J. Michael Cherry
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View article: The IGVF catalog—from genetic variation to function
The IGVF catalog—from genetic variation to function Open
Genomic variation between individuals is essential for understanding how differences in the genome sequence affect molecular and cellular processes. The Impact of Genomic Variation on Function (IGVF) Consortium aims to uncover the relation…
View article: Data navigation on the ENCODE portal
Data navigation on the ENCODE portal Open
Spanning two decades, the collaborative ENCODE project aims to identify all the functional elements within human and mouse genomes. To best serve the scientific community, the comprehensive ENCODE data including results from 23,000+ functi…
View article: Integrative chromatin state annotation of 234 human ENCODE4 cell types using Segway
Integrative chromatin state annotation of 234 human ENCODE4 cell types using Segway Open
The fourth and final phase of the ENCODE consortium has newly profiled epigenetic activity in hundreds of human tissues. Chromatin state annotations created by segmentation and genome annotation (SAGA) methods such as Segway have emerged a…
View article: Gene spatial integration: enhancing spatial transcriptomics analysis via deep learning and batch effect mitigation
Gene spatial integration: enhancing spatial transcriptomics analysis via deep learning and batch effect mitigation Open
Motivation Spatial transcriptomics (ST) is a groundbreaking technique for studying the correlation between cellular organization within a tissue and its physiological and pathological properties. Every facet of spatial information, includi…
View article: CZ CELLxGENE Discover: a single-cell data platform for scalable exploration, analysis and modeling of aggregated data
CZ CELLxGENE Discover: a single-cell data platform for scalable exploration, analysis and modeling of aggregated data Open
Hundreds of millions of single cells have been analyzed using high-throughput transcriptomic methods. The cumulative knowledge within these datasets provides an exciting opportunity for unlocking insights into health and disease at the lev…
View article: <i>Saccharomyces</i> Genome Database: advances in genome annotation, expanded biochemical pathways, and other key enhancements
<i>Saccharomyces</i> Genome Database: advances in genome annotation, expanded biochemical pathways, and other key enhancements Open
Budding yeast (Saccharomyces cerevisiae) is the most extensively characterized eukaryotic model organism and has long been used to gain insight into the fundamentals of genetics, cellular biology, and the functions of specific genes and pr…
View article: <i>Saccharomyces</i>Genome Database: Advances in Genome Annotation, Expanded Biochemical Pathways, and Other Key Enhancements
<i>Saccharomyces</i>Genome Database: Advances in Genome Annotation, Expanded Biochemical Pathways, and Other Key Enhancements Open
Budding yeast ( Saccharomyces cerevisiae ) is the most extensively characterized eukaryotic model organism and has long been used to gain insight into the fundamentals of genetics, cellular biology, and the functions of specific genes and …
View article: Updates to the Alliance of Genome Resources central infrastructure
Updates to the Alliance of Genome Resources central infrastructure Open
The Alliance of Genome Resources (Alliance) is an extensible coalition of knowledgebases focused on the genetics and genomics of intensively studied model organisms. The Alliance is organized as individual knowledge centers with strong con…
View article: Updates to the Alliance of Genome Resources Central Infrastructure Alliance of Genome Resources Consortium
Updates to the Alliance of Genome Resources Central Infrastructure Alliance of Genome Resources Consortium Open
The Alliance of Genome Resources (Alliance) is an extensible coalition of knowledgebases focused on the genetics and genomics of intensively-studied model organisms. The Alliance is organized as individual knowledge centers with strong con…
View article: CZ CELL×GENE Discover: A single-cell data platform for scalable exploration, analysis and modeling of aggregated data
CZ CELL×GENE Discover: A single-cell data platform for scalable exploration, analysis and modeling of aggregated data Open
Hundreds of millions of single cells have been analyzed to date using high throughput transcriptomic methods, thanks to technological advances driving the increasingly rapid generation of single-cell data. This provides an exciting opportu…
View article: Integrative chromatin state annotation of 234 human ENCODE4 cell types using Segway reveals disease drivers
Integrative chromatin state annotation of 234 human ENCODE4 cell types using Segway reveals disease drivers Open
Towards the goal of identifying functional elements in the human genome, the fourth and final phase of the ENCODE consortium has newly profiled hundreds of human tissues using sequencing-based measurements of genomic activity such as ChIP-…
View article: The ENCODE Uniform Analysis Pipelines
The ENCODE Uniform Analysis Pipelines Open
The Encyclopedia of DNA elements (ENCODE) project is a collaborative effort to create a comprehensive catalog of functional elements in the human genome. The current database comprises more than 19000 functional genomics experiments across…
View article: Data navigation on the ENCODE Portal
Data navigation on the ENCODE Portal Open
Spanning two decades, the Encyclopaedia of DNA Elements (ENCODE) is a collaborative research project that aims to identify all the functional elements in the human and mouse genomes. To best serve the scientific community, all data generat…
View article: Data navigation on the ENCODE portal
Data navigation on the ENCODE portal Open
Spanning two decades, the Encyclopaedia of DNA Elements (ENCODE) is a collaborative research project that aims to identify all the functional elements in the human and mouse genomes. To best serve the scientific community, all data generat…
View article: The ENCODE Uniform Analysis Pipelines
The ENCODE Uniform Analysis Pipelines Open
The Encyclopedia of DNA elements (ENCODE) project is a collaborative effort to create a comprehensive catalog of functional elements in the human genome. The current database comprises more than 19000 functional genomics experiments across…
View article: The Gene Ontology knowledgebase in 2023
The Gene Ontology knowledgebase in 2023 Open
The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and noncoding RNAs). GO annotations cover genes from organisms across the tree of life…
View article: The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models
The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models Open
Understanding how genetic variants impact molecular phenotypes is a key goal of functional genomics, currently hindered by reliance on a single haploid reference genome. Here, we present the EN-TEx resource of 1,635 open-access datasets fr…
View article: Saccharomyces genome database update: server architecture, pan-genome nomenclature, and external resources
Saccharomyces genome database update: server architecture, pan-genome nomenclature, and external resources Open
As one of the first model organism knowledgebases, Saccharomyces Genome Database (SGD) has been supporting the scientific research community since 1993. As technologies and research evolve, so does SGD: from updates in software architectur…
View article: Annotating and prioritizing human non-coding variants with RegulomeDB
Annotating and prioritizing human non-coding variants with RegulomeDB Open
Nearly 90% of the disease risk-associated variants identified from genome-wide association studies (GWAS) are in non-coding regions of the genome. The annotations obtained from analyzing functional genomics assays can provide additional in…
View article: Author Correction: Perspectives on ENCODE
Author Correction: Perspectives on ENCODE Open
In this Article, the authors Rizi Ai (Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA) and Shantao Li (Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, US…
View article: Harmonizing model organism data in the Alliance of Genome Resources
Harmonizing model organism data in the Alliance of Genome Resources Open
The Alliance of Genome Resources (the Alliance) is a combined effort of 7 knowledgebase projects: Saccharomyces Genome Database, WormBase, FlyBase, Mouse Genome Database, the Zebrafish Information Network, Rat Genome Database, and the Gene…
View article: New data and collaborations at the <i>Saccharomyces</i> Genome Database: updated reference genome, alleles, and the Alliance of Genome Resources
New data and collaborations at the <i>Saccharomyces</i> Genome Database: updated reference genome, alleles, and the Alliance of Genome Resources Open
Saccharomyces cerevisiae is used to provide fundamental understanding of eukaryotic genetics, gene product function, and cellular biological processes. Saccharomyces Genome Database (SGD) has been supporting the yeast research community si…
View article: New Data and Collaborations at the<i>Saccharomyces</i>Genome Database: Updated reference genome, alleles, and the Alliance of Genome Resources
New Data and Collaborations at the<i>Saccharomyces</i>Genome Database: Updated reference genome, alleles, and the Alliance of Genome Resources Open
Saccharomyces cerevisiae is used to provide fundamental understanding of eukaryotic genetics, gene product function, and cellular biological processes. Saccharomyces Genome Database (SGD) has been supporting the yeast research community si…
View article: Multi-tissue integrative analysis of personal epigenomes
Multi-tissue integrative analysis of personal epigenomes Open
Evaluating the impact of genetic variants on transcriptional regulation is a central goal in biological science that has been constrained by reliance on a single reference genome. To address this, we constructed phased, diploid genomes for…
View article: ClinGen Variant Curation Interface: A Variant Classification Platform for the Application of Evidence Criteria from ACMG/AMP Guidelines
ClinGen Variant Curation Interface: A Variant Classification Platform for the Application of Evidence Criteria from ACMG/AMP Guidelines Open
Background Identification of clinically significant genetic alterations involved in human disease has been dramatically accelerated by developments in next-generation sequencing technologies. However, the infrastructure and accessible comp…