ArticleBioinformatics (Oxford, England)2026
Searching the druggable genome using large language models.
Lars Schimmelpfennig, Matthew Cannon, Quentin Cody, Joshua McMichael, Adam C Coffman, Susanna Kiwala, Kilannin Krysiak, Alex H Wagner, Malachi Griffith, Obi L Griffith
Abstract read
In one paragraphArticle in Bioinformatics (Oxford, England), 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
2 · The registryThe trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
3 · Its place in the literatureWho cites it
0 citing papers in PubMed.
No citing paper in PubMed yet.
4 · The recordCorrections and comments
5 · Who and what moneyAuthors and funding
10 authors.
Lars SchimmelpfennigDivision of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, United States.ORCID 0009-0009-0585-2062 Matthew CannonInstitute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH 43205, United States.ORCID 0000-0003-1908-7292 Quentin CodyIndependent Researcher, Philadelphia, PA, United States.
Joshua McMichaelMcDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, United States.ORCID 0000-0002-0197-2245 Adam C CoffmanDivision of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, United States.ORCID 0000-0003-0944-3126 Susanna KiwalaDivision of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, United States.ORCID 0000-0003-4378-7328 Kilannin KrysiakDepartment of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, United States.ORCID 0000-0002-6299-9230 Alex H WagnerInstitute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH 43205, United States.ORCID 0000-0002-2502-8961 Malachi GriffithDivision of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, United States.ORCID 0000-0002-6388-446X Obi L GriffithDivision of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, United States.ORCID 0000-0002-0843-4271 Funding
Standardized and Genome-Wide Clinical Interpretation of Complex Genotypes for Cancer Precision MedicineU24CA237719 · NCI · WASHINGTON UNIVERSITY · PI GRIFFITH, OBI L. · 2019 to 2023
$3.8MText Mining and Large Language Models for AI-Driven Evidence-Based Functional Annotation of Clinical VariantsU24CA275783 · NCI · WASHINGTON UNIVERSITY · PI Malachi Griffith, Obi L. Griffith · 2023 to 2026
$2.6MDevelopment and validation of a computable knowledge framework for genomic medicineR35HG011949 · NHGRI · RESEARCH INST NATIONWIDE CHILDREN'S HOSP · PI WAGNER, ALEX HANDLER · 2021 to 2025
$2.4MAccelerating the expert-crowdsourcing of cancer variant interpretation in CIViCU24CA305456 · NCI · WASHINGTON UNIVERSITY · PI Malachi Griffith, Obi L. Griffith · 2025 to 2026
$2.0MGenomic Expert Curation Panels for Pediatric MalignanciesU24CA258115 · NCI · WASHINGTON UNIVERSITY · PI GRIFFITH, MALACHI, GRIFFITH, OBI L. · 2022 to 2024
$870kNational Cancer Institute (NCI) U24CA237719National Cancer Institute (NCI) U24CA258115National Cancer Institute (NCI) U24CA275783National Cancer Institute (NCI) U24CA305456National Human Genome Research Institute (NHGRI) R35HG011949NCI NIH HHS U24 CA237719NCI NIH HHS U24 CA258115NCI NIH HHS U24 CA275783NCI NIH HHS U24 CA305456NHGRI NIH HHS R35 HG011949NIH HHS
6 · The paper itselfAbstract
summaryThe druggable genome encompasses the genes that are known or predicted to interact with drugs. The Drug-Gene Interaction Database (DGIdb) provides an integrated resource for discovering and contextualizing these interactions, supporting a broad range of research and clinical applications. DGIdb is currently accessed through structured web interfaces and API calls, requiring users to translate natural-language questions into database-specific query patterns. To allow for the use of DGIdb through natural language, we developed the DGIdb Model Context Protocol (MCP) server, which allows large language models (LLMs) access to up-to-date information through the DGIdb API. We demonstrate that the MCP server improves an LLM's ability to answer questions requiring accurate, up-to-date biomedical knowledge drawn from structured external resources. AVAILABILITY AND IMPLEMENTATION: The DGIdb MCP server is detailed at https://github.com/dgidb/dgidb-mcp-server and includes instructions for accessing the server through the Claude desktop app.
Indexed as
GenomeGenomicsDatabases, GeneticLarge Language ModelsSoftware
Identifiers
PMID42631692
PMCPMC13544961
What OpenQuestion holds
Textmetadata
Read underepoch 390