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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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