Author

James Livingston Thomson

University of Wisconsin–Madison

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioinformatics· 3

Signature Assays, Organisms & Methods

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Approach:statistical model· 3 Research Focus:benchmarking· 2 Assay:ATAC-seq· 1 Assay:bulk RNA-seq· 1 Research Focus:differential expression· 1 Research Focus:gene regulatory network inference· 1 Approach:machine learning (classical)· 1 Research Focus:trajectory inference· 1

Frequent Co-Authors

Ron M. StewartiD· 3 shared Finn KuusistoiD· 2 shared Ian RossiD· 2 shared John SteilliD· 2 shared Kalpana RajaiD· 2 shared Lam C. TsoiiD· 2 shared Miron LivnyiD· 2 shared Zijian NiiD· 2 shared

Activity by Year

2020-2023 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 37 mutual co-author links

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3 shared papersBioinformatics

Ron M. StewartORCID

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3 papers

Recent·Most cited

BioinformaticsBMC BioinformaticsPeer-reviewedNov 1, 2023

Serial KinderMiner (SKiM) Discovers and Annotates Biomedical Knowledge Using Co-Occurrence and Transformer Models

Robert J. Millikin, Kalpana Raja, John Steill…·Ron M. Stewart

SKiM discovers and annotates biomedical knowledge using co-occurrence and transformer models to find A-B-C relationships between user-defined concepts.

8 citations

statistical modelbenchmarking

𝕏 PostBluesky

BioinformaticsbioRxivPreprintOct 16, 2020

SKiM - A generalized literature-based discovery system for uncovering novel biomedical knowledge from PubMed

Kalpana Raja, John Steill, Ian Ross…·Ron M. Stewart

SKiM is a literature-based discovery system that rediscovered biomedical knowledge and identified potential drug candidates by analyzing PubMed literature.

2 citations

statistical modelbenchmarking

𝕏 PostBluesky

BioinformaticsbioRxivPreprintJul 18, 2020

Dynamic regulatory module networks for inference of cell type-specific transcriptional networks

Alireza Fotuhi Siahpirani, Sara Knaack, Deborah A. Chasman…·Sushmita Roy

This paper introduces DRMN, a method to infer cell type-specific transcriptional networks from multi-omic data, showing it accurately predicts cis-regulators and models network dynamics.

6 citations

bulk RNA-seqATAC-seq

𝕏 PostBluesky