Can Neural Network Constraints in GP Provide Power to Detect Genes Associated with Human Disease?. - William S. Bush; Alison A. Motsinger; Scott M. Dudek; Marylyn D. Ritchie (EvoWorkshops, 2005)

Exploratory Visual Analysis of Pharmacogenomic Results. - David M. Reif; Scott M. Dudek; Christian M. Shaffer; Janey Wang; Jason H. Moore (Pacific Symposium on Biocomputing, 2005)

Understanding the Evolutionary Process of Grammatical Evolution Neural Networks for Feature Selection in Genetic Epidemiology. - Alison A. Motsinger; David M. Reif; Scott M. Dudek; Marylyn D. Ritchie (CIBCB, 2006)

Comparison of Neural Network Optimization Approaches for Studies of Human Genetics. - Alison A. Motsinger; Scott M. Dudek; Lance W. Hahn; Marylyn D. Ritchie (EvoWorkshops, 2006)

Alternative cross-over strategies and selection techniques for grammatical evolution optimized neural networks. - Alison A. Motsinger; Lance W. Hahn; Scott M. Dudek; Kelli K. Ryckman; Marylyn D. Ritchie (GECCO, 2006)

Data Simulation Software for Whole-Genome Association and Other Studies in Human Genetics. - Scott M. Dudek; Alison A. Motsinger; Digna R. Velez; Scott M. Williams; Marylyn D. Ritchie (Pacific Symposium on Biocomputing, 2006)

Parallel multifactor dimensionality reduction: a tool for the large-scale analysis of gene-gene interactions. - William S. Bush; Scott M. Dudek; Marylyn D. Ritchie (Bioinform., 2006)

Generating Linkage Disequilibrium Patterns in Data Simulations Using genomeSIMLA. - Todd L. Edwards; William S. Bush; Stephen D. Turner; Scott M. Dudek; Eric Torstenson; Mike Schmidt; Eden Martin; Marylyn D. Ritchie (EvoBIO, 2008)

A balanced accuracy fitness function leads to robust analysis using grammatical evolution neural networks in the case of class imbalance. - Nicholas E. Hardison; Theresa J. Fanelli; Scott M. Dudek; David M. Reif; Marylyn D. Ritchie; Alison A. Motsinger-Reif (GECCO, 2008)

Alternative contingency table measures improve the power and detection of multifactor dimensionality reduction. - William S. Bush; Todd L. Edwards; Scott M. Dudek; Brett A. McKinney; Marylyn D. Ritchie (BMC Bioinform., 2008)

Biofilter: A Knowledge-Integration System for the Multi-Locus Analysis of Genome-Wide Association Studies. - William S. Bush; Scott M. Dudek; Marylyn D. Ritchie (Pacific Symposium on Biocomputing, 2009)

Grammatical Evolution of Neural Networks for Discovering Epistasis among Quantitative Trait Loci. - Stephen D. Turner; Scott M. Dudek; Marylyn D. Ritchie (EvoBIO, 2010)

Initialization parameter sweep in ATHENA: optimizing neural networks for detecting gene-gene interactions in the presence of small main effects. - Emily Rose Holzinger; Carrie C. Buchanan; Scott M. Dudek; Eric Torstenson; Stephen D. Turner; Marylyn D. Ritchie (GECCO, 2010)

Incorporating Domain Knowledge into Evolutionary Computing for Discovering Gene-Gene Interaction. - Stephen D. Turner; Scott M. Dudek; Marylyn D. Ritchie (PPSN (1), 2010)

Finding Unique Filter Sets in PLATO: A Precursor to Efficient Interaction Analysis in GWAS Data. - Benjamin J. Grady; Eric Torstenson; Scott M. Dudek; Justin Giles; David Sexton; Marylyn D. Ritchie (Pacific Symposium on Biocomputing, 2010)

Synthesis-View: visualization and interpretation of SNP association results for multi-cohort, multi-phenotype data and meta-analysis. - Sarah A. Pendergrass; Scott M. Dudek; Dana C. Crawford; Marylyn D. Ritchie (BioData Min., 2010)

ATHENA: A knowledge-based hybrid backpropagation-grammatical evolution neural network algorithm for discovering epistasis among quantitative trait Loci. - Stephen D. Turner; Scott M. Dudek; Marylyn D. Ritchie (BioData Min., 2010)

Visualizing SNP statistics in the context of linkage disequilibrium using LD-Plus. - William S. Bush; Scott M. Dudek; Marylyn D. Ritchie (Bioinform., 2010)

ATHENA Optimization: The Effect of Initial Parameter Settings across Different Genetic Models. - Emily Rose Holzinger; Scott M. Dudek; Eric Torstenson; Marylyn D. Ritchie (EvoBio, 2011)

Visual Integration of Results from a Large Dna Biobank (Biovu) Using Synthesis-View. - Sarah A. Pendergrass; Scott M. Dudek; Dan M. Roden; Dana C. Crawford; Marylyn D. Ritchie (Pacific Symposium on Biocomputing, 2011)

Comparison of Methods for Meta-dimensional Data Analysis Using in Silico and Biological Data Sets. - Emily Rose Holzinger; Scott M. Dudek; Alex T. Frase; Brooke L. Fridley; Prabhakar Chalise; Marylyn D. Ritchie (EvoBIO, 2012)

Visually integrating and exploring high throughput Phenome-Wide Association Study (PheWAS) results using PheWAS-View. - Sarah A. Pendergrass; Scott M. Dudek; Dana C. Crawford; Marylyn D. Ritchie (BioData Min., 2012)

Evaluation of Parameter Contribution to Neural Network Size and Fitness in ATHENA for Genetic Analysis. - Ruowang Li; Emily Rose Holzinger; Scott M. Dudek; Marylyn D. Ritchie (GPTP, 2013)

ATHENA: A Tool for Meta-Dimensional Analysis Applied to Genotypes and Gene Expression Data to Predict HDL Cholesterol Levels. - Emily Rose Holzinger; Scott M. Dudek; Alex T. Frase; Ronald M. Krauss; Marisa Wong Medina; Marylyn D. Ritchie (Pacific Symposium on Biocomputing, 2013)

Next-Generation Analysis of Cataracts: Determining Knowledge Driven Gene-Gene Interactions Using Biofilter, and Gene-Environment Interactions Using the PhenX Toolkit. - Sarah A. Pendergrass; Shefali S. Verma; Emily Rose Holzinger; Carrie Moore; John R. Wallace; Scott M. Dudek; Wayne Huggins; Terrie E. Kitchner; Carol Waudby; Richard L. Berg; Catherine A. McCarty; Marylyn D. Ritchie (Pacific Symposium on Biocomputing, 2013)

ATHENA: Identifying interactions between different levels of genomic data associated with cancer clinical outcomes using grammatical evolution neural network. - Dokyoon Kim; Ruowang Li; Scott M. Dudek; Marylyn D. Ritchie (BioData Min., 2013)

Visualizing genomic information across chromosomes with PhenoGram. - Daniel Wolfe; Scott M. Dudek; Marylyn D. Ritchie; Sarah A. Pendergrass (BioData Min., 2013)

An integrated analysis of genome-wide DNA methylation and genetic variants underlying etoposide-induced cytotoxicity in European and African populations. - Ruowang Li; Do Kyoon Kim; Scott M. Dudek; Marylyn D. Ritchie (EvoApplications, 2014)

Knowledge-driven genomic interactions: an application in ovarian cancer. - Do Kyoon Kim; Ruowang Li; Scott M. Dudek; Alex T. Frase; Sarah A. Pendergrass; Marylyn D. Ritchie (BioData Min., 2014)

ATHENA: the analysis tool for heritable and environmental network associations. - Emily Rose Holzinger; Scott M. Dudek; Alex T. Frase; Sarah A. Pendergrass; Marylyn D. Ritchie (Bioinform., 2014)

Binning Somatic Mutations Based on Biological Knowledge for Predicting Survival: An Application in Renal Cell Carcinoma. - Dokyoon Kim; Ruowang Li; Scott M. Dudek; John R. Wallace; Marylyn D. Ritchie (Pacific Symposium on Biocomputing, 2015)

Predicting censored survival data based on the interactions between meta-dimensional omics data in breast cancer. - Dokyoon Kim; Ruowang Li; Scott M. Dudek; Marylyn D. Ritchie (J. Biomed. Informatics, 2015)

Integrating Clinical Laboratory Measures and ICD-9 Code Diagnoses in Phenome-Wide Association Studies. - Anurag Verma; Joseph B. Leader; Shefali S. Verma; Alex T. Frase; John R. Wallace; Scott M. Dudek; Daniel R. Lavage; Cristopher V. Van Hout; Frederick E. Dewey; John Penn; Alexander E. Lopez; John D. Overton; et al. (PSB, 2016)

Identification of genetic interaction networks via an evolutionary algorithm evolved Bayesian network. - Ruowang Li; Scott M. Dudek; Dokyoon Kim; Molly A. Hall; Yukiko Bradford; Peggy L. Peissig; Murray H. Brilliant; James G. Linneman; Catherine A. McCarty; Le Bao; Marylyn D. Ritchie (BioData Min., 2016)

Pathway analysis by randomization incorporating structure - PARIS: an update. - Mariusz Butkiewicz; Jessica Cooke Bailey; Alex T. Frase; Scott M. Dudek; Brian L. Yaspan; Marylyn D. Ritchie; Sarah A. Pendergrass; Jonathan L. Haines (Bioinform., 2016)

Discovery and replication of SNP-SNP interactions for quantitative lipid traits in over 60,000 individuals. - Emily Rose Holzinger; Shefali S. Verma; Carrie Colleen Buchanan Moore; Molly A. Hall; Rishika De; Diane Gilbert-Diamond; Matthew B. Lanktree; Nathan Pankratz; Antoinette Amuzu; Amber Burt; Caroline Dale; Scott M. Dudek; et al. (BioData Min., 2017)

Using knowledge-driven genomic interactions for multi-omics data analysis: metadimensional models for predicting clinical outcomes in ovarian carcinoma. - Dokyoon Kim; Ruowang Li; Anastasia Lucas; Shefali S. Verma; Scott M. Dudek; Marylyn D. Ritchie (J. Am. Medical Informatics Assoc., 2017)

Collective feature selection to identify crucial epistatic variants. - Shefali S. Verma; Anastasia Lucas; Xinyuan Zhang 003; Yogasudha Veturi; Scott M. Dudek; Binglan Li; Ruowang Li; Ryan J. Urbanowicz; Jason H. Moore; Dokyoon Kim; Marylyn D. Ritchie (BioData Min., 2018)

A simulation study investigating power estimates in phenome-wide association studies. - Anurag Verma; Yukiko Bradford; Scott M. Dudek; Anastasia Lucas; Shefali S. Verma; Sarah A. Pendergrass; Marylyn D. Ritchie (BMC Bioinform., 2018)

Neural network-based multiomics data integration in Alzheimer's disease. - Pankhuri Singhal; Shefali S. Verma; Scott M. Dudek; Marylyn D. Ritchie (GECCO (Companion), 2019)