J. Michael Cherry

The paper describes a collaborative submission model for building high-quality single-cell genomics data resources, emphasizing partnership between contributors and curators to improve metadata quality and resource scalability.

Saccharomyces Genome Database released two S288C annotation updates (R64.4.1, R64.5.1) adding ncRNAs, ORFs and uORFs, overhauled YeastPathways, and expanded search, GFF and web features.

The paper updates the Alliance of Genome Resources' central infrastructure, adding tools and enhancing data management and curation capabilities.

The paper presents ENCODE4 Segway annotations for 234 human cell types, improving sensitivity in capturing regulatory patterns relevant to disease and traits.

ENCODE's containerised Workflow Description Language pipelines for ChIP-seq, ATAC-seq, DNase-seq, RNA-seq variants, Hi-C and bisulfite sequencing run on cloud or local clusters, with documented compute costs and provenance.

The paper introduces the EN-TEx resource, which provides personal epigenomes and variant-impact models across multiple tissues, revealing allele-specific loci and their associations with GWAS loci.

The paper updates RegulomeDB to improve non-coding variant annotation by integrating new functional genomic data and probabilistic scores from the SURF algorithm.

The paper introduces the ClinGen Variant Curation Interface, a platform for applying ACMG/AMP guidelines to classify genetic variants, enabling collaboration and standardization in clinical variant interpretation.

The paper describes recent updates to the Saccharomyces Genome Database, including a new reference genome, allele curation system, and resources for studying human disease using yeast.

The paper quantifies privacy leakage in functional genomics data and proposes a data-sanitization protocol to reduce it while preserving utility.

The paper systematically maps chromatin state landscapes during mouse development by profiling histone modifications across 72 tissue-stages, identifying dynamic enhancers and transcriptional regulators.

A yeast-based refactoring platform (HEx) with new inducible promoters, an engineered host strain, and homology-based assembly expressed 41 cryptic fungal gene clusters; 22 yielded non-native compounds.

The paper presents a framework to evaluate the clinical validity of gene-disease associations, validated using representative gene-disease pairs.

The paper introduces SnoVault, a metadata storage system, and encodeD, a tool for genomic data storage, both designed for the ENCODE project's data management needs.