ProbeMatch: rapid alignment of oligonucleotides to genome allowing both gaps and mismatches. - You Jung Kim; Nikhil Teletia; Victor Ruotti; Christopher A. Maher; Arul M. Chinnaiyan; Ron M. Stewart; James A. Thomson; Jignesh M. Patel (Bioinform., 2009)

RNA-Seq gene expression estimation with read mapping uncertainty. - Bo Li 015; Victor Ruotti; Ron M. Stewart; James A. Thomson; Colin N. Dewey (Bioinform., 2010)

TF-Cluster: A pipeline for identifying functionally coordinated transcription factors via network decomposition of the shared coexpression connectivity matrix (SCCM). - Jeff Nie; Ron M. Stewart; Hang Zhang; James A. Thomson; Fang Ruan; Xiaoqi Cui; Hairong Wei (BMC Syst. Biol., 2011)

EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments. - Ning Leng; John A. Dawson; James A. Thomson; Victor Ruotti; Anna I. Rissman; Bart M. G. Smits; Jill D. Haag; Michael N. Gould; Ron M. Stewart; Christina Kendziorski (Bioinform., 2013)

Integrated Module and Gene-Specific Regulatory Inference Implicates Upstream Signaling Networks. - Sushmita Roy; Stephen Lagree; Zhonggang Hou; James A. Thomson; Ron M. Stewart; Audrey P. Gasch (PLoS Comput. Biol., 2013)

Comparative RNA-seq Analysis in the Unsequenced Axolotl: The Oncogene Burst Highlights Early Gene Expression in the Blastema. - Ron M. Stewart; Cynthia Alexander Rascón; Shulan Tian; Jeff Nie; Chris Barry; Li-Fang Chu; Hamisha Ardalani; Ryan J. Wagner; Mitchell D. Probasco; Jennifer M. Bolin; Ning Leng; Srikumar Sengupta; et al. (PLoS Comput. Biol., 2013)

MPBind: a Meta-motif-based statistical framework and pipeline to Predict Binding potential of SELEX-derived aptamers. - Peng Jiang; Susanne Meyer; Zhonggang Hou; Nicholas E. Propson; H. Tom Soh; James A. Thomson; Ron M. Stewart (Bioinform., 2014)

EBSeq-HMM: a Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments. - Ning Leng; Yuan Li; Brian E. McIntosh; Bao Kim Nguyen; Bret Duffin; Shulan Tian; James A. Thomson; Colin N. Dewey; Ron M. Stewart; Christina Kendziorski (Bioinform., 2015)

Baseline Regularization for Computational Drug Repositioning with Longitudinal Observational Data. - Zhaobin Kuang; James A. Thomson; Michael Caldwell; Peggy L. Peissig; Ron M. Stewart; David Page (IJCAI, 2016)

Computational Drug Repositioning Using Continuous Self-Controlled Case Series. - Zhaobin Kuang; James A. Thomson; Michael Caldwell; Peggy L. Peissig; Ron M. Stewart; David Page (KDD, 2016)

Quality control of single-cell RNA-seq by SinQC. - Peng Jiang; James A. Thomson; Ron M. Stewart (Bioinform., 2016)

OEFinder: a user interface to identify and visualize ordering effects in single-cell RNA-seq data. - Ning Leng; Jeea Choi; Li-Fang Chu; James A. Thomson; Christina Kendziorski; Ron M. Stewart (Bioinform., 2016)

A Simple Text Mining Approach for Ranking Pairwise Associations in Biomedical Applications. - Finn Kuusisto; John W. Steill; Zhaobin Kuang; James A. Thomson; David Page; Ron M. Stewart (CRI, 2017)

Machine Learning to Predict Developmental Neurotoxicity with High-Throughput Data from 2D Bio-Engineered Tissues. - Finn Kuusisto; Vítor Santos Costa; Zhonggang Hou; James A. Thomson; David Page; Ron M. Stewart (ICMLA, 2019)

Automated minute scale RNA-seq of pluripotent stem cell differentiation reveals early divergence of human and mouse gene expression kinetics. - Chris Barry; Matthew T. Schmitz; Cara Argus; Jennifer M. Bolin; Mitchell D. Probasco; Ning Leng; Bret Duffin; John W. Steill; Scott Swanson; Brian E. McIntosh; Ron M. Stewart; Christina Kendziorski; et al. (PLoS Comput. Biol., 2019)

KinderMiner Web: a simple web tool for ranking pairwise associations in biomedical applications. - Finn Kuusisto; Daniel Ng; John W. Steill; Ian Ross; Miron Livny; James A. Thomson; David Page; Ron M. Stewart (F1000Research, 2020)

Automated Extraction and Visualization of Protein-Protein Interaction Networks and Beyond: A Text-Mining Protocol. - Kalpana Raja; Jeyakumar Natarajan; Finn Kuusisto; John W. Steill; Ian Ross; James A. Thomson; Ron M. Stewart (Protein-Protein Interaction Networks, 2020)

CHARTS: a web application for characterizing and comparing tumor subpopulations in publicly available single-cell RNA-seq data sets. - Matthew N. Bernstein; Zijian Ni; Michael Collins; Mark E. Burkard; Christina Kendziorski; Ron M. Stewart (BMC Bioinform., 2021)

Interspecies chimeric conditions affect the developmental rate of human pluripotent stem cells. - Jared Brown; Chris Barry; Matthew T. Schmitz; Cara Argus; Jennifer M. Bolin; Michael P. Schwartz; Amy Van Aartsen; John W. Steill; Scott Swanson; Ron M. Stewart; James A. Thomson; Christina Kendziorski (PLoS Comput. Biol., 2021)

A Nile rat transcriptomic landscape across 22 organs by ultra-deep sequencing and comparative RNA-seq pipeline (CRSP). - Huishi Toh; Atefeh Bagheri; Colin N. Dewey; Ron M. Stewart; Lili Yan; Dennis Clegg; James A. Thomson; Peng Jiang (Comput. Biol. Chem., 2023)

Serial KinderMiner (SKiM) discovers and annotates biomedical knowledge using co-occurrence and transformer models. - Robert J. Millikin; Kalpana Raja; John W. Steill; Cannon Lock; Xuancheng Tu; Ian Ross; Lam C. Tsoi; Finn Kuusisto; Zijian Ni; Miron Livny; Brian Bockelman; James A. Thomson; et al. (BMC Bioinform., 2023)