Publications by authors named "Adam Coffman"

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ImmunoNX: a robust bioinformatics workflow to support personalized neoantigen vaccine trials.
Kartik Singhal, Evelyn Schmidt, Susanna Kiwala, S Peter Goedegebuure, Christopher A Miller, Adam Coffman

ArXiv· December 2025

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CIViC MCP: Integrating Large Language Models with the Clinical Interpretations of Variants in Cancer.
Lars Schimmelpfennig, Quentin Cody, Joshua McMichael, Adam C Coffman, Jason Saliba

bioRxiv· October 2025

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DGIdb 5.0: rebuilding the drug-gene interaction database for precision medicine and drug discovery platforms.
Matthew Cannon, James Stevenson, Kathryn Stahl, Rohit Basu, Adam Coffman

Nucleic Acids Res· January 2024

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CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase.
Kilannin Krysiak, Arpad M Danos, Jason Saliba, Joshua F McMichael, Adam C Coffman

Nucleic Acids Res· January 2023

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A community approach to the cancer-variant-interpretation bottleneck.
Kilannin Krysiak, Arpad M Danos, Susanna Kiwala, Joshua F McMichael, Adam C Coffman

Nat Cancer· May 2022

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Integration of the Drug-Gene Interaction Database (DGIdb 4.0) with open crowdsource efforts.
Sharon L Freshour, Susanna Kiwala, Kelsy C Cotto, Adam C Coffman, Joshua F McMichael

Nucleic Acids Res· January 2021

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CIViCpy: A Python Software Development and Analysis Toolkit for the CIViC Knowledgebase.
Alex H Wagner, Susanna Kiwala, Adam C Coffman, Joshua F McMichael, Kelsy C Cotto

JCO Clin Cancer Inform· March 2020

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Standard operating procedure for curation and clinical interpretation of variants in cancer.
Arpad M Danos, Kilannin Krysiak, Erica K Barnell, Adam C Coffman, Joshua F McMichael

Genome Med· November 2019

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Adapting crowdsourced clinical cancer curation in CIViC to the ClinGen minimum variant level data community-driven standards.
Arpad M Danos, Deborah I Ritter, Alex H Wagner, Kilannin Krysiak, Dmitriy Sonkin, Adam C Coffman

Hum Mutat· November 2018

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Cancer Immunogenomics: Computational Neoantigen Identification and Vaccine Design.
Jasreet Hundal, Christopher A Miller, Malachi Griffith, Obi L Griffith, Jason Walker, Adam Coffman

Cold Spring Harb Symp Quant Biol· February 2018

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DGIdb 3.0: a redesign and expansion of the drug-gene interaction database.
Kelsy C Cotto, Alex H Wagner, Yang-Yang Feng, Susanna Kiwala, Adam C Coffman

Nucleic Acids Res· January 2018

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CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer.
Malachi Griffith, Nicholas C Spies, Kilannin Krysiak, Joshua F McMichael, Adam C Coffman

Nat Genet· January 2017

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DoCM: a database of curated mutations in cancer.
Benjamin J Ainscough, Malachi Griffith, Adam C Coffman, Alex H Wagner, Jason Kunisaki

Nat Methods· September 2016

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DGIdb 2.0: mining clinically relevant drug-gene interactions.
Alex H Wagner, Adam C Coffman, Benjamin J Ainscough, Nicholas C Spies, Zachary L Skidmore

Nucleic Acids Res· January 2016

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Genome Modeling System: A Knowledge Management Platform for Genomics.
Malachi Griffith, Obi L Griffith, Scott M Smith, Avinash Ramu, Matthew B Callaway, Adam C Coffman

PLoS Comput Biol· July 2015

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DGIdb: mining the druggable genome.
Malachi Griffith, Obi L Griffith, Adam C Coffman, James V Weible, Josh F McMichael

Nat Methods· December 2013

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