PANNZER —A practical tool for protein function prediction

Transcriptomic time-series analysis of cold- and heat-shock response in psychrotrophic lactic acid bacteria

(2021) Ilhan Cem Duru et al.   BMC GENOMICS

NetQuilt: deep multispecies network-based protein function prediction using homology-informed network similarity

(2021) Meet Barot et al.   BIOINFORMATICS

Kin selection explains the evolution of cooperation in the gut microbiota

(2021) Camille Simonet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DeepGraphGO: graph neural network for large-scale, multispecies protein function prediction

(2021) Ronghui You et al.   BIOINFORMATICS

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

NetGO 2.0: improving large-scale protein function prediction with massive sequence, text, domain, family and network information

(2021) Shuwei Yao et al.   NUCLEIC ACIDS RESEARCH

Accurate prediction of protein structures and interactions using a three-track neural network

(2021) Minkyung Baek et al.   SCIENCE

Genome-wide selection and genetic improvement during modern maize breeding

(2020) Baobao Wang et al.   NATURE GENETICS

Benchmarking gene ontology function predictions using negative annotations

(2020) Alex Warwick Vesztrocy et al.   BIOINFORMATICS

Graph2GO: a multi-modal attributed network embedding method for inferring protein functions

(2020) Kunjie Fan et al.   GigaScience

UniProt: the universal protein knowledgebase in 2021

(2020) et al.   NUCLEIC ACIDS RESEARCH

The genome of Cucurbita argyrosperma (silver-seed gourd) reveals faster rates of protein-coding gene and long noncoding RNA turnover and neofunctionalization within Cucurbita

(2019) Josué Barrera-Redondo et al.   Molecular Plant

NetGO: improving large-scale protein function prediction with massive network information

(2019) Ronghui You et al.   NUCLEIC ACIDS RESEARCH

INGA 2.0: improving protein function prediction for the dark proteome

(2019) Damiano Piovesan et al.   NUCLEIC ACIDS RESEARCH

FunFam protein families improve residue level molecular function prediction

(2019) Linus Scheibenreif et al.   BMC BIOINFORMATICS

Novel comparison of evaluation metrics for gene ontology classifiers reveals drastic performance differences

(2019) Ilya Plyusnin et al.   PLoS Computational Biology

GOLabeler: improving sequence-based large-scale protein function prediction by learning to rank

(2018) Ronghui You et al.   BIOINFORMATICS

AAI-profiler: fast proteome-wide exploratory analysis reveals taxonomic identity, misclassification and contamination

(2018) Alan J Medlar et al.   NUCLEIC ACIDS RESEARCH

PANNZER2: a rapid functional annotation web server

(2018) Petri Törönen et al.   NUCLEIC ACIDS RESEARCH

The draft genome sequence of cork oak

(2018) António Marcos Ramos et al.   Scientific Data

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

(2018) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

ProLanGO: Protein Function Prediction Using Neural Machine Translation Based on a Recurrent Neural Network

(2017) Renzhi Cao et al.   MOLECULES

The Bologna Annotation Resource (BAR 3.0): improving protein functional annotation

(2017) Giuseppe Profiti et al.   NUCLEIC ACIDS RESEARCH

Enhancing protein function prediction with taxonomic constraints – The Argot2.5 web server

(2016) Enrico Lavezzo et al.   METHODS

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

FFPred 3: feature-based function prediction for all Gene Ontology domains

(2016) Domenico Cozzetto et al.   Scientific Reports

PANNZER: high-throughput functional annotation of uncharacterized proteins in an error-prone environment

(2015) Patrik Koskinen et al.   BIOINFORMATICS

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

SANSparallel: interactive homology search against Uniprot

(2015) Panu Somervuo et al.   NUCLEIC ACIDS RESEARCH

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

A close look at protein function prediction evaluation protocols

(2015) Indika Kahanda et al.   GigaScience

Categorisation of sugar acid dehydratases in Aspergillus niger

(2014) Francine A. Motter et al.   FUNGAL GENETICS AND BIOLOGY

100% Classification Accuracy Considered Harmful: The Normalized Information Transfer Factor Explains the Accuracy Paradox

(2014) Francisco J. Valverde-Albacete et al.   PLoS One

Information-theoretic evaluation of predicted ontological annotations

(2013) Wyatt T. Clark et al.   BIOINFORMATICS

Characterizing the state of the art in the computational assignment of gene function: lessons from the first critical assessment of functional annotation (CAFA)

(2013) Jesse Gillis et al.   BMC BIOINFORMATICS

A large-scale evaluation of computational protein function prediction

(2013) Predrag Radivojac et al.   NATURE METHODS

The Structure–Function Linkage Database

(2013) Eyal Akiva et al.   NUCLEIC ACIDS RESEARCH

A beginner's guide to eukaryotic genome annotation

(2012) Mark Yandell et al.   NATURE REVIEWS GENETICS

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Evolutionary Trace Annotation Server: automated enzyme function prediction in protein structures using 3D templates

(2009) R. Matthew Ward et al.   BIOINFORMATICS

Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies

(2009) Alexandra M. Schnoes et al.   PLoS Computational Biology

High-throughput functional annotation and data mining with the Blast2GO suite

(2008) S. Gotz et al.   NUCLEIC ACIDS RESEARCH

An experimental comparison of performance measures for classification

(2008) C. Ferri et al.   PATTERN RECOGNITION LETTERS

PFP: Automated prediction of gene ontology functional annotations with confidence scores using protein sequence data

(2008) Troy Hawkins et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS