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)

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)

Feature Selection using a Random Forests Classifier for the Integrated Analysis of Multiple Data Types. - David M. Reif; Alison A. Motsinger; Brett A. McKinney; James E. Crowe Jr.; Jason H. Moore (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)

Risk Factor Interactions and Genetic Effects Associated with Post-Operative Atrial Fibrillation. - Alison A. Motsinger; Brian S. Donahue; Nancy J. Brown; Dan M. Roden; Marylyn D. Ritchie (Pacific Symposium on Biocomputing, 2006)

GPNN: Power studies and applications of a neural network method for detecting gene-gene interactions in studies of human disease. - Alison A. Motsinger; Stephen L. Lee; George Mellick; Marylyn D. Ritchie (BMC Bioinform., 2006)

Linkage Disequilibrium in Genetic Association Studies Improves the Performance of Grammatical Evolution Neural Networks. - Alison A. Motsinger; David M. Reif; Theresa J. Fanelli; Anna C. Davis; Marylyn D. Ritchie (CIBCB, 2007)

Genetic programming neural networks: A powerful bioinformatics tool for human genetics. - Marylyn D. Ritchie; Alison A. Motsinger; William S. Bush; Christopher S. Coffey; Jason H. Moore (Appl. Soft Comput., 2007)

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)

Neural networks for genetic epidemiology: past, present, and future. - Alison A. Motsinger-Reif; Marylyn D. Ritchie (BioData Min., 2008)

Grammatical Evolution Decision Trees for Detecting Gene-Gene Interactions. - Sushamna Deodhar; Alison A. Motsinger-Reif (EvoBIO, 2010)

Grammatical evolution decision trees for detecting gene-gene interactions. - Alison A. Motsinger-Reif; Sushamna Deodhar; Stacey J. Winham; Nicholas E. Hardison (BioData Min., 2010)

A comparison of internal validation techniques for multifactor dimensionality reduction. - Stacey J. Winham; Andrew J. Slater; Alison A. Motsinger-Reif (BMC Bioinform., 2010)

The power of quantitative grammatical evolution neural networks to detect gene-gene interactions. - Nicholas E. Hardison; Alison A. Motsinger-Reif (GECCO, 2011)

Optimization of grammatical evolution decision trees. - Kristopher Hoover; Rachel Marceau; Tyndall Harris; Nicholas E. Hardison; David M. Reif; Alison A. Motsinger-Reif (GECCO (Companion), 2011)

An R package implementation of multifactor dimensionality reduction. - Stacey J. Winham; Alison A. Motsinger-Reif (BioData Min., 2011)

A comparison of GE optimized neural networks and decision trees. - Kristopher Hoover; Rachel Marceau; Tyndall Harris; David M. Reif; Alison A. Motsinger-Reif (GECCO (Companion), 2012)

Grammatical evolution support vector machines for predicting human genetic disease association. - Skylar W. Marvel; Alison A. Motsinger-Reif (GECCO (Companion), 2012)

Multivariate methods and software for association mapping in dose-response genome-wide association studies. - Chad C. Brown; Tammy M. Havener; Marisa Wong Medina; Ronald M. Krauss; Howard L. McLeod; Alison A. Motsinger-Reif (BioData Min., 2012)

Global tests of P-values for multifactor dimensionality reduction models in selection of optimal number of target genes. - Hongying Dai; Madhusudan Bhandary; Mara Becker; J. Steven Leeder; Roger Gaedigk; Alison A. Motsinger-Reif (BioData Min., 2012)

Risk score modeling of multiple gene to gene interactions using aggregated-multifactor dimensionality reduction. - Hongying Dai; Richard J. Charnigo; Mara Becker; J. Steven Leeder; Alison A. Motsinger-Reif (BioData Min., 2013)

An adaptive permutation approach for genome-wide association study: evaluation and recommendations for use. - Ronglin Che; John R. Jack; Alison A. Motsinger-Reif; Chad C. Brown (BioData Min., 2014)

PGxClean: a quality control GUI for the Affymetrix DMET chip and other candidate gene studies with non-biallelic alleles. - Daniel M. Rotroff; John R. Jack; Nathan Campbell; Scott Clark; Alison A. Motsinger-Reif (BioData Min., 2014)

Bayesian neural networks for detecting epistasis in genetic association studies. - Andrew L. Beam; Alison A. Motsinger-Reif; Jon Doyle (BMC Bioinform., 2014)

An investigation of gene-gene interactions in dose-response studies with Bayesian nonparametrics. - Andrew L. Beam; Alison A. Motsinger-Reif; Jon Doyle (BioData Min., 2015)

Gene set analysis methods: a systematic comparison. - Ravi Mathur; Daniel M. Rotroff; Jun Ma 032; Ali Shojaie; Alison A. Motsinger-Reif (BioData Min., 2018)

Cheminformatics approach to exploring and modeling trait-associated metabolite profiles. - Jeremy R. Ash; Mélaine A. Kuenemann; Daniel M. Rotroff; Alison A. Motsinger-Reif; Denis Fourches (J. Cheminformatics, 2019)

Identifying individual risk rare variants using protein structure guided local tests (POINT). - Rachel Marceau West; Wenbin Lu; Daniel M. Rotroff; Mélaine A. Kuenemann; Sheng-Mao Chang; Michael C. Wu; Michael J. Wagner; John B. Buse; Alison A. Motsinger-Reif; Denis Fourches; Jung-Ying Tzeng (PLoS Comput. Biol., 2019)

Prediction of synergistic drug combinations using PCA-initialized deep learning. - Jun Ma 032; Alison A. Motsinger-Reif (BioData Min., 2021)

Knockoff boosted tree for model-free variable selection. - Tao Jiang; Yuanyuan Li; Alison A. Motsinger-Reif (Bioinform., 2021)

Visualization, benchmarking and characterization of nested single-cell heterogeneity as dynamic forest mixtures. - Benedict Anchang; Raul Mendez-Giraldez; Xiaojiang Xu; Trevor K. Archer; Qing Chen; Guang Hu; Sylvia K. Plevritis; Alison Anne Motsinger-Reif; Jian-Liang Li (Briefings Bioinform., 2022)

Model-based evaluation of spatiotemporal data reduction methods with unknown ground truth through optimal visualization and interpretability metrics. - Komlan Atitey; Alison A. Motsinger-Reif; Benedict Anchang (Briefings Bioinform., 2024)

Predicting nutrition and environmental factors associated with female reproductive disorders using a knowledge graph and random forests. - Lauren E. Chan; Elena Casiraghi; Justin T. Reese; Quaker E. Harmon; Kevin Schaper; Harshad Hegde; Giorgio Valentini; Charles Schmitt; Alison A. Motsinger-Reif; Janet E. Hall; Christopher J. Mungall; Peter N. Robinson; et al. (Int. J. Medical Informatics, 2024)

Taxanorm: a novel taxa-specific normalization approach for microbiome data. - Ziyue Wang; Dillon Lloyd; Shanshan Zhao; Alison A. Motsinger-Reif (BMC Bioinform., 2024)

Differences in brain spindle density during sleep between patients with and without type 2 diabetes. - Deryck Yeung; Amlan Talukder; Min Shi 002; David M. Umbach; Yuanyuan Li; Alison A. Motsinger-Reif; Janice J. Hwang; Zheng Fan; Leping Li (Comput. Biol. Medicine, 2025)