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Scott M. Dudek - Publications

Affiliations: 
Center for Human Genetics Research, Departments of Molecular Physiology & Biophysics and Biomedical Informatics Vanderbilt University, Nashville, TN 
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42 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Singhal P, Veturi Y, Dudek SM, Lucas A, Frase A, van Steen K, Schrodi SJ, Fasel D, Weng C, Pendergrass R, Schaid DJ, Kullo IJ, Dikilitas O, Sleiman PMA, Hakonarson H, et al. Evidence of epistasis in regions of long-range linkage disequilibrium across five complex diseases in the UK Biobank and eMERGE datasets. American Journal of Human Genetics. 110: 575-591. PMID 37028392 DOI: 10.1016/j.ajhg.2023.03.007  0.436
2019 Pendergrass SA, Buyske S, Jeff JM, Frase A, Dudek S, Bradford Y, Ambite JL, Avery CL, Buzkova P, Deelman E, Fesinmeyer MD, Haiman C, Heiss G, Hindorff LA, Hsu CN, et al. A phenome-wide association study (PheWAS) in the Population Architecture using Genomics and Epidemiology (PAGE) study reveals potential pleiotropy in African Americans. Plos One. 14: e0226771. PMID 31891604 DOI: 10.1371/Journal.Pone.0226771  0.452
2018 Li R, Kim D, Wheeler HE, Dudek SM, Dolan ME, Ritchie MD. Integration of genetic and functional genomics data to uncover chemotherapeutic induced cytotoxicity. The Pharmacogenomics Journal. PMID 29795408 DOI: 10.1038/S41397-018-0024-6  0.444
2018 Verma SS, Lucas A, Zhang X, Veturi Y, Dudek S, Li B, Li R, Urbanowicz R, Moore JH, Kim D, Ritchie MD. Collective feature selection to identify crucial epistatic variants. Biodata Mining. 11: 5. PMID 29713383 DOI: 10.1186/S13040-018-0168-6  0.318
2018 Verma A, Bradford Y, Dudek S, Lucas AM, Verma SS, Pendergrass SA, Ritchie MD. A simulation study investigating power estimates in phenome-wide association studies. Bmc Bioinformatics. 19: 120. PMID 29618318 DOI: 10.1186/S12859-018-2135-0  0.374
2017 Hall MA, Wallace J, Lucas A, Kim D, Basile AO, Verma SS, McCarty CA, Brilliant MH, Peissig PL, Kitchner TE, Verma A, Pendergrass SA, Dudek SM, Moore JH, Ritchie MD. PLATO software provides analytic framework for investigating complexity beyond genome-wide association studies. Nature Communications. 8: 1167. PMID 29079728 DOI: 10.1038/S41467-017-00802-2  0.426
2017 Holzinger ER, Verma SS, Moore CB, Hall M, De R, Gilbert-Diamond D, Lanktree MB, Pankratz N, Amuzu A, Burt A, Dale C, Dudek S, Furlong CE, Gaunt TR, Kim DS, et al. Discovery and replication of SNP-SNP interactions for quantitative lipid traits in over 60,000 individuals. Biodata Mining. 10: 25. PMID 28770004 DOI: 10.1186/S13040-017-0145-5  0.316
2016 Kim D, Li R, Lucas A, Verma SS, Dudek SM, Ritchie MD. Using knowledge-driven genomic interactions for multi-omics data analysis: metadimensional models for predicting clinical outcomes in ovarian carcinoma. Journal of the American Medical Informatics Association : Jamia. PMID 28040685 DOI: 10.1093/Jamia/Ocw165  0.38
2016 Li R, Dudek SM, Kim D, Hall MA, Bradford Y, Peissig PL, Brilliant MH, Linneman JG, McCarty CA, Bao L, Ritchie MD. Identification of genetic interaction networks via an evolutionary algorithm evolved Bayesian network. Biodata Mining. 9: 18. PMID 27168765 DOI: 10.1186/S13040-016-0094-4  0.477
2016 Butkiewicz M, Cooke Bailey JN, Frase A, Dudek S, Yaspan BL, Ritchie MD, Pendergrass SA, Haines JL. Pathway analysis by randomization incorporating structure-PARIS: an update. Bioinformatics (Oxford, England). PMID 27153576 DOI: 10.1093/Bioinformatics/Btw130  0.344
2016 Hohman TJ, Bush WS, Jiang L, Brown-Gentry KD, Torstenson ES, Dudek SM, Mukherjee S, Naj A, Kunkle BW, Ritchie MD, Martin ER, Schellenberg GD, Mayeux R, Farrer LA, Pericak-Vance MA, et al. Discovery of gene-gene interactions across multiple independent data sets of late onset Alzheimer disease from the Alzheimer Disease Genetics Consortium. Neurobiology of Aging. 38: 141-50. PMID 26827652 DOI: 10.1016/J.Neurobiolaging.2015.10.031  0.465
2016 Verma A, Leader JB, Verma SS, Frase A, Wallace J, Dudek S, Lavage DR, VAN Hout CV, Dewey FE, Penn J, Lopez A, Overton JD, Carey DJ, Ledbetter DH, Kirchner HL, et al. INTEGRATING CLINICAL LABORATORY MEASURES AND ICD-9 CODE DIAGNOSES IN PHENOME-WIDE ASSOCIATION STUDIES. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 21: 168-79. PMID 26776183  0.311
2015 Kim D, Li R, Dudek SM, Ritchie MD. Predicting censored survival data based on the interactions between meta-dimensional omics data in breast cancer. Journal of Biomedical Informatics. PMID 26048077 DOI: 10.1016/J.Jbi.2015.05.019  0.36
2015 Pendergrass SA, Verma SS, Hall MA, Holzinger ER, Moore CB, Wallace JR, Dudek SM, Huggins W, Kitchner T, Waudby C, Berg R, Mccarty CA, Ritchie MD. Next-generation analysis of cataracts: determining knowledge driven gene-gene interactions using biofilter, and gene-environment interactions using the Phenx Toolkit*. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 495-505. PMID 25741542  0.385
2014 Kim D, Li R, Dudek SM, Frase AT, Pendergrass SA, Ritchie MD. Knowledge-driven genomic interactions: an application in ovarian cancer. Biodata Mining. 7: 20. PMID 25214892 DOI: 10.1186/1756-0381-7-20  0.371
2014 Holzinger ER, Dudek SM, Frase AT, Pendergrass SA, Ritchie MD. ATHENA: the analysis tool for heritable and environmental network associations. Bioinformatics (Oxford, England). 30: 698-705. PMID 24149050 DOI: 10.1093/Bioinformatics/Btt572  0.477
2013 Kim D, Li R, Dudek SM, Ritchie MD. ATHENA: Identifying interactions between different levels of genomic data associated with cancer clinical outcomes using grammatical evolution neural network. Biodata Mining. 6: 23. PMID 24359638 DOI: 10.1186/1756-0381-6-23  0.399
2013 Wolfe D, Dudek S, Ritchie MD, Pendergrass SA. Visualizing genomic information across chromosomes with PhenoGram. Biodata Mining. 6: 18. PMID 24131735 DOI: 10.1186/1756-0381-6-18  0.319
2013 Holzinger ER, Dudek SM, Frase AT, Krauss RM, Medina MW, Ritchie MD. ATHENA: a tool for meta-dimensional analysis applied to genotypes and gene expression data to predict HDL cholesterol levels. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 385-96. PMID 23424143  0.33
2013 Pendergrass SA, Verma SS, Holzinger ER, Moore CB, Wallace J, Dudek SM, Huggins W, Kitchner T, Waudby C, Berg R, McCarty CA, Ritchie MD. Next-generation analysis of cataracts: determining knowledge driven gene-gene interactions using Biofilter, and gene-environment interactions using the PhenX Toolkit. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 147-58. PMID 23424120  0.386
2013 Pendergrass SA, Brown-Gentry K, Dudek S, Frase A, Torstenson ES, Goodloe R, Ambite JL, Avery CL, Buyske S, Bůžková P, Deelman E, Fesinmeyer MD, Haiman CA, Heiss G, Hindorff LA, et al. Phenome-wide association study (PheWAS) for detection of pleiotropy within the Population Architecture using Genomics and Epidemiology (PAGE) Network. Plos Genetics. 9: e1003087. PMID 23382687 DOI: 10.1371/Journal.Pgen.1003087  0.434
2012 Pendergrass SA, Dudek SM, Crawford DC, Ritchie MD. Visually integrating and exploring high throughput Phenome-Wide Association Study (PheWAS) results using PheWAS-View. Biodata Mining. 5: 5. PMID 22682510 DOI: 10.1186/1756-0381-5-5  0.397
2012 Thornton-Wells T, Brown-Gentry K, Baker A, Torstenson E, Dudek S, Jiang L, Ritchie M, Martin E, Pericak-Vance M, Haines J. Biological knowledge-driven approach to gene-gene interaction analysis in the Alzheimer's Disease Genetics Consortium Alzheimers & Dementia. 8. DOI: 10.1016/J.Jalz.2012.05.1843  0.417
2011 Pendergrass SA, Brown-Gentry K, Dudek SM, Torstenson ES, Ambite JL, Avery CL, Buyske S, Cai C, Fesinmeyer MD, Haiman C, Heiss G, Hindorff LA, Hsu CN, Jackson RD, Kooperberg C, et al. The use of phenome-wide association studies (PheWAS) for exploration of novel genotype-phenotype relationships and pleiotropy discovery. Genetic Epidemiology. 35: 410-22. PMID 21594894 DOI: 10.1002/Gepi.20589  0.443
2011 Bush WS, McCauley JL, DeJager PL, Dudek SM, Hafler DA, Gibson RA, Matthews PM, Kappos L, Naegelin Y, Polman CH, Hauser SL, Oksenberg J, Haines JL, Ritchie MD. A knowledge-driven interaction analysis reveals potential neurodegenerative mechanism of multiple sclerosis susceptibility. Genes and Immunity. 12: 335-40. PMID 21346779 DOI: 10.1038/Gene.2011.3  0.429
2011 Cattaert T, Calle ML, Dudek SM, Mahachie John JM, Van Lishout F, Urrea V, Ritchie MD, Van Steen K. Model-based multifactor dimensionality reduction for detecting epistasis in case-control data in the presence of noise. Annals of Human Genetics. 75: 78-89. PMID 21158747 DOI: 10.1111/J.1469-1809.2010.00604.X  0.446
2011 Thornton-Wells T, Torstenson E, Dudek S, Ritchie M, Martin E, Pericak-Vance M, Haines J. Discovery and Replication of Gene-Gene Interactions in Multiple Independent Datasets from the Alzheimer Disease Genetics Consortium Alzheimers & Dementia. 7. DOI: 10.1016/J.Jalz.2011.05.548  0.432
2010 Pendergrass SA, Dudek SM, Crawford DC, Ritchie MD. Synthesis-View: visualization and interpretation of SNP association results for multi-cohort, multi-phenotype data and meta-analysis. Biodata Mining. 3: 10. PMID 21162740 DOI: 10.1186/1756-0381-3-10  0.415
2010 Holzinger ER, Buchanan CC, Dudek SM, Torstenson EC, Turner SD, Ritchie MD. Initialization Parameter Sweep in ATHENA: Optimizing Neural Networks for Detecting Gene-Gene Interactions in the Presence of Small Main Effects. Genetic and Evolutionary Computation Conference : [Proceedings] / Sponsored by Acm Sigevo. Genetic and Evolutionary Computation Conference. 12: 203-210. PMID 21152364 DOI: 10.1145/1830483.1830519  0.373
2010 Turner SD, Dudek SM, Ritchie MD. ATHENA: A knowledge-based hybrid backpropagation-grammatical evolution neural network algorithm for discovering epistasis among quantitative trait Loci. Biodata Mining. 3: 5. PMID 20875103 DOI: 10.1186/1756-0381-3-5  0.446
2010 Edwards TL, Turner SD, Torstenson ES, Dudek SM, Martin ER, Ritchie MD. A general framework for formal tests of interaction after exhaustive search methods with applications to MDR and MDR-PDT. Plos One. 5: e9363. PMID 20186329 DOI: 10.1371/Journal.Pone.0009363  0.322
2010 Bush WS, Dudek SM, Ritchie MD. Visualizing SNP statistics in the context of linkage disequilibrium using LD-Plus. Bioinformatics (Oxford, England). 26: 578-9. PMID 20130027 DOI: 10.1093/Bioinformatics/Btp678  0.377
2010 Edwards TL, Torstensen E, Dudek S, Martin ER, Ritchie MD. A cross-validation procedure for general pedigrees and matched odds ratio fitness metric implemented for the multifactor dimensionality reduction pedigree disequilibrium test. Genetic Epidemiology. 34: 194-9. PMID 19697353 DOI: 10.1002/Gepi.20447  0.361
2009 Bush WS, Dudek SM, Ritchie MD. Biofilter: a knowledge-integration system for the multi-locus analysis of genome-wide association studies. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 368-79. PMID 19209715  0.406
2009 Edwards TL, Lewis K, Velez DR, Dudek S, Ritchie MD. Exploring the performance of Multifactor Dimensionality Reduction in large scale SNP studies and in the presence of genetic heterogeneity among epistatic disease models. Human Heredity. 67: 183-92. PMID 19077437 DOI: 10.1159/000181157  0.406
2008 Bush WS, Edwards TL, Dudek SM, McKinney BA, Ritchie MD. Alternative contingency table measures improve the power and detection of multifactor dimensionality reduction. Bmc Bioinformatics. 9: 238. PMID 18485205 DOI: 10.1186/1471-2105-9-238  0.342
2008 Motsinger-Reif AA, Dudek SM, Hahn LW, Ritchie MD. Comparison of approaches for machine-learning optimization of neural networks for detecting gene-gene interactions in genetic epidemiology. Genetic Epidemiology. 32: 325-40. PMID 18265411 DOI: 10.1002/Gepi.20307  0.426
2006 Motsinger AA, Reif DM, Dudek SM, Ritchie MD. Understanding the Evolutionary Process of Grammatical Evolution Neural Networks for Feature Selection in Genetic Epidemiology. Proceedings of the ... Ieee Symposium On Computational Intelligence in Bioinformatics and Computational Biology. Ieee Symposium On Computational Intelligence in Bioinformatics and Computational Biology. 2006: 1-8. PMID 20634919 DOI: 10.1109/CIBCB.2006.330945  0.317
2006 Dudek SM, Motsinger AA, Velez DR, Williams SM, Ritchie MD. Data simulation software for whole-genome association and other studies in human genetics. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 499-510. PMID 17094264  0.39
2006 Bush WS, Dudek SM, Ritchie MD. Parallel multifactor dimensionality reduction: a tool for the large-scale analysis of gene-gene interactions. Bioinformatics (Oxford, England). 22: 2173-4. PMID 16809395 DOI: 10.1093/Bioinformatics/Btl347  0.356
2006 Motsinger AA, Dudek SM, Hahn LW, Ritchie MD. Comparison of neural network optimization approaches for studies of human genetics Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3907: 103-114. DOI: 10.1007/11732242_10  0.443
2005 Bush WS, Motsinger AA, Dudek SM, Ritchie MD. Can neural network constraints in GP provide power to detect genes associated with human disease Lecture Notes in Computer Science. 44-53. DOI: 10.1007/978-3-540-32003-6_5  0.424
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