Lista de obras - Paul D Thomas - Dominio Público Uruguay

A simple protein folding algorithm using a binary code and secondary structure constraints.

artículo científico publicado en 1995

A systems biology network model for genetic association studies of nicotine addiction and treatment.

artículo científico

Accurate prediction of the functional significance of single nucleotide polymorphisms and mutations in the ABCA1 gene

artículo científico publicado en 2005

Advances and Applications in the Quest for Orthologs

scientific article published on 01 October 2019

An iterative method for extracting energy-like quantities from protein structures.

artículo científico publicado en 1996

Ancestral Genomes: a resource for reconstructed ancestral genes and genomes across the tree of life

article

Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools

artículo científico publicado en 2006

Assessment of genome-wide protein function classification for Drosophila melanogaster

artículo científico

Bayesian parameter estimation for automatic annotation of gene functions using observational data and phylogenetic trees

artículo científico publicado en 2021

Big data and other challenges in the quest for orthologs

artículo científico publicado en 2014

BioPAX support in CellDesigner

artículo científico publicado en 2011

CAFA and the open world of protein function predictions.

artículo científico publicado en 2013

CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination

scientific article published on 01 October 2019

Coding single-nucleotide polymorphisms associated with complex vs. Mendelian disease: evolutionary evidence for differences in molecular effects.

scholarly article

Corrigendum: The BioPAX community standard for pathway data sharing

correction; published 7 December 2010

DRD1 associations with smoking abstinence across slow and normal nicotine metabolizers

artículo científico publicado en 2012

Dopamine genes and nicotine dependence in treatment-seeking and community smokers

artículo científico publicado en 2009

Erratum: Corrigendum: The BioPAX community standard for pathway data sharing

scholarly article published in Nature Biotechnology

GIGA: a simple, efficient algorithm for gene tree inference in the genomic age.

artículo científico publicado en 2010

GO functional similarity clustering depends on similarity measure, clustering method, and annotation completeness

artículo científico publicado en 2019

Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems

scientific article published on 01 October 2019

Gene Ontology Consortium: going forward

artículo científico publicado en 2015

Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire

artículo científico publicado en 2010

InterPro in 2011: new developments in the family and domain prediction database

artículo científico publicado en 2012

InterPro in 2011: new developments in the family and domain prediction database

artículo científico publicado en 2012

InterPro in 2017-beyond protein family and domain annotations

artículo científico publicado en 2016

InterPro in 2019: improving coverage, classification and access to protein sequence annotations

article by Alex Mitchell et al published 6 November 2018 in Nucleic Acids Research

InterPro: the integrative protein signature database

artículo científico publicado en 2009

Kat3 coactivators in somatic stem cells and cancer stem cells: biological roles, evolution, and pharmacologic manipulation.

artículo científico publicado en 2016

Large-scale gene function analysis with the PANTHER classification system

artículo científico publicado en 2013

Large-scale inference of gene function through phylogenetic annotation of Gene Ontology terms: case study of the apoptosis and autophagy cellular processes

artículo científico publicado en 2016

New developments in the InterPro database

artículo científico publicado en 2007

Nicotinic acetylcholine receptor beta2 subunit gene implicated in a systems-based candidate gene study of smoking cessation

artículo científico publicado en 2008

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

artículo científico publicado en 2012

On the quality of tree-based protein classification.

artículo científico

Ontologies and standards in bioscience research: for machine or for human

artículo científico

Ontology annotation: mapping genomic regions to biological function

artículo científico publicado en 2007

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

artículo científico publicado en 2013

PANTHER pathway: an ontology-based pathway database coupled with data analysis tools

artículo científico publicado en 2009

PANTHER version 10: expanded protein families and functions, and analysis tools.

artículo científico publicado en 2015

PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements

artículo científico publicado en 2016

PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools

artículo científico publicado en 2019

PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API

scientific article published on 08 December 2020

PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways

artículo científico publicado en 2007

PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium

artículo científico publicado en 2010

PANTHER-PSEP: predicting disease-causing genetic variants using position-specific evolutionary preservation

artículo científico publicado en 2016

PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification

artículo científico publicado en 2003

Perspectives on tracking data reuse across biodata resources

PhyloGenes: An online phylogenetics and functional genomics resource for plant gene function inference

scientific article published on 30 December 2020

Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium

artículo científico publicado en 2011

PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools

PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools.

artículo científico publicado en 2013

Principles of protein folding--a perspective from simple exact models.

artículo científico publicado en 1995

Protocol Update for large-scale genome and gene function analysis with the PANTHER classification system (v.14.0)

scientific article published on 25 February 2019

Reactome and the Gene Ontology: digital convergence of data resources

artículo científico publicado en 2021

Standardized benchmarking in the quest for orthologs

artículo científico publicado en 2016

SynGO: An Evidence-Based, Expert-Curated Knowledge Base for the Synapse

artículo científico publicado en 2019

The BioPAX community standard for pathway data sharing

artículo científico publicado en 2010

The Gene Ontology and the Meaning of Biological Function.

artículo científico

The Gene Ontology knowledgebase in 2023

scientific article published in 2023

The InterPro protein families database: the classification resource after 15 years

artículo científico publicado en 2015

The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database.

artículo científico publicado en 2017

The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST)

artículo científico publicado en 2020

The PANTHER database of protein families, subfamilies, functions and pathways

artículo científico publicado en 2005

The use of orthologous sequences to predict the impact of amino acid substitutions on protein function

artículo científico publicado en 2010

Tools for Predicting the Functional Impact of Nonsynonymous Genetic Variation

artículo científico publicado en 2016

TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations

article

Lista de obras de Paul D Thomas

A simple protein folding algorithm using a binary code and secondary structure constraints.

A systems biology network model for genetic association studies of nicotine addiction and treatment.

Accurate prediction of the functional significance of single nucleotide polymorphisms and mutations in the ABCA1 gene

Advances and Applications in the Quest for Orthologs

An iterative method for extracting energy-like quantities from protein structures.

Ancestral Genomes: a resource for reconstructed ancestral genes and genomes across the tree of life

Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools

Assessment of genome-wide protein function classification for Drosophila melanogaster

Bayesian parameter estimation for automatic annotation of gene functions using observational data and phylogenetic trees

Big data and other challenges in the quest for orthologs

BioPAX support in CellDesigner

CAFA and the open world of protein function predictions.

CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination

Coding single-nucleotide polymorphisms associated with complex vs. Mendelian disease: evolutionary evidence for differences in molecular effects.

Corrigendum: The BioPAX community standard for pathway data sharing

DRD1 associations with smoking abstinence across slow and normal nicotine metabolizers

Dopamine genes and nicotine dependence in treatment-seeking and community smokers

Erratum: Corrigendum: The BioPAX community standard for pathway data sharing

GIGA: a simple, efficient algorithm for gene tree inference in the genomic age.

GO functional similarity clustering depends on similarity measure, clustering method, and annotation completeness

Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems

Gene Ontology Consortium: going forward

Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire

InterPro in 2011: new developments in the family and domain prediction database

InterPro in 2011: new developments in the family and domain prediction database

InterPro in 2017-beyond protein family and domain annotations

InterPro in 2019: improving coverage, classification and access to protein sequence annotations

InterPro: the integrative protein signature database

Kat3 coactivators in somatic stem cells and cancer stem cells: biological roles, evolution, and pharmacologic manipulation.

Large-scale gene function analysis with the PANTHER classification system

Large-scale inference of gene function through phylogenetic annotation of Gene Ontology terms: case study of the apoptosis and autophagy cellular processes

New developments in the InterPro database

Nicotinic acetylcholine receptor beta2 subunit gene implicated in a systems-based candidate gene study of smoking cessation

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

On the quality of tree-based protein classification.

Ontologies and standards in bioscience research: for machine or for human

Ontology annotation: mapping genomic regions to biological function

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

PANTHER pathway: an ontology-based pathway database coupled with data analysis tools

PANTHER version 10: expanded protein families and functions, and analysis tools.

PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements

PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools

PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API

PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways

PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium

PANTHER-PSEP: predicting disease-causing genetic variants using position-specific evolutionary preservation

PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification

Perspectives on tracking data reuse across biodata resources

PhyloGenes: An online phylogenetics and functional genomics resource for plant gene function inference

Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium

PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools

PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools.

Principles of protein folding--a perspective from simple exact models.

Protocol Update for large-scale genome and gene function analysis with the PANTHER classification system (v.14.0)

Reactome and the Gene Ontology: digital convergence of data resources

Standardized benchmarking in the quest for orthologs

SynGO: An Evidence-Based, Expert-Curated Knowledge Base for the Synapse

The BioPAX community standard for pathway data sharing

The Gene Ontology and the Meaning of Biological Function.

The Gene Ontology knowledgebase in 2023

The InterPro protein families database: the classification resource after 15 years

The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database.

The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST)

The PANTHER database of protein families, subfamilies, functions and pathways

The use of orthologous sequences to predict the impact of amino acid substitutions on protein function

Tools for Predicting the Functional Impact of Nonsynonymous Genetic Variation

TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations