Biomedical and Translational Informatics Laboratory

Publications - 2010

  • Synthesis-View: visualization and interpretation of SNP association results for multi-cohort, multi-phenotype data and meta-analysis. Sarah A. Pendergrass, Scott M. Dudek, Dana C. Crawford, Marylyn D. Ritchie, 3, BioData mining, 2010, PMID: 21162740 PMCID: PMC3012023,
  • Assessing the accuracy of observer-reported ancestry in a biorepository linked to electronic medical records. Logan Dumitrescu, Marylyn D. Ritchie, Kristin Brown-Gentry, Jill M. Pulley, Melissa Basford, Joshua C. Denny, Jorge R. Oksenberg, Dan M. Roden, Jonathan L. Haines, Dana C. Crawford, 12, 10, 648-650, Genetics in medicine : official journal of the American College of Medical Genetics, 2010 Oct, PMID: 20733501 PMCID: PMC2952033,
  • Grammatical Evolution of Neural Networks for Discovering Epistasis among Quantitative Trait Loci Book Section, Stephen D. Turner, Scott M. Dudek, Marylyn D. Ritchie, Clara Pizzuti, Marylyn D. Ritchie, Mario Giacobini, http://link.springer.com/chapter/10.1007/978-3-642-12211-8_8, ©2010 Springer-Verlag Berlin Heidelberg, Lecture Notes in Computer Science, Springer Berlin Heidelberg, 86-97, 978-3-642-12210-1, 978-3-642-12211-8, 2010/01/01, 2014-02-24 18:05:57, 6023, link.springer.com, Growing interest and burgeoning technology for discovering genetic mechanisms that influence disease processes have ushered in a flood of genetic association studies over the last decade, yet little heritability in highly studied complex traits has been explained by genetic variation. Non-additive gene-gene interactions, which are not often explored, are thought to be one source of this “missing” heritability. Here we present our assessment of the performance of grammatical evolution to evolve neural networks (GENN) for discovering gene-gene interactions which contribute to a quantitative heritable trait. We present several modifications to the GENN procedure which result in modest improvements in performance., Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics,
  • FAM-MDR: a flexible family-based multifactor dimensionality reduction technique to detect epistasis using related individuals. Tom Cattaert, Victor Urrea, Adam C. Naj, Lizzy De Lobel, Vanessa De Wit, Mao Fu, Jestinah M. Mahachie John, Haiqing Shen, M. Luz Calle, Marylyn D. Ritchie, Todd L. Edwards, Kristel Van Steen, 5, 4, PloS one, 2010, PMID: 20421984 PMCID: PMC2858665,
  • ATHENA: A knowledge-based hybrid backpropagation-grammatical evolution neural network algorithm for discovering epistasis among quantitative trait Loci. Stephen D. Turner, Scott M. Dudek, Marylyn D. Ritchie, 3, 1, BioData mining, 2010, PMID: 20875103 PMCID: PMC2955681,
  • Visualizing SNP statistics in the context of linkage disequilibrium using William S. Bush, Scott M. Dudek, Marylyn D. Ritchie, 26, 4, 578-579, Bioinformatics (Oxford, England), 2010 Feb 15, PMID: 20130027 PMCID: PMC2820673,
  • Robust replication of genotype-phenotype associations across multiple diseases in an electronic medical record. Marylyn D. Ritchie, Joshua C. Denny, Dana C. Crawford, Andrea H. Ramirez, Justin B. Weiner, Jill M. Pulley, Melissa A. Basford, Kristin Brown-Gentry, Jeffrey R. Balser, Daniel R. Masys, Jonathan L. Haines, Dan M. Roden, (c) 2010 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved., 86, 4, 560-572, American journal of human genetics, 2010 Apr 9, PMID: 20362271 PMCID: PMC2850440,
  • A general framework for formal tests of interaction after exhaustive search methods with applications to MDR and MDR-PDT. Todd L. Edwards, Stephen D. Turner, Eric S. Torstenson, Scott M. Dudek, Eden R. Martin, Marylyn D. Ritchie, 5, 2, PloS one, 2010, PMID: 20186329 PMCID: PMC2826406,
  • Genome simulation approaches for synthesizing in silico datasets for human genomics. Marylyn D. Ritchie, William S. Bush, Copyright (c) 2010 Elsevier Inc. All rights reserved., 72, Advances in genetics, 2010, PMID: 21029846,
  • Quantification of the clinical modifiers impacting high-density lipoprotein cholesterol in the community: Personalized Medicine Research Project. Russell A. Wilke, Richard L. Berg, James G. Linneman, Peggy Peissig, Justin Starren, Marilyn D. Ritchie, Catherine A. McCarty, 13, 2, 63-68, Preventive cardiology, 2010 Spring, PMID: 20377807,
  • Identification of genomic predictors of atrioventricular conduction: using electronic medical records as a tool for genome science. Joshua C. Denny, Marylyn D. Ritchie, Dana C. Crawford, Jonathan S. Schildcrout, Andrea H. Ramirez, Jill M. Pulley, Melissa A. Basford, Daniel R. Masys, Jonathan L. Haines, Dan M. Roden, 122, 20, 2016-2021, Circulation, 2010 Nov 16, PMID: 21041692 PMCID: PMC2991609,
  • Effect of CYP2B6, ABCB1, and CYP3A5 polymorphisms on efavirenz pharmacokinetics and treatment response: an AIDS Clinical Trials Group study. Heather J. Ribaudo, Huan Liu, Matthias Schwab, Elke Schaeffeler, Michel Eichelbaum, Alison A. Motsinger-Reif, Marylyn D. Ritchie, Ulrich M. Zanger, Edward P. Acosta, Gene D. Morse, Roy M. Gulick, Gregory K. Robbins, David Clifford, David W. Haas, 202, 5, 717-722, The of infectious diseases, 2010 Sep 1, PMID: 20662624 PMCID: PMC2919241,
  • Incorporating Domain Knowledge into Evolutionary Computing for Discovering Gene-gene Interaction Conference Paper, Stephen D. Turner, Scott M. Dudek, Marylyn D. Ritchie, http://dl.acm.org/citation.cfm?id=1885031.1885074, PPSN'10, Berlin, Heidelberg, Springer-Verlag, 394–403, 3-642-15843-9, 978-3-642-15843-8, 2010, 2014-02-24 18:06:46, ACM Digital Library, Understanding the genetic underpinnings of common heritable human traits has enormous public health benefits with implications for risk prediction, development of novel drugs, and personalized medicine. Many complex human traits are highly heritable, yet little of the variability in such traits can be accounted for by examining single DNA variants at a time. Seldom explored non-additive gene-gene interactions are thought to be one source of this "missing" heritability. Approaches that can account for this complexity are more aptly suited to find combinations of genetic and environmental exposures that can lead to disease. Stochastic methods employing evolutionary algorithms have demonstrated promise in being able to detect and model gene-gene interactions that influence human traits, yet the search space is nearly infinite because of the vast number of variables collected in contemporary human genetics studies. In this work we assess the performance and feasibility of sensible initialization of an evolutionary algorithm using domain knowledge., Proceedings of the 11th International Conference on Parallel Problem Solving from Nature: Part I,
  • Warfarin pharmacogenetics: a single VKORC1 polymorphism is predictive of dose across 3 racial groups Nita A Limdi, Mia Wadelius, Larisa Cavallari, Niclas Eriksson, Dana C Crawford, Ming-Ta M Lee, Chien-Hsiun Chen, Alison Motsinger-Reif, Hersh Sagreiya, Nianjun Liu, Alan H B Wu, Brian F Gage, Andrea Jorgensen, Munir Pirmohamed, Jae-Gook Shin, Guilherme Suarez-Kurtz, Stephen E Kimmel, Julie A Johnson, Teri E Klein, Michael J Wagner, International Warfarin Pharmacogenetics Consortium, 115, 18, 3827-3834, Blood, 1528-0020, May 6, 2010, PMID: 20203262 PMCID: PMC2865873,
  • Initialization Parameter Sweep in ATHENA: Optimizing Neural Networks for Detecting Gene-Gene Interactions in the Presence of Small Main Effects. Emily R. Holzinger, Carrie C. Buchanan, Scott M. Dudek, Eric C. Torstenson, Stephen D. Turner, Marylyn D. Ritchie, 12, Genetic and Evolutionary Computation Conference : [proceedings] / sponsored by ACM SIGEVO. Genetic and Evolutionary Computation Conference, 2010, PMID: 21152364 PMCID: PMC2997651,
  • Finding unique filter sets in PLATO: a precursor to efficient interaction analysis in GWAS data. Benjamin J. Grady, Eric Torstenson, Scott M. Dudek, Justin Giles, David Sexton, Marylyn D. Ritchie, 315-326, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 2010, PMID: 19908384 PMCID: PMC2903053,
  • PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene-disease associations. Joshua C. Denny, Marylyn D. Ritchie, Melissa A. Basford, Jill M. Pulley, Lisa Bastarache, Kristin Brown-Gentry, Deede Wang, Dan R. Masys, Dan M. Roden, Dana C. Crawford, 26, 9, 1205-1210, Bioinformatics (Oxford, England), 2010 May 1, PMID: 20335276 PMCID: PMC2859132,
  • A cross-validation procedure for general pedigrees and matched odds ratio fitness metric implemented for the multifactor dimensionality reduction pedigree disequilibrium test. Todd L. Edwards, Eric Torstensen, Scott Dudek, Eden R. Martin, Marylyn D. Ritchie, 2009 Wiley-Liss, Inc., 34, 2, 194-199, Genetic epidemiology, 2010 Feb, PMID: 19697353 PMCID: PMC2811750,
  • African mitochondrial DNA subhaplogroups and peripheral neuropathy during antiretroviral therapy. Jeffrey A. Canter, Gregory K. Robbins, Doug Selph, David B. Clifford, Asha R. Kallianpur, Robert Shafer, Shawn Levy, Deborah G. Murdock, Marylyn D. Ritchie, David W. Haas, Todd Hulgan, 201, 11, 1703-1707, The of infectious diseases, 2010 Jun 1, PMID: 20402593 PMCID: PMC2862090,

Publications