Fabregat A, Sidiropoulos K, Garapati P, Gillespie M, Hausmann K, Haw R, Jassal B, Jupe S, Korninger F, McKay S, Matthews L, May B, Milacic M, Rothfels K, Shamovsky V, Webber M, Weiser J, Williams M, Wu G, Stein L, Hermjakob H and D'Eustachio P. 2015. The Reactome pathway Knowledgebase Nucl. Acids Res. doi:10.1093/nar/gkv1351

Tello-Ruiz MK, Stein J, Wei S, Preece J, Olson A, Naithani S, Amarasinghe V, Dharmawardhana P, Jiao Y, Mulvaney J, Kumari S, Chougule K, Elser J, Wang B, Thomason J, M. D, Kerhornou A, Walts B, A. N, Huerta L, Keays M, Amy Y, Parkinson H, Fabregat A, McKay S, Weiser J, D'Eustachio P, Stein L, Petryszak R, J. P, Jaiswal P and Ware D. 2015.  Gramene 2016: comparative plant genomics and pathway resources. Nucl. Acids Res. doi:10.1093/nar/gkv1179

Mckay SJ and Weiser J. 2015. Installing a Local Copy of the Reactome Web Site and Knowledgebase.  Current Protocols in Bioinformatics 50:9.10.1-9.10.10 doi 10.1002/0471250953.bi0910s50

Ramani AK, Verster AJ, McKay SJ and AG Fraser. 2013. Comparative RNAi screens in C. elegans and C. briggsae reveal the impact of Developmental System Drift on gene function.  PLOS Genetics  10(2): e1004077 doi:10.1371/journal.pgen.1004077

Hilgert U, McKay SJ, Ghiban C, Khalfan M, Micklos D, and Williams J.  2014. DNA Subway: Making genome analysis egalitarian. In ACM International Conference Proceeding Series. [70] Association for Computing Machinery. doi 10.1145/2616498.2616575

McKay SJ, Skidmore EJ, LaRose CJ, Mercer AW and C Noutsos.  2013. Cloud-based bioinformatics with iPlant Atmosphere. Current Protocols in Bioinformatics 43:9.15.1-9.15.20 doi: 10.1002/0471250953.bi0915s43


Deck CA, McKay SJ, Fiedler TJ, LeMoine CMR, Kajimura M, Nawata CM, Wood CM and PM Walsh. 2013.  Transcriptome responses in the rectal gland of fed and fasted spiny dogfish shark (Squalus acanthias) determined by suppression subtractive hybridization.  Comp. Biochem. Physiol. Part D: Genomics and Proteomics  8:334-343 doi: 10.1016/j.cbd.2013.09.003

Oliver SL, Lenards AJ, Barthelson RA, Merchant N and McKay SJ.  2013. Using the iPlant Collaborative Discovery Environment.  Current Protocols in Bioinformatics 42:1.22.1–1.22.26 doi: 10.1002/0471250953.bi0122s42


Matasci N and SJ McKay.  2013. Phylogenetic Analysis with the iPlant Discovery Environment.  Current Protocols in Bioinformatics 42:6.13.1–6.13.13 doi: 10.1002/0471250953.bi0613s42

Boyle BL, Hopkins N, Lu Z, Garay JAR, Mozzherin D, Rees T, Matasci N, Narro ML, Piel WH, McKay SJ, Lowry S, Freeland C, Peet RK and Enquist BJ. 2013. The Taxonomic Name Resolution Service: an online tool for automated standardization of plant names.  BMC Bionformatics 14:16 doi: 10.1186/1471-2105-14-16

Washington NL, Stinson EO, et al., McKay SJ, Micklem G, Stein LD, and Lewis SE. 2011. The modENCODE Data Coordination Center: Lessons in Harvesting Comprehensive Experimental Details. Database. doi:10.1093/database/bar023

Goff SA, Vaughn M, McKay S, et al.  2011. The iPlant Collaborative: Cyberinfrastructure for Plant Biology. Front. Plant Sci. 2:34. doi: 10.3389/fpls.2011.00034

McKay SJ, Vergara IA and Stajich J. 2010. "Using the Generic Synteny Browser (Gbrowse_syn).  Current Protocols in Bioinformatics 9.12.1-9.12.25. doi: 10.1002/0471250953.bi0912s31

Gerstein MB, Lu ZJ, et al., McKay, SJ, Stein LD, Lieb JD, Waterston RH. (2010) Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project. Science 330: 1775-87.

The modENCODE Consortium, Roy S, et al. Stein L, White KP, Kellis M. (2010) Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 330:1787-97 (Corresponding authors listed).

Fiedler TJ, Hudder A, McKay SJ, Shivkumar S, Capo TR, Schmale MC and Walsh PJ. 2010. The transcriptome of early life history stages of the California Sea Hare Aplysia californica.  Comp. Biochem. Physiol. Part D: Genomics and Proteomics 5: 165-170

Celniker SE, Dillon LA, Gerstein MB, et al., Waterston RH; modENCODE Consortium.  2009.  Unlocking the secrets of the genome.  Nature 459:927-30.

Stephen J. Robinson, Lily H. Tang, Brent A. G. Mooney, McKay SJ, et al. and Parkin IAP. 2009. An archived activation tagged population of Arabidopsis to facilitate forward genetics approaches.  BMC Plant Biology 9:101 doi:10.1186/1471-2229-9-101

Meissner B, Warner A, et al.,
McKay SJ, et al., Jones SJM, Marra MA and Moerman DG, 2009. An Integrated Strategy to Study Muscle Development and Myofilament Structure in Caenorhabditis elegans. PLoS Genet 5: e1000537. doi:10.1371/journal.pgen.1000537

Coghlan A, Fiedler TJ, McKay SJ, Flicec P, Harris TW, Blasiar D, the nGASP Consortium and LD Stein. 2008. nGASP - the nematode genome annotation assessment project. BMC Bioinformatics 9:549 (

Rogers A, Antoshechkin I, Bieri T, et al., McKay S, et al., Stein LD, Spieth J and Sternberg PW. 2008. WormBase 2007. Nucleic Acids Research: doi:10.1093/nar/gkm975

Hunt-Newbury R, Viveiros R, Johnsen R, et al., McKay S, et al., Jones SJ, Marra MA, Baillie DL and Moerman DG. 2007. High-throughput in vivo analysis of gene expression in Caenorhabditis elegans. PLoS Biol. 5:e237

McGhee JD, Sleumer MC, Bilenky M, Wong K, McKay SJ, et al., Marra MA, Jones SJM, Moerman DG and Robertson AG. 2007. The ELT-2 GATA-factor and the global regulation of transcription in the C. elegans intestine. Developmental Biology 302: 627-645

Ruzanov P, Riddle DL, Marra MA, McKay SJ and SJM Jones. 2007. Genes that may modulate longevity in C. elegans in both dauer larvae and long-lived daf-2 adults. Aging Cell 42: 825-839

Bieri T, Blasiar D, Ozersky P, et al., McKay S, et al., Durbin R, Stein L, Sternberg PW and Spieth J. 2007. WormBase: new content and better access. Nucleic Acids Research:doi:10.1093/nar/gkl818.

Blacque OE, Perens EA, Boroevich KA, et al., McKay SJ, et al. and Leroux MR. 2005. Functional genomics of the cilium, a sensory organelle. Current Biology 15:935-941

Halaschek-Wiener J, Khattra JS, McKay SJ, Pouzyrev A, Stott JM, Yang GS, Holt RA, Jones SJ, Marra MA, Brooks-Wilson AR and DL Riddle. 2005. Analysis of long-lived C. elegans daf-2 mutants using serial analysis of gene expression. Genome Research. 15:603-615

McKay SJ, Trautner J, Smith MJ, Koop BF and RH Devlin. 2004. Evolution of duplicated growth hormone genes in autotetraploid salmonid fishes. Genome 47:714-723

Baross A, Butterfield YS, Coughlin SM, Zeng T, Griffith M, Griffith OL, Petrescu AS, Smailus DE, Khattra J, McDonald HL, McKay SJ, Moksa M, Holt RA and Marra MA. 2004. Systematic recovery and analysis of full-ORF human cDNA clones. Genome Research 14:2083-2092

Phillips, RB, MP Matsuoka, NR Konkol, and McKay SJ. 2003. Molecular systematics and evolution of the growth hormone introns in the Salmoninae. Environmental Biology of Fishes 69:433-440

Edgley M, D'Souza A, Moulder G, McKay SJ, Shen B, Gilchrist E, Moerman D and Barstead R. 2002. Improved detection of small deletions in complex pools of DNA. Nucleic Acids Research 30:e52

McKay SJ and Jones SJM. 2002. AcePrimer: automation of PCR primer design based on gene structure. Bioinformatics 18:1538-1539.

Smith CT, Nelson RJ, Pollard S, Rubidge E, McKay SJ, Rodzen J, May B and Koop BF. 2002. Population genetic analysis of white sturgeon (Acipenser transmontanus) in the Fraser River. Journal of Applied Ichthyology 18:307-312

McKay SJ, Nakayama I, Smith MJ, and Devlin RH. 1998. Relationship between amago and masu salmon examined through DNA sequence analysis of nuclear and mitochondrial loci. Zoological Science 15: 971-979

McKay SJ, Smith MJ, and Devlin RH. 1997. Polymerase chain reaction-based species identification of salmon and coastal trout in British Columbia. Molecular Marine Biology and Biotechnology 6: 131-140

McKay SJ, Devlin, RH and Smith MJ. 1996. Phylogeny of Pacific Salmon and Trout based on Growth Hormone Type-2 (GH2) and Mitochondrial NADH Dehydrogenase Subunit 3 (ND3) DNA Sequences. Canadian Journal of Fisheries and Aquatic Sciences 53: 1165-1176


McKay SJ and Cain S. 2009. “Genome Browsers” in Bioinformatics: Tools and Applications (Edwards D, Stajich J and Hansen D, Eds).  Springer. doi: 10.1007/978-0-387-92738-1


Byun-McKay SA, Duggan R, Carroll B,  Geeta R and McKay SJ . 2009.  “Missing the Subcellular Target: A mechanism for the evolution of Eukaryotic Genes” in Evolutionary Biology, from Concept to Application II (Pontarotti EP, Ed.) Springer. doi: 10.1007/978-3-642-00952-5_10

McKay SJ, Johnsen, R., Khattra, J., Asano, J., Baillie, D.L., Chan, S., Dube, N., Fang, L., Goszczynski, B., Ha, E., et al. 2003. Gene expression profiling of cells, tissues, and developmental stages of the nematode C. elegans . Cold Spring Harbor Symposium on Quantitative Biology 68, 159-169.


Abigail Cabunoc and Sheldon McKay (eds):Software Carpentry: Using Databases and SQL.  Software Carpentry Foundation, Version 5.3, May 2015, 10.5281/zenodo.27356.