomic sequencing-based diagnostics. We are working on a software pipeline to rapidly identify pathogens and detect antimicrobial resistance genes in metagenomic sequence data, to inform antimicrobial use in feedlot cattle.

Creating user-friendly software for rapid bacterial genome interpretation. We continue to develop Proksee, a popular web-based system that uses high-performance computing to quickly deliver high-quality and comprehensively annotated bacterial genome assemblies.

Our paper on a new SNP array for bison has been published in Frontiers in Genetics and the array is available to bison producers through Neogen Canada.

Feed efficiency genetic evaluations created by our Genome Canada-funded research with the University of Guelph have been released by Lactanet Canada.

Our Proksee bacterial genome analysis server is now online.

Our Bison Integrated Genomics (BIG) Project is now underway.

AFNS 508 - Applied Bioinformatics

Introduction to databases, software tools, and analysis methods used to characterize DNA and protein sequences and to measure gene expression. Topics include information retrieval from sequence databases, protein function prediction, assessing sequence similarity, measuring gene expression, and the analysis of high-throughput sequencing data using command-line tools. Prerequisite: consent of instructor.

AN SC 384 - Principles of Animal Genetics

An introduction to the basic principles of animal genetics and their practical application in selection strategies, breeding systems, and methods of improvement for domestic animals. Prerequisites: BIOL 207 and AN SC 101 or consent of instructor.

AN SC 485 - Animal Genetics and Breeding

Application of genetic/genomic principles and methods to the improvement of livestock and poultry. Prerequisite: AN SC 384 or consent of instructor.

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