List of works by J. Michael Cherry

A gene ontology inferred from molecular networks

scientific article published on January 2013

A guide to best practices for Gene Ontology (GO) manual annotation.

scientific article published on 09 July 2013

A systematic approach to reconstructing transcription networks in Saccharomycescerevisiae

scientific article

AGAPE (Automated Genome Analysis PipelinE) for pan-genome analysis of Saccharomyces cerevisiae.

scientific article published on 17 March 2015

Active Interaction Mapping Reveals the Hierarchical Organization of Autophagy

scientific article published on 23 January 2017

An atlas of dynamic chromatin landscapes in mouse fetal development

scientific article published on 29 July 2020

Annotation of functional variation in personal genomes using RegulomeDB

scientific article (publication date: September 2012)

Arabidopsis thaliana: a model plant for genome analysis.

scientific article

AtDB, the Arabidopsis thaliana database, and graphical-web-display of progress by the Arabidopsis Genome Initiative.

scientific article published in January 1998

Author Correction: An atlas of dynamic chromatin landscapes in mouse fetal development

scientific article published on 10 October 2020

Author Correction: An atlas of dynamic chromatin landscapes in mouse fetal development

scientific article published on 04 January 2021

CNN-Peaks: ChIP-Seq peak detection pipeline using convolutional neural networks that imitate human visual inspection

scientific article published on 13 May 2020

CZ CELLxGENE Discover: A single-cell data platform for scalable exploration, analysis and modeling of aggregated data

Characteristics of amino acids.

scientific article published on May 2001

Codon usage table for Xenopus laevis

scientific article

Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function

scientific article published on 27 June 2008

Comparative genomics of the eukaryotes

scientific article (publication date: 24 March 2000)

Comparison of the complete protein sets of worm and yeast: orthology and divergence

scientific article

Computational Methods and Bioinformatic Tools

Computer manipulation of DNA and protein sequences

scientific article published in May 2001

Considerations for creating and annotating the budding yeast Genome Map at SGD: a progress report

scientific article published on 20 March 2012

Correction: AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome Analysis of Saccharomyces cerevisiae.

scientific article published on 27 May 2015

Cross-organism analysis using InterMine

scientific article

Curated protein information in the Saccharomyces genome database

scientific article

CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations.

scientific article published on 20 March 2012

DATABASE, The Journal of Biological Databases and Curation, is now the official journal of the International Society for Biocuration.

scientific article published on 6 December 2013

DNA termini in ciliate macronuclei

scientific article published on 01 January 1983

Data Sanitization to Reduce Private Information Leakage from Functional Genomics

scientific article published on 01 November 2020

Detection of herpes simplex virus thymidine kinase and latency-associated transcript gene sequences in human herpetic corneas by polymerase chain reaction amplification

scientific article published in May 1991

ENCODE data at the ENCODE portal

scientific article

Erratum: CORRIGENDUM: InterMOD: integrated data and tools for the unification of model organism research

scientific article published in Scientific Reports

Evaluating the Clinical Validity of Gene-Disease Associations: An Evidence-Based Framework Developed by the Clinical Genome Resource

scientific article published on 24 May 2017

Evaluating the clinical validity of gene-disease associations: an evidence-based framework developed by the Clinical Genome Resource

article

Evidence for a plasma membrane redox system on intact ascites tumor cells with different metastatic capacity

scientific article published on 01 January 1981

Expanded encyclopaedias of DNA elements in the human and mouse genomes

scientific article published on 29 July 2020

Expanded protein information at SGD: new pages and proteome browser.

scientific article

Expanding yeast knowledge online

scientific article

Expressions of hepatic genes, especially IGF-binding protein-1, correlating with serum corticosterone in microarray analysis.

scientific article published on February 2004

From one to many: expanding the Saccharomyces cerevisiae reference genome panel

scientific article published on 17 March 2016

Functional annotations for the Saccharomyces cerevisiae genome: the knowns and the known unknowns

scientific article

Fungal BLAST and Model Organism BLASTP Best Hits: new comparison resources at the Saccharomyces Genome Database (SGD)

scientific article

GA4GH: International policies and standards for data sharing across genomic research and healthcare

scientific article published on 10 November 2021

GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes

scientific article (publication date: 12 December 2004)

Gene Ontology annotations and resources

scientific article

Gene Ontology annotations at SGD: new data sources and annotation methods

scientific article

Gene ontology: tool for the unification of biology

scientific article

Genetic and physical maps of Saccharomyces cerevisiae

scientific article

Genetic dissection of an RNA enzyme

scientific article published on 01 January 1987

Genetic nomenclature guide. Saccharomyces cerevisiae

scientific article published on March 1, 1995

Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome

scientific article

Genome comparisons highlight similarity and diversity within the eukaryotic kingdoms

scientific article

Genome maps 9. Arabidopsis thaliana. Wall chart

scientific article published in October 1998

H3K4me3 Breadth Is Linked to Cell Identity and Transcriptional Consistency

scientific article published on 19 November 2015

H3K4me3 breadth is linked to cell identity and transcriptional consistency.

scientific article published on July 2014

Identification of unstable transcripts in Arabidopsis by cDNA microarray analysis: rapid decay is associated with a group of touch- and specific clock-controlled genes

scientific article

In the beginning there was babble..

scientific article (publication date: August 2012)

Incorporation of a unified protein abundance dataset into the Saccharomyces genome database

scientific article published on 01 January 2020

Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation

scientific article

Integrating functional genomic information into the Saccharomyces genome database

scientific article

Integration of macromolecular complex data into the Saccharomyces Genome Database

scientific article published on 01 January 2019

Integration of new alternative reference strain genome sequences into the Saccharomyces genome database.

scientific article published on June 2016

Integrative Meta-Assembly Pipeline (IMAP): Chromosome-level genome assembler combining multiple de novo assemblies

scientific article published on 27 August 2019

InterMOD: integrated data and tools for the unification of model organism research

scientific article (publication date: 2013)

Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote

scientific article

Making Linked Data SPARQL with the InterMine Biological Data Warehouse ⬇️

Microarray data quality analysis: lessons from the AFGC project

scholarly article published 2002

Microarray data quality analysis: lessons from the AFGC project. Arabidopsis Functional Genomics Consortium.

scientific article

Mining experimental evidence of molecular function claims from the literature.

scientific article

Molecular linguistics: extracting information from gene and protein sequences

scientific article

Mutational analysis of conserved nucleotides in a self-splicing group I intron

scientific article published on 01 October 1990

New developments on the Encyclopedia of DNA Elements (ENCODE) data portal

scientific article published on 01 January 2020

New mutant phenotype data curation system in the Saccharomyces Genome Database

article

Ontology application and use at the ENCODE DCC

scientific article

Outreach and online training services at the Saccharomyces Genome Database

scientific article

PatMatch: a program for finding patterns in peptide and nucleotide sequences

scientific article

Perspectives on ENCODE

scientific article published on 29 July 2020

Plant biology in the post-Gutenberg era. Everything you wanted to know and more on the World Wide Web.

scientific article

Prevention of data duplication for high throughput sequencing repositories.

scientific article

Principles of metadata organization at the ENCODE data coordination center.

scientific article

Providing Access to Genomic Variant Knowledge in a Healthcare Setting: A Vision for the ClinGen Electronic Health Records Workgroup

scientific article

RNAcentral: a comprehensive database of non-coding RNA sequences

scientific article (publication date: 4 January 2017)

RNAcentral: a hub of information for non-coding RNA sequences

scientific article published on 5 November 2018

RNAcentral: a hub of information for non-coding RNA sequences

scholarly article published in Nucleic Acids Research

SGD: Saccharomyces Genome Database

scientific article (publication date: 1998)

SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data

scientific article

Saccharomyces Genome Database

scientific article published in January 2002

Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins

scientific article published on January 2003

Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO)

scientific article

Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms

scientific article (publication date: 2004)

Saccharomyces Genome Database provides mutant phenotype data.

scientific article

Saccharomyces Genome Database provides tools to survey gene expression and functional analysis data

scientific article

Saccharomyces Genome Database: the genomics resource of budding yeast

scientific article (publication date: 2012)

Saccharomyces cerevisiae S288C genome annotation: a working hypothesis

scientific article

Saccharomyces cerevisiae homoserine kinase is homologous to prokaryotic homoserine kinases

scientific journal article

Saccharomyces genome database informs human biology.

scientific article published on 11 November 2017

Saccharomyces genome database provides new regulation data

scientific article

Saccharomyces genome database: underlying principles and organisation

scientific article

SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata

scientific article

SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata

Tetrahymena Genome Database (TGD): a new genomic resource for Tetrahymena thermophila research.

scientific article

The ENCODE Portal as an Epigenomics Resource

scientific article published on 01 December 2019

The Encyclopedia of DNA elements (ENCODE): data portal update

scientific article published on 6 November 2017

The Gene Ontology (GO) database and informatics resource

scientific article (publication date: 2004)

The Gene Ontology knowledgebase in 2023

scientific article published in 2023

The Saccharomyces Genome Database Variant Viewer

scientific article

The Saccharomyces Genome Database: A Tool for Discovery.

scientific article published on 02 December 2015

The Saccharomyces Genome Database: Advanced Searching Methods and Data Mining.

scientific article

The Saccharomyces Genome Database: Exploring Biochemical Pathways and Mutant Phenotypes

scientific article published on 2 December 2015

The Saccharomyces Genome Database: Exploring Genome Features and Their Annotations.

scientific article published on 2 December 2015

The Saccharomyces Genome Database: Gene Product Annotation of Function, Process, and Component

scientific article published on 02 December 2015

The Stanford Microarray Database

scientific article

The YeastGenome app: the Saccharomyces Genome Database at your fingertips

scientific article

The genome sequence of Drosophila melanogaster

scientific article

The internally located telomeric sequences in the germ-line chromosomes of Tetrahymena are at the ends of transposon-like elements

scientific article published in December 1985

The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple Saccharomyces cerevisiae strains at the Saccharomyces Genome Database

scientific article published on 13 March 2013

The nucleotide sequence of Saccharomyces cerevisiae chromosome V.

scientific article published on May 1997

The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI.

scientific article published in May 1997

The reference genome sequence of Saccharomyces cerevisiae: then and now.

scientific article published on 20 March 2014

Toward an interactive article: integrating journals and biological databases.

scientific article

Towards BioDBcore: a community-defined information specification for biological databases

scientific article

Towards BioDBcore: a community-defined information specification for biological databases

scientific article (publication date: 2011)

Transcriptome visualization and data availability at the Saccharomyces Genome Database

scientific article published on 01 January 2020

Unified display of Arabidopsis thaliana physical maps from AtDB, the A.thaliana database

scientific article published on January 1999

Updated regulation curation model at the Saccharomyces Genome Database.

scientific article published in January 2018

Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study

scientific article

Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure

scientific article

Visualization of expression clusters using Sammon's non-linear mapping

scientific article published on 01 July 2001

XenMine: A genomic interaction tool for the Xenopus community

scientific article published on 03 May 2016

Yeast as a model organism

scientific article

YeastMine--an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit.

scientific article

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