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Brett Whitty

Owner/Operator - GNŌMATIX

Position - Company  
Manager, International Cancer Genome Consortium Data Coordination Centre, & Senior Bioinformatician/Data Manager - Ontario Institute for Cancer Research

Manager & Senior Bioinformatician/Data Manager, International Cancer Genome Consortium Data Coordination Centre, Ontario Institute for Cancer Research, Informatics and Bio-Computing platform

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Apr 2011 - Jun 2013
Research Assistant III (Bioinformatics Engineer) - Michigan State University

Lead bioinformatics developer/analyst and web developer on USDA Solanaceae Comparative Genomics Resource project. Performed bioinformatics work, including NGS transcriptomics, as part of the International Potato Genome Sequencing Consortium. Provided bioinformatics support and analysis for the Solanaceae Co-ordinated Agricultural Project (SolCAP), which received the 2011 USDA Secretary's Honor Award. Contributed to the Pythium ultimum genome project. Provided bioinformatics support to collaborators. Built and administered 450+ core grid computing cluster running Rocks Linux cluster distribution (and using SGE).

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Jan 2008 - Apr 2011
Bioinformatics Engineer II - J. Craig Venter Institute

Developed metagenomic annotation and analysis pipeline for the CAMERA marine metagenomics web portal (including the Global Ocean Sequencing expeditions). Microbial pan-genome analysis pipeline development.

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Oct 2005 - Jan 2008
Graduate Student / Teaching Assistant - McMaster University

* Bioinformatics support for Thellungiella salsuginea EST/microarray/metabolomics joint project with University of Waterloo. Developed a software pipeline for quality control, processing, clustering, assembly, and annotation of EST data. Designed and implemented a MySQL-based relational database and PHP web interface to access, analyze, and visualize the data.
* Developed sequence-based computational methods to predict protein functional associations for complete proteome of Sinorhizobium meliloti. Predicted novel functional associations of conserved hypothetical proteins through phylogenomics methods, and integration of public database information. Developed software for web-based display of results. Supervisor: Dr. G. Brian Golding
* Conducted labs for Biology I, Cell Biology, Eukaryotic Genetics. Conducted tutorials for Genetics, Bioinformatics. Developed course materials for Bioinformatics. Presented guest lectures for Eukaryotic Genetics.

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Sep 2002 - Sep 2005
Computer Lab Advisor / Network Technician / Teaching Assistant - Brock University

* Installation and troubleshooting of Ethernet network in campus residences.
* Supervised general access computer labs (PC and Mac). Instructed/assisted students with software and hardware use and troubleshooting.
* Conducted labs, graded assignments and exams for Intermediate Computer Applications, Introduction to Computer Science, and Data Structures and Abstraction.

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Sep 2000 - Sep 2002
Marine Mammal Trainer - Marineland Canada

Training, care and public demonstration of orca and beluga whales at Friendship Cove.

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Jan 2000 - Sep 2000
Owner/Operator - GNŌMATIX

Offering project support in genomics/informatics; development of software solutions to meet project needs.

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Aug 2013 - Present
Degree - University  
M. Sc. (in progress), Biology - McMaster University

Withdrawn in good standing.

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2002 - 2005
BSc, Computer Science - Brock University

with distinction

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2000 - 2002
Hons. B. Sc., Biology - University of Waterloo 1995 - 1999
Publication Info
Genome sequence and analysis of the tuber crop potato. Xu X, Pan S, Cheng S, Zhang B, Mu D, Ni P, Zhang G and 91 others Nature. 475(7355):189-95. doi: 10.1038/nature10158. July 10, 2011. View on PubMed.
Single nucleotide polymorphism discovery in elite north american potato germplasm. Hamilton JP, Hansey CN, Whitty BR, Stoffel K, Massa AN, Van Deynze A, De Jong WS, Douches DS, Buell CR BMC Genomics. 12:302. doi: 10.1186/1471-2164-12-302. June 9, 2011. View on PubMed.
Suppression of the vacuolar invertase gene prevents cold-induced sweetening in potato. Bhaskar PB, Wu L, Busse JS, Whitty BR, Hamernik AJ, Jansky SH, Buell CR, Bethke PC, Jiang J Plant Physiol. 154(2):939-48. doi: 10.1104/pp.110.162545. August 24, 2010. View on PubMed.
Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire. Lévesque CA, Brouwer H, Cano L, Hamilton JP, Holt C, Huitema E, Raffaele S and 41 others Genome Biol. 11(7):R73. doi: 10.1186/gb-2010-11-7-r73. July 13, 2010. View on PubMed.
Ergatis: a web interface and scalable software system for bioinformatics workflows. Orvis J, Crabtree J, Galens K, Gussman A, Inman JM, Lee E, Nampally S and 8 others Bioinformatics. 26(12):1488-92. doi: 10.1093/bioinformatics/btq167. June 15, 2010. View on PubMed.
Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus. Fedorova ND, Khaldi N, Joardar VS, Maiti R, Amedeo P, Anderson MJ, Crabtree J and 32 others PLoS Genet. 4(4):e1000046. doi: 10.1371/journal.pgen.1000046. April 11, 2008. View on PubMed.
Transcriptional profiling implicates novel interactions between abiotic stress and hormonal responses in Thellungiella, a close relative of Arabidopsis. Wong CE, Li Y, Labbe A, Guevara D, Nuin P, Whitty B, Diaz C and 5 others Plant Physiol. 140(4):1437-50. doi: 10.1104/pp.105.070508. February 24, 2006. View on PubMed.
Sex-specific functional specialization and the evolutionary rates of essential fertility genes. Torgerson DG, Whitty BR, Singh RS J Mol Evol. 61(5):650-8. doi: 10.1007/s00239-005-0007-5. October 20, 2005. View on PubMed.
Expressed sequence tags from the Yukon ecotype of Thellungiella reveal that gene expression in response to cold, drought and salinity shows little overlap. Wong CE, Li Y, Whitty BR, Díaz-Camino C, Akhter SR, Brandle JE, Golding GB, Weretilnyk EA, Moffatt BA, Griffith M Plant Mol Biol. 58(4):561-74. doi: 10.1007/s11103-005-6163-6. July 2005. View on PubMed.
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