Biomedical and Translational Informatics Laboratory

Publications - 2006

  • Alternative Cross-Over Strategies and Selection Techniques for Grammatical Evolution Optimized Neural Networks. Alison A. Motsinger, Lance W. Hahn, Scott M. Dudek, Kelli K. Ryckman, Marylyn D. Ritchie, 2006, Genetic and Evolutionary Computation Conference : [proceedings] / sponsored by ACM SIGEVO. Genetic and Evolutionary Computation Conference, 2006, PMID: 20634918 PMCID: PMC2903763,
  • Multilocus genetic interactions and response to efavirenz-containing regimens: an adult AIDS clinical trials group study. Alison A. Motsinger, Marylyn D. Ritchie, Robert W. Shafer, Gregory K. Robbins, Gene D. Morse, Line Labbe, Grant R. Wilkinson, David B. Clifford, Richard T. D'Aquila, Victoria A. Johnson, Richard B. Pollard, Thomas C. Merigan, Martin S. Hirsch, John P. Donahue, Richard B. Kim, David W. Haas, 16, 11, 837-845, Pharmacogenetics and genomics, 2006 Nov, PMID: 17047492,
  • Different contributions of polymorphisms in VKORC1 and CYP2C9 to intra- and inter-population differences in maintenance dose of warfarin in Japanese, Caucasians and African-Americans. Harumi Takahashi, Grant R. Wilkinson, Edith A. Nutescu, Takashi Morita, Marylyn D. Ritchie, Maria G. Scordo, Vittorio Pengo, Martina Barban, Roberto Padrini, Ichiro Ieiri, Kenji Otsubo, Toshitaka Kashima, Sosuke Kimura, Shinichi Kijima, Hirotoshi Echizen, 16, 2, 101-110, Pharmacogenetics and genomics, 2006 Feb, PMID: 16424822,
  • Clinical applications of whole-genome association studies: future applications at the bedside. Alison A. Motsinger, Marylyn D. Ritchie, Seth E. Dobrin, 6, 4, 551-565, Expert review of molecular diagnostics, 2006 Jul, PMID: 16824029,
  • Estrogens, enzyme variants, and breast cancer: a risk model. Philip S. Crooke, Marylyn D. Ritchie, David L. Hachey, Sheila Dawling, Nady Roodi, Fritz F. Parl, 15, 9, 1620-1629, Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology, 2006 Sep, PMID: 16985022,
  • Multifactor dimensionality reduction: an analysis strategy for modelling and detecting gene-gene interactions in human genetics and pharmacogenomics studies. Alison A. Motsinger, Marylyn D. Ritchie, 2, 5, 318-328, Human genomics, 2006 Mar, PMID: 16595076 PMCID: PMC3500181,
  • The effect of reduction in cross-validation intervals on the performance of multifactor dimensionality reduction. Alison A. Motsinger, Marylyn D. Ritchie, Copyright (c) 2006 Wiley-Liss, Inc., 30, 6, 546-555, Genetic epidemiology, 2006 Sep, PMID: 16800004,
  • GPNN: power studies and applications of a neural network method for detecting gene-gene interactions in studies of human disease. Alison A. Motsinger, Stephen L. Lee, George Mellick, Marylyn D. Ritchie, 7, BMC bioinformatics, 2006, PMID: 16436204 PMCID: PMC1388239,
  • Risk factor interactions and genetic effects associated with post-operative atrial fibrillation. Alison A. Motsinger, Brian S. Donahue, Nancy J. Brown, Dan M. Roden, Marylyn D. Ritchie, 584-595, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 2006, PMID: 17094271,
  • A novel method to identify gene-gene effects in nuclear families: the MDR-PDT. E. R. Martin, M. D. Ritchie, L. Hahn, S. Kang, J. H. Moore, (c) 2005 Wiley-Liss, Inc., 30, 2, 111-123, Genetic epidemiology, 2006 Feb, PMID: 16374833,
  • Single-nucleotide polymorphisms for diagnosis of salt-sensitive hypertension. Hironobu Sanada, Junichi Yatabe, Sanae Midorikawa, Shigeatsu Hashimoto, Tsuyoshi Watanabe, Jason H. Moore, Marylyn D. Ritchie, Scott M. Williams, John C. Pezzullo, Midori Sasaki, Gilbert M. Eisner, Pedro A. Jose, Robin A. Felder, 52, 3, 352-360, Clinical chemistry, 2006 Mar, PMID: 16439609,
  • Hemochromatosis (HFE) gene mutations and peripheral neuropathy during antiretroviral therapy. Asha R. Kallianpur, Todd Hulgan, Jeffrey A. Canter, Marylyn D. Ritchie, Jonathan L. Haines, Gregory K. Robbins, Robert W. Shafer, David B. Clifford, David W. Haas, 20, 11, 1503-1513, AIDS (London, England), 2006 Jul 13, PMID: 16847405,
  • Drug transporter and metabolizing enzyme gene variants and nonnucleoside reverse-transcriptase inhibitor hepatotoxicity. Marylyn D. Ritchie, David W. Haas, Alison A. Motsinger, John P. Donahue, Huso Erdem, Stephen Raffanti, Peter Rebeiro, Alfred L. George, Richard B. Kim, Jonathan L. Haines, Timothy R. Sterling, 43, 6, 779-782, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 2006 Sep 15, PMID: 16912956,
  • Immunogenetics of CD4 lymphocyte count recovery during antiretroviral therapy: An AIDS Clinical Trials Group study. David W. Haas, Daniel E. Geraghty, Janet Andersen, Jessica Mar, Alison A. Motsinger, Richard T. D'Aquila, Derya Unutmaz, Constance A. Benson, Marylyn D. Ritchie, Alan Landay, 194, 8, 1098-1107, The of infectious diseases, 2006 Oct 15, PMID: 16991084,
  • Understanding the Evolutionary Process of Grammatical Evolution Neural Networks for Feature Selection in Genetic Epidemiology. Alison A. Motsinger, David M. Reif, Scott M. Dudek, Marylyn D. Ritchie, 2006, Proceedings of the ... IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology. IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, 2006 Sep 28, PMID: 20634919 PMCID: PMC2903766,
  • Data simulation software for whole-genome association and other studies in human genetics. Scott M. Dudek, Alison A. Motsinger, Digna R. Velez, Scott M. Williams, Marylyn D. Ritchie, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 2006, PMID: 17094264,
  • Comparison of Neural Network Optimization Approaches for Studies of Human Genetics Book Section, Alison A. Motsinger, Scott M. Dudek, Lance W. Hahn, Marylyn D. Ritchie, Franz Rothlauf, Jürgen Branke, Stefano Cagnoni, Ernesto Costa, Carlos Cotta, Rolf Drechsler, Evelyne Lutton, Penousal Machado, Jason H. Moore, Juan Romero, George D. Smith, Giovanni Squillero, Hideyuki Takagi, http://link.springer.com/chapter/10.1007/11732242_10, ©2006 Springer-Verlag Berlin Heidelberg, Lecture Notes in Computer Science, Springer Berlin Heidelberg, 103-114, 978-3-540-33237-4, 978-3-540-33238-1, 2006/01/01, 2014-02-24 17:59:22, 3907, link.springer.com, A major goal of human genetics is the identification of susceptibility genes associated with common, complex diseases. The preponderance of gene-gene and gene-environment interactions comprising the genetic architecture of common diseases presents a difficult challenge. To address this, novel computational approaches have been applied to studies of human disease. These novel approaches seek to capture the complexity inherent in common diseases. Previously, we developed a genetic programming neural network (GPNN) to optimize network architecture for the detection of disease susceptibility genes in association studies. While GPNN was a successful endeavor, we wanted to address the limitations in its flexibility and ease of development. To this end, we developed a grammatical evolution neural network (GENN) approach that accounts for the drawbacks of GPNN. In this study we show that this new method has high power to detect gene-gene interactions in simulated data. We also compare the performance of GENN to GPNN, a traditional back-propagation neural network (BPNN) and a random search algorithm. GENN outperforms both BPNN and the random search, and performs at least as well as GPNN. This study demonstrates the utility of using GE to evolve NN in studies of complex human disease., Applications of Evolutionary Computing,
  • Parallel multifactor dimensionality reduction: a tool for the large-scale analysis of gene-gene interactions. William S. Bush, Scott M. Dudek, Marylyn D. Ritchie, 22, 17, 2173-2174, Bioinformatics (Oxford, England), 2006 Sep 1, PMID: 16809395,
  • Machine learning for detecting gene-gene interactions: a review. Brett A. McKinney, David M. Reif, Marylyn D. Ritchie, Jason H. Moore, 5, 2, Applied bioinformatics, 2006, PMID: 16722772 PMCID: PMC3244050,
  • Multifactor dimensionality reduction reveals gene-gene interactions associated with multiple sclerosis susceptibility in African Americans. D. Brassat, A. A. Motsinger, S. J. Caillier, H. A. Erlich, K. Walker, L. L. Steiner, B. A. C. Cree, L. F. Barcellos, M. A. Pericak-Vance, S. Schmidt, S. Gregory, S. L. Hauser, J. L. Haines, J. R. Oksenberg, M. D. Ritchie, 7, 4, 310-315, Genes and immunity, 2006 Jun, PMID: 16625214,
  • An analysis paradigm for investigating multi-locus effects in complex disease: examination of three GABA receptor subunit genes on 15q11-q13 as risk factors for autistic disorder. A. E. Ashley-Koch, H. Mei, J. Jaworski, D. Q. Ma, M. D. Ritchie, M. M. Menold, G. R. Delong, R. K. Abramson, H. H. Wright, J. P. Hussman, M. L. Cuccaro, J. R. Gilbert, E. R. Martin, M. A. Pericak-Vance, 70, Pt 3, 281-292, Annals of human genetics, 2006 May, PMID: 16674551,

Publications