Picture of                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    Matthew Links

Matthew Links Assistant Professor

6D30 - Agriculture Building

Research Area(s)

  • Microbiome
  • Microbiology
  • Bioinformatics
  • Genomics
  • Metagenomics


Animal and Poultry Science

Other Affiliations/positions

Department of Computer Science



Ph.D. Veterinary Microbiology, University of Saskatchewan.


M.Sc. Department of Biological Sciences, University of Windsor.


B.Sc. Biochemistry & Computer Science, University of Saskatchewan.

Selected Recent Publications

LRolfe Sa, Strelkov S, Links MG, Clarke WE, Robinson SJ, Djavaheri M, Malinowski R, Haddadi P, Kagale S, Parkin IA, Taheri A, Borhan H. The compact genome of the plant pathogen Plasmodiophora brassicae is adapted to intracellular interaction with its host Brassica napus. BMC Genomics. 2016 Mar 31;17(1):272.


Links MG. Big Data is changing the battle against infectious disease. CCDR September 3, 2015 Volume 41-9. ISSN 1481-8531. 


Lévesque CA, Chen W, Hambleton S, Seifert KA, Adam Z, Bilodeau GJ, Cullis J, Demeke T, Dumonceaux TJ, Gagnon M, Graefenhan T, Kawchuk LM, Khan IUH, Lewis CT, Li X, Links MG, Mimee B, Rott M, Tambong JT, Topp E, Yu Q, and Yuan K. (2015). Project CRTI 09-462RD - Next generation sequencing, direct detection and genotyping of fungi, bacteria and nematodes in the agri-food system. DRDC-RDDC-2015-C148.


Links MG, Demeke T, Gräfenhan T, Hill JE, Hemmingsen SM, and Dumonceaux TJ. Simultaneous profiling of seed-associated bacteria and fungi reveals antagonistic interactions between microorganisms within a shared epiphytic microbiome on Triticum and Brassica seeds. New Phytologist, 2014. doi: 10.1111/nph.12693.


Links MG, Chaban B, Hemmingsen SM, Muirhead K, and Hill JE. mPUMA: a computational approach to microbiota analysis by de novo assembly of OTUs based on protein-coding barcode sequences. Microbiome, 2013. 1:23.


Links MG, Dumonceaux TJ, Hemmingsen SM, and Hill JE. The chaperonin-60 universal target is a barcode for bacteria that enables de novo assembly of metagenomic sequence data. PLoS ONE, 2012. 7(11): e49755.


Selected Awards


AAFC Gold Harvest Award in Innovation, Collaboration and Service Excellence


Governor General’s Gold Medal

Funding Sources

Canada First Research Excellence Fund http://www.cfref-apogee.gc.ca/

Agriculture and AgriFood Canada http://agr.gc.ca/

Genomics Research and Development Initiative http://grdi-irdg.collaboration.gc.ca/eng/about/index.html

Canadian Institutes of Health Research http://cihr-irsc.gc.ca/

Defence Research and Development Canada http://www.drdc-rddc.gc.ca/

SaskCanola http://www.saskcanola.com/

Agriculture Development Fund http://www.saskatchewan.ca/business/agriculture-natural-resources-and-industry/agribusiness-farmers-and-ranchers/agricultural-research-programs

Courses Taught

CMPT 857 - Readings in Bioinformatics