Sean R. Davis

MetaHarmonizer: robust biomedical metadata harmonization and a contamination control for inflated LLM performance on public benchmarks

MetaHarmonizer improves metadata harmonization and addresses LLM contamination in biomedical data, outperforming existing methods on benchmark tasks.

Large-scale Manual Curation and Harmonization of Metadata from Metagenomic and Cancer Genomic Repositories: Challenges and Solutions

The paper curates and harmonizes metadata from metagenomic and cancer genomic repositories to improve data reusability and cross-study integration.

A pivotal role for Wnt antagonists in constraining Wnt activity to promote digit joint specification.

The paper shows that Wnt antagonists, working with Fgfs, prevent premature pSmad1/5 accumulation to maintain mesenchymal plasticity and balance digit phalanx and joint formation.

bamSliceR: a Bioconductor package for rapid, cross-cohort variant analysis

bamSliceR enables rapid, cross-cohort variant analysis by extracting and analyzing aligned reads from GDC data, identifying clinically relevant variants in leukemia cohorts.

GenomicSuperSignature: interpretation of RNA-seq experiments through robust, efficient comparison to public databases

GenomicSuperSignature compares new RNA-seq datasets to public archives for rapid interpretation using precomputed axes of variation.

HGNChelper: Identification and correction of invalid gene symbols for human and mouse

HGNChelper identifies and corrects invalid gene symbols in human and mouse data by leveraging authoritative databases and addressing spreadsheet-related errors.

Towards a gold standard for benchmarking gene set enrichment analysis

The paper benchmarks gene set enrichment methods using a curated compendium of disease datasets, identifying performance differences and providing recommendations for improved analysis.

BiocPkgTools: Toolkit for Mining the Bioconductor Package Ecosystem

BiocPkgTools provides a toolkit to access and analyze metadata from the Bioconductor package ecosystem, enabling downstream applications like data mining and graph analytics.

recount-brain: a curated repository of human brain RNA-seq datasets metadata

The paper curates a database of human brain RNA-seq metadata to improve reproducibility and analysis of gene expression data.

Software For The Integration Of Multi-Omics Experiments In Bioconductor

The paper introduces MultiAssayExperiment, a Bioconductor package for integrating multi-omics data, demonstrating its use with TCGA datasets to simplify analysis and visualization.

Resources For Interpreting Variants In Precision Genomic Oncology Applications

The paper reviews variant interpretation resources for precision genomic oncology, including catalogs, annotation tools, and databases for clinical actionability and hypothesis generation.

GenomicDataCommons: a Bioconductor Interface to the NCI Genomic Data Commons

The paper introduces a Bioconductor package for accessing NCI Genomic Data Commons datasets, enabling integration with Bioconductor tools for cancer genomics analysis.