Deidre Beavers
9 Papers
Deidre Beavers is an academic researcher. The author has contributed to research in topics: Medicine & Computer science. The author has co-authored 3 publications.
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Papers
The Reactome Pathway Knowledgebase 2024.
Marija Milacic,Deidre Beavers,P. Conley,Chuqiao Gong,Marc Gillespie,Johannes Griss,Robin Haw,Bijay Jassal,Lisa Matthews,Bruce May,Robert Petryszak,Eliot Ragueneau,Karen Rothfels,Cristoffer Sevilla,Veronica Shamovsky,Ralf Stephan,Krishna Tiwari,Thawfeek M. Varusai,Joel Weiser,Adam Wright,Guanming Wu,Lincoln Stein,H. Hermjakob,Peter D'Eustachio +23 more
TL;DR: Progress towards annotation of the entire human proteome, targeted annotation of disease-causing genetic variants of proteins and of small-molecule drugs in a pathway context, and towards supporting explicit annotation of cell- and tissue-specific pathways are reviewed.
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Using the Reactome Database
Karen Rothfels,Marija Milacic,Lisa Matthews,Robin Haw,Cristoffer Sevilla,Marc Gillespie,Ralf Stephan,Chuqiao Gong,Eliot Ragueneau,Bruce May,Veronica Shamovsky,Adam Wright,Joel Weiser,Deidre Beavers,P. Conley,Krishna Tiwari,Bijay Jassal,Johannes Griss,Andrea Senff-Ribeiro,Timothy Brunson,Robert Petryszak,Henning Hermjakob,Peter D'Eustachio,Lincoln Stein +23 more
TL;DR: The Reactome project as mentioned in this paper is a pathway database that collects detailed information on biological pathways and processes in humans from the primary literature, covering the gamut from simple intermediate metabolism to signaling pathways and complex cellular events.
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Illuminate the Functions of Dark Proteins Using the Reactome-IDG Web Portal.
Deidre Beavers,Timothy Brunson,Nasim Sanati,Lisa Matthews,Robin Haw,Solomon Shorser,Cristoffer Sevilla,Guilherme Viteri,P. Conley,Karen Rothfels,Henning Hermjakob,Lincoln Stein,Peter D'Eustachio,Guanming Wu +13 more
TL;DR: The Reactome-IDG web portal as mentioned in this paper provides a simple, interactive web page for users to search pathways that may functionally interact with dark proteins, enabling the prediction of functions of dark proteins in the context of Reactome pathways.
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Illuminating Dark Proteins using Reactome Pathways
Lisa Matthews,Robin Haw,Timothy Brunson,Nasim Sanati,Solomon Shorser,Deidre Beavers,P. Conley,Lincoln Stein,Peter D'Eustachio +8 more
TL;DR: A random forest is trained with 106 protein/gene pairwise features collected from multiple resources to predict functional interactions between dark proteins and proteins annotated in Reactome and three scores are developed to measure the interactions betweendark proteins and Reactome pathways based on enrichment analysis and fuzzy logic simulations.
Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes.
Marija Orlic-Milacic,Karen Rothfels,Lisa Matthews,Adam Wright,Bijay Jassal,Veronica Shamovsky,Quang Trinh,Marc E Gillespie,Cristoffer Sevilla,Krishna Tiwari,Eliot Ragueneau,Chuqiao Gong,Ralf Stephan,Bruce May,Robin Haw,Joel Weiser,Deidre Beavers,P. Conley,H. Hermjakob,Lincoln D. Stein,Peter D'Eustachio,Guanming Wu +21 more
- 01 Jan 2023
TL;DR: Pathway-based, reaction-specific annotation of disease variants provides a standardized overview of molecular phenotypes of pathogenic variants that is amenable to computational mining and mathematical modeling.
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