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Bioinformatics Publications (2009)

  1. Dorfman R, Li W, Sun L, Lin F, Wang Y, Sandford A, Paré PD, McKay K, Kayserova H, Piskackova T, Macek M, Czerska K, Sands D, Tiddens H, Margarit S, Repetto G, Sontag MK, Accurso FJ, Blackman S, Cutting GR, Tsui L-C, Corey M, Durie P, Zielenski J, Strug L. Modifier gene study of meconium ileus in cystic fibrosis: statistical considerations and gene mapping results. Human Genetics, 2009, Aug 7.
  2. Strug LJ, Hodge SE, Chiang T, Pal DK, Corey PN, Rohde C: A Pure Likelihood Approach to the Analysis of Genetic Association Data: An alternative to Bayesian and Frequentist analysis. European Journal of Human Genetics 2009: Submitted.
  3. Goos LM, Crosbie J, Payne S, Schachar R: Validation and extension of the endophenotype model in ADHD patterns of inheritance in a family study of inhibitory control. American Journal of Psychiatry, 2009, 166:711-717.
  4. Soreni N, Crosbie J, Ickowicz A, Schachar R: Stop signal and Conners' continuous performance tasks: test--retest reliability of two inhibition measures in ADHD children. Journal of Attention Disorders, 2009, 13:137-143.
  5. Strug LJ, Clarke T, Chiang T, Chien MC, Baskurt Z, Li WL, Dorfman R, Bali B, Wirrell E, Kugler SL, et al.: Centrotemporal sharp wave EEG trait in rolandic epilepsy maps to Elongator Protein Complex 4 (ELP4). European Journal of Human Genetics 2009, 17:1171-1181.
  6. Fairn GD, Ogata K, Botelho RJ, Stahl PD, Anderson RA, De Camilli P, Meyer T, Wodak SJ, Grinstein S: An electrostatic switch displaces phosphatidylinositol phosphate kinases. Journal of Cell Biology 2009, in press.

Bioinformatics Conference Presentations (2009)

  1. Taylor C, Dorfman R, Strug LJ, Li W, Cojocaru A, Anderson N, Sandford A, Paré PD, Zielenski J, Durie P, Corey M., Development of a lung disease severity phenotype in Cystic Fibrosis and its application in the Canadian CF Modifier study. American Society of Human Genetics, 2009, Hawaii.
  2. Li W, Sun L, Taylor C, Dorfman R, Cojocaru A, Zielenski J, Durie P, Corey M, Strug LJ.Cystic fibrosis: an 'inclusive' disease - demonstrated by analysis of population stratification. American Society of Human Genetics, 2009, Hawaii.
  3. Cojocaru1 A, Sun L, Corey M, Li W, Taylor C, Dorfman R, Zielenski J, Durie P, Keenan K, Strug LJ. Association analysis for meconium ileus incorporating phenotype misclassification. 4rd Canadian Genetic Epidemiology and Statistical Genetics Meeting, 2009, Harrison Hot Springs BC.
  4. Li W, Sun L, Taylor C, Dorfman R, Cojocaru A, Zielenski J, Durie P, Corey M, Strug LJ.Cystic fibrosis: an 'inclusive' disease - demonstrated by analysis of population stratification. 4rd Canadian Genetic Epidemiology and Statistical Genetics Meeting, 2009, Harrison Hot Springs BC.
  5. Taylor C, Dorfman R, Strug LJ, Li W, Cojocaru A, Anderson N, Sandford A, Paré PD, Zielenski J, Durie P, Corey M., Development of a lung disease severity phenotype in Cystic Fibrosis and its application in the Canadian CF Modifier study. 4rd Canadian Genetic Epidemiology and Statistical Genetics Meeting, 2009, Harrison Hot Springs BC.
  6. Taylor C, Webel A, Cutting G, Knowles M, Corey M.  A new CF lung disease severity phenotype for genetic modifier studies. North American CF Conference, 2009, Minneapolis.
  7. Li W, Zou F, Lee S, Corey M, Sun L, Wright FA, Strug LJ, Analysis of population tratification in North American CF patients. North American CF Conference, 2009, Minneapolis.

Bioinformatics Conference Presentations (2008)

  1. Strug LJ, Hodge SE, Chiang T: Evidential Analysis of Genome-Wide Association Studies: Sample Size and Multiple Testing Implications. In American Society of Human Genetics abstract, November 2008, Philadelphia, Pennsylvania.
  2. Sun L, Chiang T: PREST-plus: detection of pedigree error and cryptic relatedness among individuals that allows for high-throughput genotype data and adjusts for large-scale multiple hypothesis testing. In American Society of Human Genetics abstract, November 2008, Philadelphia, Pennsylvania.
  3. Pal DK, Strug LJ, Clarke T, B.ali B, Chiang T, Chien M, Russo JJ: Genomewide linkage and fine mapping identifies ELP4 as a major susceptibility gene for Rolandic epilepsy in two independent samples. In American Society of Human Genetics abstract, November 2008, Philadelphia, Pennsylvania.
  4. Abdel-Rahman R, Zogopolous G, Farrington A, Gropper K, K. H, Hyeja S, Moore G, Bader R, Gryfe B, Zanke A, Montpetit  P, Laflamme J, Hurley T, Chiang A, Tenesa D, Farhat T, Hudson M, Dunlop G, Steve H, Campbell H: A Common Genomic Copy Number Variant Locus Is Associated with Colorectal Cancer Risk and Poor Survival. In American Society of Human Genetics abstract, November 2008, Philadelphia, Pennsylvania.

Database Application Publications (2009)

  1. Soreni N, Crosbie J, Ickowicz A, Schachar R: Stop signal and Conners' continuous performance tasks: test--retest reliability of two inhibition measures in ADHD children. Journal of Attention Disorders, 2009, 13:137-143.
  2. Sharan S, Dupuis A, Hébert D, Levin AV: The effect of oral acetazolamide on growth in children. Canadian Journal of Ophthalmology 2009, in press.
  3. Mrkonjic M, Chappell E, Pethe VV, Manno M, Daftary D, Greenwood CM, Gallinger S, Zanke BW, Knight JA, Bapat B: Association of apolipoprotein E polymorphisms and dietary factors in colorectal cancer. British Journal of Cancer 2009, 100:1966-1974.
  4. Amlie-Lefond C, Bernard TJ, Sébire G, Friedman NR, Heyer GL, Lerner NB, DeVeber G, Fullerton HJ: Predictors of cerebral arteriopathy in children with arterial ischemic stroke: results of the International Pediatric Stroke Study. Circulation 2009, 119:1417-1423.
  5. Amlie-Lefond C, deVeber G, Chan AK, Benedict S, Bernard T, Carpenter J, Dowling M, Fullerton H, Hovinga C, Kirton A, et al.: Use of alteplase in childhood arterial ischemic stroke: A multicenter observational cohort study. Lancet Neurology 2009, 8:530-536.
  6. Amlie-Lefond C, Chan AK, Kirton A, deVeber G, Hovinga CA, Ichord R, Stephens D, Zaidat OO: Thrombolysis in acute childhood stroke: design and challenges of the thrombolysis in pediatric stroke clinical trial. Neuroepidemiology 2009, 32:279-286.
  7. Goldenberg NA, Bernard TJ, Fullerton HJ, Gordon A, deVeber G: Treatments, outcome and prognostic factors in acute childhood arterial ischemic stroke: International Pediatric Stroke Study findings.  Lancet Neurology. Lancet Neurology 2009, in press.
  8. Hanwell H, Vieth R, Bar-Or A, Sadovnick D, Arnold D, Banwell B, Network atCPDD: Serum 25-hydroxyvitamin D status as a determinant of MS outcome following an initial acquired demyelinating event in children. Journal Of the American Medical Association 2009, manuscript in preparation.
  9. Golomb MR, Fullerton HJ, Nowak-Gottl U, Deveber G: Male predominance in childhood ischemic stroke: findings from the international pediatric stroke study. Stroke 2009, 40:52-57.
  10. Cabral DA, Uribe AG, Benseler S, O'Neil KM; Hashkes PJ, Higgins G, et al.: Classification, presentation and initial treatment of Wegener's granulomatosis in childhood. Arthritis Rheum 2009 (in Press)

Database Application Publications (2008)

  1. Elbers J, Benseler SM: Central nervous system vasculitis in children. Current Opinion in Rheumatology 2008, 20:47-54.
  2. Cantez S, Benseler SM: Childhood CNS vasculitis: a treatable cause of new neurological deficit in children. Nature Clinical Practice Rheumatology 2008, 4:460-461.
  3. Houlston RS, Webb E, Broderick P, Pittman AM, Di Bernardo MC, Lubbe S, Chandler I, Vijayakrishnan J, Sullivan K, Penegar S, et al.: Meta-analysis of genome-wide association data identifies four new susceptibility loci for colorectal cancer. Nature Genetics 2008, 40:1426-1435.
  4. Tenesa A, Farrington SM, Prendergast JG, Porteous ME, Walker M, Haq N, Barnetson RA, Theodoratou E, Cetnarskyj R, Cartwright N, et al.: Genome-wide association scan identifies a colorectal cancer susceptibility locus on 11q23 and replicates risk loci at 8q24 and 18q21. Nature Genetics 2008, 40:631-637.
  5. Au F, Prahardhi S, Shiell A: Reliability of two instruments for critical assessment of economic evaluations. Value Health 2008, 11:435-439.

Database Application Conference Presentations (2009)

  1. Amlie-Lefond C BT, Sébire G, Friedman N, Heyer G, Lerner N, deVeber G, Fullerton H, on behalf of the International Pediatric Stroke Study Group.  Predictors of Cerebral Arteriopathy in Children with Arterial Ischemic Stroke:  Results of the International Pediatric Stroke Study.  AHA, San Diego CA, February 2009.  Stroke 2009, 40, e105-e276 (Abstract # 71).
  2. Harrison D, Hutchinson A, Stevens B, Estabrooks CA, Yamada J, Latimer M, Cummings G, Scott S, Kang S.  Is there a relationship between nurses’ use of evidence-based paediatric pain assessment tools and characteristics of organizational context? KU09 Knowledge Utilization Colloquium, June 2009, Deganway, Wales, United Kingdom.
  3. Jordan L SS, Rafay M, Zamel K, Askalon R, Ashwal S and Members of the IPSS.  Predictors of Antithrombotic Treatment in Neonatal Cerebral Sinovenous Thrombosis: Results of the International Pediatric Stroke Study.  AHA, San Diego CA, Februrary 2009. Stroke 2009, 40, e105-e276, (Abstract # 75).
  4. Stevens B, CIHR Team in Children’s Pain. Variability in pain assessment and management practices across Canadian paediatric health care centres. IASP 12th World Congress on Pain; August 2008, Glasgow, Scotland. Also presented at: 2009 SickKids Nursing Research Day, February 2009, Toronto, Ontario.
  5. Stevens B, CIHR Team in Children’s Pain. Management of acute procedural pain in hospitalized Canadian children. Pediatric Academic Societies Annual Meeting, May 2009, Baltimore, USA.
  6. Stevens B, CIHR Team in Children’s Pain, Kang S, Hutchinson A, Watt-Watson J, Dionne K, McNair C, Oliver-Homewood S, Lee KS, de Silva N. Knowledge Translation: Lessons Learned from the CIHR Team in Children’s Pain. 29th Annual CPS Conference: Pain – Translating Science into Care, May 2009, Québec City, Québec.
  7. Stevens B, Harrison D, Yamada J, Abbott L, CIHR Team in Children’s Pain. Current paediatric pain assessment practices in Canada. Pain in Europe VI: 6th Congress of the European Federation of IASP Chapters (EFIC), September 2009, Lisbon, Portugal.
  8. Stevens B, CIHR Team in Children’s Pain. Paediatric pain management strategies across Canada: Findings from the CIHR Team in Children’s Pain. CAPHC Annual Meeting, October 2008, Edmonton, Alberta. Also presented at: CHEO Annual Clinical Research Day, October 2008, Ottawa, Ontario and Child Health – The Next 100 Years, June 2009, Winnipeg, Manitoba.

Database Application Conference Presentations (2009)

  1. CIHR Team in Children’s Pain. Translating Research on Pain in Children. Nursing Week (Children’s Hospital – Health Sciences Centre Winnipeg), May 2008, Winnipeg, Manitoba.
  2. Goldenberg N BT, Gordon A, Fullerton H, deVeber G. Acute treatments of early outcomes of childhood arterial ischemic stroke. Bood (ASH Annual Meeting Abstracts) 2008, 112 (Abstract #1978).
  3. Rashotte J, Cohen J, Stevens B. Inter- and intra-hospital variability in paediatric pain assessment and management practices: A preliminary report from the new Canadian Paediatric Pain Research database comparing CHEO practices to other paediatric centres. CHEO Annual Clinical Research Day, October 2008, Ottawa, Ontario.

HPF Publications (2009)

  1. Al-Abdul-Wahid MS, Neale C, Pomes R, Prosser RS: A Solution NMR Approach to the Measurement of Amphiphile Immersion Depth and Orientation in Membrane Model Systems. Journal of the American Chemical Society 2009, 131:6452-6459.
  2. Henry RM, Yu CH, Rodinger T, Pomes R: Functional Hydration and Conformational Gating of Proton Uptake in Cytochrome c Oxidase. Journal of Molecular Biology 2009, 387:1165-1185.
  3. Pu S, Wong J, Turner B, Cho E, Wodak SJ: Up-to-date catalogues of yeast protein complexes. Nucleic Acids Research 2009, 37:825-831.
  4. Vlasblom J, Wodak SJ: Markov clustering versus affinity propagation for the partitioning of protein interaction graphs. BMC Bioinformatics 2009, 10.
  5. Wilkins O, Nahal H, Foong J, Provart NJ, Campbell MM: Expansion and diversification of the Populus R2R3-MYB family of transcription factors. Plant Physiology 2009, 149:981-993.
  6. Husted JA, Lim S, Chow EWC, Greenwood C, Bassett AS: Heritability of Neurocognitive Traits in Familial Schizophrenia. American Journal of Medical Genetics Part B-Neuropsychiatric Genetics 2009, 150B:845-853.
  7. Grant SF, Qu HQ, Bradfield JP, Marchand L, Kim CE, Glessner JT, Grabs R, Taback SP, Frackelton EC, Eckert AW, Annaiah K, Lawson ML, Otieno FG, Santa E, Shaner JL, Smith RM, Skraban R, Imielinski M, Chiavacci RM, Grundmeier RW, Stanley CA, Kirsch SE, Waggott D, Paterson AD, Monos DS; DCCT/EDIC Research Group, Polychronakos C, Hakonarson H.: Follow-up analysis of genome-wide association data identifies novel loci for type 1 diabetes. Diabetes 2009, 58:290-295.
  8. Nolte IM, Wallace C, Newhouse SJ, Waggott D, Fu J, Soranzo N, Gwilliam R, Deloukas P, Savelieva I, Zheng D, Dalageorgou C, Farrall M, Samani NJ, Connell J, Brown M, Dominiczak A, Lathrop M, Zeggini E, Wain LV; Wellcome Trust Case Control Consortium; DCCT/EDIC Research Group, Newton-Cheh C, Eijgelsheim M, Rice K, de Bakker PI; QTGEN consortium, Pfeufer A, Sanna S, Arking DE; QTSCD consortium, Asselbergs FW, Spector TD, Carter ND, Jeffery S, Tobin M, Caulfield M, Snieder H, Paterson AD, Munroe PB, Jamshidi Y.: Common genetic variation near the phospholamban gene is associated with cardiac repolarisation: meta-analysis of three genome-wide association studies. PLoS One. 2009,4(7):e6138.
  9. Paterson AD, Waggott D, Boright A, Hosseini M, Shen E, Sylvestre MP, Wong I, Bharaj B, Cleary P, Lachin J, MAGIC, Bellow JE, Nicolae D, Cox NJ, Canty A, Sun L, Bull SB, the DCCT/EDIC Research Group. A genome-wide association study identifies a novel major locus for glycemic control in type 1 diabetes, as measured by both HbA1c and glucose. Diabetes 2009, October 29.
  10. Paterson AD, Lopes-Virella MF, Waggott D, Boright AP, Hosseini SM, Carter RE, Shen E, Mirea L, Bharaj B, Sun L, Bull SB; the DCCT/EDIC Research Group. Genome-Wide Association Identifies the ABO Blood Group as a Major Locus Associated With Serum Levels of Soluble E-Selectin. Arteriosclerosis Thrombosis and Vascular Biology 2009, 29:1958-U1609.
  11. Pezzolesi MG, Poznik GD, Mychaleckyj JC, Paterson AD, Barati MT, Klein JB, Ng DP, Placha G, Canani LH, Bochenski J, Waggott D, Merchant ML, Krolewski B, Mirea L, Wanic K, Katavetin P, Kure M, Wolkow P, Dunn JS, Smiles A, Walker WH, Boright AP, Bull SB; DCCT/EDIC Research Group, Doria A, Rogus JJ, Rich SS, Warram JH, Krolewski AS.: Genome-wide association scan for diabetic nephropathy susceptibility genes in type 1 diabetes. Diabetes 2009, 58:1403-1410.
  12. Yoo YJ, Bull SB, Paterson AD, Waggott D, Sun L, the DCCT/EDIC Research Group. Were genome-wide linkage studies a waste of time? Exploiting candidate regions within genome-wide association studies. Genetic Epidemiology, 2009, July 22.

HPF Publications (2008)

  1. Malevanets A, Sirota FL, Wodak SJ: Mechanism and energy landscape of domain swapping in the B1 domain of protein G. Journal of Molecular Biology 2008, 382:223-235.
  2. Neale C, Rodinger T, Pomes R: Equilibrium exchange enhances the convergence rate of umbrella sampling. Chemical Physics Letters 2008, 460:375-381.
  3. Sirota FL, Hery-Huynh S, Maurer-Stroh S, Wodak SJ: Role of the amino acid sequence in domain swapping of the B1 domain of protein G. Proteins: Structure, Function, and Bioinformatics 2008, 72:88-104.
  4. Marshall CR, Noor A, Vincent JB, Lionel AC, Feuk L, Skaug J, Shago M, Moessner R, Pinto D, Ren Y, Thiruvahindrapduram B, Fiebig A, Schreiber S, Friedman J, Ketelaars, C E J, Vos Y J, Ficicioglu C, Kirkpatrick S, Nicolson R, Sloman L, Surnmers A, Gibbons C A, Teebi A, Chitayat D, Weksberg R, Thompson A, Vardy C, Crosbie V, Luscombe S, Baatjes R, Zwaigenbaum L, Roberts W, Fernandez B, Szatmari P, Scherer SW: Structural variation of chromosomes in autism spectrum disorder. American Journal of Human Genetics 2008, 82:477-488.
  5. Kim T, Kim TH, Lee HJ, Peddle L, Rahman P, Hu P, Greenwood CMT, Inman RD: Interleukin 1 polymorphisms in patients with ankylosing spondylitis in Korea. Journal of Rheumatology 2008, 35:1603-1608.
  6. Okamura K, Wintle RF, Scherer SW: Characterization of the differentially methylated region of the Impact gene that exhibits Glires-specific imprinting. Genome Biology 2008, 9.
  7. Goobie S, Knijnenburg J, FitzPatrick D, Sharkey FH, Lionel AC, Marshall CR, Azam T, Shago M, Chong K, Mendoza-Londono R, et al.: Molecular and clinical characterization of de novo and familial cases with microduplication 3q29: guidelines for copy number variation case reporting. Cytogenetic and Genome Research 2008, 123:65-78.
  8. Al-Kateb H, Boright AP, Mirea L, Xie X, Sutradhar R, Mowjoodi A, Bharaj B, Liu M, Bucksa JM, Arends VL, Steffes MW, Cleary PA, Sun W, Lachin JM, Thorner PS, Ho M, McKnight AJ, Maxwell AP, Savage DA, Kidd KK, Kidd JR, Speed WC, Orchard TJ, Miller RG, Sun L, Bull SB, Paterson AD: Multiple superoxide dismutase 1/splicing factor serine alanine 15 variants are associated with the development and progression of diabetic nephropathy: the Diabetes Control and Complications Trial/Epidemiology of Diabetes Interventions and Complications Genetics study. Diabetes 2008, 57:218-228

HPF Conference Presentations (2009)

  1. Vlasblom J, Pu S, Wodak SJ: Increasing the reliability and coverage of protein-protein interaction data from tandem affinity purification experiments. In International Conference on Intelligent Systems for Molecular Biology: 2009, Stockholm, Sweden.
  2. Hu P, Matei I, Parkhomenko E, Guidos C, Danska J, Beyene J: Evaluation of CNV calling algorithms in identifying T-ALL related cancer genes. In 17th Annual Meeting of the International-Genetic-Epidemiology-Society, September 2008, St. Louis, MO:93.
  3. Allen U, Hu P, Barton M, Beyene J, Khodai-Booran N, Hebert D, Dipchand A, Ng V, Solomon M, Grant D: Differentially expressed host B cell-associated genes in high/intermediate versus low/undetectable viral load states in Epstein-Barr (EBV) virus infection after pediatric organ transplantation. In 26th International Congress of Chemotherapy and Infection June 2009, Toronto, CANADA: O21.

HPF Conference Presentations (2008)

  1. Parkhomenko E, Tritchler D, Hu P, Guidos C, Danska J, Beyene J: Studying genomic impact of copy number variation on gene expression profiles using Sparse Canonical Correlation Analysis. In 17th Annual Meeting of the International-Genetic-Epidemiology-Society, September 2008, St. Louis, MO: 142.

Papers Coauthored by CCB Bioinformatics Analysts

  1. GD Fairn, K Ogata, RJ Botelho, PD Stahl, RA Anderson, P De Camilli, T Meyer, S Wodak, S Grinstein,  An electrostatic switch displaces phosphatidylinositol phosphate kinases.  J. Cell. Biol. accepted 2009 Sep.
  2. Strug L.J, Clarke T, Chiang T, Chien M, Baskurt Z, Li W, Dorfman R, Bali B, Wirrell E, Kugler SL, Mandel-baum DE, Wolf SM, McGoldrick P, Hardison H, Novotny EJ, Ju J, Greenberg DA, Russo JJ, Pal DK.
    Centrotemporal sharp wave EEG trait in rolandic epilepsy maps to Elongator Protein Complex 4 (ELPH) European Journal of Human Genetics. (2009) 17:1171
  3. Zanke BW, Greenwood CM, Rangrej J, Kustra R, Tenesa A, Farrington SM, Prendergast J, Olschwang S, Chiang T, Crowdy E, Ferretti V, Laflamme P, Sundararajan S, Roumy, S, Olivier JF, Robidoux F, Sladek R, Montpetit A, Campbell P, Bezieau S, O'Shea AM, Zogopoulos G, Cotterchio M, Newcomb P, McLaughlin J, Younghusband B, Green R, Green J, Porteous ME, Campbell H, Blanche H, Sahbatou M, Tubacher E, Bonaiti-Pellié C, Buecher B, Riboli E, Kury S, Chanock SJ, Potter J, Thomas G, Gallinger S, Hudson TJ, Dunlop MG.
    Genome-wide association scan identifies a colorectal cancer susceptibility locus on chromosome 8q24.
    Nat Genet. 2007 Aug;39(8):989-94. Epub 2007 Jul 8.