Brendan McConkey

Dr. Brendan McConkey is an Associate Professor in the Department of Biology at the University of Waterloo with extensive expertise in computational biology, bioinformatics and integrative omics analysis.

His research program integrates experimental and computational approaches to understand gene and protein expression across diverse biological systems, with particular emphasis on non-model organisms. The McConkey lab combines high-throughput RNA sequencing and proteomics with advanced statistical and bioinformatics methods to study genome assembly, RNA-seq power and differential expression analysis, comparative genomics and structural bioinformatics. These approaches are applied to a wide range of problems, including plant–microbe interactions, microbial and plant pathogen genomics and environmental metagenomics. McConkey has led and contributed to a substantial portfolio of externally funded research supported by NSERC, the New Frontiers in Research Fund, Polar Knowledge Canada and industry and government partners. He has published close to 100 peer-reviewed articles with over 8,600 citations and counting (h-index 40), including work in Nature and other leading journals. He is also an experienced educator and mentor in bioinformatics and computational biology and has provided extensive service through graduate supervision and leadership roles at departmental, faculty and national levels.

McConkey studies gene expression patterns and host–pathogen interactions, with a focus on plant viruses, using experimental and bioinformatics approaches. His research aims to improve how scientists measure and interpret gene and protein expression. By deepening our understanding of how plant pathogens function, his work supports long‑term advances in crop improvement, enhanced food safety and reduced pesticide use, contributing to global efforts to strengthen food security and public health.

• Bioinformatics, systematics and protein evolution

• Protein structure and interaction modeling

• Gene expression pattern analysis

• Molecular genetics

• Biochemistry and biophysics

• Bioinformatics, systematics and evolution

• Molecular genetics

• Microbiology

• 2002, PhD Biology, Waterloo, Canada

• 2000, BSc Applied Physics, Waterloo, Canada

• 2012, Early Researcher Award, Ontario Ministry of Research and Innovation

• 1999, W.B. Pearson Medal for creative thesis research (Biology), University of Waterloo

• 2024 – Present, Graduate Studies Curriculum Committee

• 2020 – 2024, Undergraduate Studies Curriculum Committee

• 2020 – 2023, Associate Chair of Undergraduate Studies

• International Society for Computational Biology (Member)

• UW Bioinformatics Research Group (Member)

• Waterloo Centre for Microbial Research (Member)

• BIOL 130L - Cell Biology Laboratory
  • Taught in 2022
• BIOL 365 - Methods in Bioinformatics
  • Taught in 2021, 2022, 2023, 2024, 2026
• BIOL 465 - Structural Bioinformatics
  • Taught in 2024
• BIOL 631 - Statistical Methods in Ecology
  • Taught in 2025
• BME 285L - Engineering Biology Laboratory
  • Taught in 2022

* Only courses taught in the past 5 years are displayed.

• For the full list of Brendan McConkey's publications, please see Google Scholar.

• Cheng, Z., Li, JF., Niu, Y. et al. (2015). Pathogen-secreted proteases activate a novel plant immune pathway. Nature 521, 213–216 https://doi.org/10.1038/nature14243

• Duncker BP, Chesnokov IN, McConkey BJ. (2009) The origin recognition complex protein family. Genome Biol. 2009;10(3):214 Epub Mar 17. PMID: 19344485; PMCID: PMC2690993. https://doi.org/10.1186/gb-2009-10-3-214.

• Lorv, J.S., McConkey, B.J. Kastor (2025): a reference-based comparative approach for assessment and correction of gene-fragmenting errors in long-read assemblies of small genomes. BMC Genomics 26, 388 https://doi.org/10.1186/s12864-025-11569-y

• Mooney SM, Talebian V, Jolly MK, Jia D, Gromala M, Levine H, McConkey BJ (2017). The GRHL2/ZEB Feedback Loop-A Key Axis in the Regulation of EMT in Breast Cancer. J Cell Biochem. 2017 Sep;118(9):2559-2570. Epub 2017 May 3. PMID: 28266048. https://doi.org/10.1002/jcb.25974

• Collington EL, Doxey AC, McConkey BJ, Glerum DM. Widespread gene fusion artifacts in helminth genome annotations. BMC Genomics. 2026 Feb 4;27(1):253. PMID: 41634541; PMCID: PMC12964723. https://doi.org/10.1186/s12864-026-12589-y

• Hajaniriana, E., Ruffell, S., McConkey, B.J., Muller, K.M. Sterile Methods and Products: Provisional Patent for Anti‑bacterial Algae Fatty Acids. PCT International Patent Application PCT/CA2015/051288, jurisdiction PCT (WO), patent type Provisional