Author

Reagon Karki

Fraunhofer Institute for Translational Medicine and PharmacologyORCID 0000-0002-1815-0037Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 4 Systems Biology· 1

Signature Assays, Organisms & Methods

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Research Focus:drug response / drug discovery· 3 Research Focus:database / resource· 2 Organism:human· 2 Approach:benchmark study· 1 Approach:experimental assay· 1 Assay:imaging· 1 Approach:large language model· 1 Approach:machine learning (classical)· 1

Frequent Co-Authors

Yojana GadiyaiD· 4 shared Andrea ZalianiiD· 3 shared Philip M. GribboniD· 3 shared Alpha Tom KodamulliliD· 2 shared Bruce T. SchultziD· 2 shared Christian EbelingiD· 2 shared Daniel Domingo‐FernándéziD· 2 shared Martin Hofmann‐ApitiusiD· 2 shared

Activity by Year

2020-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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4 shared papersBioinformatics

Yojana GadiyaORCID

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Author profile →

5 papers

Recent·Most cited

Human-supervised Agentic AI for Hypothesis Generation and Experimental Assistance in Drug Repurposing

Dinh-Long Huynh, Elin Asp, Flavio Ballante, Jordi Carreras Puigvert, Alisa Nicole DeGrave, Reagon Karki, Kristen Michelle Nader, Päivi Östling, B.K. Pokharel, Jonne Rietdijk, Lars Schlotawa, Lina Schmidt, Srijit Seal, Brinton A. Seashore-Ludlow, Tero A. Aittokallio, Ola Spjuth

A human-supervised multi-agent LLM system covered drug repurposing from knowledge graph building to assay analysis in three case studies; retrospective COVID-19 screen AUC-ROC 0.986 without predefined thresholds.

bioRxiv · Aug 17, 2026 · PreprintBioinformatics✦ In-depth digest

Pharmacophoric-based ML model to filter candidate E3 ligands and predict E3 Ligase binding probabilities

Reagon Karki, Yojana Gadiya, Simran Shetty, Philip M. Gribbon, Andrea Zaliani

bioRxiv · Aug 10, 2023 · PreprintBioinformatics

Monkeypox Knowledge Graph: A comprehensive representation embedding chemical entities and associated biology of Monkeypox

Reagon Karki, Andrea Zaliani, Yojana Gadiya, Philip M. Gribbon

This paper constructs a Monkeypox knowledge graph to represent chemical entities and biological aspects of MPXV, integrating data for comprehensive analysis.

bioRxiv · Aug 2, 2022 · PreprintSystems Biology

The COVID-19 PHARMACOME: A method for the rational selection of drug repurposing candidates from multimodal knowledge harmonization

Bruce T. Schultz, Andrea Zaliani, Christian Ebeling, Jeanette Reinshagen, Denisa Bojková, Vanessa Lage‐Rupprecht, Reagon Karki, Soeren Lukassen, Yojana Gadiya, Neal G. Ravindra, Sayoni Das, Shounak Baksi, Daniel Domingo‐Fernándéz, Manuel Lentzen, Mark A. Strivens, , Martin Hofmann‐Apitius

The paper presents a drug-target-mechanism graph to identify synergistic drug combinations for SARS-CoV-2 treatment, validated through experimental testing.

bioRxiv · Sep 23, 2020 · PreprintBioinformatics

COVID-19 Knowledge Graph: a computable, multi-modal, cause-and-effect knowledge model of COVID-19 pathophysiology

Daniel Domingo‐Fernándéz, Shounak Baksi, Bruce T. Schultz, Yojana Gadiya, Reagon Karki, Tamara Raschka, Christian Ebeling, Martin Hofmann‐Apitius, Alpha Tom Kodamullil

The paper constructs a cause-and-effect knowledge graph of COVID-19 pathophysiology from scientific literature and provides it as a public resource.

Bioinformatics · Sep 11, 2020Peer-reviewedBioinformatics