Author

Scott W. Simpkins

University of MinnesotaORCID 0000-0002-5997-2838Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Research Focus:benchmarking· 4 Organism:yeast· 4 Approach:statistical model· 3 Approach:experimental assay· 2 Research Focus:database / resource· 1 Research Focus:differential expression· 1 Research Focus:drug response / drug discovery· 1 Research Focus:gene regulatory network inference· 1

Frequent Co-Authors

Chad L. MyersiD· 5 shared Jeff S. PiotrowskiiD· 5 shared Justin NelsoniD· 5 shared Sheena Claire LiiD· 5 shared Charles M. BooneiD· 4 shared Hamid SafizadehiD· 4 shared Hiroyuki OsadaiD· 4 shared Minoru YoshidaiD· 4 shared

Activity by Year

2017-2021 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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5 shared papersSystems Biology

Chad L. MyersORCID

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5 papers

Recent·Most cited

Improving prediction of compound function from chemical structure using chemical-genetic networks

Hamid Safizadeh, Scott W. Simpkins, Justin Nelson, Sheena Claire Li, Jeff S. Piotrowski, Mami Yoshimura, Yoko Yashiroda, Hiroyuki Hirano, Hiroyuki Osada, Minoru Yoshida, Charles M. Boone, Chad L. Myers

The paper benchmarks structure descriptors and similarity coefficients using chemical-genetic interaction data to improve compound function prediction.

Journal of Chemical Information and Modeling · Jul 28, 2021Peer-reviewedSystems Biology

Predicting bioprocess targets of chemical compounds through integration of chemical-genetic and genetic interaction networks

Scott W. Simpkins, Justin Nelson, Raamesh Deshpande, Sheena Claire Li, Jeff S. Piotrowski, Erin H. Wilson, Abraham Abera Gebre, Hamid Safizadeh, Reika Okamoto, Mami Yoshimura, Michael Costanzo, Yoko Yashiroda, Yoshikazu Ohya, Hiroyuki Osada, Minoru Yoshida, , Chad L. Myers

The paper develops CG-TARGET to predict compound biological processes by integrating chemical-genetic and genetic interaction networks, showing improved accuracy and FDR control.

PLoS Computational Biology · Oct 30, 2018Peer-reviewedSystems Biology

MOSAIC: a chemical-genetic interaction data repository and web resource for exploring chemical modes of action

Justin Nelson, Scott W. Simpkins, Hamid Safizadeh, Sheena Claire Li, Jeff S. Piotrowski, Hiroyuki Hirano, Yoko Yashiroda, Hiroyuki Osada, Minoru Yoshida, Charles M. Boone, Chad L. Myers

The paper introduces MOSAIC, a database and web resource for chemical-genetic interaction data, enabling mode-of-action prediction and discovery of compound effects in yeast.

Bioinformatics · Nov 29, 2017Peer-reviewedBioinformatics

Functional Annotation of Chemical Libraries across Diverse Biological Processes

Jeff S. Piotrowski, Sheena Claire Li, Raamesh Deshpande, Scott W. Simpkins, Justin Nelson, Yoko Yashiroda, Jacqueline M. Barber, Hamid Safizadeh, Erin H. Wilson, Hiroki Okada, Abraham Abera Gebre, Karen Kubo, Nikko P. Torres, Marissa A. LeBlanc, Kerry Andrusiak, , Charles M. Boone

This study develops a yeast-based chemical-genetic screening system to annotate compound functionality across biological processes and identifies compounds with dual modes of action.

Nature Chemical Biology · Jul 24, 2017Peer-reviewedSystems Biology

Efficient strategies for screening large-scale genetic interaction networks

Raamesh Deshpande, Justin Nelson, Scott W. Simpkins, Michael Costanzo, Jeff S. Piotrowski, Sheena Claire Li, Charlie Boone, Chad L. Myers

The paper introduces COMPRESS-GI, an algorithm that efficiently selects informative genes for genetic interaction screens, enabling large-scale chemical genetic screens with high throughput.

bioRxiv · Jul 5, 2017 · PreprintSystems Biology