James A. Thomson

26 papers A* 2C 1Journal 21Unranked 1
YearRankTypeTitle / Venue / Authors
2023 J jnl
A Nile rat transcriptomic landscape across 22 organs by ultra-deep sequencing and comparative RNA-seq pipeline (CRSP).
Comput. Biol. Chem.
Huishi Toh, Atefeh Bagheri, Colin N. Dewey, Ron M. Stewart, Lili Yan, Dennis Clegg, James A. Thomson, Peng Jiang
2023 J jnl
Serial KinderMiner (SKiM) discovers and annotates biomedical knowledge using co-occurrence and transformer models.
BMC Bioinform.
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
2021 J jnl
Interspecies chimeric conditions affect the developmental rate of human pluripotent stem cells.
PLoS Comput. Biol.
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
2020 — ch.
Automated Extraction and Visualization of Protein-Protein Interaction Networks and Beyond: A Text-Mining Protocol.
Protein-Protein Interaction Networks
Kalpana Raja, Jeyakumar Natarajan, Finn Kuusisto, John W. Steill, Ian Ross, James A. Thomson, Ron M. Stewart
2020 J jnl
KinderMiner Web: a simple web tool for ranking pairwise associations in biomedical applications.
F1000Research
Finn Kuusisto, Daniel Ng, John W. Steill, Ian Ross, Miron Livny, James A. Thomson, David Page, Ron M. Stewart
2019 J jnl
A Simple Text Mining Approach for Ranking Pairwise Associations in Biomedical Applications.
CoRR
Finn Kuusisto, John W. Steill, Zhaobin Kuang, James A. Thomson, David Page, Ron M. Stewart
2019 J jnl
Assessment of Drug-Induced Toxicity Biomarkers in the Brain Microphysiological System (MPS) Using Targeted and Untargeted Molecular Profiling.
Frontiers Big Data
Sara G. Mina, Begum Alaybeyoglu, William L. Murphy, James A. Thomson, Cynthia L. Stokes, Murat Cirit
2019 J jnl
Automated minute scale RNA-seq of pluripotent stem cell differentiation reveals early divergence of human and mouse gene expression kinetics.
PLoS Comput. Biol.
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
2019 C conf
Machine Learning to Predict Developmental Neurotoxicity with High-Throughput Data from 2D Bio-Engineered Tissues.
ICMLA
Finn Kuusisto, Vítor Santos Costa, Zhonggang Hou, James A. Thomson, David Page, Ron M. Stewart
2019 J jnl
Machine Learning to Predict Developmental Neurotoxicity with High-throughput Data from 2D Bio-engineered Tissues.
CoRR
Finn Kuusisto, Vítor Santos Costa, Zhonggang Hou, James A. Thomson, David Page, Ron M. Stewart
2017 — conf
A Simple Text Mining Approach for Ranking Pairwise Associations in Biomedical Applications.
CRI
Finn Kuusisto, John W. Steill, Zhaobin Kuang, James A. Thomson, David Page, Ron M. Stewart
2016 A* conf
Baseline Regularization for Computational Drug Repositioning with Longitudinal Observational Data.
IJCAI
Zhaobin Kuang, James A. Thomson, Michael Caldwell, Peggy L. Peissig, Ron M. Stewart, David Page
2016 A* conf
Computational Drug Repositioning Using Continuous Self-Controlled Case Series.
KDD
Zhaobin Kuang, James A. Thomson, Michael Caldwell, Peggy L. Peissig, Ron M. Stewart, David Page
2016 J jnl
OEFinder: a user interface to identify and visualize ordering effects in single-cell RNA-seq data.
Bioinform.
Ning Leng, Jeea Choi, Li-Fang Chu, James A. Thomson, Christina Kendziorski, Ron M. Stewart
2016 J jnl
Quality control of single-cell RNA-seq by SinQC.
Bioinform.
Peng Jiang, James A. Thomson, Ron M. Stewart
2015 J jnl
Chromatin architecture reorganization during stem cell differentiation Open.
Nat.
Jesse R. Dixon, Inkyung Jung, Siddarth Selvaraj, Yin Shen, Jessica E. Antosiewicz-Bourget, Ahyoung Lee, Zhen Ye, Audrey Kim, Nisha Rajagopal, Wei Xie, Yarui Diao, Jing Liang, Huimin Zhao, Victor V. Lobanenkov, Joseph R. Ecker, James A. Thomson, Bing Ren
2015 J jnl
EBSeq-HMM: a Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments.
Bioinform.
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
2015 J jnl
Integrative analysis of 111 reference human epigenomes Open.
Nat.
Roadmap Epigenomics Consortium, Anshul Kundaje, Wouter Meuleman, Jason Ernst, Misha Bilenky, Angela Yen, Alireza Heravi Moussavi, Pouya Kheradpour, ZhiZhuo Zhang, Jianrong Wang, Michael J. Ziller, Viren Amin, John W. Whitaker, Matthew D. Schultz, Lucas D. Ward, Abhishek Sarkar, Gerald T. Quon, Richard S. Sandstrom, Matthew L. Eaton, Yi-Chieh Wu, Andreas R. Pfenning, Xinchen Wang, Melina Claussnitzer, Yaping Liu, Cristian Coarfa, R. Alan Harris, Noam Shoresh, Charles B. Epstein, Elizabeta Gjoneska, Danny Leung, Wei Xie, R. David Hawkins, Ryan Lister, Chibo Hong, Philippe Gascard, Andrew J. Mungall, Richard A. Moore, Eric Chuah, Angela Tam, Theresa K. Canfield, R. Scott Hansen, Rajinder Kaul, Peter J. Sabo, Mukul S. Bansal, Annaick Carles, Jesse R. Dixon, Kyle Kai-How Farh, Soheil Feizi, Rosa Karlic, Ah-Ram Kim, Ashwinikumar Kulkarni, Daofeng Li, Rebecca F. Lowdon, GiNell Elliott, Tim R. Mercer, Shane J. Neph, Vitor Onuchic, Paz Polak, Nisha Rajagopal, Pradipta Ray, Richard C. Sallari, Kyle T. Siebenthall, Nicholas A. Sinnott-Armstrong, Michael Stevens, Robert E. Thurman, Jie Wu, Bo Zhang, Xin Zhou, Arthur E. Beaudet, Laurie A. Boyer, Philip L. De Jager, Peggy J. Farnham, Susan J. Fisher, David Haussler, Steven J. M. Jones, Wei Li, Marco A. Marra, Michael T. McManus, Shamil R. Sunyaev, James A. Thomson, Thea D. Tlsty, Li-Huei Tsai, Wei Wang, Robert A. Waterland, Michael Q. Zhang, Lisa H. Chadwick, Bradley E. Bernstein, Joseph F. Costello, Joseph R. Ecker, Martin Hirst, Alexander Meissner, Aleksandar Milosavljevic, Bing Ren, John A. Stamatoyannopoulos, Ting Wang, Manolis Kellis
2014 J jnl
MPBind: a Meta-motif-based statistical framework and pipeline to Predict Binding potential of SELEX-derived aptamers.
Bioinform.
Peng Jiang, Susanne Meyer, Zhonggang Hou, Nicholas E. Propson, H. Tom Soh, James A. Thomson, Ron M. Stewart
2013 J jnl
Comparative RNA-seq Analysis in the Unsequenced Axolotl: The Oncogene Burst Highlights Early Gene Expression in the Blastema.
PLoS Comput. Biol.
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
2013 J jnl
EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments.
Bioinform.
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
2013 J jnl
EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments.
Bioinform.
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
2013 J jnl
Integrated Module and Gene-Specific Regulatory Inference Implicates Upstream Signaling Networks.
PLoS Comput. Biol.
Sushmita Roy, Stephen Lagree, Zhonggang Hou, James A. Thomson, Ron M. Stewart, Audrey P. Gasch
2011 J jnl
TF-Cluster: A pipeline for identifying functionally coordinated transcription factors via network decomposition of the shared coexpression connectivity matrix (SCCM).
BMC Syst. Biol.
Jeff Nie, Ron M. Stewart, Hang Zhang, James A. Thomson, Fang Ruan, Xiaoqi Cui, Hairong Wei
2010 J jnl
RNA-Seq gene expression estimation with read mapping uncertainty.
Bioinform.
Bo Li, Victor Ruotti, Ron M. Stewart, James A. Thomson, Colin N. Dewey
2009 J jnl
ProbeMatch: rapid alignment of oligonucleotides to genome allowing both gaps and mismatches.
Bioinform.
You Jung Kim, Nikhil Teletia, Victor Ruotti, Christopher A. Maher, Arul M. Chinnaiyan, Ron M. Stewart, James A. Thomson, Jignesh M. Patel