PLEASE NOTE SPEAKER CHANGE

Plant Gene Annotation Enrichment and Data Visualization via Comparative Genomics: Challenges and Solutions

by Dr. Dan Tulpan, University of Guelph

LOCATION: Room 202, Crop Sci
DATE & TIME: Thursday, March 21, 2019 @ 11:00 AM

ABSTRACT

Worldwide genome sequencing efforts for plants with medium and large genomes require identification and visualization of orthologous genes and corresponding enriched annotations, while their syntenic conservation becomes the pinnacle of any comparative and functional genomics study. Previous experimental studies carried out on model plant organisms such as Arabidopsis, Brachypodium, sorghum and rice provide a plethora of gene annotations that can be used to prime wheat gene annotations, proven that solid cross-species gene-to-gene and protein-to-protein orthology relationships are identified. The talk will include two studies. First, I show how a novel comparative genomics approach enriches existing wheat gene annotations based on cliques of predicted 1-to-1 orthologs, phylogenetic relationships and existing gene ontologies from 9 other plant species. Second, we present a web-based orthology and annotation visualization tool, which currently supports 20 completely sequenced plant species with considerably large genomes and offers intuitive and highly interactive pairwise comparison and visualization of genomic traits via gene orthology. I will also discuss potential ways to improve these approaches and how they can be extended to other areas of research.

Biography

Dan Tulpan’s research interests range from computational biology and bioinformatics to mathematical modelling and computer vision (using computers to extract and process data from images). His expertise has application across a broad range of topics, but at U of G, Dan is applying his skills to livestock breeding and other areas of plant and animal science. Previously, Dan was a research officer in the Scientific Data Mining Team, Digital Technologies Research Center of the National Research Council in Moncton, New Brunswick. There, he headed the NRC Atlantic Bioinformatics Laboratory. He has held numerous research and academic positions across Canada and worked in the software industry internationally.