Research Topics
Species | Marylyn RitchieSummaryAffiliation: Vanderbilt University Country: USA Publications
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Publications
Rule based classifier for the analysis of gene-gene and gene-environment interactions in genetic association studiesThorsten Lehr
Boehringer Ingelheim Pharma GmbH and Co, KG, Department of Drug Metabolism and Pharmacokinetics, 88397 Biberach an der Riss, Germany
BioData Min 4:4. 2011..abstract:..- Power of grammatical evolution neural networks to detect gene-gene interactions in the presence of errorAlison A Motsinger-Reif
Bioinformatics Research Center, Department of Statistics, North Carolina State University, Raleigh, NC 27695, USA
BMC Res Notes 1:65. 2008..Additionally, we compare the performance of GENN to that of another computational method - Multifactor Dimensionality Reduction (MDR)... - Alternative contingency table measures improve the power and detection of multifactor dimensionality reductionWilliam S Bush
Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
BMC Bioinformatics 9:238. 2008..We sought to improve the ability of MDR to detect gene-gene interactions by replacing classification error with a different measure to score model quality... - An application of conditional logistic regression and multifactor dimensionality reduction for detecting gene-gene interactions on risk of myocardial infarction: the importance of model validationChristopher S Coffey
Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL 35294 0022, USA
BMC Bioinformatics 5:49. 2004..One advantage of the MDR method is that it provides an internal prediction error for validation. We summarize our use of this internal prediction error for model validation... - LD-Spline: Mapping SNPs on genotyping platforms to genomic regions using patterns of linkage disequilibriumWilliam S Bush
Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
BioData Min 2:7. 2009..CONCLUSION: LD-Spline is an integrated database routine that quickly and effectively defines the genomic region marked by a SNP using linkage disequilibrium, with a SNP-centric block definition algorithm... 
Trends in genomic variation: a view of some of the latest technologiesMarylyn D Ritchie
Vanderbilt University, Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Nashville, TN 37232, USA
Drug Discov Today 10:1417-8. 2005- Multifactor dimensionality reduction for detecting gene-gene and gene-environment interactions in pharmacogenomics studiesMarylyn D Ritchie
Vanderbilt University Medical Center, Department of Molecular Physiology and Biophysics, 519 Light Hall, Center for Human Genetics Research, Nashville, TN 37232 0700, USA
Pharmacogenomics 6:823-34. 2005..This computational technology is described in detail in this review, and its application in pharmacogenomic studies is demonstrated... - Using prior knowledge and genome-wide association to identify pathways involved in multiple sclerosisMarylyn D Ritchie
Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University, 519 Light Hall, Nashville, TN 37232 0700, USA
Genome Med 1:65. 2009..This and other pathway-based approaches are likely to continue to emerge in the GWAS literature, as they provide a powerful strategy to detect important modest single-locus effects and gene-gene interaction effects... - The effects of linkage disequilibrium in large scale SNP datasets for MDRBenjamin J Grady
Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, TN 37232, USA
BioData Min 4:11. 2011..abstract:.. - Exploring epistasis in candidate genes for rheumatoid arthritisMarylyn D Ritchie
Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University Medical Center, 21st Avenue South and Garland Avenue, Nashville, Tennessee 37232, USA
BMC Proc 1:S70. 2007..This comparison should be extended in future studies with both simulated and real data... - Bioinformatics approaches for detecting gene-gene and gene-environment interactions in studies of human diseaseMarylyn D Ritchie
Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University Medical School, Nashville, Tennessee 37232 0700, USA
Neurosurg Focus 19:E2. 2005..Finally, the author describes the future directions for this technique and related methodologies... - ATHENA: A knowledge-based hybrid backpropagation-grammatical evolution neural network algorithm for discovering epistasis among quantitative trait LociStephen D Turner
Center for Human Genetics Research, Departments of Molecular Physiology and Biophysics and Biomedical Informatics, Vanderbilt University, Nashville, TN, USA
BioData Min 3:5. 2010..Non-additive gene-gene interactions, which are not often explored, are thought to be one source of this "missing" heritability... - Synthesis-View: visualization and interpretation of SNP association results for multi-cohort, multi-phenotype data and meta-analysisSarah A Pendergrass
Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville TN, USA
BioData Min 3:10. 2010.... - Using biological knowledge to uncover the mystery in the search for epistasis in genome-wide association studiesMarylyn D Ritchie
Department of Molecular Physiology, Center for Human Genetics Research, Vanderbilt University, Nashville, TN 37232 0700, USA
Ann Hum Genet 75:172-82. 2011..I discuss a number of these approaches and propose that a comprehensive approach will likely be most fruitful for searching for epistasis in large-scale genomic studies of the current state-of-the-art and into the future... - Robust replication of genotype-phenotype associations across multiple diseases in an electronic medical recordMarylyn D Ritchie
Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
Am J Hum Genet 86:560-72. 2010.... - Multifactor dimensionality reduction software for detecting gene-gene and gene-environment interactionsLance W Hahn
Program in Human Genetics and Department of Molecular Physiology and Biophysics, Vanderbilt University Medical School, Nashville, TN 37232-0700, USA
Bioinformatics 19:376-82. 2003..SUPPLEMENTARY INFORMATION: All supplementary information can be found at http://phg.mc.vanderbilt.edu/Software/MDR... - Machine learning for detecting gene-gene interactions: a reviewBrett A McKinney
Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University Medical School, Nashville, Tennessee, USA
Appl Bioinformatics 5:77-88. 2006..We conclude with some ideas about how these methods and others can be integrated into a comprehensive and flexible framework for data mining and knowledge discovery in human genetics... - Genetic variation in the rhythmonome: ethnic variation and haplotype structure in candidate genes for arrhythmiasWilliam S Bush
Center for Human Genetics Research and Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN, USA
Pharmacogenomics 10:1043-53. 2009..Here, we report an evaluation of the variation and haplotype structure in six key components of the rhythmonome... - Multilocus analysis of hypertension: a hierarchical approachScott M Williams
Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
Hum Hered 57:28-38. 2004..5% of the time. Thus, our data indicate epistatic interactions play a major role in hypertension susceptibility. Our data also support a model where multiple pathways need to be affected in order to predispose to hypertension... 
Genetic determinants of response to warfarin during initial anticoagulationUte I Schwarz
Department of Medicine, Vanderbilt University School of Medicine, Nashville, USA
N Engl J Med 358:999-1008. 2008....- An association analysis of Alzheimer disease candidate genes detects an ancestral risk haplotype clade in ACE and putative multilocus association between ACE, A2M, and LRRTM3Todd L Edwards
Department of Molecular Physiology and Biophysics and Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee 37232, USA
Am J Med Genet B Neuropsychiatr Genet 150:721-35. 2009.... - Exploring the performance of Multifactor Dimensionality Reduction in large scale SNP studies and in the presence of genetic heterogeneity among epistatic disease modelsTodd L Edwards
Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, Tenn, USA
Hum Hered 67:183-92. 2009..Previously unknown aspects of MDR performance were the power to detect interactive effects given large numbers of non-model loci or varying degrees of heterogeneity among multiple epistatic disease models... - Interaction between interleukin 3 and dystrobrevin-binding protein 1 in schizophreniaTodd L Edwards
Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, TN 37232, USA
Schizophr Res 106:208-17. 2008..We also observed a significant main effect in DTNBP1, which survived correction for multiple comparisons, and numerous nominally significant effects in several genes... - Human genomic association studies: a primer for the infectious diseases specialistAlison A Motsinger
School of Medicine, Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University, Nashville, TN 37232, USA
J Infect Dis 195:1737-44. 2007..Our goal is to provide the infectious diseases specialist with information that will aid in the critical evaluation of publications that include human genomic analyses... - Genome simulation approaches for synthesizing in silico datasets for human genomicsMarylyn D Ritchie
Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, USA
Adv Genet 72:1-24. 2010..Many of the hallmark features of biological datasets can be synthesized in silico; still much research is needed to enhance our capabilities to create datasets that capture the natural complexity of biological datasets... - A balanced accuracy function for epistasis modeling in imbalanced datasets using multifactor dimensionality reductionDigna R Velez
Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, Tennessee
Genet Epidemiol 31:306-15. 2007..These results suggest that balanced accuracy should be used instead of accuracy for the MDR analysis of epistasis in imbalanced datasets... - Persistent atrial fibrillation is associated with reduced risk of torsades de pointes in patients with drug-induced long QT syndromeDawood Darbar
Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee 37323 6602, USA
J Am Coll Cardiol 51:836-42. 2008..The goal of this study was to identify markers of torsades de pointes (TdP) in patients with drug-associated long QT syndrome (LQTS)... - Polymorphism modulates symptomatic response to antiarrhythmic drug therapy in patients with lone atrial fibrillationDawood Darbar
Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee 37323 6602, USA
Heart Rhythm 4:743-9. 2007.... - PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene-disease associationsJoshua C Denny
Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA
Bioinformatics 26:1205-10. 2010..The primary outcome of this study was replication of seven previously known SNP-disease associations for these SNPs... - Visualizing SNP statistics in the context of linkage disequilibrium using LD-PlusWilliam S Bush
Department of Molecular Physiology, Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, TN, USA
Bioinformatics 26:578-9. 2010.... - African mitochondrial DNA subhaplogroups and peripheral neuropathy during antiretroviral therapyJeffrey A Canter
Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, 345 24th Ave North, Nashville, TN 37203, USA
J Infect Dis 201:1703-7. 2010..7 [95% confidence interval, 1.1-12.0]). An African mtDNA subhaplogroup is for the first time implicated in susceptibility to nucleoside reverse-transcriptase inhibitor-associated toxicity... - Identifying the genotype behind the phenotype: a role model found in VKORC1 and its association with warfarin dosingDana C Crawford
Vanderbilt University, Center for Human Genetics Research, 519 Light Hall, Nashville, TN 37232, USA
Pharmacogenomics 8:487-96. 2007..These future avenues will be best explored using diverse approaches encompassing clinical, statistical and genomic methods currently being developed for genotype-phenotype studies in human populations... - Drug transporter and metabolizing enzyme gene variants and nonnucleoside reverse-transcriptase inhibitor hepatotoxicityMarylyn D Ritchie
Center for Human Genetics Research, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
Clin Infect Dis 43:779-82. 2006..Decreased risk of hepatotoxicity was associated with MDR1 3435C-->T (odds ratio, 0.254; P=.021). An interaction between MDR1 and hepatitis B surface antigen status predicted risk with 82% accuracy (P<.001)... - GPNN: power studies and applications of a neural network method for detecting gene-gene interactions in studies of human diseaseAlison A Motsinger
Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University Medical School, Nashville, TN 37232 0700, USA
BMC Bioinformatics 7:39. 2006..The goal of this study was to evaluate the power of GPNN for identifying high-order gene-gene interactions. We were also interested in applying GPNN to a real data analysis in Parkinson's disease... - Clinical applications of whole-genome association studies: future applications at the bedsideAlison A Motsinger
Vanderbilt University, Center for Human Genetics Research Department of Molecular Physiology and Biophysics, 519 Light Hall, Nashville, TN 37232, USA
Expert Rev Mol Diagn 6:551-65. 2006.... - Immunogenetics of CD4 lymphocyte count recovery during antiretroviral therapy: An AIDS Clinical Trials Group studyDavid W Haas
Center for Human Genetics Research, Vanderbilt University, Nashville, TN, 37203, USA
J Infect Dis 194:1098-107. 2006..Immune recovery during antiretroviral therapy is a complex phenotype that is influenced by multiple genetic variants. Future studies should validate these tentative associations and define underlying mechanisms... - Complex gene-gene interactions in multiple sclerosis: a multifactorial approach reveals associations with inflammatory genesAlison A Motsinger
Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, 519 Light Hall, Vanderbilt University Medical School, Nashville, TN 37232 0700, USA
Neurogenetics 8:11-20. 2007..These results suggest that significant epistasis, or gene-gene interactions, may exist even in the absence of statistically significant individual main effects... - Multilocus genetic interactions and response to efavirenz-containing regimens: an adult AIDS clinical trials group studyAlison A Motsinger
Vanderbilt University School of Medicine, Nashville, Tennessee 37203, USA
Pharmacogenet Genomics 16:837-45. 2006..We examined whether long-term responses to efavirenz, and/or plasma efavirenz exposure, are better predicted by multilocus genetic interactions than by individual polymorphisms... - Parallel multifactor dimensionality reduction: a tool for the large-scale analysis of gene-gene interactionsWilliam S Bush
Center for Human Genetics Research, Vanderbilt University, Nashville, TN, USA
Bioinformatics 22:2173-4. 2006..AVAILABILITY: Parallel MDR is freely available for non-commercial research institutions. For full details see http://chgr.mc.vanderbilt.edu/ritchielab/pMDR. An open-source version of MDR software is available at http://www.epistasis.org... - The effect of reduction in cross-validation intervals on the performance of multifactor dimensionality reductionAlison A Motsinger
Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, Tennessee 37232-0700, USA
Genet Epidemiol 30:546-55. 2006..The validity of this reduction was confirmed with data from an Alzheimer's disease (AD) study... - Multifactor dimensionality reduction: an analysis strategy for modelling and detecting gene-gene interactions in human genetics and pharmacogenomics studiesAlison A Motsinger
Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, TN 37232 0700, USA
Hum Genomics 2:318-28. 2006..MDR can be a powerful tool in reaching these goals when used appropriately... - Mitochondrial haplogroups and peripheral neuropathy during antiretroviral therapy: an adult AIDS clinical trials group studyTodd Hulgan
Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee 37203, USA
AIDS 19:1341-9. 2005..The objective of this study was to determine if NRTI-associated peripheral neuropathy is associated with European mitochondrial haplogroups... - Optimization of neural network architecture using genetic programming improves detection and modeling of gene-gene interactions in studies of human diseasesMarylyn D Ritchie
Program in Human Genetics and Department of Molecular Physiology and Biophysics, Vanderbilt University Medical School, Nashville, TN, 37232 0700, USA
BMC Bioinformatics 4:28. 2003.... - Power of multifactor dimensionality reduction for detecting gene-gene interactions in the presence of genotyping error, missing data, phenocopy, and genetic heterogeneityMarylyn D Ritchie
Program in Human Genetics and Department of Molecular Physiology and Biophysics, Vanderbilt University Medical School, Nashville, TN 37232-0700, USA
Genet Epidemiol 24:150-7. 2003..Extending MDR to address genetic heterogeneity should be a priority for the continued methodological development of this new approach... - Genetic variation in the mitochondrial enzyme carbamyl-phosphate synthetase I predisposes children to increased pulmonary artery pressure following surgical repair of congenital heart defects: a validated genetic association studyJeffrey A Canter
Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN, USA
Mitochondrion 7:204-10. 2007..In conclusion, the CPSI T1405N genotype appears to be an important new factor in predicting susceptibility to increased PAP following surgical repair of congenital cardiac defects in children... - Hemochromatosis (HFE) gene mutations and peripheral neuropathy during antiretroviral therapyAsha R Kallianpur
Department of Medicine, Divisions of General Internal Medicine and Public Health, Nashville, TN, USA
AIDS 20:1503-13. 2006..Since iron deficiency is associated with some types of PN, and iron is essential for mitochondrial function, we tested the hypothesis that hemochromatosis (HFE) gene mutations influence susceptibility to NRTI-induced PN... - Relative contribution of CYP2C9 and VKORC1 genotypes and early INR response to the prediction of warfarin sensitivity during initiation of therapyChun Li
Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN, USA
Blood 113:3925-30. 2009..08) and VKORC1 (P = .30) were not associated with stable warfarin dose. Thus, much of the information provided by CYP2C9 and VKORC1 genotypes during warfarin initiation is captured by the early INR response... - STUDENTJAMA. The challenges of whole-genome approaches to common diseasesJason H Moore
Vanderbilt University Medical School, Nashville, Tenn, USA
JAMA 291:1642-3. 2004 - Nephrocystin-conserved domains involved in targeting to epithelial cell-cell junctions, interaction with filamins, and establishing cell polarityJohn C Donaldson
Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
J Biol Chem 277:29028-35. 2002.... - Estrogens, enzyme variants, and breast cancer: a risk modelPhilip S Crooke
Department of Pathology, TVC 4918, Vanderbilt University, Nashville, TN 37232, USA
Cancer Epidemiol Biomarkers Prev 15:1620-9. 2006..The model offers the opportunity to combine metabolic, genetic, and lifetime exposure data in assessing estrogens as a breast cancer risk factor... - Subsets of the major tyrosine phosphorylation sites in Crk-associated substrate (CAS) are sufficient to promote cell migrationNah Young Shin
Department of Cell and Developmental Biology, Vanderbilt Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
J Biol Chem 279:38331-7. 2004..Effective wound healing was achieved by CAS variants containing as few as four of the major sites, indicating sufficiency of partial SD signaling function in this cell migration response... - Renin-angiotensin system gene polymorphisms and coronary artery disease in a large angiographic cohort: detection of high order gene-gene interactionChia Ti Tsai
Division of Cardiology, Department of Internal Medicine, National Taiwan, University Hospital, Taipei, Taiwan
Atherosclerosis 195:172-80. 2007..These results are compatible with the concept of multilocus and multi-gene effects in complex diseases that would be missed with conventional approaches... - Problems with genome-wide association studiesScott M Williams
Science 316:1840-2. 2007 - Renin-angiotensin system gene polymorphisms and atrial fibrillationChia Ti Tsai
Division of Cardiology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
Circulation 109:1640-6. 2004..We hypothesized that RAS genes might be among the susceptibility genes of nonfamilial structural AF and conducted a genetic case-control study to demonstrate this... - Susceptibility and modifier genes in Portuguese transthyretin V30M amyloid polyneuropathy: complexity in a single-gene diseaseMiguel L Soares
Department of Molecular and Experimental Medicine, Division of Rheumatology Research and the WM Keck Autoimmune Disease Center, The Scripps Research Institute, La Jolla, CA 92037, USA
Hum Mol Genet 14:543-53. 2005..Thus, although the TTR V30M mutation is required for the disease in Portuguese patients, different genetic factors may govern the age of onset, as well as the occurrence of anticipation... - Pacific Symposium on Biocomputing--computational approaches for pharmacogenomicsRussell A Wilke
Marshfield Clinic, Center for Human Genetics, and Department of Internal Medicine, 1000 N Oak Ave, Marshfield, WI 54449, and Department of Genetics, Stanford University, CA 94305-5120, USA
Pharmacogenomics 6:111-3. 2005 - Investigation of potential gene-gene interactions between APOE and RELN contributing to autism riskAllison E Ashley-Koch
Center for Human Genetics, Department of Medicine, Duke University Medical Center, Snyderman Genomic Sciences Building, Durham, NC 27710, USA
Psychiatr Genet 17:221-6. 2007..RELN shares a common biological pathway with APOE, and Persico et al. have observed transmission distortion of the APOE-2 allele in autism families... - A genome-wide scan for common genetic variants with a large influence on warfarin maintenance doseGregory M Cooper
Department of Genome Sciences, University of Washington, Seattle, WA98195, USA
Blood 112:1022-7. 2008..Randomized clinical trials that account for these 2 genes should therefore produce results that are definitive and broadly applicable... - Different contributions of polymorphisms in VKORC1 and CYP2C9 to intra- and inter-population differences in maintenance dose of warfarin in Japanese, Caucasians and African-AmericansHarumi Takahashi
Department of Pharmacotherapy, Meiji Pharmaceutical University, Kiyose, Tokyo, Japan
Pharmacogenet Genomics 16:101-10. 2006.... - Single-nucleotide polymorphisms for diagnosis of salt-sensitive hypertensionHironobu Sanada
Third Department of Internal Medicine, Fukushima Medical University, School of Medicine, Fukushima City, Japan
Clin Chem 52:352-60. 2006..Like low-renin testing, screening for GRK4 variants may be a useful diagnostic adjunct for detection of SS hypertension... - Novel methods for detecting epistasis in pharmacogenomics studiesAlison A Motsinger
North Carolina State University, Bioinformatics Research Center, Department of Statistics, Raleigh, NC 27695, USA
Pharmacogenomics 8:1229-41. 2007..The overall goal of this paper is to aid researchers in developing an analysis plan that accounts for gene-gene and gene-environment in their own work... - Discussing gene-gene interaction: warning--translating equations to English may result in jabberwockyChristopher W Bartlett
Center for Quantitative and Computational Biology and Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, OH, USA
Genet Epidemiol 31:S61-7. 2007..The difficulty of using (primarily) affected sib pair data in a gene x gene interaction analysis is explored... - Comparison of approaches for machine-learning optimization of neural networks for detecting gene-gene interactions in genetic epidemiologyAlison A Motsinger-Reif
Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA
Genet Epidemiol 32:325-40. 2008..Finally, we demonstrate the scalability of the GENN method with increasing numbers of variables--as many as 500,000 single nucleotide polymorphisms... - ABCB1 and GST polymorphisms associated with TP53 status in breast cancerSilje H Nordgard
Department of Genetics, The Norwegian Radium Hospital, University of Oslo, Oslo, Norway
Pharmacogenet Genomics 17:127-36. 2007..The goal of this study was to characterize the genetic variation in the ABCB1, GSTM1, GSTT1 and GSTP1 genes, as well as the haplotype structure in the ABCB1 gene... - Genetic heterogeneity is not as threatening as you might thinkMarylyn D Ritchie
Genet Epidemiol 31:797-800. 2007
Research Grants
- Analysis Tool for Heritable and Envirnonmental Network AssociationsMarylyn D Ritchie; Fiscal Year: 2010..As the field gains experience in analyzing large scale genomic data, it is crucial that we learn from each other and develop and codify the best strategies. ..