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James A. Thomson
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2020 – today
- 2023
- [j18]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) - [j17]Huishi Toh, Atefeh Bagheri
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
- [j16]Jared Brown
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
KinderMiner Web: a simple web tool for ranking pairwise associations in biomedical applications. F1000Research 9: 832 (2020)
2010 – 2019
- 2019
- [j15]Sara G. Mina, Begum Alaybeyoglu
Assessment of Drug-Induced Toxicity Biomarkers in the Brain Microphysiological System (MPS) Using Targeted and Untargeted Molecular Profiling. Frontiers Big Data 2: 23 (2019) - [j14]Chris Barry, Matthew T. Schmitz
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
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
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
- [j13]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) - [j12]Peng Jiang
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
- [j11]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) - [j10]Roadmap Epigenomics Consortium, Anshul Kundaje
Integrative analysis of 111 reference human epigenomes Open. Nat. 518(7539): 317-330 (2015) - [j9]Jesse R. Dixon, Inkyung Jung
Chromatin architecture reorganization during stem cell differentiation Open. Nat. 518(7539): 331-336 (2015) - 2014
- [j8]Peng Jiang
MPBind: a Meta-motif-based statistical framework 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
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
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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