Biomedical and Translational Informatics Laboratory

Publications - 2008

  • Genetic determinants of response to warfarin during initial anticoagulation. Ute I. Schwarz, Marylyn D. Ritchie, Yuki Bradford, Chun Li, Scott M. Dudek, Amy Frye-Anderson, Richard B. Kim, Dan M. Roden, C. Michael Stein, Copyright 2008 Massachusetts Medical Society., 358, 10, The New England journal of medicine, 2008 Mar 6, PMID: 18322281 PMCID: PMC3894627,
  • Power of grammatical evolution neural networks to detect gene-gene interactions in the presence of error. Alison A. Motsinger-Reif, Theresa J. Fanelli, Anna C. Davis, Marylyn D. Ritchie, 1, BMC research notes, 2008, PMID: 18710518 PMCID: PMC2531119,
  • Neural networks for genetic epidemiology: past, present, and future. Alison A. Motsinger-Reif, Marylyn D. Ritchie, 1, 1, BioData mining, 2008, PMID: 18822147 PMCID: PMC2553772,
  • Comparison of approaches for machine-learning optimization of neural networks for detecting gene-gene interactions in genetic epidemiology. Alison A. Motsinger-Reif, Scott M. Dudek, Lance W. Hahn, Marylyn D. Ritchie, 32, 4, 325-340, Genetic epidemiology, 2008 May, PMID: 18265411,
  • Expectations and challenges stemming from genome-wide association studies Paolo Vineis, Paul Brennan, Federico Canzian, John P A Ioannidis, Giuseppe Matullo, Marylyn Ritchie, Ulf Stromberg, Emanuela Taioli, John Thompson, 23, 6, 439-444, Mutagenesis, 1464-3804, Nov 2008, PMID: 18765424,
  • Generating Linkage Disequilibrium Patterns in Data Simulations Using genomeSIMLA Conference Paper, Todd L. Edwards, William S. Bush, Stephen D. Turner, Scott M. Dudek, Eric S. Torstenson, Mike Schmidt, Eden Martin, Marylyn D. Ritchie,, EvoBIO'08, Berlin, Heidelberg, Springer-Verlag, 24–35, 3-540-78756-9, 978-3-540-78756-3, 2008, 2014-02-24 18:00:08, ACM Digital Library, Whole-genome association (WGA) studies are becoming a common tool for the exploration of the genetic components of common disease. The analysis of such large scale data presents unique analytical challenges, including problems of multiple testing, correlated independent variables, and large multivariate model spaces. These issues have prompted the development of novel computational approaches. Thorough, extensive simulation studies are a necessity for methods development work to evaluate the power and validity of novel approaches. Many data simulation packages exist, however, the resulting data is often overly simplistic and does not compare to the complexity of real data; especially with respect to linkage disequilibrium (LD). To overcome this limitation, we have developed genomeSIMLA. GenomeSIMLA is a forward-time population simulation method that can simulate realistic patterns of LD in both family-based and case-control datasets. In this manuscript, we demonstrate how LD patterns of the simulated data change under different population growth curve parameter initialization settings. These results provide guidelines to simulate WGA datasets whose properties resemble the HapMap., Proceedings of the 6th European Conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics,
  • A Balanced Accuracy Fitness Function Leads to Robust Analysis using Grammatical Evolution Neural Networks in the Case of Class Imbalance. Nicholas E. Hardison, Theresa J. Fanelli, Scott M. Dudek, David M. Reif, Marylyn D. Ritchie, Alison A. Motsinger-Reif, 2008, Genetic and Evolutionary Computation Conference : [proceedings] / sponsored by ACM SIGEVO. Genetic and Evolutionary Computation Conference, 2008, PMID: 21197143 PMCID: PMC3011228,
  • Persistent atrial fibrillation is associated with reduced risk of torsades de pointes in patients with drug-induced long QT syndrome. Dawood Darbar, John Kimbrough, Asif Jawaid, Robert McCray, Marylyn D. Ritchie, Dan M. Roden, 51, 8, 836-842, of the American College of Cardiology, 2008 Feb 26, PMID: 18294569 PMCID: PMC2271078,
  • Filling the gap between biology and computer science. Jesus S. Aguilar-Ruiz, Jason H. Moore, Marylyn D. Ritchie, 1, 1, BioData mining, 2008, PMID: 18822148 PMCID: PMC2547862,
  • A genome-wide scan for common genetic variants with a large influence on warfarin maintenance dose. Gregory M. Cooper, Julie A. Johnson, Taimour Y. Langaee, Hua F Ian B. Stanaway, Ute I. Schwarz, Marylyn D. Ritchie, C. Michael Stein, Dan M. Roden, Joshua D. Smith, David L. Veenstra, Allan E. Rettie, Mark J. Rieder, 112, 4, 1022-1027, Blood, 2008 Aug 15, PMID: 18535201 PMCID: PMC2515139,
  • The bradykinin type 2 receptor BE1 polymorphism and ethnicity influence systolic blood pressure and vascular resistance. M. M. Pretorius, J. V. Gainer, G. P. Van Guilder, E. B. Coelho, J. M. Luther, P. Fong, D. D. Rosenbaum, H. A. Malave, C. Yu, M. D. Ritchie, D. E. Vaughan, N. J. Brown, 83, 1, 122-129, Clinical pharmacology and therapeutics, 2008 Jan, PMID: 17522594,
  • The mitochondrial pharmacogenomics of haplogroup T: MTND2*LHON4917G and antiretroviral therapy-associated peripheral neuropathy. J. A. Canter, D. W. Haas, A. R. Kallianpur, M. D. Ritchie, G. K. Robbins, R. W. Shafer, D. B. Clifford, D. G. Murdock, T. Hulgan, 8, 1, 71-77, The pharmacogenomics journal, 2008 Feb, PMID: 17684475,
  • A comparison of analytical methods for genetic association studies. Alison A. Motsinger-Reif, David M. Reif, Theresa J. Fanelli, Marylyn D. Ritchie, 32, 8, 767-778, Genetic epidemiology, 2008 Dec, PMID: 18561203,
  • Alternative contingency table measures improve the power and detection of multifactor dimensionality reduction. William S. Bush, Todd L. Edwards, Scott M. Dudek, Brett A. McKinney, Marylyn D. Ritchie, 9, BMC bioinformatics, 2008, PMID: 18485205 PMCID: PMC2412877,
  • Interaction between interleukin 3 and dystrobrevin-binding protein 1 in schizophrenia. Todd L. Edwards, Xu Wang, Qi Chen, Brandon Wormly, Brien Riley, F. Anthony O'Neill, Dermot Walsh, Marylyn D. Ritchie, Kenneth S. Kendler, Xiangning Chen, 106, 2-3, 208-217, Schizophrenia research, 2008 Dec, PMID: 18804346 PMCID: PMC2746913,