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

PhosPred-RF: A Novel Sequence-Based Predictor for Phosphorylation Sites Using Sequential Information Only

(2017) Leyi Wei et al.   IEEE TRANSACTIONS ON NANOBIOSCIENCE

CPPred-RF: A Sequence-based Predictor for Identifying Cell-Penetrating Peptides and Their Uptake Efficiency

(2017) Leyi Wei et al.   JOURNAL OF PROTEOME RESEARCH

Accurate prediction of functional effects for variants by combining gradient tree boosting with optimal neighborhood properties

(2017) Yuliang Pan et al.   PLoS One

HPSLPred: An Ensemble Multi-Label Classifier for Human Protein Subcellular Location Prediction with Imbalanced Source

(2017) Shixiang Wan et al.   PROTEOMICS

Sequence-based predictive modeling to identify cancerlectins

(2017) Hong-Yan Lai et al.   Oncotarget

QAcon: single model quality assessment using protein structural and contact information with machine learning techniques

(2016) Renzhi Cao et al.   BIOINFORMATICS

DeepQA: improving the estimation of single protein model quality with deep belief networks

(2016) Renzhi Cao et al.   BMC BIOINFORMATICS

Integrated protein function prediction by mining function associations, sequences, and protein–protein and gene–gene interaction networks

(2016) Renzhi Cao et al.   METHODS

iOri-Human: identify human origin of replication by incorporating dinucleotide physicochemical properties into pseudo nucleotide composition

(2016) Chang-Jian Zhang et al.   Oncotarget

Identification of Bacterial Cell Wall Lyases via Pseudo Amino Acid Composition

(2016) Xin-Xin Chen et al.   Biomed Research International

Identification of Secretory Proteins inMycobacterium tuberculosisUsing Pseudo Amino Acid Composition

(2016) Huan Yang et al.   Biomed Research International

ProFET: Feature engineering captures high-level protein functions

(2015) Dan Ofer et al.   BIOINFORMATICS

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

(2015) Patrik Koskinen et al.   BIOINFORMATICS

Deciphering the association between gene function and spatial gene-gene interactions in 3D human genome conformation

(2015) Renzhi Cao et al.   BMC GENOMICS

Integrative approaches for predicting microRNA function and prioritizing disease-related microRNA using biological interaction networks

(2015) Xiangxiang Zeng et al.   BRIEFINGS IN BIOINFORMATICS

Predicting the subcellular localization of mycobacterial proteins by incorporating the optimal tripeptides into the general form of pseudo amino acid composition

(2015) Pan-Pan Zhu et al.   Molecular BioSystems

Deep learning

(2015) Yann LeCun et al.   NATURE

Random Forest-Based Protein Model Quality Assessment (RFMQA) Using Structural Features and Potential Energy Terms

(2014) Balachandran Manavalan et al.   PLoS One

A large-scale evaluation of computational protein function prediction

(2013) Predrag Radivojac et al.   NATURE METHODS

A Protein Domain Co-Occurrence Network Approach for Predicting Protein Function and Inferring Species Phylogeny

(2011) Zheng Wang et al.   PLoS One

Analysis of protein function and its prediction from amino acid sequence

(2011) Wyatt T. Clark et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Bayesian Markov Random Field Analysis for Protein Function Prediction Based on Network Data

(2010) Yiannis A. I. Kourmpetis et al.   PLoS One

HIERARCHICAL CLASSIFICATION OF GENE ONTOLOGY TERMS USING THE GOstruct METHOD

(2010) ARTEM SOKOLOV et al.   Journal of Bioinformatics and Computational Biology

The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata

(2009) Konstantinos Liolios et al.   NUCLEIC ACIDS RESEARCH

Protein function prediction – the power of multiplicity

(2009) Robert Rentzsch et al.   TRENDS IN BIOTECHNOLOGY

The FEATURE framework for protein function annotation: modeling new functions, improving performance, and extending to novel applications

(2008) Inbal Halperin et al.   BMC GENOMICS

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