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

por Thomas, Paul D
Publicado 2010

Ontologies and Standards in Bioscience Research: For Machine or for Human

por Mi, Huaiyu, Thomas, Paul D.
Publicado 2011

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

por Liu, Meng, Thomas, Paul D.
Publicado 2019

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

por Mi, Huaiyu, Muruganujan, Anushya, Thomas, Paul D.
Publicado 2013

The Use of Orthologous Sequences to Predict the Impact of Amino Acid Substitutions on Protein Function

por Marini, Nicholas J., Thomas, Paul D., Rine, Jasper
Publicado 2010

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

por Tang, Haiming, Finn, Robert D, Thomas, Paul D
Publicado 2019

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

por Mi, Huaiyu, Guo, Nan, Kejariwal, Anish, Thomas, Paul D.
Publicado 2007

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

por Gaudet, Pascale, Livstone, Michael S., Lewis, Suzanna E., Thomas, Paul D.
Publicado 2011

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

por Mi, Huaiyu, Poudel, Sagar, Muruganujan, Anushya, Casagrande, John T., Thomas, Paul D.
Publicado 2016

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

por Mi, Huaiyu, Muruganujan, Anushya, Ebert, Dustin, Huang, Xiaosong, Thomas, Paul D
Publicado 2019

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

por Feuermann, Marc, Gaudet, Pascale, Mi, Huaiyu, Lewis, Suzanna E., Thomas, Paul D.
Publicado 2016

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

por Mi, Huaiyu, Dong, Qing, Muruganujan, Anushya, Gaudet, Pascale, Lewis, Suzanna, Thomas, Paul D.
Publicado 2010

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

por Thomas, Paul D., Wood, Valerie, Mungall, Christopher J., Lewis, Suzanna E., Blake, Judith A.
Publicado 2012

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

por Huang, Xiaosong, Albou, Laurent-Philippe, Mushayahama, Tremayne, Muruganujan, Anushya, Tang, Haiming, Thomas, Paul D
Publicado 2019

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

por Mi, Huaiyu, Huang, Xiaosong, Muruganujan, Anushya, Tang, Haiming, Mills, Caitlin, Kang, Diane, Thomas, Paul D.
Publicado 2017

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

por Rawlings, Neil D, Barrett, Alan J, Thomas, Paul D, Huang, Xiaosong, Bateman, Alex, Finn, Robert D
Publicado 2018

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

por Mi, Huaiyu, Ebert, Dustin, Muruganujan, Anushya, Mills, Caitlin, Albou, Laurent-Philippe, Mushayamaha, Tremayne, Thomas, Paul D
Publicado 2020

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

por Vega Yon, George G., Thomas, Duncan C., Morrison, John, Mi, Huaiyu, Thomas, Paul D., Marjoram, Paul
Publicado 2021

Accurate Prediction of the Functional Significance of Single Nucleotide Polymorphisms and Mutations in the ABCA1 Gene

por Brunham, Liam R, Singaraja, Roshni R, Pape, Terry D, Kejariwal, Anish, Thomas, Paul D, Hayden, Michael R
Publicado 2005

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

por Thomas, Paul D., Kejariwal, Anish, Guo, Nan, Mi, Huaiyu, Campbell, Michael J., Muruganujan, Anushya, Lazareva-Ulitsky, Betty
Publicado 2006