SDN2GO: An Integrated Deep Learning Model for Protein Function Prediction

DMfold: A Novel Method to Predict RNA Secondary Structure With Pseudoknots Based on Deep Learning and Improved Base Pair Maximization Principle

(2019) Linyu Wang et al.   Frontiers in Genetics

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

Protein Function Prediction: From Traditional Classifier to Deep Learning

(2019) Zhibin Lv et al.   PROTEOMICS

DEEPred: Automated Protein Function Prediction with Multi-task Feed-forward Deep Neural Networks

(2019) Ahmet Sureyya Rifaioglu et al.   Scientific Reports

iProEP: A Computational Predictor for Predicting Promoter

(2019) Hong-Yan Lai et al.   Molecular Therapy-Nucleic Acids

DeepMiR2GO: Inferring Functions of Human MicroRNAs Using a Deep Multi-Label Classification Model

(2019) Jiacheng Wang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

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

(2018) Ronghui You et al.   BIOINFORMATICS

MetaGO: Predicting Gene Ontology of Non-homologous Proteins Through Low-Resolution Protein Structure Prediction and Protein–Protein Network Mapping

(2018) Chengxin Zhang et al.   JOURNAL OF MOLECULAR BIOLOGY

Prediction of human protein subcellular localization using deep learning

(2018) Leyi Wei et al.   JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING

Predicting protein structural classes for low-similarity sequences by evaluating different features

(2018) Xiao-Juan Zhu et al.   KNOWLEDGE-BASED SYSTEMS

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

Gene expression inference with deep learning

(2016) Yifei Chen et al.   BIOINFORMATICS

Systematic Functional Annotation and Visualization of Biological Networks

(2016) Anastasia Baryshnikova   Cell Systems

A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction

(2015) Matt Spencer et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

The I-TASSER Suite: protein structure and function prediction

(2015) Jianyi Yang et al.   NATURE METHODS

A deep learning framework for modeling structural features of RNA-binding protein targets

(2015) Sai Zhang et al.   NUCLEIC ACIDS RESEARCH

Continuous Distributed Representation of Biological Sequences for Deep Proteomics and Genomics

(2015) Ehsaneddin Asgari et al.   PLoS One

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

STRING v10: protein–protein interaction networks, integrated over the tree of life

(2014) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Homology-based inference sets the bar high for protein function prediction

(2013) Tobias Hamp et al.   BMC 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 Review on Multi-Label Learning Algorithms

(2013) Min-Ling Zhang et al.   IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING

A large-scale evaluation of computational protein function prediction

(2013) Predrag Radivojac et al.   NATURE METHODS

Predicting Protein Function by Multi-Label Correlated Semi-Supervised Learning

(2011) J. Q. Jiang et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Protein annotation from protein interaction networks and Gene Ontology

(2011) Cao D. Nguyen et al.   JOURNAL OF BIOMEDICAL INFORMATICS

The NCBI Taxonomy database

(2011) S. Federhen   NUCLEIC ACIDS RESEARCH

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Predicting protein function from domain content

(2008) Kristoffer Forslund et al.   BIOINFORMATICS

PredGPI: a GPI-anchor predictor

(2008) Andrea Pierleoni et al.   BMC BIOINFORMATICS

The GOA database in 2009--an integrated Gene Ontology Annotation resource

(2008) D. Barrell et al.   NUCLEIC ACIDS RESEARCH

InterPro: the integrative protein signature database

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