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Canadian Bioinformatics Workshops

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TCAG Acknowledgments

Informatics & Biostatistics Facility

  • Genetic Analysis Workshop 18 single-nucleotide variant prioritization based on protein impact, sequence conservation, and gene annotation. Nalpathamkalam T, Derkach A, Paterson AD, Merico D. BMC Proceedings. 2014 8(Suppl 1):S11 (TCAG authors Nalpathamkalam, Paterson and Merico). Full text
  • Dynamic pathway analysis of genes associated with blood pressure using whole genome sequence data. Hu P, Paterson AD. BMC Proceedings. 2014 8(Suppl 1):S106 (TCAG authors Hu and Paterson). Full text
  • Genome-wide single nucleotide polymorphism and Insertion-Deletion discovery through next generation sequencing of reduced representation libraries in common bean. Zou X, Shi X, Austin RS, Merico D, Munholland S, Marsolais F, Navabi A, Crosby WL, Pauls KP, Yu K, Cui Y. Molecular Breeding. 2014 33: 769-778 (TCAG author Daniele Merico) Abstract
  • Enrichment Map - a Cytoscape app to visualize and explore OMICs pathway enrichment results. Isserlin R, Merico D, Voisin V, Bader GD. F1000Res. 2014 Jul 1;3:141. (TCAG authors Merico and Bader) Full text

Cytogenomics & Genome Resources Facility

  • ETV6/FLT3 fusion in a mixed-phenotype acute leukemia arising in lymph nodes in a patient with myeloproliferative neoplasm with eosinophilia. Hosseini N, Craddock KJ, Salehi-rad S, Brennan S, Bailey DJ, Brandwein JM, Porwit A. Journal of Hematopathology. 2014 7: 71-77 (BAC Probes) Abstract
  • MuLV-related endogenous retroviral elements and Flt3 participate in aberrant end-joining events that promote B-cell leukemogenesis. Johnson RM, Papp E, Grandal I, Kowalski PE, Nutter L, Wong RC, Joseph-George AM, Danska JS, Guidos CJ. Genes Dev. 2014 Jun 1;28(11):1179-90. (TCAG authors Wong, George and Danska). Abstract | Full text
  • Loss of the mammalian DREAM complex deregulates chondrocyte proliferation. Forristal C, Henley SA, MacDonald JI, Bush JR, Ort C, Passos DT, Talluri S, Ishak CA, Thwaites MJ, Norley CJ, Litovchick L, DeCaprio JA, DiMattia G, Holdsworth DW, Beier F, Dick FA. Mol Cell Biol. 2014 Jun 15;34(12):2221-34. (BAC clone). Abstract

Microarray & Genotyping Facility

  • Whole blood gene expression profile associated with spontaneous preterm birth in women with threatened preterm labor. Heng YJ, Pennell CE, Chua HN, Perkins JE, Lye SJ. PLoS One. 2014 May 14;9(5):e96901 (Affymetrix expression arrays) Abstract | Full text
  • Preeclampsia and cardiovascular disease share genetic risk factors on chromosome 2q22. Loset M, Johnson MP, et al. Pregnancy Hypertension. 2014 4: 178-185 (Illumina SNP Arrays) Abstract | Full text
  • Estradiol increases mucus synthesis in bronchial epithelial cells. Tam A, Wadsworth S, Dorscheid D, Man SF, Sin DD. PLoS One. 2014 Jun 25;9(6):e100633. (Bioanalyzer) Abstract | Full text
  • Clonal genetic structure and diversity in populations of an aquatic plant with combined vs. separate sexes. Yakimowski SB, Barrett SC. Mol Ecol. 2014 Jun;23(12):2914-28. (SSR genotyping) Abstract | Full text
  • Investigation of genetic variants, birthweight and hypothalamic-pituitary-adrenal axis function suggests a genetic variant in the SERPINA6 gene is associated with corticosteroid binding globulin in the western Australia pregnancy cohort (Raine) study. Anderson LN, Briollais L, Atkinson HC, Marsh JA, Xu J, Connor KL, Matthews SG, Pennell CE, Lye SJ. PLoS One. 2014 Apr 1;9(4):e92957 (Illumina GoldenGate genotyping) Abstract | Full text
  • Functional analysis of the TRIB1 associated locus linked to plasma triglycerides and coronary artery disease. Douvris A, Soubeyrand S, Naing T, Martinuk A, Nikpay M, Williams A, Buick J, Yauk C, McPherson R. J Am Heart Assoc. 2014 Jun 3;3(3):e000884. (Affymetrix expression arrays) Abstract | Full text
  • A putative de-N-acetylase of the PIG-L superfamily affects fluoroquinolone tolerance in Pseudomonas aeruginosa. Liebens V, Defraine V, Van der Leyden A, De Groote VN, Fierro C, Beullens S, Verstraeten N, Kint C, Jans A, Frangipani E, Visca P, Marchal K, Versées W, Fauvart M, Michiels J. Pathog Dis. 2014 Jun;71(1):39-54 (Affymetrix arrays) Abstract

Sequencing Facility

  • Appetite regulating peptides in red-bellied piranha, Pygocentrus nattereri: cloning, tissue distribution and effect of fasting on mRNA expression levels. Volkoff H. Peptides. 2014 Jun;56:116-24 (Sanger sequencing) Abstract | Full text
  • Group 1 LEA proteins contribute to the desiccation and freeze tolerance of Artemia franciscana embryos during diapause. Toxopeus J, Warner AH, MacRae TH. Cell Stress Chaperones. 2014 May 21. [Epub ahead of print] Abstract | Full text
  • SNARE zippering and synaptic strength. Prashad RC, Charlton MP. PLoS One. 2014 Apr 18;9(4):e95130 (Sanger sequencing) Abstract | Full text
  • High-quality draft whole-genome sequences of 162 Salmonella enterica subsp. enterica Serovar Enteritidis strains isolated from diverse sources in Canada. Rehman MA, Ziebell K, Nash JH, Kropinski AM, Zong Z, Nafziger E, Boerlin P, Chui L, Devenish J, Bekal S, Graham M, Johnson RP. Genome Announc. 2014 May 1;2(2). pii: e00348-14. (Illumina NGS) Abstract | Full text
  • Seroprevalence of feline immunodeficiency virus (FIV) and feline leukemia virus (FeLV) in shelter cats on the island of Newfoundland, Canada. Munro HJ, Berghuis L, Lang AS, Rogers L, Whitney H. Can J Vet Res. 2014 Apr;78(2):140-4. (Sanger sequencing) Abstract
  • De novo WNT5A-associated autosomal dominant Robinow syndrome suggests specificity of genotype and phenotype. Roifman M, Marcelis CL, Paton T, Marshall C, Silver R, Lohr JL, Yntema HG, Venselaar H, Kayserili H, van Bon B, Seaward G; FORGE Canada Consortium, Brunner HG, Chitayat D. Clin Genet. 2014 Apr 9. [Epub ahead of print] (exome sequencing; TCAG authors Paton and Marshall) Abstract |

Collaborative Work

  • Novel population specific autosomal copy number variation and its functional analysis amongst Negritos from Peninsular Malaysia. Mokhtar SS, Marshall CR, Phipps ME, Thiruvahindrapuram B, Lionel AC, Scherer SW, Peng HB. PLoS One. 2014 Jun 23;9(6):e100371. (Collaborative work with former visiting scientist Peng; TCAG authors Marshall, Thiruvahindrapuram, Lionel, Scherer). Abstract | Full text