List of works - Judith A. Blake

A Resource of Quantitative Functional Annotation for Homo sapiens Genes

scientific article published on February 2012

A critical assessment of Mus musculus gene function prediction using integrated genomic evidence

scientific article

A domain ontology for the Non-Coding RNA field

A method for increasing expressivity of Gene Ontology annotations using a compositional approach

scientific article

A procedure for assessing GO annotation consistency

scientific article published on June 2005

A promoter-level mammalian expression atlas

scientific article

A semantic approach for knowledge capture of MIcroRNA-Target gene interactions

article

A short study on the success of the Gene Ontology

2004 article

Access to immunology through the Gene Ontology

scientific article published on October 2008

An effective biomedical document classification scheme in support of biocuration: addressing class imbalance

An en masse phenotype and function prediction system for Mus musculus

scientific article published on 27 June 2008

An ontology-based MicroRNA knowledge sharing and acquisition framework

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

scientific article (publication date: 5 December 2002)

Application of comparative biology in GO functional annotation: the mouse model

scientific article

Autism candidate genes via mouse phenomics

scientific article published on 21 March 2011

Automated Annotation-Based Bio-Ontology Alignment with Structural Validation

scientific article published on 30 July 2009

Beyond the data deluge: data integration and bio-ontologies

scientific article

Bio-ontologies-fast and furious

scientific article published on June 2004

Biological nomenclatures: a source of lexical knowledge and ambiguity

scientific article published on January 2004

Cisplatin-resistant triple-negative breast cancer subtypes: multiple mechanisms of resistance

scientific article published on 04 November 2019

Concept annotation in the CRAFT corpus

scientific article

Connecting sequence and biology in the laboratory mouse

scientific article

Corralling conditional mutations: A unified resource for mouse phenotypes

article

Curating gene sets: challenges and opportunities for integrative analysis

article

DFLAT: functional annotation for human development

scientific article

Disease model curation improvements at Mouse Genome Informatics

scientific article published on 20 March 2012

Effective biomedical document classification for identifying publications relevant to the mouse Gene Expression Database (GXD)

scientific article published on 01 January 2020

Effective biomedical document classification for identifying publications relevant to the mouse Gene Expression Database (GXD).

scientific article published on January 2017

Equipping and organizing comparative molecular genetics laboratories

scientific article

Extension and integration of the gene ontology (GO): combining GO vocabularies with external vocabularies

scientific article published on December 2002

Finding our way through phenotypes

scientific article

Framework for a protein ontology

scientific article

Framework for a protein ontology

Functional annotation of a full-length mouse cDNA collection

scientific article (publication date: 8 February 2001)

Gearing up to handle the mosaic nature of life in the quest for orthologs

scientific article published on 30 August 2017

Gene Ontology annotation of sequence-specific DNA binding transcription factors: setting the stage for a large-scale curation effort

scientific article published on 27 August 2013

Gene Ontology annotations and resources

scientific article

Gene Ontology annotations: what they mean and where they come from

scientific article

Gene ontology: tool for the unification of biology

scientific article

Gene regulation knowledge commons: community action takes care of DNA binding transcription factors

scientific article

GlyGen: Computational and Informatics Resources for Glycoscience

scientific article published on 01 January 2020

Hematopoietic cell types: prototype for a revised cell ontology

scientific article

Human disease genes and their cloned mouse orthologs: exploration of the FANTOM2 cDNA sequence data set

scientific article

Improving Interpretation of Cardiac Phenotypes and Enhancing Discovery With Expanded Knowledge in the Gene Ontology

scientific article published in February 2018

Informatics for mouse genetics and genome mapping

scientific article published on February 1998

Integrating image caption information into biomedical document classification in support of biocuration

scientific article published on 01 January 2020

Integrating text mining into the MGI biocuration workflow

scientific article

Integration of Mouse Phenome Data Resources

Investigation of COVID-19 comorbidities reveals genes and pathways coincident with the SARS-CoV-2 viral disease

scientific article published on 21 September 2020

Investigation of COVID-19 comorbidities reveals genes and pathways coincident with the SARS-CoV-2 viral disease

scientific article published on 30 November 2020

Logical development of the cell ontology

scientific article

MEETING REPORT

scientific article published on 01 October 1997

MGD: the Mouse Genome Database

scientific article published on January 2003

Manual Gene Ontology annotation workflow at the Mouse Genome Informatics Database

scientific article

Methodology for the inference of gene function from phenotype data

scientific article

Model organism data evolving in support of translational medicine

scientific article published on 17 September 2018

Modeling biochemical pathways in the gene ontology

scientific article published on September 2016

Mouse Genome Database (MGD) 2019

scholarly article by Carol J Bult et al published 8 November 2018 in Nucleic Acids Research

Mouse Genome Database (MGD)-2017: community knowledge resource for the laboratory mouse

scientific article

Mouse Genome Database (MGD)-2018: knowledgebase for the laboratory mouse

scientific article published on 30 October 2017

Mouse Genome Database (MGD): Knowledgebase for mouse-human comparative biology

scientific article published on 24 November 2020

Mouse Genome Database: From sequence to phenotypes and disease models

scientific article

Mouse Genome Informatics (MGI): Resources for Mining Mouse Genetic, Genomic, and Biological Data in Support of Primary and Translational Research.

scientific article

Mouse Genome Informatics (MGI): latest news from MGD and GXD

scientific article published on 26 October 2021

Mouse Genome Informatics (MGI): reflecting on 25 years

scientific article

Mouse genome database 2016.

scientific article

Mouse genome informatics (MGI) resources for pathology and toxicology

scientific article

OMIT: dynamic, semi-automated ontology development for the microRNA domain

scientific article

OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data

scientific article

On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report

scientific article

Ontological visualization of protein-protein interactions

scientific article

Ontology based molecular signatures for immune cell types via gene expression analysis

scientific article

Ontology development for biological systems: immunology

scientific article

Ontology engineering

scientific article

Orthology for comparative genomics in the mouse genome database

scientific article (publication date: August 2015)

Pax genes: regulators of lineage specification and progenitor cell maintenance

scientific article published on February 2014

Pax3 transcripts in melanoblast development

scientific article published in December 2005

Perplexing Pax: from puzzle to paradigm.

scientific article

Phylogeny and relationships of pleurotomariid gastropods (Mollusca: Gastropoda): an assessment based on partial 18S rDNA and cytochrome c oxidase I sequences.

scientific article published on March 1997

Program description: Strategies for biological annotation of mammalian systems: implementing gene ontologies in mouse genome informatics.

scientific article published on May 2001

Protein Ontology (PRO): enhancing and scaling up the representation of protein entities

scientific article

Protein Ontology: a controlled structured network of protein entities

scientific article

Providing the missing link: the exposure science ontology ExO

scientific article published on 12 March 2012

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

Reactome and the Gene Ontology: digital convergence of data resources

scientific article

Recent advances in biocuration: meeting report from the Fifth International Biocuration Conference

scientific article (publication date: 2012)

Report of the Second International Nomenclature Workshop. Cambridge, United Kingdom, May 1-2, 1999.

scientific article published in December 1999

Representing kidney development using the gene ontology

scientific article

Rules and guidelines for mouse gene nomenclature: a condensed version. International Committee on Standardized Genetic Nomenclature for Mice.

scientific article

Rules and guidelines for mouse gene, allele, and mutation nomenclature: a condensed version

scientific article

Sensing the cilium, digital capture of ciliary data for comparative genomics investigations.

scientific article

Standardized description of scientific evidence using the Evidence Ontology (ECO)

scientific article

Supplementary data need to be kept in public repositories

scientific article published in Nature

TGF-beta signaling proteins and the Protein Ontology

scientific article

TOWARDS COORDINATED INTERNATIONAL SUPPORT OF CORE DATA RESOURCES FOR THE LIFE SCIENCES

scientific article (publication date: 23 February 2017)

Ten quick tips for using the gene ontology

scientific article

Text mining for biology - the way forward: opinions from leading scientists

scientific article (publication date: 2008)

The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability

scientific article

The Characterisation of Pax3 Expressant Cells in Adult Peripheral Nerve ⬇️

scientific article published on March 19, 2013

The Gene Ontology (GO) Project: Structured Vocabularies for Molecular Biology and Their Application to Genome and Expression Analysis

article

The Gene Ontology (GO) database and informatics resource

scientific article (publication date: 2004)

The Gene Ontology (GO) project: structured vocabularies for molecular biology and their application to genome and expression analysis

scientific article

The Gene Ontology knowledgebase in 2023

scientific article published in 2023

The Mouse Genome Database (MGD): a community resource. Status and enhancements. The Mouse Genome Informatics Group ⬇️

scientific article published on January 1, 1998

The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse

scientific article published on 10 November 2011

The Mouse Genome Database (MGD): expanding genetic and genomic resources for the laboratory mouse. The Mouse Genome Database Group

scientific article published on January 2000

The Mouse Genome Database (MGD): facilitating mouse as a model for human biology and disease

scientific article

The Mouse Genome Database (MGD): from genes to mice--a community resource for mouse biology

scientific article

The Mouse Genome Database (MGD): genetic and genomic information about the laboratory mouse. The Mouse Genome Database Group.

scientific article published on January 1999

The Mouse Genome Database (MGD): integrating biology with the genome.

scientific article

The Mouse Genome Database (MGD): integration nexus for the laboratory mouse

scientific article

The Mouse Genome Database (MGD): mouse biology and model systems

scientific article published on 23 December 2007

The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics

scientific article

The Mouse Genome Database (MGD): the model organism database for the laboratory mouse ⬇️

scientific article published on January 1, 2002

The Mouse Genome Database (MGD): updates and enhancements

scientific article

The Mouse Genome Database genotypes::phenotypes

scientific article published on 3 November 2008

The Mouse Genome Database: enhancements and updates

scientific article

The Mouse Genome Database: integration of and access to knowledge about the laboratory mouse

scientific article

The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology

scientific article

The Protein Ontology: a structured representation of protein forms and complexes

scientific article

The development of non-coding RNA ontology

scientific article published on January 2016

The mouse Gene Expression Database (GXD): updates and enhancements

scientific article published on January 2004

The mouse genome database (MGD): new features facilitating a model system

scientific article

The mouse genome database: a resource for today and tomorrow

scientific article

The mouse genome database: genotypes, phenotypes, and models of human disease

scientific article

The representation of protein complexes in the Protein Ontology (PRO).

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)

Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon

scientific article

List of works by Judith A. Blake

A Resource of Quantitative Functional Annotation for Homo sapiens Genes

A critical assessment of Mus musculus gene function prediction using integrated genomic evidence

A domain ontology for the Non-Coding RNA field

A method for increasing expressivity of Gene Ontology annotations using a compositional approach

A procedure for assessing GO annotation consistency

A promoter-level mammalian expression atlas

A semantic approach for knowledge capture of MIcroRNA-Target gene interactions

A short study on the success of the Gene Ontology

Access to immunology through the Gene Ontology

An effective biomedical document classification scheme in support of biocuration: addressing class imbalance

An en masse phenotype and function prediction system for Mus musculus

An ontology-based MicroRNA knowledge sharing and acquisition framework

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

Application of comparative biology in GO functional annotation: the mouse model

Autism candidate genes via mouse phenomics

Automated Annotation-Based Bio-Ontology Alignment with Structural Validation

Beyond the data deluge: data integration and bio-ontologies

Bio-ontologies-fast and furious

Biological nomenclatures: a source of lexical knowledge and ambiguity

Cisplatin-resistant triple-negative breast cancer subtypes: multiple mechanisms of resistance

Concept annotation in the CRAFT corpus

Connecting sequence and biology in the laboratory mouse

Corralling conditional mutations: A unified resource for mouse phenotypes

Curating gene sets: challenges and opportunities for integrative analysis

DFLAT: functional annotation for human development

Disease model curation improvements at Mouse Genome Informatics

Effective biomedical document classification for identifying publications relevant to the mouse Gene Expression Database (GXD)

Effective biomedical document classification for identifying publications relevant to the mouse Gene Expression Database (GXD).

Equipping and organizing comparative molecular genetics laboratories

Extension and integration of the gene ontology (GO): combining GO vocabularies with external vocabularies

Finding our way through phenotypes

Framework for a protein ontology

Framework for a protein ontology

Functional annotation of a full-length mouse cDNA collection

Gearing up to handle the mosaic nature of life in the quest for orthologs

Gene Ontology annotation of sequence-specific DNA binding transcription factors: setting the stage for a large-scale curation effort

Gene Ontology annotations and resources

Gene Ontology annotations: what they mean and where they come from

Gene ontology: tool for the unification of biology

Gene regulation knowledge commons: community action takes care of DNA binding transcription factors

GlyGen: Computational and Informatics Resources for Glycoscience

Hematopoietic cell types: prototype for a revised cell ontology

Human disease genes and their cloned mouse orthologs: exploration of the FANTOM2 cDNA sequence data set

Improving Interpretation of Cardiac Phenotypes and Enhancing Discovery With Expanded Knowledge in the Gene Ontology

Informatics for mouse genetics and genome mapping

Integrating image caption information into biomedical document classification in support of biocuration

Integrating text mining into the MGI biocuration workflow

Integration of Mouse Phenome Data Resources

Investigation of COVID-19 comorbidities reveals genes and pathways coincident with the SARS-CoV-2 viral disease

Investigation of COVID-19 comorbidities reveals genes and pathways coincident with the SARS-CoV-2 viral disease

Logical development of the cell ontology

MEETING REPORT

MGD: the Mouse Genome Database

Manual Gene Ontology annotation workflow at the Mouse Genome Informatics Database

Methodology for the inference of gene function from phenotype data

Model organism data evolving in support of translational medicine

Modeling biochemical pathways in the gene ontology

Mouse Genome Database (MGD) 2019

Mouse Genome Database (MGD)-2017: community knowledge resource for the laboratory mouse

Mouse Genome Database (MGD)-2018: knowledgebase for the laboratory mouse

Mouse Genome Database (MGD): Knowledgebase for mouse-human comparative biology

Mouse Genome Database: From sequence to phenotypes and disease models

Mouse Genome Informatics (MGI): Resources for Mining Mouse Genetic, Genomic, and Biological Data in Support of Primary and Translational Research.

Mouse Genome Informatics (MGI): latest news from MGD and GXD

Mouse Genome Informatics (MGI): reflecting on 25 years

Mouse genome database 2016.

Mouse genome informatics (MGI) resources for pathology and toxicology

OMIT: dynamic, semi-automated ontology development for the microRNA domain

OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data

On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report

Ontological visualization of protein-protein interactions

Ontology based molecular signatures for immune cell types via gene expression analysis

Ontology development for biological systems: immunology

Ontology engineering

Orthology for comparative genomics in the mouse genome database

Pax genes: regulators of lineage specification and progenitor cell maintenance

Pax3 transcripts in melanoblast development

Perplexing Pax: from puzzle to paradigm.

Phylogeny and relationships of pleurotomariid gastropods (Mollusca: Gastropoda): an assessment based on partial 18S rDNA and cytochrome c oxidase I sequences.