Brendan J. McConkey

Undergraduate Advisor (Bioinformatics)

Cross-appointed (Chemical Engineering, School of Computer Science)
Bachelor of Science (BSc) Physics, Doctor of Philosophy (PhD) Biology Waterloo

Email: mcconkey@uwaterloo.ca

Telephone: (519) 888-4567 ext. 37020

Office: Biology 1 165A

Research interests

The research in my lab is focused on two complementary areas – experimental techniques for proteomics analysis, and the use of computational and bioinformatics approaches for investigating protein function.

We use the proteomics techniques of differential in-gel electrophoresis and mass spectrometry to identify changes in protein expression in a variety of biological systems. For example, my lab has applied this approach for the quantification of cell cycle proteins in yeast, recombinant protein production in mammalian cell lines, and identification of proteins mediating plant-bacterial interactions.

Computational and bioinformatics approaches are also used in the McConkey lab to investigate protein structure and expression patterns, and to investigate how protein function changes and diversifies within protein families. Recently we have applied structural pattern recognition algorithms to predict protein functions such as carbohydrate binding and antifreeze activity, and have used publicly available high-throughput data sets to map the evolution of protein function within homologous protein groups.

Selected publications

• Broom, A.R., Doxey, A.C., Lobsanov, Y., Howell, P.L., Rose, D.R., McConkey, B.J. and Meiering, E.M.  (2011) Modular subdomain evolution and the computational design of a threefold symmetric globular protein (in press)
• Lee S, Doxey AC, McConkey BJ, Moffat BA. (2011) Nuclear Targeting of Methyl-Recycling Enzymes in Arabidopsis thaliana is Mediated by Specific Protein Interactions. Mol Plant. (in press)
• Meshram M, Naderi S, McConkey B, Budman H, Scharer J, Ingalls B (2011). Pupulation based modeling of the progression of apoptosis in mammalian cell culture. Biotechnology and Bioengineering. (in press)
• Cheng Z, Woody OZ, McConkey BJ, Glick BR (2011). Combined effects of the plant growth-promoting bacterium Pseudomonas putida UW4 and salinity stress on the Brassica napus proteome. Applied Soil Ecology (in press)
• Stearns JC, Woody OZ, McConkey BJ, Glick BR (2011). Effects of bacterial ACC deamiase on Brassica napus gene expression measured with an Arabidopsis thaliana microarray. Mol Plant Microbe Interact. (in press)
• Kim DR, Gidvani RD, Ingalls BP, Duncker BP, McConkey BJ. (2011)  Differential chromatin proteomics of the MMS-induced DNA damage response in yeast. Proteome Sci. 9:62.
• Wei, Y.Y.C., Naderi, S, Meshram, M., Budman H, Scharer JM, Ingalis BP, McConkey, B.J. (2011) Proteomics analysis of chinese hamster ovary cells undergoing apoptosis during prolonged cultivation. Cytotechnology, 63(6):663-77. 
• Naderi, S., Meshram, M., Wei, Y.Y.C., McConkey, B.J., Ingalls, B.P., Budman, H.M. and Scharer, J.  (2011) Development of a mathematical model for evaluating the dynamic response of normal and apoptotic CHO cells in batch culture. Biotechnology Progress. 27: 1197-1205. 
• Ho, R, McConkey, B.J. (2011)  Modulating glycosylation of recombinant monoclonal antibodies for therapeutic applications. Curent Topics in Biotechnology, 6:57-69. 
• Doxey, A.C., Cheng,  Z., Moffatt, B.A. and McConkey, B.J. (2010). Structural motif screening reveals a novel, conserved carbohydrate-binding surface in the pathogenesis-related protein PR-5d. BMC Struct. Biol. 10: 23.
• Cheng, Z., Woody, O.Z., Glick, B.R. and McConkey, B.J. (2010). Characterization of Plant-Bacterial Interactions Using Proteomic Approaches. Curr. Proteomics 7: 244-257.
• Sun, Z., Cheng, Z., Taylor, C.A., McConkey, B.J. and Thompson, J.E. (2010). Apoptosis induction by eIF5A1 involves activation of the intrinsic mitochondrial pathway. J. Cell Physiol. 223:  798-809.
• Cheng, Z., McConkey, B.J. and Glick, B.R. (2010). Proteomic studies of plant-bacterial interactions. Soil Biol. Biochem. 42: 1673-1684.
• Cheng, Z., Woody, O.Z., Song, J., Glick, B.R. and  McConkey B.J. (2009). Proteome reference map for the plant growth-promoting bacterium Pseudomonas putida UW4. Proteomics. 9: 4271-4.
• Cheng, Z., Duan, J., Hao, Y., McConkey, B.J. and Glick, B.R. (2009). Identification of bacterial proteins mediating the interactions between Pseudomonas putida UW4 and Brassica napus (Canola). Mol. Plant Microbe Interact. 22: 686-94.
• Jostrup, R., Shen, W., Burrows, J.T.A., Sivak, J.G., McConkey, B.J. and Singer, T.D. (2009). Identification of myopia-related marker proteins in tilapia retinal, RPE, and choroidal tissue following induced form deprivation. Curr. Eye Res. 34: 966-975.
• Cheng, Z., Wei, Y.Y., Sung, W.W,, Glick, B.R. and McConkey, B.J. (2009). Proteomic analysis of the response of the plant growth-promoting bacterium Pseudomonas putida UW4 to nickel stress. Proteome Sci. 7: 18.
• Duncker, B.P., Chesnokov, I.N. and McConkey, B.J. (2009). The origin recognition complex protein family. Genome Biol. 10: 214.
• Kabash,i E., Valdmanis, P.N., Dion, P., Spiegelman, D., McConkey, B.J., Bouchard, J-P, Salachas, F., Meininger, V., Camu, W. , Dupre, N. and Rouleau G.A. (2008). TDP-43 mutations in sporadic and familial ALS patients. Nat. Genet. 40: 572-574.
• Cheng, Z.Y., Duncker, B.P., McConkey, B.J. and Glick, B.R. (2008). Transcriptional regulation of ACC deaminase gene expression in Pseudomonas putida UW4. Can. J. Microbiol. 54: 128-136.
• Doxey, A.C., Lynch. M.D., Müller, K.M., Meiering, E.M. and McConkey, B.J. (2008). Insights into the evolutionary origins of clostridial neurotoxins from analysis of the Clostridium botulinum strain A neurotoxin gene cluster. BMC Evol. Biol. 8: 316.
• Woody, O.Z., Doxey, A.C. and  McConkey, B.J. (2008). Assessing the evolution of gene expression using microarray data.  Evol. Bioinform. Online 4: 139-152
• Doxey, A.C., Yaish, M.W., Moffatt, B.A., Griffith, M. and McConkey, B.J. (2007). Functional divergence in the Arabidopsis ß-1,3-glucanase gene family revealed by integrated expression and phylogenetic analysis. Mol. Biol. Evol. 24: 1045-1055.
• Ingalls, B.P., Duncker, B.P., Kim, D.R. and McConkey, B.J. (2007). Systems level modeling of the cell cycle using budding yeast. Cancer Informatics. 3: 367–380.
• Glick,B.R., Todorovic, B., Czarny, J., Cheng, Z., Duan, J. and McConkey, B.J. (2007). Promotion of plant growth by bacterial ACC deaminase. Crit. Rev. Plant Sci. 26: 227-242.
• Doxey, A.C., Yaish, M.W., Griffith, M. and McConkey, B.J. (2006). Ordered surface carbons distinguish antifreeze proteins and their ice-binding regions. Nat. Biotech. 24: 852-855.
• Doxey, A.C. and McConkey, B.J. (2006). AFPredictor: A computational screening protocol for antifreeze/ice-structuring proteins. Nat. Protoc. DOI: 10.1038/ nprot.2006.213.
• Yaish, M.W., Doxey, A.C., McConkey, B.J., Moffatt, B.A. and Griffith, M. (2006). Cold active winter rye glucanases with ice-binding capacity. Plant Phys. 141: 1459-1472
• Eyal, E., Najmanovich, R., McConkey, B.J., Edelman, M. and Sobolev, V. (2004). Importance of solvent accessibility and contact surfaces in modeling side-chain conformations in proteins. J. Comput. Chem. 25: 712-724.
• McConkey, B.J., Sobolev, V. and Edelman, M. (2003). Discrimination of native protein structures using atom-atom contact scoring. Proc. Natl Acad. Sci. U.S.A. 100: 3215-3220.
• McConkey, B.J., Sobolev, V. and Edelman, M. (2002). Quantification of protein surfaces, volumes, and atom-atom contacts using a constrained Voronoi procedure. Bioinformatics 18:1365-1373.
• McConkey, B.J., Sobolev, V. and Edelman, M. (2002). The performance of current methods in ligand-protein docking. Curr. Sci. 83: 845-856.
• McConkey, B.J., Hewitt, L.M., Dixon, D.G. and Greenberg, B.M. (2002). Natural sunlight induced photooxidation of naphthalene in aqueous solution. Water Air Soil Poll. 136: 347-359.
• El-Alawi,Y.S., McConkey, B.J., Dixon, D.G. and Greenberg, B.M. (2002). Measurement of short- and long-term toxicity of polycyclic aromatic hydrocarbons using luminescent bacteria. Ecotox. Environ. Safe. 51(1): 12-21.
• McConkey, B.J., Mezey,P.G., Dixon, D.G. and Greenberg, B.M. (2000). Fractional simplex designs for interaction screening within complex mixtures. Biometrics 56: 824-832.
• Mallakin, A., McConkey, B.J., Miao, G.B., McKibbe, B., Snieckus, V., Dixon, D.G. and Greenberg, B.M. (1999). Impacts of structural photomodification on the toxicity of environmental contaminants: Anthracene photooxidation products. Ecotox. Environ. Safe. 43: 204-212.
• McConkey, B.J., Duxbury, C.L., Dixon, D.G. and Greenberg, B.M. (1997). Toxicity of a PAH photo-oxidation product to the bacteria Photobacterium phosphoreum and the duckweed Lemna gibba: Effects of phenanthrene and its primary photoproduct, phenanthrenequinone. Environ. Toxicol. Chem. 16: 892-899.
• Huang, X-D., Krylov, S.N., Ren, L., McConkey, B.J., Dixon, D.G. and Greenberg, B.M. (1997). Mechanistic QSAR model for the photoinduced toxicity of polycyclic aromatic hydrocarbons: II An empirical model for the toxicity of 16 polycyclic aromatic hydrocarbons to the duckweed Lemna gibba L. G3. Environ. Toxicol. Chem. 16:2296-2303.
• Huang. X-D., McConkey, B.J., Babu, T.S. and Greenberg, B.M. (1997). Mechanisms of photoinduced toxicity of photomodified anthracene to plants: Inhibition of photosynthesis in the aquatic higher plant Lemna gibba (duckweed) Environ. Toxicol. Chem. 16:1707-1715.
• Greenberg,B.M., Dixon, D.G., Wilson, M.I., Huang, X-D., McConkey, B.J., Duxbury, C.L., Gerhardt, K. and Gensemer, B. (1995). Use of artificial lighting in environmental assessment studies. In Environmental Toxicology and Risk Assessment: 4th Volume, STP 1262. Thomas W. La Point, Fred T. Price and Edward E. Little, Eds. American Society for Testing and Materials, Philadelphia, 55-70.