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Canadian Bioinformatics Workshops

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Publications 2014

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 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 Full text

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 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. Full text

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 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 Abstract

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. 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. Abstract | Full text

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. 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. Abstract

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. Abstract | Full text

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. 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. 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

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 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. Abstract

Preeclampsia and cardiovascular disease share genetic risk factors on chromosome 2q22.
Loset M, Johnson MP, et al. Pregnancy Hypertension. 2014 4: 178-185 Abstract | 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 Abstract

SNARE zippering and synaptic strength.
Prashad RC, Charlton MP. PLoS One. 2014 Apr 18;9(4):e95130 Abstract | Full text

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. Abstract |

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 Abstract | Full text

Cellular actions of nesfatin-1 in the subfornical organ.
Kuksis M, Ferguson AV. J Neuroendocrinol. doi: 10.1111/jne.12143 [Epub ahead of print] Abstract

Whole-genome array CGH evaluation for replacing prenatal karyotyping in Hong Kong.
Kan AS, Lau ET, Tang WF, Chan SS, Ding SC, Chan KY, Lee CP, Hui PW, Chung BH, Leung KY, Ma T, Leung WC, Tang MH. PLoS One. 2014 Feb 5;9(2):e87988. PMID: 2450534 Full text

Transgenic expression of Map3k4 rescues T-associated sex reversal (Tas) in mice.
Warr N, Siggers P, Carré GA, Bogani D, Brixey R, Akiyoshi M, Tachibana M, Teboul L, Wells S, Sanderson J, Greenfield A. Hum Mol Genet. 2014 Feb 11. [Epub ahead of print] PMID: 24452333 Abstract

Genetic and functional evidence for a locus controlling otitis media at chromosome 10q26.3.
Rye MS, Scaman ES, Thornton RB, Vijayasekaran S, Coates HL, Francis RW, Pennell CE, Blackwell JM, Jamieson SE. BMC Med Genet. 2014 Feb 6;15(1):18. PMID: 24499112 Full text

Genetic contributors to otitis media: agnostic discovery approaches.
Allen EK, Manichaikul A, Sale MM. Curr Allergy Asthma Rep. 2014 Feb;14(2):411. PMID: 24415464 Abstract

PPAR-γ regulates trophoblast differentiation in the BeWo cell model.
Levytska K, Drewlo S, Baczyk D, Kingdom J. PPAR Research 2014, Article ID 637251, 13 pages, 2014. doi:10.1155/2014/637251 Full text

Reproductive fitness and genetic transmission of tetralogy of fallot in the molecular age.
Chin-Yee NJ, Costain G, Swaby JA, Silversides CK, Bassett AS. Circ Cardiovasc Genet. 2014 Feb 21. [Epub ahead of print] PMID: 24563425 Abstract

Novel CYP2A6 variants identified in African Americans are associated with slow nicotine metabolism in vitro and in vivo.
Piliguian M, Zhu AZ, Zhou Q, Benowitz NL, Ahluwalia JS, Sanderson Cox L, Tyndale RF. Pharmacogenet Genomics. 2014 Feb;24(2):118-28. PMID: 24305170 Abstract

Novel protein interactions with endoglin and activin receptor-like kinase 1: potential role in vascular networks.
Xu G, Barrios-Rodiles M, Jerkic M, Turinsky AL, Nadon R, Vera S, Voulgaraki D, Wrana JL, Toporsian M, Letarte M. Mol Cell Proteomics. 2014 Feb;13(2):489-502. PMID: 24319055 Abstract

Characterization of the Pseudomonas sp. DF41 quorum sensing locus and its role in fungal antagonism.
Berry CL, Nandi M, Manuel J, Brassinga AKC, Fernando WGD, Loewen PC, de Kievit TR. Biological Control 2014 Feb;69:82-89 Abstract

Expression of the Pseudomonas chlororaphis strain PA23 Rsm system is under control of GacA, RpoS, PsrA, quorum sensing and the stringent response.
Selin C, Manuel J, Fernando WGD, de Kievit T. Biological Control 2014 Feb;69:24-33 Abstract

Genome re-sequencing and functional analysis places the Phytophthora sojae avirulence genes avr1c and avr1a in a tandem repeat at a single locus.
Na R, Yu D, Chapman BP, Zhang Y, Kuflu K, Austin R, Qutob D, Zhao J, Wang Y, Gijzen M. PLoS One 2014 Feb 24. doi:10.1371/journal.pone.0089738 Full text

Genetic structure of avian influenza viruses from ducks of the Atlantic flyway of North America.
Huang Y, Wille M, Dobbin A, Walzthöni NM, Robertson GJ, Ojkic D, Whitney H, Lang AS. PLoS One. 2014 Jan 30;9(1):e86999. PMID: 24498009 Full text

Glucose sensing mechanisms in hypothalamic cell models: glucose inhibition of AgRP synthesis and secretion.
Chalmers JA, Jang JJ, Belsham DD. Mol Cell Endocrinol. 2014 Jan 25;382(1):262-70. PMID: 24145125 Abstract

Glucocorticoid receptor-mediated regulation of Rfrp (GnIH) and Gpr147 (GnIH-R) synthesis in immortalized hypothalamic neurons.
Gojska NM, Belsham DD. Mol Cell Endocrinol. 2014 Jan 8;384(1-2):23-31. PMID: 24412804 Abstract

A phospholipase A2 gene is linked to Jack bean urease toxicity in the Chagas' disease vector Rhodnius prolixus.
Defferrari MS, Lee DH, Fernandes CL, Orchard I, Carlini CR. Biochim Biophys Acta. 2014 Jan;1840(1):396-405. PMID: 24055375 Abstract

Genome-wide association study of bipolar disorder in Canadian and UK populations corroborates disease loci including SYNE1 and CSMD1.
Xu W, Cohen-Woods S, Chen Q, Noor A, Knight J, Hosang G, Parikh SV, De Luca V, Tozzi F, Muglia P, Forte J, McQuillin A, Hu P, Gurling HM, Kennedy JL, McGuffin P, Farmer A, Strauss J, Vincent JB. BMC Med Genet. 2014 Jan 4;15(1):2. PMID: 24387768 (TCAG author Pingzhao Hu, and Associate Investigator John Vincent) Full text

Higher activity of the inducible nitric oxide synthase contributes to very early onset inflammatory bowel disease.
Dhillon SS, Mastropaolo LA, Murchie R, Griffiths C, Thöni C, Elkadri A, Xu W, Mack A, Walters T, Guo C, Mack D, Huynh H, Baksh S, Silverberg MS, Brumell JH, Snapper SB, Muise AM. Clin Transl Gastroenterol. 2014 Jan 16;5:e46. PMID: 24430113 Full text

The MoxR ATPase RavA and its cofactor ViaA interact with the NADH:ubiquinone oxidoreductase I in Escherichia coli.
Wong KS, Snider JD, Graham C, Greenblatt JF, Emili A, Babu M, Houry WA. PLoS One. 2014 Jan 15;9(1):e85529. PMID: 24454883 Full text

Altered IFN-γ-mediated immunity and transcriptional expression patterns in N-Ethyl-N-nitrosourea-induced STAT4 mutants confer susceptibility to acute typhoid-like disease.
Eva MM, Yuki KE, Dauphinee SM, Schwartzentruber JA, Pyzik M, Paquet M, Lathrop M, Majewski J, Vidal SM, Malo D. J Immunol. 2014 Jan 1;192(1):259-70. PMID: 24285835 Full text

Leri's pleonosteosis, a congenital rheumatic disease, results from microduplication at 8q22.1 encompassing GDF6 and SDC2 and provides insight into systemic sclerosis pathogenesis.
Banka S, Cain SA, Carim S, Daly SB, Urquhart JE, Erdem G, Harris J, Bottomley M, Donnai D, Kerr B, Kingston H, Superti-Furga A, Unger S, Ennis H, Worthington J, Herrick AL, Merry CL, Yue WW, Kielty CM, Newman WG. Ann Rheum Dis. 2014 Jan 17. doi: 10.1136/annrheumdis-2013-204309. [Epub ahead of print] PMID: 24442880 Abstract

A CARD9 polymorphism is associated with decreased likelihood of persistent conjugated hyperbilirubinemia in intestinal failure.
Burghardt KM, Avinashi V, Kosar C, Xu W, Wales PW, Avitzur Y, Muise A. PLoS One. 2014 Jan 21;9(1):e85915. PMID: 24465786 Full text