PANTHER : Making genome‐scale phylogenetics accessible to all

Updates to HCOP: the HGNC comparison of orthology predictions tool

(2021) Bethan Yates et al.   BRIEFINGS IN BIOINFORMATICS

The Quest for Orthologs benchmark service and consensus calls in 2020

(2020) Adrian M Altenhoff et al.   NUCLEIC ACIDS RESEARCH

Expanded encyclopaedias of DNA elements in the human and mouse genomes

(2020) Jill E. Moore et al.   NATURE

SBML Level 3: an extensible format for the exchange and reuse of biological models

(2020) Sarah M Keating et al.   Molecular Systems Biology

FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs

(2020) Imad Abugessaisa et al.   NUCLEIC ACIDS RESEARCH

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

(2020) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

PEREGRINE: A genome-wide prediction of enhancer to gene relationships supported by experimental evidence

(2020) Caitlin Mills et al.   PLoS One

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

(2020) Peifen Zhang et al.   Plant Direct

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

(2019) Huaiyu Mi et al.   Nature Protocols

Advances and Applications in the Quest for Orthologs

(2019) Natasha Glover et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Alliance of Genome Resources: Building a Modern Data Ecosystem for Model Organism Databases

(2019)   GENETICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

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

(2018) Xiaosong Huang et al.   NUCLEIC ACIDS RESEARCH

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

(2018) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

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

(2016) Haiming Tang et al.   BIOINFORMATICS

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

(2016) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

Event inference in multidomain families with phylogenetic reconciliation

(2015) Maureen Stolzer et al.   BMC BIOINFORMATICS

Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream

(2015) Brigitte Boeckmann et al.   Genome Biology and Evolution

From genome to function by studying eQTLs

(2014) Harm-Jan Westra et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Large-scale gene function analysis with the PANTHER classification system

(2013) Huaiyu Mi et al.   Nature Protocols

TreeFam v9: a new website, more species and orthology-on-the-fly

(2013) Fabian Schreiber et al.   NUCLEIC ACIDS RESEARCH

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

(2011) P. Gaudet et al.   BRIEFINGS IN BIOINFORMATICS

Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development

(2010) Jennifer I Deegan (née Clark) et al.   BMC BIOINFORMATICS

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

(2010) Paul D Thomas   BMC BIOINFORMATICS

The BioPAX community standard for pathway data sharing

(2010) Emek Demir et al.   NATURE BIOTECHNOLOGY

The Systems Biology Graphical Notation

(2009) Nicolas Le Novère et al.   NATURE BIOTECHNOLOGY

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

(2009) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

The Gene Ontology's Reference Genome Project: A Unified Framework for Functional Annotation across Species

(2009)   PLoS Computational Biology