Jason H Moore

Summary

Affiliation: Dartmouth Medical School
Country: USA

Publications

  1. doi request reprint Influence networks based on coexpression improve drug target discovery for the development of novel cancer therapeutics
    Nadia M Penrod
    Department of Genetics, Geisel School of Medicine at Dartmouth College, HB7937 One Medical Center Dr, Lebanon, NH 03766, USA
    BMC Syst Biol 8:12. 2014
  2. pmc Multifactor dimensionality reduction reveals a three-locus epistatic interaction associated with susceptibility to pulmonary tuberculosis
    Ryan L Collins
    Institute for Quantitative Biomedical Sciences, Dartmouth College, Hanover NH 03755, USA
    BioData Min 6:4. 2013
  3. pmc GAMETES: a fast, direct algorithm for generating pure, strict, epistatic models with random architectures
    Ryan J Urbanowicz
    Department of Genetics, Institute for Quantitative Biomedical Sciences, Dartmouth Medical School, Lebanon, NH, USA
    BioData Min 5:16. 2012
  4. pmc Identification of SNPs associated with variola virus virulence
    Anne Gatewood Hoen
    Department of Community and Family Medicine, The Geisel School of Medicine at Dartmouth, Dartmouth College, One Medical Center Drive, Lebanon, NH 03756, USA
    BioData Min 6:3. 2013
  5. doi request reprint Genome-wide association studies for the identification of biomarkers in metabolic diseases
    Kristine A Pattin
    Dartmouth Medical School, Departments of Genetics, 706 Rubin Building, HB 7937, One Medical Center Drive, Lebanon, NH 03756, USA 1 603 653 9939 1 603 653 9900
    Expert Opin Med Diagn 4:39-51. 2010
  6. pmc Predicting the difficulty of pure, strict, epistatic models: metrics for simulated model selection
    Ryan J Urbanowicz
    Department of Genetics, Institute for Quantitative Biomedical Sciences, Dartmouth Medical School, Lebanon, NH, USA
    BioData Min 5:15. 2012
  7. pmc Gene ontology analysis of pairwise genetic associations in two genome-wide studies of sporadic ALS
    Nora Chung Kim
    Institute for Quantitative Biomedical Sciences, Department of Genetics, Dartmouth Medical School, One Medical Center Dr, Lebanon, NH 03756, USA
    BioData Min 5:9. 2012
  8. pmc A role for CETP TaqIB polymorphism in determining susceptibility to atrial fibrillation: a nested case control study
    Folkert W Asselbergs
    Department of Cardiology, University Medical Center Groningen, Groningen, The Netherlands
    BMC Med Genet 7:39. 2006
  9. pmc A gene expression fingerprint of C. elegans embryonic motor neurons
    Rebecca M Fox
    Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232 8240, USA
    BMC Genomics 6:42. 2005
  10. pmc Dissecting trait heterogeneity: a comparison of three clustering methods applied to genotypic data
    Tricia A Thornton-Wells
    Neuroscience Graduate Program, Vanderbilt Brain Institute, Vanderbilt University Medical Center, Nashville, TN, USA
    BMC Bioinformatics 7:204. 2006

Research Grants

  1. Machine Learning Prediction of Cancer Susceptibility
    Jason Moore; Fiscal Year: 2009
  2. Genetics Basis of Trauma Recovery
    Jason Moore; Fiscal Year: 2009
  3. Machine Learning Prediction of Cancer Susceptibility
    Jason Moore; Fiscal Year: 2009
  4. Bioinformatics Strategies: Biodefense Vaccine Research
    Jason H Moore; Fiscal Year: 2010
  5. Bioinformatics Strategies for Genome-Wide Association Studies
    SCOTT MATTHEW WILLIAMS; Fiscal Year: 2010
  6. Machine Learning Prediction of Cancer Susceptibility
    Jason Moore; Fiscal Year: 2007
  7. Bioinformatics Strategies: Biodefense Vaccine Research
    Jason Moore; Fiscal Year: 2007
  8. GENETIC ARCHITECTURE OF PLASMA T-PA AND PAI-1
    Jason Moore; Fiscal Year: 2004
  9. Parallel Computer
    Jason Moore; Fiscal Year: 2004
  10. Machine Learning Prediction of Cancer Susceptibility
    Jason H Moore; Fiscal Year: 2010

Detail Information

Publications123 found, 100 shown here

  1. doi request reprint Influence networks based on coexpression improve drug target discovery for the development of novel cancer therapeutics
    Nadia M Penrod
    Department of Genetics, Geisel School of Medicine at Dartmouth College, HB7937 One Medical Center Dr, Lebanon, NH 03766, USA
    BMC Syst Biol 8:12. 2014
    ..Here, we introduce influence networks and demonstrate how they can be used to generate influence scores as a network-based metric to rank genes as potential drug targets...
  2. pmc Multifactor dimensionality reduction reveals a three-locus epistatic interaction associated with susceptibility to pulmonary tuberculosis
    Ryan L Collins
    Institute for Quantitative Biomedical Sciences, Dartmouth College, Hanover NH 03755, USA
    BioData Min 6:4. 2013
    ..The goal of the present study was to apply MDR to mining high-order epistatic interactions in a population-based genetic study of tuberculosis (TB)...
  3. pmc GAMETES: a fast, direct algorithm for generating pure, strict, epistatic models with random architectures
    Ryan J Urbanowicz
    Department of Genetics, Institute for Quantitative Biomedical Sciences, Dartmouth Medical School, Lebanon, NH, USA
    BioData Min 5:16. 2012
    ..This makes them an attractive gold standard for simulation studies considering complex multi-locus effects...
  4. pmc Identification of SNPs associated with variola virus virulence
    Anne Gatewood Hoen
    Department of Community and Family Medicine, The Geisel School of Medicine at Dartmouth, Dartmouth College, One Medical Center Drive, Lebanon, NH 03756, USA
    BioData Min 6:3. 2013
    ..We aimed to identify genome-wide single nucleotide polymorphisms associated with CFR. We evaluated unadjusted and outbreak geographic location-adjusted models of single SNPs and two- and three-way interactions between SNPs...
  5. doi request reprint Genome-wide association studies for the identification of biomarkers in metabolic diseases
    Kristine A Pattin
    Dartmouth Medical School, Departments of Genetics, 706 Rubin Building, HB 7937, One Medical Center Drive, Lebanon, NH 03756, USA 1 603 653 9939 1 603 653 9900
    Expert Opin Med Diagn 4:39-51. 2010
    ....
  6. pmc Predicting the difficulty of pure, strict, epistatic models: metrics for simulated model selection
    Ryan J Urbanowicz
    Department of Genetics, Institute for Quantitative Biomedical Sciences, Dartmouth Medical School, Lebanon, NH, USA
    BioData Min 5:15. 2012
    ..abstract:..
  7. pmc Gene ontology analysis of pairwise genetic associations in two genome-wide studies of sporadic ALS
    Nora Chung Kim
    Institute for Quantitative Biomedical Sciences, Department of Genetics, Dartmouth Medical School, One Medical Center Dr, Lebanon, NH 03756, USA
    BioData Min 5:9. 2012
    ..abstract:..
  8. pmc A role for CETP TaqIB polymorphism in determining susceptibility to atrial fibrillation: a nested case control study
    Folkert 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...
  9. pmc A gene expression fingerprint of C. elegans embryonic motor neurons
    Rebecca 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...
  10. pmc Dissecting trait heterogeneity: a comparison of three clustering methods applied to genotypic data
    Tricia 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...
  11. ncbi request reprint Connecting the dots between genes, biochemistry, and disease susceptibility: systems biology modeling in human genetics
    Jason 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...
  12. ncbi request reprint Computational analysis of gene-gene interactions using multifactor dimensionality reduction
    Jason 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...
  13. pmc Epistasis and its implications for personal genetics
    Jason 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...
  14. ncbi request reprint Traversing the conceptual divide between biological and statistical epistasis: systems biology and a more modern synthesis
    Jason 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...
  15. pmc Bioinformatics challenges for genome-wide association studies
    Jason 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...
  16. pmc Evolving hard problems: Generating human genetics datasets with a complex etiology
    Daniel S Himmelstein
    Department of Genetics, Dartmouth Medical School, One Medical Center Drive, Lebanon, NH 03756, USA
    BioData Min 4:21. 2011
    ..abstract:..
  17. ncbi request reprint Bioinformatics
    Jason 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...
  18. ncbi request reprint A flexible computational framework for detecting, characterizing, and interpreting statistical patterns of epistasis in genetic studies of human disease susceptibility
    Jason 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...
  19. pmc Accelerating epistasis analysis in human genetics with consumer graphics hardware
    Nicholas 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...
  20. pmc A computationally efficient hypothesis testing method for epistasis analysis using multifactor dimensionality reduction
    Kristine 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...
  21. pmc Examination of polymorphic glutathione S-transferase (GST) genes, tobacco smoking and prostate cancer risk among men of African descent: a case-control study
    Nicole 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...
  22. pmc Polymorphisms in the brain-derived neurotrophic factor gene influence memory and processing speed one month after brain injury
    Thomas W McAllister
    Section of Neuropsychiatry, Department of Psychiatry, Dartmouth Medical School, Lebanon, New Hampshire 05756, USA
    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...
  23. pmc Bladder cancer SNP panel predicts susceptibility and survival
    Angeline 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...
  24. ncbi request reprint Symbolic modeling of epistasis
    Jason 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...
  25. pmc An information-gain approach to detecting three-way epistatic interactions in genetic association studies
    Ting Hu
    Computational Genetics Laboratory, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
    J Am Med Inform Assoc 20:630-6. 2013
    ..Quantifying epistasis of orders higher than two is very challenging due to both the computational complexity of enumerating all possible combinations in genome-wide data and the lack of efficient and effective methodologies...
  26. pmc No association between variant DNA repair genes and prostate cancer risk among men of African descent
    Nicole A Lavender
    Department of Pharmacology and Toxicology, School of Medicine, University of Louisville, Louisville, Kentucky 40202, USA
    Prostate 70:113-9. 2010
    ..However, studies identifying high-risk cancer-related genes use single gene approaches that lack the statistical rigor to model higher order interactions...
  27. pmc Breast cancer risk-associated SNPs modulate the affinity of chromatin for FOXA1 and alter gene expression
    Richard Cowper-Sal Lari
    Department of Genetics, Norris Cotton Cancer Center, Dartmouth Medical School, Lebanon, New Hampshire, USA
    Nat Genet 44:1191-8. 2012
    ..1 risk locus...
  28. pmc A simple and computationally efficient sampling approach to covariate adjustment for multifactor dimensionality reduction analysis of epistasis
    Jiang 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...
  29. pmc DNA repair polymorphisms modify bladder cancer risk: a multi-factor analytic strategy
    Angeline 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...
  30. pmc Failure to replicate a genetic association may provide important clues about genetic architecture
    Casey 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...
  31. pmc Multifactor dimensionality reduction for graphics processing units enables genome-wide testing of epistasis in sporadic ALS
    Casey 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...
  32. pmc COMT Val158Met Genotype and Individual Differences in Executive Function in Healthy Adults
    Heather 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...
  33. pmc A robust multifactor dimensionality reduction method for detecting gene-gene interactions with application to the genetic analysis of bladder cancer susceptibility
    Jiang 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...
  34. pmc Interaction among apoptosis-associated sequence variants and joint effects on aggressive prostate cancer
    Nicole A Lavender
    Department of Pharmacology and Toxicology, School of Medicine, University of Louisville UofL, Louisville, KY, USA
    BMC Med Genomics 5:11. 2012
    ..This statistical conundrum stems from the prohibitive amount of data needed to account for multiple hypothesis testing...
  35. pmc SLC39A2 and FSIP1 polymorphisms as potential modifiers of arsenic-related bladder cancer
    Margaret 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...
  36. pmc A novel survival multifactor dimensionality reduction method for detecting gene-gene interactions with application to bladder cancer prognosis
    Jiang 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
    ....
  37. pmc Single nucleotide polymorphisms in ANKK1 and the dopamine D2 receptor gene affect cognitive outcome shortly after traumatic brain injury: a replication and extension study
    Thomas W McAllister
    Department of Psychiatry, Section of Neuropsychiatry, Dartmouth Hitchcock Medical Center, Lebanon, NH 03756, USA
    Brain Inj 22:705-14. 2008
    ....
  38. pmc Ecogeographic genetic epidemiology
    Chantel D Sloan
    Computational Genetics Laboratory, Department of Genetics, Dartmouth Medical School, Lebanon, New Hampshire, USA
    Genet Epidemiol 33:281-9. 2009
    ....
  39. doi request reprint Epistasis, complexity, and multifactor dimensionality reduction
    Qinxin Pan
    Computational Genetics Laboratory, Dartmouth Medical School, Dartmouth College, Lebanon, NH, USA
    Methods Mol Biol 1019:465-77. 2013
    ..We focus on multifactor dimensionality reduction (MDR) as an approach for modeling one of these complexities: epistasis or gene-gene interaction...
  40. pmc Key genes for modulating information flow play a temporal role as breast tumor coexpression networks are dynamically rewired by letrozole
    Nadia M Penrod
    Department of Pharmacology and Toxicology, Geisel School of Medicine at Dartmouth College, HB7937 One Medical Center Dr, Lebanon, NH 03766, USA
    BMC Med Genomics 6:S2. 2013
    ..To understand how breast tumors adapt to the presence of the drug letrozole, at the molecular level, it is necessary to consider how the expression levels of genes in these networks change relative to one another...
  41. pmc Role of genetic heterogeneity and epistasis in bladder cancer susceptibility and outcome: a learning classifier system approach
    Ryan John Urbanowicz
    Department of Genetics, Geisel School of Medicine, Dartmouth College, Lebanon, New Hampshire 03756, USA
    J Am Med Inform Assoc 20:603-12. 2013
    ..In particular, strategies that provide multifactor interactions or heterogeneous patterns of association can offer new insights into association studies for which traditional analytic tools have had limited success...
  42. pmc HSD3B and gene-gene interactions in a pathway-based analysis of genetic susceptibility to bladder cancer
    Angeline S Andrew
    Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States of America
    PLoS ONE 7:e51301. 2012
    ..This biologic process-based analysis suggests candidate susceptibility markers and supports the theory that disrupted hormone regulation plays a role in bladder carcinogenesis...
  43. doi request reprint Detecting, characterizing, and interpreting nonlinear gene-gene interactions using multifactor dimensionality reduction
    Jason 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...
  44. pmc Genetic population structure analysis in New Hampshire reveals Eastern European ancestry
    Chantel 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...
  45. pmc Integrative functional genomics identifies an enhancer looping to the SOX9 gene disrupted by the 17q24.3 prostate cancer risk locus
    Xiaoyang Zhang
    Department of Genetics and Institute for Quantitative Biomedical Sciences, Norris Cotton Cancer Center, Dartmouth Medical School, Lebanon, New Hampshire 03756, USA
    Genome Res 22:1437-46. 2012
    ..This further supports the notion that an integrative genomics approach can identify the functional biology disrupted by genetic risk variants...
  46. pmc ViSEN: methodology and software for visualization of statistical epistasis networks
    Ting Hu
    Institute for Quantitative Biomedical Sciences, Dartmouth College, New Hampshire, USA
    Genet Epidemiol 37:283-5. 2013
    ..ViSEN is implemented in Java and freely available at https://sourceforge.net/projects/visen/...
  47. pmc Characterizing genetic interactions in human disease association studies using statistical epistasis networks
    Ting Hu
    Department of Genetics, Dartmouth Medical School, Dartmouth College, Lebanon, NH, USA
    BMC Bioinformatics 12:364. 2011
    ....
  48. pmc Cancer heterogeneity: origins and implications for genetic association studies
    Davnah Urbach
    Institute for Quantitative Biomedical Sciences, The Geisel School of Medicine, Dartmouth College, One Medical Center Drive, Lebanon, NH 03756, USA
    Trends Genet 28:538-43. 2012
    ....
  49. pmc SMAD4-dependent polysome RNA recruitment in human pancreatic cancer cells
    Jessica A Thornley
    Norris Cotton Cancer Center, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire 03756, USA
    Mol Carcinog 51:771-82. 2012
    ....
  50. pmc Genetic pathway-based hierarchical clustering analysis of older adults with cognitive complaints and amnestic mild cognitive impairment using clinical and neuroimaging phenotypes
    Chantel 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...
  51. pmc Drinking-water arsenic exposure modulates gene expression in human lymphocytes from a U.S. population
    Angeline 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
    ....
  52. doi request reprint A system-level pathway-phenotype association analysis using synthetic feature random forest
    Qinxin Pan
    Department of Genetics, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, United States of America
    Genet Epidemiol 38:209-19. 2014
    ..The bladder cancer associated pathways we found are both consistent with existing biological knowledge and reveal novel and plausible hypotheses for future biological validations. ..
  53. doi request reprint Interaction among variant vascular endothelial growth factor (VEGF) and its receptor in relation to prostate cancer risk
    Tiva T VanCleave
    Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky, USA
    Prostate 70:341-52. 2010
    ..This study evaluates the interplay among three highly variant genes (i.e., IL-10, TGFbetaR-1, VEGF), their receptors and their influence on PCa within a case-control study consisting of an under-served population...
  54. pmc The influence of assortativity on the robustness of signal-integration logic in gene regulatory networks
    Dov A Pechenick
    Computational Genetics Laboratory, Dartmouth College, Hanover, NH 03755, USA
    J Theor Biol 296:21-32. 2012
    ....
  55. pmc Systems genetics for drug target discovery
    Nadia M Penrod
    Computational Genetics Laboratory Dartmouth Medical School, One Medical Center Drive, Lebanon, NH 03756, USA
    Trends Pharmacol Sci 32:623-30. 2011
    ....
  56. pmc Shadows of complexity: what biological networks reveal about epistasis and pleiotropy
    Anna 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...
  57. pmc Genetic basis for adverse events after smallpox vaccination
    David M Reif
    Computational Genetics Laboratory, Dartmouth Medical School, Lebanon, New Hampshire, USA
    J Infect Dis 198:16-22. 2008
    ....
  58. pmc Microarray analysis of cytoplasmic versus whole cell RNA reveals a considerable number of missed and false positive mRNAs
    Heidi W Trask
    Norris Cotton Cancer Center, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire 03756, USA
    RNA 15:1917-28. 2009
    ....
  59. pmc Multifactor dimensionality reduction analysis identifies specific nucleotide patterns promoting genetic polymorphisms
    Eric Arehart
    Computational Genetics Laboratory, Department of Genetics, Norris Cotton Cancer Center, Dartmouth Medical School, Lebanon, NH, USA
    BioData Min 2:2. 2009
    ....
  60. pmc Distinct patterns of DNA methylation in conventional adenomas involving the right and left colon
    Devin C Koestler
    Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth College, Lebanon, NH, USA
    Mod Pathol 27:145-55. 2014
    ..1, P=0.004) exhibited a methylation profile similar to right-colon adenomas. In summary, our results indicate distinct patterns of DNA methylation, independent of CIMP genes, in adenomas of the right and left colon. ..
  61. pmc The influence of assortativity on the robustness and evolvability of gene regulatory networks upon gene birth
    Dov A Pechenick
    Computational Genetics Laboratory, Dartmouth College, Hanover, NH, USA
    J Theor Biol 330:26-36. 2013
    ..By providing a mechanistic explanation for these observations, this work extends our understanding of how the assortativity of a GRN influences its robustness and evolvability upon gene birth...
  62. pmc Obesity is mediated by differential aryl hydrocarbon receptor signaling in mice fed a Western diet
    Joanna S Kerley-Hamilton
    Dartmouth Hitchcock Medical Center, Lebanon, Norris Cotton Cancer Center, Lebanon, New Hampshire, USA
    Environ Health Perspect 120:1252-9. 2012
    ..The AHR is a nuclear receptor/transcription factor that is best known for responding to environmental toxicant exposures to induce a battery of xenobiotic-metabolizing genes...
  63. pmc Exploiting graphics processing units for computational biology and bioinformatics
    Joshua 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...
  64. doi request reprint Analysis of gene-gene interactions
    Jason 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...
  65. doi request reprint Analysis of gene-gene interactions
    Diane 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...
  66. pmc Role for protein-protein interaction databases in human genetics
    Kristine 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...
  67. pmc Epistatic interactions in genetic regulation of t-PA and PAI-1 levels in a Ghanaian population
    Nadia 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...
  68. pmc Selective repression of retinoic acid target genes by RIP140 during induced tumor cell differentiation of pluripotent human embryonal carcinoma cells
    Kelly 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...
  69. pmc Exploiting the proteome to improve the genome-wide genetic analysis of epistasis in common human diseases
    Kristine 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...
  70. pmc Layers of epistasis: genome-wide regulatory networks and network approaches to genome-wide association studies
    Richard 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...
  71. pmc Exploratory visual analysis of statistical results from microarray experiments comparing high and low grade glioma
    David 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...
  72. ncbi request reprint Visual analysis of statistical results from microarray studies of human breast cancer
    David 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...
  73. doi request reprint Effect of genetic variants, especially CYP2C9 and VKORC1, on the pharmacology of warfarin
    Erik Fung
    Section of Cardiology, Heart and Vascular Center, Lebanon, New Hampshire 03756, USA
    Semin Thromb Hemost 38:893-904. 2012
    ..Additional genome-wide association studies may help us to improve and refine dosing algorithms and potentially identify novel biological pathways...
  74. ncbi request reprint Concordance of multiple analytical approaches demonstrates a complex relationship between DNA repair gene SNPs, smoking and bladder cancer susceptibility
    Angeline 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...
  75. pmc Additive functions in boolean models of gene regulatory network modules
    Christian 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...
  76. ncbi request reprint Transcriptional profiling in coronary artery disease: indications for novel markers of coronary collateralization
    Thomas W Chittenden
    Angiogenesis Research Center, Dartmouth Medical School, Hanover, NH 03755, USA
    Circulation 114:1811-20. 2006
    ..The present study was undertaken to determine transcriptional profiles of circulating monocytes in CAD patients with different extents of collateral growth...
  77. ncbi request reprint Characterization of microRNA expression levels and their biological correlates in human cancer cell lines
    Arti 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...
  78. pmc Acceleration of cardiovascular disease by a dysfunctional prostacyclin receptor mutation: potential implications for cyclooxygenase-2 inhibition
    Eric 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...
  79. ncbi request reprint Multilocus analysis of hypertension: a hierarchical approach
    Scott 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...
  80. ncbi request reprint The interaction of four genes in the inflammation pathway significantly predicts prostate cancer risk
    Jianfeng 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
    ....
  81. ncbi request reprint Single-nucleotide polymorphisms for diagnosis of salt-sensitive hypertension
    Hironobu Sanada
    Third Department of Internal Medicine, Fukushima Medical University, School of Medicine, Fukushima City, Japan
    Clin Chem 52:352-60. 2006
    ..Salt-sensitive (SS) hypertension affects >30 million Americans and is often associated with low plasma renin activity. We tested the diagnostic validity of several candidate genes for SS and low-renin hypertension...
  82. ncbi request reprint Petri net modeling of high-order genetic systems using grammatical evolution
    Jason 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...
  83. ncbi request reprint Evidence for epistasis between SLC6A4 and ITGB3 in autism etiology and in the determination of platelet serotonin levels
    Ana M Coutinho
    Instituto Gulbenkian de Ciencia, R Quinta Grande 6, Ap 14, 2781 901 Oeiras, Portugal
    Hum Genet 121:243-56. 2007
    ....
  84. ncbi request reprint STUDENTJAMA. The challenges of whole-genome approaches to common diseases
    Jason H Moore
    Vanderbilt University Medical School, Nashville, Tenn, USA
    JAMA 291:1642-3. 2004
  85. ncbi request reprint A balanced accuracy function for epistasis modeling in imbalanced datasets using multifactor dimensionality reduction
    Digna 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...
  86. ncbi request reprint Genetics, statistics and human disease: analytical retooling for complexity
    Tricia 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...
  87. ncbi request reprint Problems with genome-wide association studies
    Scott M Williams
    Science 316:1840-2. 2007
  88. ncbi request reprint Ideal discrimination of discrete clinical endpoints using multilocus genotypes
    Lance 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...
  89. doi request reprint Genetic interactions model among Eotaxin gene polymorphisms in asthma
    June 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...
  90. doi request reprint Ability of epistatic interactions of cytokine single-nucleotide polymorphisms to predict susceptibility to disease subsets in systemic sclerosis patients
    Lorenzo 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...
  91. doi request reprint Detecting pathway-based gene-gene and gene-environment interactions in pancreatic cancer
    Eric J Duell
    International Agency for Research Cancer, 150 cours Albert Thomas, 69008 Lyon, France
    Cancer Epidemiol Biomarkers Prev 17:1470-9. 2008
    ....
  92. ncbi request reprint Renin-angiotensin system gene polymorphisms and atrial fibrillation
    Chia 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...
  93. ncbi request reprint Power of multifactor dimensionality reduction for detecting gene-gene interactions in the presence of genotyping error, missing data, phenocopy, and genetic heterogeneity
    Marylyn 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...
  94. ncbi request reprint Multifactor dimensionality reduction software for detecting gene-gene and gene-environment interactions
    Lance 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
    ..In this paper, we describe the MDR approach and an MDR software package...
  95. pmc Optimization of neural network architecture using genetic programming improves detection and modeling of gene-gene interactions in studies of human diseases
    Marylyn 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
    ....
  96. pmc A high-density admixture map for disease gene discovery in african americans
    Michael 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...
  97. pmc An application of conditional logistic regression and multifactor dimensionality reduction for detecting gene-gene interactions on risk of myocardial infarction: the importance of model validation
    Christopher 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...
  98. ncbi request reprint Profiles of gene expression in human autoimmune disease
    Thomas 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...
  99. ncbi request reprint 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...
  100. ncbi request reprint The ubiquitous nature of epistasis in determining susceptibility to common human diseases
    Jason 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...
  101. ncbi request reprint A training-testing approach to the molecular classification of resected non-small cell lung cancer
    Noboru Yamagata
    Vanderbilt Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37232 6838, USA
    Clin Cancer Res 9:4695-704. 2003
    ....

Research Grants27

  1. Machine Learning Prediction of Cancer Susceptibility
    Jason Moore; Fiscal Year: 2009
    ....
  2. Genetics Basis of Trauma Recovery
    Jason Moore; Fiscal Year: 2009
    ..abstract_text> ..
  3. Machine Learning Prediction of Cancer Susceptibility
    Jason Moore; Fiscal Year: 2009
    ....
  4. Bioinformatics Strategies: Biodefense Vaccine Research
    Jason H Moore; Fiscal Year: 2010
    ..All bioinformatics methods and tools will be provided in a timely manner for free as open-source software. ..
  5. Bioinformatics Strategies for Genome-Wide Association Studies
    SCOTT MATTHEW WILLIAMS; Fiscal Year: 2010
    ..Our working hypothesis is that we will obtain more validated and hence more real SNPs using the bioinformatics approach. ..
  6. Machine Learning Prediction of Cancer Susceptibility
    Jason Moore; Fiscal Year: 2007
    ....
  7. Bioinformatics Strategies: Biodefense Vaccine Research
    Jason Moore; Fiscal Year: 2007
    ..abstract_text> ..
  8. GENETIC ARCHITECTURE OF PLASMA T-PA AND PAI-1
    Jason 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. ..
  9. Parallel Computer
    Jason 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. ..
  10. Machine Learning Prediction of Cancer Susceptibility
    Jason 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. ..