Large-scale automated function prediction of protein sequences and an experimental case study validation on PTEN transcript variants

NegGOA: negative GO annotations selection using ontology structure

(2016) Guangyuan Fu et al.   BIOINFORMATICS

UniProt-DAAC: domain architecture alignment and classification, a new method for automatic functional annotation in UniProtKB

(2016) Tunca Doğan et al.   BIOINFORMATICS

Prediction of Metabolic Pathway Involvement in Prokaryotic UniProtKB Data by Association Rule Mining

(2016) Imane Boudellioua et al.   PLoS One

Functional classification of CATH superfamilies: a domain-based approach for protein function annotation

(2015) Sayoni Das et al.   BIOINFORMATICS

The PI3K/AKT/mTOR interactive pathway

(2015) Tulin Ersahin et al.   Molecular BioSystems

CATH FunFHMMer web server: protein functional annotations using functional family assignments

(2015) Sayoni Das et al.   NUCLEIC ACIDS RESEARCH

INGA: protein function prediction combining interaction networks, domain assignments and sequence similarity

(2015) Damiano Piovesan et al.   NUCLEIC ACIDS RESEARCH

SIFTER search: a web server for accurate phylogeny-based protein function prediction

(2015) Sayed M. Sahraeian et al.   NUCLEIC ACIDS RESEARCH

PFP/ESG: automated protein function prediction servers enhanced with Gene Ontology visualization tool

(2014) Ishita K. Khan et al.   BIOINFORMATICS

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

(2014) B. E. Suzek et al.   BIOINFORMATICS

Disruptive CHD8 Mutations Define a Subtype of Autism Early in Development

(2014) Raphael Bernier et al.   CELL

The GOA database: Gene Ontology annotation updates for 2015

(2014) Rachael P. Huntley et al.   NUCLEIC ACIDS RESEARCH

Computational Prediction of Protein Function Based on Weighted Mapping of Domains and GO Terms

(2014) Zhixia Teng et al.   Biomed Research International

Parametric Bayesian priors and better choice of negative examples improve protein function prediction

(2013) Noah Youngs et al.   BIOINFORMATICS

Protein function prediction by massive integration of evolutionary analyses and multiple data sources

(2013) Domenico Cozzetto et al.   BMC BIOINFORMATICS

A novel function prediction approach using protein overlap networks

(2013) Shide Liang et al.   BMC Systems Biology

A large-scale evaluation of computational protein function prediction

(2013) Predrag Radivojac et al.   NATURE METHODS

Argot2: a large scale function prediction tool relying on semantic similarity of weighted Gene Ontology terms

(2012) Marco Falda et al.   BMC BIOINFORMATICS

EnzML: multi-label prediction of enzyme classes using InterPro signatures

(2012) Luna De Ferrari et al.   BMC BIOINFORMATICS

CombFunc: predicting protein function using heterogeneous data sources

(2012) Mark N. Wass et al.   NUCLEIC ACIDS RESEARCH

HAMAP in 2013, new developments in the protein family classification and annotation system

(2012) I. Pedruzzi et al.   NUCLEIC ACIDS RESEARCH

COFACTOR: an accurate comparative algorithm for structure-based protein function annotation

(2012) Ambrish Roy et al.   NUCLEIC ACIDS RESEARCH

LIBSVM

(2012) Chih-Chung Chang et al.   ACM Transactions on Intelligent Systems and Technology

Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study

(2011) M. C. Costanzo et al.   Database-The Journal of Biological Databases and Curation

Inhibition of Akt signaling in hepatoma cells induces apoptotic cell death independent of Akt activation status

(2010) Francesca Buontempo et al.   INVESTIGATIONAL NEW DRUGS

GOPred: GO Molecular Function Prediction by Combined Classifiers

(2010) Ömer Sinan Saraç et al.   PLoS One

ESG: extended similarity group method for automated protein function prediction

(2009) Meghana Chitale et al.   BIOINFORMATICS

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