Alex Handler Wagner

Searching the Druggable Genome using Large Language Models

The paper develops a server enabling large language models to access drug-gene interaction data through natural language queries.

Taming the reference genome jungle: the refget sequence collection standard

The paper introduces a standard for unambiguously representing, retrieving, and comparing reference genomes and transcriptomes, revealing inconsistencies across 60 human and 36 mouse references.

The GA4GH Categorical Variation Representation Specification: A Unified Computational Framework for Reasoning over Genomic Variant Categories

The paper introduces Cat-VRS, a framework for computable representation of genomic variant categories to improve data interoperability and clinical interpretation.

dgiLIT: A Method for Prioritization and AI Curation of Drug-Gene Interactions

The paper introduces dgiLIT, an AI-driven method to prioritize and curate drug-gene interactions from biomedical literature for inclusion in DGIdb, achieving high validation rates.

The Clinical Genomic Variation Landscape

The paper evaluates challenges in genomic variant representation across resources and develops normalization methods to improve clinical outcome associations.

PEDIA-BRAIN: A single nuclei multiomic encyclopedia of the human pons provides a resource for normal development and disease vulnerability

PEDIA-BRAIN provides a single nuclei multiomic resource of the human pons across development, revealing oligodendrocyte maturation trajectories and disease-related perturbations in DMG and MS.

Mapping MAVE data for use in human genomics applications

The paper maps MAVE data to human reference sequences to improve variant functional assay utility for genomics applications.

AI-readiness criteria for biomedical data

The paper defines AI-readiness criteria for biomedical data, encompassing seven dimensions, and evaluates them across flagship datasets to ensure ethical and explainable AI practices.

Development and application of a computable genotype model in the GA4GH Variation Representation Specification

The paper develops and applies a computable genotype model within the GA4GH Variation Representation Specification to enable precise and interoperable representation of genomic variation data.

The GA4GH Phenopacket schema: A computable representation of clinical data for precision medicine

The paper introduces the GA4GH Phenopacket schema to standardize the exchange of phenotypic data for precision medicine applications.

Discovery of Clinically Relevant Fusions in Pediatric Cancer

The paper develops an ensemble fusion-calling pipeline to improve the detection of clinically relevant gene fusions in pediatric cancer, identifying 67 fusions with a 29.3% diagnostic yield.

The GA4GH Variation Representation Specification (VRS): a Computational Framework for the Precise Representation and Federated Identification of Molecular Variation

The paper introduces the GA4GH Variation Representation Specification (VRS), a framework for precise and federated representation of molecular variation, with a reference implementation and community resources available online.

Evolution of the open-access CIViC knowledgebase is driven by the needsof the cancer variant interpretation community

The paper describes the evolution of the CIViC knowledgebase to meet the needs of the cancer variant interpretation community by expanding its functionality and data types.

Integration of the Drug-Gene Interaction Database (DGIdb) with open crowdsource efforts

DGIdb 4.0 aggregates drug-gene interaction and druggability claims from 41 sources, adding crowd-sourced Drug Target Commons, Wikidata-based drug normalization, search-relative query scores, and NDEx export.

A harmonized meta-knowledgebase of clinical interpretations of cancer genomic variants

The paper harmonizes clinical interpretations of cancer genomic variants across six knowledgebases, improving overlap and matching with patient cohorts.

CIViCpy: a Python software development and analysis toolkit for the CIViC knowledgebase

CIViCpy is a Python SDK for accessing and analyzing the CIViC knowledgebase, enabling efficient variant annotation in cancer genomics.

The CIViC knowledge model and standard operating procedures for curation and clinical interpretation of variants in cancer

The paper describes the CIViC knowledge model and curation procedures for systematically organizing and interpreting cancer-related genetic variants.

Standard operating procedure for somatic variant refinement of tumor sequencing data

This paper establishes a standard operating procedure for manual refinement of somatic variants in tumor sequencing data to improve consistency and reproducibility.

DGIdb 3.0: a redesign and expansion of the drug-gene interaction database

DGIdb 3.0 updates and expands the drug-gene interaction database by adding new sources, improving the codebase, and enhancing API features.