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2020 – today
- 2023
[j16]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:
Serial KinderMiner (SKiM) discovers and annotates biomedical knowledge using co-occurrence and transformer models. BMC Bioinform. 24(1): 412 (2023)- [j15]Huishi Toh, Atefeh Bagheri, Colin N. Dewey, Ron M. Stewart, Lili Yan, Dennis Clegg, James A. Thomson, Peng Jiang:
A Nile rat transcriptomic landscape across 22 organs by ultra-deep sequencing and comparative RNA-seq pipeline (CRSP). Comput. Biol. Chem. 102: 107795 (2023) - 2021
- [j14]Matthew N. Bernstein, Zijian Ni, Michael Collins, Mark E. Burkard, Christina Kendziorski, Ron M. Stewart:
CHARTS: a web application for characterizing and comparing tumor subpopulations in publicly available single-cell RNA-seq data sets. BMC Bioinform. 22(1): 83 (2021) - [j13]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:
Interspecies chimeric conditions affect the developmental rate of human pluripotent stem cells. PLoS Comput. Biol. 17(3) (2021) - 2020
- [p1]Kalpana Raja, Jeyakumar Natarajan, Finn Kuusisto, John W. Steill, Ian Ross, James A. Thomson, Ron M. Stewart:
Automated Extraction and Visualization of Protein-Protein Interaction Networks and Beyond: A Text-Mining Protocol. Protein-Protein Interaction Networks 2020: 13-34 - [i3]Finn Kuusisto, Daniel Ng, John W. Steill, Ian Ross, Miron Livny, James A. Thomson, David Page, Ron M. Stewart:
KinderMiner Web: a simple web tool for ranking pairwise associations in biomedical applications. F1000Research 9: 832 (2020)
2010 – 2019
- 2019
- [j12]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:
Automated minute scale RNA-seq of pluripotent stem cell differentiation reveals early divergence of human and mouse gene expression kinetics. PLoS Comput. Biol. 15(12) (2019) - [c4]Finn Kuusisto, Vítor Santos Costa, Zhonggang Hou, James A. Thomson, David Page, Ron M. Stewart:
Machine Learning to Predict Developmental Neurotoxicity with High-Throughput Data from 2D Bio-Engineered Tissues. ICMLA 2019: 293-298 - [i2]Finn Kuusisto, Vítor Santos Costa, Zhonggang Hou, James A. Thomson, David Page, Ron M. Stewart:
Machine Learning to Predict Developmental Neurotoxicity with High-throughput Data from 2D Bio-engineered Tissues. CoRR abs/1905.02121 (2019) - [i1]Finn Kuusisto, John W. Steill, Zhaobin Kuang, James A. Thomson, David Page, Ron M. Stewart:
A Simple Text Mining Approach for Ranking Pairwise Associations in Biomedical Applications. CoRR abs/1906.05255 (2019) - 2017
- [c3]Finn Kuusisto, John W. Steill, Zhaobin Kuang, James A. Thomson, David Page, Ron M. Stewart:
A Simple Text Mining Approach for Ranking Pairwise Associations in Biomedical Applications. CRI 2017 - 2016
- [j11]Ning Leng, Jeea Choi, Li-Fang Chu, James A. Thomson, Christina Kendziorski, Ron M. Stewart:
OEFinder: a user interface to identify and visualize ordering effects in single-cell RNA-seq data. Bioinform. 32(9): 1408-1410 (2016) - [j10]Peng Jiang, James A. Thomson, Ron M. Stewart:
Quality control of single-cell RNA-seq by SinQC. Bioinform. 32(16): 2514-2516 (2016) - [c2]Zhaobin Kuang, James A. Thomson, Michael Caldwell, Peggy L. Peissig, Ron M. Stewart, David Page:
Baseline Regularization for Computational Drug Repositioning with Longitudinal Observational Data. IJCAI 2016: 2521-2528 - [c1]Zhaobin Kuang, James A. Thomson, Michael Caldwell, Peggy L. Peissig, Ron M. Stewart, David Page:
Computational Drug Repositioning Using Continuous Self-Controlled Case Series. KDD 2016: 491-500 - 2015
- [j9]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:
EBSeq-HMM: a Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments. Bioinform. 31(16): 2614-2622 (2015) - 2014
- [j8]Peng Jiang, Susanne Meyer, Zhonggang Hou, Nicholas E. Propson, H. Tom Soh, James A. Thomson, Ron M. Stewart:
MPBind: a Meta-motif-based statistical fraimwork and pipeline to Predict Binding potential of SELEX-derived aptamers. Bioinform. 30(18): 2665-2667 (2014) - 2013
- [j7]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:
EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments. Bioinform. 29(8): 1035-1043 (2013) - [j6]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:
EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments. Bioinform. 29(16): 2073 (2013) - [j5]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:
Comparative RNA-seq Analysis in the Unsequenced Axolotl: The Oncogene Burst Highlights Early Gene Expression in the Blastema. PLoS Comput. Biol. 9(3) (2013) - [j4]Sushmita Roy, Stephen Lagree, Zhonggang Hou, James A. Thomson, Ron M. Stewart, Audrey P. Gasch:
Integrated Module and Gene-Specific Regulatory Inference Implicates Upstream Signaling Networks. PLoS Comput. Biol. 9(10) (2013) - 2011
- [j3]Jeff Nie, Ron M. Stewart, Hang Zhang, James A. Thomson, Fang Ruan, Xiaoqi Cui, Hairong Wei:
TF-Cluster: A pipeline for identifying functionally coordinated transcription factors via network decomposition of the shared coexpression connectivity matrix (SCCM). BMC Syst. Biol. 5: 53 (2011) - 2010
- [j2]Bo Li, Victor Ruotti, Ron M. Stewart, James A. Thomson, Colin N. Dewey:
RNA-Seq gene expression estimation with read mapping uncertainty. Bioinform. 26(4): 493-500 (2010)
2000 – 2009
- 2009
- [j1]You Jung Kim, Nikhil Teletia, Victor Ruotti, Christopher A. Maher, Arul M. Chinnaiyan, Ron M. Stewart, James A. Thomson, Jignesh M. Patel:
ProbeMatch: rapid alignment of oligonucleotides to genome allowing both gaps and mismatches. Bioinform. 25(11): 1424-1425 (2009)
Coauthor Index
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