Ron M. Stewart

According to our database, Ron M. Stewart authored at least 21 papers between 2009 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

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, Ron M. Stewart

BMC Bioinform., December, 2023

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., February, 2023

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

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

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

Proceedings of the Protein-Protein Interaction Networks, Methods and Protocols., 2020

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

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, James A. Thomson, Rhonda Bacher

PLoS Comput. Biol., 2019

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

Proceedings of the 18th IEEE International Conference On Machine Learning And Applications, 2019

2017

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

Proceedings of the Summit on Clinical Research Informatics, 2017

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

Quality control of single-cell RNA-seq by SinQC.

Peng Jiang, James A. Thomson, Ron M. Stewart

Bioinform., 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

Proceedings of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 2016

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

Proceedings of the Twenty-Fifth International Joint Conference on Artificial Intelligence, 2016

2015

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

2014

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

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, Michael Volkmer, Bianca Habermann, Elly M. Tanaka, James A. Thomson, Colin N. Dewey

PLoS Comput. Biol., 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

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

2011

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

2010

RNA-Seq gene expression estimation with read mapping uncertainty.

Bo Li, Victor Ruotti, Ron M. Stewart, James A. Thomson, Colin N. Dewey

Bioinform., 2010

2009

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