Using genetic algorithms for the inference of motifs that are represented in only a subset of sequences of interest. - Jeffrey A. Thompson; Clare Bates Congdon (BIBM Workshops, 2011)

Initial Results In Using de Novo Motif Inference to Detect Cis-Regulatory Modules. - Jeffrey A. Thompson; Clare Bates Congdon (BCB, 2013)

An exploration into improving DNA motif inference by looking for highly conserved core regions. - Jeffrey A. Thompson; Clare Bates Congdon (CIBCB, 2013)

An automated pipeline for discovering gene expression patterns associated with increased cancer survival time. - Jeffrey A. Thompson; Christine Duarte; Peter Marks; Clare Bates Congdon (BCB, 2014)

A workflow for the computational identification of candidate regulatory elements in noncoding DNA. - Jeffrey A. Thompson; Craig R. Lessard; Samuel McFarland; Robert L. Morris; Clare Bates Congdon (BCB, 2014)

GAMI-CRM: Using de novo motif inference to detect cis-regulatory modules. - Jeffrey A. Thompson; Clare Bates Congdon (IEEE Congress on Evolutionary Computation, 2014)

A Methylation-to-Expression Feature Model for Generating Accurate Prognostic Risk Scores and Identifying Disease Targets in Clear Cell Kidney Cancer. - Jeffrey A. Thompson; Carmen J. Marsit (PSB, 2017)

Relevant Word Order Vectorization for Improved Natural Language Processing in Electronic Healthcare Records. - Jeffrey A. Thompson; Jinxiang Hu; Dinesh Pal Mudaranthakam; David Streeter; Lisa Neums; Michele Park; Devin C. Koestler; Byron Gajewski; Matthew S. Mayo (CoRR, 2018)

pwrEWAS: a user-friendly tool for comprehensive power estimation for epigenome wide association studies (EWAS). - Stefan Graw; Rosalyn Henn; Jeffrey A. Thompson; Devin C. Koestler (BMC Bioinform., 2019)

Improving Survival Prediction Using a Novel Feature Selection and Feature Reduction FrameworkBased on the Integration of Clinical and Molecular Data. - Lisa Neums; Richard Meier; Devin C. Koestler; Jeffrey A. Thompson (PSB, 2020)

A Novel Framework for the Identification of Reference DNA Methylation Libraries for Reference-Based Deconvolution of Cellular Mixtures. - Shelby Bell-Glenn; Jeffrey A. Thompson; Lucas A. Salas; Devin C. Koestler (Frontiers Bioinform., 2022)

Assessing equivalent and inverse change in genes between diverse experiments. - Lisa Neums; Devin C. Koestler; Qing Xia; Jinxiang Hu; Shachi Patel; Shelby Bell-Glenn; Dong Pei; Bo Zhang; Samuel Boyd; Prabhakar Chalise; Jeffrey A. Thompson (Frontiers Bioinform., 2022)

AMEND: active module identification using experimental data and network diffusion. - Samuel Boyd; Chad Slawson; Jeffrey A. Thompson (BMC Bioinform., 2023)

AMEND 2.0: module identification and multi-omic data integration with multiplex-heterogeneous graphs. - Samuel Boyd; Chad Slawson; Jeffrey A. Thompson (BMC Bioinform., 2025)