Research Topics
Genomes and Genes
| Jason H MooreSummaryAffiliation: Dartmouth Medical School Country: USA Publications
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Detail Information
Publications
A role for CETP TaqIB polymorphism in determining susceptibility to atrial fibrillation: a nested case control studyFolkert W Asselbergs
Department of Cardiology, University Medical Center Groningen, Groningen, The Netherlands
BMC Med Genet 7:39. 2006..We aimed to investigate the association between several environmental factors and loci of candidate genes, which might be related to the presence of AF...- A gene expression fingerprint of C. elegans embryonic motor neuronsRebecca M Fox
Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232 8240, USA
BMC Genomics 6:42. 2005..Here we describe a powerful strategy, Micro-Array Profiling of C. elegans cells (MAPCeL), and confirm that this approach provides a comprehensive gene expression profile of unc-4::GFP motor neurons in vivo... - Examination of polymorphic glutathione S-transferase (GST) genes, tobacco smoking and prostate cancer risk among men of African descent: a case-control studyNicole A Lavender
Department of Pharmacology and Toxicology, University of Louisville UofL, School of Medicine, 500 South Preston Street, Room 1319 Research Tower, UofL Health Science Center, Louisville, KY 40202, USA
BMC Cancer 9:397. 2009..Thus, we evaluated the effects of polymorphic GSTs (M1, T1, and P1) alone and combined with cigarette smoking on PCA susceptibility... - Characterizing genetic interactions in human disease association studies using statistical epistasis networksTing Hu
Department of Genetics, Dartmouth Medical School, Dartmouth College, Lebanon, NH, USA
BMC Bioinformatics 12:364. 2011.... - Dissecting trait heterogeneity: a comparison of three clustering methods applied to genotypic dataTricia A Thornton-Wells
Neuroscience Graduate Program, Vanderbilt Brain Institute, Vanderbilt University Medical Center, Nashville, TN, USA
BMC Bioinformatics 7:204. 2006..To determine the efficacy of applying the Bayesian Classification method to real data, the reliability of its internal clustering metrics at finding good clusterings was evaluated using permutation testing... - Bioinformatics challenges for genome-wide association studiesJason H Moore
Department of Genetics, Department of Community and Family Medicine, Dartmouth Medical School, Lebanon, NH 03756, USA
Bioinformatics 26:445-55. 2010..The goal of this review is to identify and discuss those GWAS challenges that will require computational methods... - Computational analysis of gene-gene interactions using multifactor dimensionality reductionJason H Moore
Dartmouth Medical School, Computational Genetics Laboratory, 706 Rubin Building, HB7937, One Medical Center Drive, Lebanon, NH 03756, USA
Expert Rev Mol Diagn 4:795-803. 2004..Several case studies that demonstrate the detection of gene-gene interactions in common diseases such as atrial fibrillation, Type II diabetes and essential hypertension are also discussed... - Connecting the dots between genes, biochemistry, and disease susceptibility: systems biology modeling in human geneticsJason H Moore
Computational Genetics Laboratory, Department of Genetics, Norris Cotton Cancer Center, Dartmouth Medical School, Lebanon, NH 03756, USA
Mol Genet Metab 84:104-11. 2005..We review here this approach and then discuss how it can be used to model biochemical and metabolic data in the context of genetic studies of human disease susceptibility... - Traversing the conceptual divide between biological and statistical epistasis: systems biology and a more modern synthesisJason H Moore
Department of Genetics, Norris Cotton Cancer Center, Dartmouth Medical School, Lebanon, NH, USA
Bioessays 27:637-46. 2005..We propose that systems biology will provide the necessary information for addressing these questions and that model systems such as bacteria, yeast and digital organisms will be a useful place to start... - Epistasis and its implications for personal geneticsJason H Moore
Computational Genetics Laboratory, Department of Genetics and Department of Community and Family Medicine, Dartmouth Medical School, Lebanon, NH 03756, USA
Am J Hum Genet 85:309-20. 2009..We provide some thoughts on the implications of epistasis for personal genetics and some recommendations for improving personal genetics in light of this complexity... - Accelerating epistasis analysis in human genetics with consumer graphics hardwareNicholas A Sinnott Armstrong
Computational Genetics Lab, Department of Genetics, Norris Cotton Cancer Center, Dartmouth Medical School, Lebanon, NH, USA
BMC Res Notes 2:149. 2009..CONCLUSION: Graphics hardware based computing provides a cost effective means to perform genetic analysis of epistasis using MDR on large datasets without the infrastructure of a computing cluster... - A flexible computational framework for detecting, characterizing, and interpreting statistical patterns of epistasis in genetic studies of human disease susceptibilityJason H Moore
Computational Genetics Laboratory, Department of Genetics, Dartmouth Hitchcock Medical Center, One Medical Center Dr, 706 Rubin Bldg, HB7937, Lebanon, NH 03756, USA
J Theor Biol 241:252-61. 2006..We then apply this strategy to detecting, characterizing, and interpreting epistatic models in a genetic study (n = 500) of atrial fibrillation and show that both classification and model interpretation are significantly improved... - BioinformaticsJason H Moore
Computational Genetics Laboratory, Departments of Genetics and Community and Family Medicine, Dartmouth Medical School, Lebanon, New Hampshire, USA
J Cell Physiol 213:365-9. 2007..We review database resources as well as data mining software tools... - Evolving hard problems: Generating human genetics datasets with a complex etiologyDaniel S Himmelstein
Department of Genetics, Dartmouth Medical School, One Medical Center Drive, Lebanon, NH 03756, USA
BioData Min 4:21. 2011..abstract:.. - A computationally efficient hypothesis testing method for epistasis analysis using multifactor dimensionality reductionKristine A Pattin
Computational Genetics Laboratory, Department of Genetics, Dartmouth Medical School, Lebanon, New Hampshire 03756, USA
Genet Epidemiol 33:87-94. 2009..We then demonstrate this new method by applying it to a genetic epidemiology study of bladder cancer susceptibility that was previously analyzed using MDR and assessed using a 1,000-fold permutation test... - Symbolic modeling of epistasisJason H Moore
Computational Genetics Laboratory, Norris Cotton Cancer Center, Dartmouth Medical School, Lebanon, NH 03756, USA
Hum Hered 63:120-33. 2007..We illustrate this five step SDA modeling process with a real case-control dataset... - Bladder cancer SNP panel predicts susceptibility and survivalAngeline S Andrew
Section of Biostatistics and Epidemiology, Department of Community and Family Medicine, Dartmouth Medical School, Lebanon, NH 03756, USA
Hum Genet 125:527-39. 2009..8 95% CI 1.1-3.0). Variants in the detoxification gene EPHX1 experienced longer survival (HR 0.4 (95% CI 0.2-0.8). These genes can now be assessed in multiple study populations to identify and validate SNPs appropriate for clinical use... - A simple and computationally efficient sampling approach to covariate adjustment for multifactor dimensionality reduction analysis of epistasisJiang Gui
Community and Family Medicine, Norris Cotton Cancer Center, Dartmouth Medical School, Lebanon, NH 03756, USA
Hum Hered 70:219-25. 2010..The results suggest that our proposed method performs similarly, but is more computationally efficient. We then apply this new method to an analysis of a population-based bladder cancer study in New Hampshire... - DNA repair polymorphisms modify bladder cancer risk: a multi-factor analytic strategyAngeline S Andrew
Department of Community and Family Medicine, Section of Biostatistics and Epidemiology, Dartmouth Medical School, Lebanon, NH 03756, USA
Hum Hered 65:105-18. 2008..These include: APE1-Asn148Gln, XRCC1-Arg399Gln and XRCC1-Arg194Trp in the BER pathway, XPD-Gln751Lys in the NER pathway and XRCC3-Thr241Met in the DSB repair pathway... - Polymorphisms in the brain-derived neurotrophic factor gene influence memory and processing speed one month after brain injuryThomas W McAllister
1 Section of Neuropsychiatry, Department of Psychiatry, Dartmouth Medical School, Lebanon, New Hampshire
J Neurotrauma 29:1111-8. 2012..Polymorphisms in BDNF influence cognitive performance shortly after mTBI. The results raise the possibility that a functional polymorphism other than rs6265 may contribute to memory function after mTBI... - A robust multifactor dimensionality reduction method for detecting gene-gene interactions with application to the genetic analysis of bladder cancer susceptibilityJiang Gui
Dartmouth Medical School, Lebanon, NH 03756, USA
Ann Hum Genet 75:20-8. 2011..We show that there is no loss of success rate when this is not the case. We then apply the RMDR method to the detection of gene-gene interactions in genotype data from a population-based study of bladder cancer in New Hampshire... - COMT Val158Met Genotype and Individual Differences in Executive Function in Healthy AdultsHeather A Wishart
Department of Psychiatry, Dartmouth Medical School, Lebanon, New Hampshire 03756 0001, USA
J Int Neuropsychol Soc 17:174-80. 2011..This study suggests the heterogeneity in COMT effects reported in the literature may be due in part to gene-gene interactions that influence central dopaminergic systems... - SLC39A2 and FSIP1 polymorphisms as potential modifiers of arsenic-related bladder cancerMargaret R Karagas
Section of Biostatistics and Epidemiology, Dartmouth Medical School, Lebanon, NH 03756, USA
Hum Genet 131:453-61. 2012..03). Our findings suggest novel variants that may influence risk of arsenic-associated bladder cancer and those who may be at greatest risk from this widespread exposure... - Multifactor dimensionality reduction for graphics processing units enables genome-wide testing of epistasis in sporadic ALSCasey S Greene
Department of Genetics, Dartmouth Medical School, Lebanon, NH 03756, USA
Bioinformatics 26:694-5. 2010..Graphics processing units (GPUs), the hardware responsible for rendering computer games, are powerful parallel processors. Using GPUs to run MDR on a genome-wide dataset allows for statistically rigorous testing of epistasis... - Failure to replicate a genetic association may provide important clues about genetic architectureCasey S Greene
Department of Genetics, Dartmouth College, Lebanon, New Hampshire, United States of America
PLoS ONE 4:e5639. 2009..We recommend that polymorphisms that fail to replicate be checked for interactions with other polymorphisms, particularly when samples are collected from groups with distinct ethnic backgrounds or different geographic regions... - Ecogeographic genetic epidemiologyChantel D Sloan
Computational Genetics Laboratory, Department of Genetics, Dartmouth Medical School, Lebanon, New Hampshire, USA
Genet Epidemiol 33:281-9. 2009.... - A novel survival multifactor dimensionality reduction method for detecting gene-gene interactions with application to bladder cancer prognosisJiang Gui
Department of Community and Family Medicine, Norris Cotton Cancer Center, Dartmouth Medical School, One Medical Center Drive, Lebanon, NH 03756, USA
Hum Genet 129:101-10. 2011.... - Single nucleotide polymorphisms in ANKK1 and the dopamine D2 receptor gene affect cognitive outcome shortly after traumatic brain injury: a replication and extension studyThomas W McAllister
Department of Psychiatry, Section of Neuropsychiatry, Dartmouth Hitchcock Medical Center, Lebanon, NH 03756, USA
Brain Inj 22:705-14. 2008.... - Genetic population structure analysis in New Hampshire reveals Eastern European ancestryChantel D Sloan
Computational Genetics Laboratory, Department of Genetics, Dartmouth Medical School, Lebanon, New Hampshire, United States of America
PLoS ONE 4:e6928. 2009..To our knowledge, this is the first time such an investigation has uncovered a strong link between genetic structure and ancestry in what would otherwise be considered a homogenous US population... - Detecting, characterizing, and interpreting nonlinear gene-gene interactions using multifactor dimensionality reductionJason H Moore
Institute for Quantitative Biomedical Sciences, Departments of Genetics and Community and Family Medicine, Dartmouth Medical School, Lebanon, New Hampshire, USA
Adv Genet 72:101-16. 2010..Third, visualization methods are needed to help interpret computational models and results. We provide here an overview of the multifactor dimensionality reduction (MDR) method that was developed for addressing each of these challenges... - Drinking-water arsenic exposure modulates gene expression in human lymphocytes from a U.S. populationAngeline S Andrew
Dartmouth Medical School Section of Biostatistics and Epidemiology, 7927 Rubin 860, One Medical Center Dr, Lebanon, NH 03756, USA
Environ Health Perspect 116:524-31. 2008.... - Genetic pathway-based hierarchical clustering analysis of older adults with cognitive complaints and amnestic mild cognitive impairment using clinical and neuroimaging phenotypesChantel D Sloan
Department of Genetics and Community and Family Medicine, Computational Genetics Laboratory, Dartmouth Medical School, Lebanon, New Hampshire, USA
Am J Med Genet B Neuropsychiatr Genet 153:1060-9. 2010..The results are consistent with polygenic influences on early neurodegenerative changes and demonstrate the effectiveness of hierarchical clustering in identifying genetic associations among multiple related phenotypic endpoints... - The influence of assortativity on the robustness of signal-integration logic in gene regulatory networksDov A Pechenick
Computational Genetics Laboratory, Dartmouth College, Hanover, NH 03755, USA
J Theor Biol 296:21-32. 2012.... - Systems genetics for drug target discoveryNadia M Penrod
Computational Genetics Laboratory Dartmouth Medical School, One Medical Center Drive, Lebanon, NH 03756, USA
Trends Pharmacol Sci 32:623-30. 2011.... - Shadows of complexity: what biological networks reveal about epistasis and pleiotropyAnna L Tyler
Computational Genetics Laboratory, Department of Genetics, Dartmouth Medical School, Lebanon, NH 03756, USA
Bioessays 31:220-7. 2009..Finally, graph theory offers an intuitive and powerful set of tools with which to study the network bases of these important genetic phenomena... - Genetic basis for adverse events after smallpox vaccinationDavid M Reif
Computational Genetics Laboratory, Dartmouth Medical School, Lebanon, New Hampshire, USA
J Infect Dis 198:16-22. 2008.... - Microarray analysis of cytoplasmic versus whole cell RNA reveals a considerable number of missed and false positive mRNAsHeidi W Trask
Norris Cotton Cancer Center, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire 03756, USA
RNA 15:1917-28. 2009.... - Multifactor dimensionality reduction analysis identifies specific nucleotide patterns promoting genetic polymorphismsEric Arehart
Computational Genetics Laboratory, Department of Genetics, Norris Cotton Cancer Center, Dartmouth Medical School, Lebanon, NH, USA
BioData Min 2:2. 2009.... - Exploiting graphics processing units for computational biology and bioinformaticsJoshua L Payne
Computational Genetics Laboratory, Department of Genetics, Dartmouth Medical School, Lebanon, NH 03756, USA
Interdiscip Sci 2:213-20. 2010..We conclude with a runtime analysis of the GPU and CPU implementations of the all-pairs distance calculation. We show our final GPU implementation to outperform the CPU implementation by a factor of 1700... - Concordance of multiple analytical approaches demonstrates a complex relationship between DNA repair gene SNPs, smoking and bladder cancer susceptibilityAngeline S Andrew
Department of Community and Family Medicine, Section of Biostatistics and Epidemiology, Dartmouth Medical School, Lebanon, NH 03756, USA
Carcinogenesis 27:1030-7. 2006..These results support the hypothesis that common polymorphisms in DNA repair genes modify bladder cancer risk and emphasize the need for a multifaceted statistical approach to identify gene-gene and gene-environment interactions... - Selective repression of retinoic acid target genes by RIP140 during induced tumor cell differentiation of pluripotent human embryonal carcinoma cellsKelly C Heim
Department of Pharmacology and Toxicology, Dartmouth Medical School, Hanover, USA
Mol Cancer 6:57. 2007..This implies that RIP140 represses key genes required for RA-mediated tumor cell differentiation. Identification of these genes would be of considerable interest... - Epistatic interactions in genetic regulation of t-PA and PAI-1 levels in a Ghanaian populationNadia M Penrod
Department of Genetics, Dartmouth Medical School, Lebanon, New Hampshire, United States of America
PLoS ONE 6:e16639. 2011..Therefore, it is necessary to consider the relationship between interacting polymorphisms of pathway specific genes that predict t-PA and PAI-1 levels... - Analysis of gene-gene interactionsDiane Gilbert-Diamond
Computational Genetics Laboratory, Departments of Genetics and Community and Family Medicine, Dartmouth Medical School, Lebanon, New Hampshire, USA
Curr Protoc Hum Genet . 2011..The focus of this unit is genetic association studies of discrete and quantitative traits because most of the methods for detecting gene-gene interactions have been developed specifically for these study designs... - Analysis of gene-gene interactionsJason H Moore
Computational Genetics Laboratory, Department of Genetics, Dartmouth Medical School, Lebanon, New Hampshire, USA
Curr Protoc Hum Genet . 2008..The focus of this unit is genetic association studies of discrete and quantitative traits because most of the methods for detecting gene-gene interactions have been developed specifically for these study designs... - Role for protein-protein interaction databases in human geneticsKristine A Pattin
Computational Genetics Laboratory and Department of Genetics, Dartmouth Medical School, Lebanon, NH, USA
Expert Rev Proteomics 6:647-59. 2009..In this review, we will discuss some of the fundamentals of protein interactions, the databases that are publicly available and how information from these databases can be used to facilitate genome-wide genetic studies... - Visual analysis of statistical results from microarray studies of human breast cancerDavid M Reif
Computational Genetics Laboratory, Norris Cotton Cancer Center, Department of Genetics, Dartmouth Medical School, One MedicalCenter Drive, Lebanon, NH 03756, USA
Oncol Rep 15:1043-7. 2006..Thus, we anticipate EVA will prove a useful addition to the repertoire of computational methods for microarray data analysis. The EVA software is freely available to academic users... - Layers of epistasis: genome-wide regulatory networks and network approaches to genome-wide association studiesRichard Cowper-Sal Lari
Department of Genetics, Norris Cotton Cancer Center, Dartmouth Medical School, Lebanon, NH, USA
Wiley Interdiscip Rev Syst Biol Med 3:513-26. 2011..This will give GWAS re-analysis efforts the most current and relevant substrates, and root them firmly on our knowledge of human disease... - Exploratory visual analysis of statistical results from microarray experiments comparing high and low grade gliomaDavid M Reif
Graduate Student, Computational Genetics Laboratory, Dartmouth Hitchcock Medical Center, Lebanon, NH 03756
Cancer Inform 5:19-24. 2007..EVA is available at no charge to academic users and can be found at http://www.epistasis.org... - Additive functions in boolean models of gene regulatory network modulesChristian Darabos
Computational Genetics Laboratory, Dartmouth Medical School, Lebanon, New Hampshire, United States of America
PLoS ONE 6:e25110. 2011..The update function confers additional realism to the model, while reducing the complexity and solution space, thus making it easier to investigate... - Characterization of microRNA expression levels and their biological correlates in human cancer cell linesArti Gaur
Norris Cotton Cancer Center, Dartmouth Medical School, Lebanon, New Hampshire 03755, USA
Cancer Res 67:2456-68. 2007..These findings call attention to the potential of microRNAs to provide etiologic insights as well as to serve as both diagnostic markers and therapeutic targets for many different tumor types... - Transcriptional profiling in coronary artery disease: indications for novel markers of coronary collateralizationThomas W Chittenden
Angiogenesis Research Center, Dartmouth Medical School, Hanover, NH 03755, USA
Circulation 114:1811-20. 2006..Thus, genetic factors may heavily influence coronary collateral vessel growth in CAD and affect prognosis and response to therapeutic interventions... - Exploiting the proteome to improve the genome-wide genetic analysis of epistasis in common human diseasesKristine A Pattin
Computational Genetics Laboratory, Norris Cotton Cancer Center, Dartmouth Medical School, Lebanon, NH, USA
Hum Genet 124:19-29. 2008..We explore some of the fundamentals of protein interactions and the databases that are publicly available... - Acceleration of cardiovascular disease by a dysfunctional prostacyclin receptor mutation: potential implications for cyclooxygenase-2 inhibitionEric Arehart
Department of Pharmacology and Toxicology, Dartmouth Hitchcock Medical Center, Hanover, NH 03755, USA
Circ Res 102:986-93. 2008..Combining both biochemical and clinical approaches, we conclude that diminished prostacyclin receptor signaling may contribute, in part, to the underlying adverse cardiovascular outcomes observed with cyclooxygenase-2 inhibition... - Ability of epistatic interactions of cytokine single-nucleotide polymorphisms to predict susceptibility to disease subsets in systemic sclerosis patientsLorenzo Beretta
Referral Center for Systemic Autoimmune Diseases, IRCCS Fondazione Policlinico Mangiagalli Regina Elena and University of Milan, Milan, Italy
Arthritis Rheum 59:974-83. 2008..Epistasis is difficult to model by traditional parametric approaches; therefore, nonparametric computational algorithms, such as multifactor dimensionality reduction (MDR), have been developed... - 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... - Genetic interactions model among Eotaxin gene polymorphisms in asthmaJune Hyuk Lee
Department of Internal Medicine, Genome Research Center for Allergy and Respiratory Diseases, Soonchunhyang University Bucheon Hospital, Gyeonggi Do, 420 021, South Korea
J Hum Genet 53:867-75. 2008..Although the models are limited to determining statistical interactions within a population, they may be useful for identifying groups at high risk of developing asthma... - 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... - Genetics, statistics and human disease: analytical retooling for complexityTricia A Thornton-Wells
Neuroscience Graduate Program, Vanderbilt Brain Institute, Vanderbilt University Medical Center, Nashville, TN 37240, USA
Trends Genet 20:640-7. 2004..Finally, we propose a comprehensive two-step approach to analysis that systemically addresses the different genetic factors that are likely to underlie complex diseases... - Ideal discrimination of discrete clinical endpoints using multilocus genotypesLance W Hahn
Center for Human Genetics Research, 519 Light Hall, Vanderbilt University, Nashville, TN 37232-0700, USA
In Silico Biol 4:183-94. 2004..This study provides a theoretical foundation for the continued development, evaluation, and application of the MDR as a data mining tool in the domain of statistical genetics and genetic epidemiology... - The interaction of four genes in the inflammation pathway significantly predicts prostate cancer riskJianfeng Xu
Center for Human Genomics, Wake Forest University School of Medicine, Medical Center Boulevard, Winston Salem, NC 27157, USA
Cancer Epidemiol Biomarkers Prev 14:2563-8. 2005.... - 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... - STUDENTJAMA. The challenges of whole-genome approaches to common diseasesJason H Moore
Vanderbilt University Medical School, Nashville, Tenn, USA
JAMA 291:1642-3. 2004 - Evidence for epistasis between SLC6A4 and ITGB3 in autism etiology and in the determination of platelet serotonin levelsAna M Coutinho
Instituto Gulbenkian de Ciencia, R Quinta Grande 6, Ap 14, 2781 901 Oeiras, Portugal
Hum Genet 121:243-56. 2007.... - 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... - Petri net modeling of high-order genetic systems using grammatical evolutionJason H Moore
Program in Human Genetics, Department of Molecular Physiology and Biophysics, Vanderbilt University Medical School, 519 Light Hall, Nashville, TN 37232 0700, USA
Biosystems 72:177-86. 2003..The results indicate that our model-building approach is capable of routinely identifying good, but not perfect, Petri net models. Ideas for improving the algorithm for this high-dimensional problem are presented... - Problems with genome-wide association studiesScott M Williams
Science 316:1840-2. 2007 - Detecting pathway-based gene-gene and gene-environment interactions in pancreatic cancerEric J Duell
International Agency for Research Cancer, 150 cours Albert Thomas, 69008 Lyon, France
Cancer Epidemiol Biomarkers Prev 17:1470-9. 2008.... - 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... - 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... - 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.... - A training-testing approach to the molecular classification of resected non-small cell lung cancerNoboru Yamagata
Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-6838, USA
Clin Cancer Res 9:4695-704. 2003.... - Symbolic discriminant analysis of microarray data in autoimmune diseaseJason H Moore
Program in Human Genetics, Vanderbilt University Medical School, Nashville, Tennessee 37232 0700, USA
Genet Epidemiol 23:57-69. 2002..In the present study, we demonstrate that SDA is capable of identifying combinations of gene expression variables that are able to classify and predict autoimmune diseases... - 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... - A high-density admixture map for disease gene discovery in african americansMichael W Smith
Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD, USA
Am J Hum Genet 74:1001-13. 2004..The map is especially appropriate for those diseases that differ in incidence between the parental African and European populations... - Proteomic patterns of tumour subsets in non-small-cell lung cancerKiyoshi Yanagisawa
Vanderbilt-Ingram Cancer Center, Nashville, Tennessee 37232-6838, USA
Lancet 362:433-9. 2003.... - Profiles of gene expression in human autoimmune diseaseThomas M Aune
Division of Rheumatology, Department of Medicine, Department of Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
Cell Biochem Biophys 40:81-96. 2004..These data argue that that there is a constant pattern of gene expression in autoimmunity that is independent of the specific autoimmune disease and clinical parameters associated with any individual autoimmune disease... - The use of animal models in the study of complex disease: all else is never equal or why do so many human studies fail to replicate animal findings?Scott M Williams
Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
Bioessays 26:170-9. 2004..This article contains supplementary material, which may be viewed at the BioEssays website at http://www.interscience.wiley.com/jpages/0265-9247/suppmat/index.html... - MnSOD polymorphism and breast cancer in a population-based case-control studyKathleen M Egan
Department of Medicine, Vanderbilt University Medical Center, Suite 6000 Medical Center East, Nashville, TN 37232 8300, USA
Cancer Lett 199:27-33. 2003..91-1.77) or two (RR: 1.18; 95% CI: 0.81-1.73) Ala alleles compared to those homozygous for the wild-type Val genotype. Results do not support any overall association of the Ala-9Val MnSOD polymorphism to the development of breast cancer... - The ubiquitous nature of epistasis in determining susceptibility to common human diseasesJason H Moore
Program in Human Genetics, Department of Molecular Physiology and Biophysics, Vanderbilt University Medical School, Nashville, TN 37232 0700, USA
Hum Hered 56:73-82. 2003..If this working hypothesis is true, it suggests that we need a research strategy for identifying common disease susceptibility genes that embraces, rather than ignores, the complexity of the genotype to phenotype relationship... - Reporting of model validation procedures in human studies of genetic interactionsChristopher S Coffey
Department of Biostatistics, University of Alabama at Birmingham, Birmingham, Alabama, USA
Nutrition 20:69-73. 2004 - Gene expression signatures for autoimmune disease in peripheral blood mononuclear cellsNancy J Olsen
Division of Rheumatology, T 3219 Medical Center North, Vanderbilt University, Nashville, Tennessee, USA
Arthritis Res Ther 6:120-8. 2004..Furthermore, the genes that are identified provide clues to possible pathogenetic mechanisms and are likely to be useful in developing tests to establish diagnostic categories and predict therapeutic responses... - Co-localization of differentially expressed genes and shared susceptibility loci in human autoimmunityThomas M Aune
Division of Rheumatology, Department of Medicine, Vanderbilt University Medical School, Nashville, Tennessee 37232, USA
Genet Epidemiol 27:162-72. 2004..To our knowledge, this is the first study showing concordance between gene expression and genetic linkage results in common complex multifactorial human diseases... - Analysis of gene-gene interactionsJason H Moore
Vanderbilt University Medical School, Nashville, Tennessee, USA
Curr Protoc Hum Genet . 2004..The focus of this unit is genetic association studies of discrete and quantitative traits since most of the methods for detecting gene-gene interactions have been developed specifically for these study designs... - Bases, bits and disease: a mathematical theory of human geneticsJason H Moore
Eur J Hum Genet 16:143-4. 2008 - Specific polymorphic variation in the mitochondrial genome and increased in-hospital mortality after severe traumaJeffrey A Canter
Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, Tennessee 37212, USA
Ann Surg 246:406-11; discussion 411-4. 2007..To determine whether specific genetic variations in the mtDNA that impact energy production and free-radical generation are potential new risk factors for in-hospital mortality after severe trauma... - The gender-specific role of polymorphisms from the fibrinolytic, renin-angiotensin, and bradykinin systems in determining plasma t-PA and PAI-1 levelsFolkert W Asselbergs
Department of Cardiology, University Medical Center Groningen, Groningen, The Netherlands
Thromb Haemost 96:471-7. 2006..In addition, the results support the idea that the biology of t-PA and PAI-1 is different between females and males... - Genomics and proteomics of lung disease: conference summaryJ Usha Raj
Division of Neonatology, Harbor-UCLA Medical Center, Geffen School of Medicine at University of California, and Los Angeles Biomedical Research Institute, Los Angeles, California, USA
Am J Physiol Lung Cell Mol Physiol 293:L45-51. 2007 - Application of HapMap data to the evaluation of 8 candidate genes for pediatric slow transit constipationMerce Garcia-Barcelo
Division of Paediatric Surgery, Department of Surgery, The University of Hong Kong, Hong Kong SAR, China
J Pediatr Surg 42:666-71. 2007..We conducted a pilot study to investigate whether genes encoding neurotransmitters (TAC1, TAC3, VIP, NOS1) and receptors (TACR1, TACR2, TACR3, KIT) could be responsible for STC... - Interleukin-1 gene complex single nucleotide polymorphisms in systemic sclerosis: a further step aheadLorenzo Beretta
Referral Center for Systemic Autoimmune Diseases, IRCCS Fondazione Policlinico Mangiagalli Regina Elena and University of Milan, Milan, Italy
Hum Immunol 69:187-92. 2008..Epistatic interactions among IL-1 gene complex SNPs and clinical or environmental factors are more important than the singe attributes in the development of severe ventilatory restriction in SSc patients... - 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... - Epistatic effects of polymorphisms in genes from the renin-angiotensin, bradykinin, and fibrinolytic systems on plasma t-PA and PAI-1 levelsFolkert W Asselbergs
Department of Cardiology, University Medical Center Groningen, Groningen, The Netherlands
Genomics 89:362-9. 2007..These results support the idea that the interplay between the renin-angiotensin, bradykinin, and fibrinolytic systems might play an important role in t-PA and PAI-1 biology... - 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... - Diabetic nephropathy is associated with gene expression levels of oxidative phosphorylation and related pathwaysChunmei Huang
Department of Pediatrics, University of Minnesota Medical School, Minneapolis, Minnesota, USA
Diabetes 55:1826-31. 2006..Whether these findings reflect inherent genetic cellular characteristics, "cell memory," or both requires further study... - 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... - Combinatorial pharmacogeneticsRussell A Wilke
Center for Human Genetics, Marshfield Clinic Research Foundation, Marshfield, Wisconsin, USA
Nat Rev Drug Discov 4:911-8. 2005..The high-dimensionality of the resulting analysis problem will often overwhelm traditional analysis methods. Novel analysis techniques, such as multifactor dimensionality reduction, offer viable options for evaluating such data... - Integrated analysis of genetic, genomic and proteomic dataDavid M Reif
Center for Human Genetics Research, Vanderbilt University Medical School, 519 Light Hall, Nashville, TN 37232 0700, USA
Expert Rev Proteomics 1:67-75. 2004..The idea that the integrated analysis of multiple data types will improve the identification of biomarkers of clinical endpoints, such as disease susceptibility, is presented as a working hypothesis... - New strategies for identifying gene-gene interactions in hypertensionJason H Moore
Department of Molecular Physiology and Biophysics, Vanderbilt University Medical School, Nashville, TN 37232 0700, USA
Ann Med 34:88-95. 2002..Here, we review the general problem of identifying gene-gene interactions and describe several traditional and several newer methods that are being used to assess complex genetic interactions in essential hypertension... - Confronting complexity in late-onset Alzheimer disease: application of two-stage analysis approach addressing heterogeneity and epistasisTricia A Thornton-Wells
Biobehavioral Intervention Training Program, Vanderbilt Kennedy Center for Research on Human Development, Vanderbilt University Institute for Imaging Science, Vanderbilt University, Nashville, Tennessee 37203, USA
Genet Epidemiol 32:187-203. 2008..Further studies are needed to replicate these statistical findings and to elucidate possible biological interaction mechanisms between LRRTM3 and these genes...
Research Grants
- Machine Learning Prediction of Cancer SusceptibilityJason Moore; Fiscal Year: 2009....
- Genetics Basis of Trauma RecoveryJason Moore; Fiscal Year: 2009..abstract_text> ..
- Machine Learning Prediction of Cancer SusceptibilityJason Moore; Fiscal Year: 2009....
- Bioinformatics Strategies: Biodefense Vaccine ResearchJason H Moore; Fiscal Year: 2010..All bioinformatics methods and tools will be provided in a timely manner for free as open-source software. ..
- Bioinformatics Strategies for Genome-Wide Association StudiesSCOTT MATTHEW WILLIAMS; Fiscal Year: 2010..Our working hypothesis is that we will obtain more validated and hence more real SNPs using the bioinformatics approach. ..
- Machine Learning Prediction of Cancer SusceptibilityJason Moore; Fiscal Year: 2007....
- Bioinformatics Strategies: Biodefense Vaccine ResearchJason Moore; Fiscal Year: 2007..abstract_text> ..
- GENETIC ARCHITECTURE OF PLASMA T-PA AND PAI-1Jason Moore; Fiscal Year: 2004..This collaborative proposal provides a robust mechanism for highly focused translational research in the molecular genetics and biology of the role of the fibrinolytic system in arterial and cerebral thrombosis. ..
- Parallel ComputerJason Moore; Fiscal Year: 2004..This resource will make it possible to carry out computationally intensive biomedical investigations otherwise not feasible thus significantly increasing the rate of scientific discovery in a variety of biomedical disciplines. ..
- Machine Learning Prediction of Cancer SusceptibilityJason H Moore; Fiscal Year: 2010..We anticipate the proposed machine learning methods will provide powerful new approaches for identifying genetic variations that are predictive of cancer susceptibility. ..