Monica C. Muñoz-Torres

The paper describes the Common Fund Data Ecosystem (CFDE), which integrates NIH Common Fund data resources to enable discovery, analysis, and collaboration across heterogeneous datasets.

The paper introduces GPSEA, a tool using GA4GH Phenopackets to analyze genotype-phenotype correlations in Mendelian disorders, identifying 225 significant associations across 85 cohorts.

The paper introduces uPheno, a framework for cross-species phenomics integration by harmonizing phenotype data across species and ontologies.

The paper introduces FAIRSCAPE, a framework for packaging biomedical datasets with metadata to enhance AI-readiness, explainability, and FAIR compliance.

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.

The paper presents a large-scale corpus of standardized phenopackets for genomic diagnostics and discovery, curated from literature and useful for software testing and genotype-phenotype analysis.

Phenomics Assistant is a chat-based interface that uses LLMs to query the Monarch knowledge graph, improving reliability for non-expert users to explore disease-gene-phenotype relationships.

This paper introduces OBA, a formalized ontology for biological attributes to facilitate data integration across phenotypic, genetic, and environmental data.

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

KG-COVID-19 creates customizable knowledge graphs for COVID-19 response by integrating siloed biomedical data into structured formats for various research applications.

The paper analyzes gene and protein domain content changes across 76 arthropod genomes to understand evolutionary patterns and their association with phenotypic adaptations.

The paper presents the milkweed bug genome and comparative analyses to study molecular evolution and feeding ecology in Hemiptera.

Apollo is an open-source software tool that enables researchers to collaboratively annotate and refine genomic features through a graphical interface.

The paper reports the sequencing and manual annotation of the Gerris buenoi genome, identifying gene expansions linked to adaptations for aquatic life.

The paper presents the genome of the Colorado potato beetle to study its rapid evolutionary changes, herbivory adaptations, and insecticide resistance mechanisms.

The paper manually curates gene models in the Asian citrus psyllid genome to improve annotation for HLB control research.

WikiGenomes provides a web platform for community curation of gene annotations in Wikidata, addressing the lack of resources for comprehensive genomic data curation.