Author

Patrick Conley

Oregon Health & Science University

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· 1 Developmental Biology· 1 Systems Biology· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 3 Research Focus:database / resource· 2 Research Focus:gene regulatory network inference· 2 Research Focus:cell type annotation· 1 Research Focus:clustering· 1 Research Focus:differential expression· 1 Approach:experimental assay· 1 Organism:human· 1

Frequent Co-Authors

Guanming WuiD· 3 shared Cristoffer SevillaiD· 2 shared Deidre BeaversiD· 2 shared Henning HermjakobiD· 2 shared Karen RothfelsiD· 2 shared Lincoln David SteiniD· 2 shared Lisa R. MatthewsiD· 2 shared Nasim SanatiiD· 2 shared

Activity by Year

2022-2024 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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3 shared papersSystems Biology

Guanming WuORCID

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Author profile →

3 papers

Recent·Most cited

Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes

Marija Orlic-Milacic, Karen Rothfels, Lisa R. Matthews, Adam Wright, Bijay Jassal, Veronica Shamovsky, Quang M. Trinh, Marc E. Gillespie, Cristoffer Sevilla, Krishna Kumar Tiwari, Eliot Ragueneau, Chuqiao Gong, Ralf Stephan, Bruce May, Robin Haw, , Guanming Wu

The paper annotates disease variants in the context of biological pathways to infer molecular phenotypes and model variant impacts.

Database · Jan 1, 2024Peer-reviewedSystems Biology

Illuminating Dark Proteins using Reactome Pathways

Timothy Brunson, Nasim Sanati, Lisa R. Matthews, Robin Haw, Deidre Beavers, Solomon I. Shorser, Cristoffer Sevilla, Guilherme Viteri, Patrick Conley, Karen Rothfels, Henning Hermjakob, Lincoln David Stein, Peter D’Eustachio, Guanming Wu

The paper predicts functional interactions of dark proteins with Reactome pathways using a random forest classifier and develops a web portal to visualize these interactions.

bioRxiv · Jun 5, 2023 · PreprintBioinformatics

Dual states of Bmi1-expressing intestinal stem cells drive epithelial development and tissue regeneration

Nicholas R. Smith, Sidharth K. Sengupta, Patrick Conley, Nicole R. Giske, Christopher D. Klocke, Brett S. Walker, Noelle McPhail, John R. Swain, Yeon Jung Yoo, Ashley N. Anderson, Paige S. Davies, Nasim Sanati, Theresa N. Nguyen, Kristof A. Torkenczy, Andrew Adey, , Melissa Hirose Wong

The paper identifies a dual state of Bmi1-expressing intestinal stem cells that drive epithelial development and tissue regeneration through dynamic Wnt signaling.

bioRxiv · Sep 30, 2022 · PreprintDevelopmental Biology