Positive-unlabeled learning in bioinformatics and computational biology: a brief review

DeepS: A web server for image optical sectioning and super resolution microscopy based on a deep learning framework

(2021) Qingjie Zhu et al.   BIOINFORMATICS

iDHS-Deep: an integrated tool for predicting DNase I hypersensitive sites by deep neural network

(2021) Fu-Ying Dao et al.   BRIEFINGS IN BIOINFORMATICS

iLearnPlus: a comprehensive and automated machine-learning platform for nucleic acid and protein sequence analysis, prediction and visualization

(2021) Zhen Chen et al.   NUCLEIC ACIDS RESEARCH

HEAL: an automated deep learning framework for cancer histopathology image analysis

(2021) Yanan Wang et al.   BIOINFORMATICS

PCprophet: a framework for protein complex prediction and differential analysis using proteomic data

(2021) Andrea Fossati et al.   NATURE METHODS

A deep-learning pipeline for the diagnosis and discrimination of viral, non-viral and COVID-19 pneumonia from chest X-ray images

(2021) Guangyu Wang et al.   Nature Biomedical Engineering

S2L-PSIBLAST: a supervised two-layer search framework based on PSI-BLAST for protein remote homology detection

(2021) Xiaopeng Jin et al.   BIOINFORMATICS

Porpoise: a new approach for accurate prediction of RNA pseudouridine sites

(2021) Fuyi Li et al.   BRIEFINGS IN BIOINFORMATICS

Deep learning boosts sensitivity of mass spectrometry-based immunopeptidomics

(2021) Mathias Wilhelm et al.   Nature Communications

Attention-based multi-label neural networks for integrated prediction and interpretation of twelve widely occurring RNA modifications

(2021) Zitao Song et al.   Nature Communications

Structure-based protein function prediction using graph convolutional networks

(2021) Vladimir Gligorijević et al.   Nature Communications

iMRM:a platform for simultaneously identifying multiple kinds of RNA modifications

(2020) Kewei Liu et al.   BIOINFORMATICS

DNA4mC-LIP: a linear integration method to identify N4-methylcytosine site in multiple species

(2020) Qiang Tang et al.   BIOINFORMATICS

PASSION: an ensemble neural network approach for identifying the binding sites of RBPs on circRNAs

(2020) Cangzhi Jia et al.   BIOINFORMATICS

Machine learning-based analysis of multi-omics data on the cloud for investigating gene regulations

(2020) Minsik Oh et al.   BRIEFINGS IN BIOINFORMATICS

iPiDi-PUL: identifying Piwi-interacting RNA-disease associations based on positive unlabeled learning

(2020) Hang Wei et al.   BRIEFINGS IN BIOINFORMATICS

Learning from positive and unlabeled data: a survey

(2020) Jessa Bekker et al.   MACHINE LEARNING

A reference map of the human binary protein interactome

(2020) Katja Luck et al.   NATURE

PROSPECT: A web server for predicting protein histidine phosphorylation sites

(2020) Zhen Chen et al.   Journal of Bioinformatics and Computational Biology

Procleave: Predicting Protease-specific Substrate Cleavage Sites by Combining Sequence and Structural Information

(2020) Fuyi Li et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Modern Deep Learning in Bioinformatics

(2020) Haoyang Li et al.   Journal of Molecular Cell Biology

A deep learning model to predict RNA-Seq expression of tumours from whole slide images

(2020) Benoît Schmauch et al.   Nature Communications

A Literature Review of Gene Function Prediction by Modeling Gene Ontology

(2020) Yingwen Zhao et al.   Frontiers in Genetics

Computational identification of eukaryotic promoters based on cascaded deep capsule neural networks

(2020) Yan Zhu et al.   BRIEFINGS IN BIOINFORMATICS

Anthem: a user customised tool for fast and accurate prediction of binding between peptides and HLA class I molecules

(2020) Shutao Mei et al.   BRIEFINGS IN BIOINFORMATICS

Inferring the molecular and phenotypic impact of amino acid variants with MutPred2

(2020) Vikas Pejaver et al.   Nature Communications

Positive-unlabelled learning of glycosylation sites in the human proteome

(2019) Fuyi Li et al.   BMC BIOINFORMATICS

Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning

(2019) Siegfried Gessulat et al.   NATURE METHODS

Deep learning: new computational modelling techniques for genomics

(2019) Gökcen Eraslan et al.   NATURE REVIEWS GENETICS

MOLI: multi-omics late integration with deep neural networks for drug response prediction

(2019) Hossein Sharifi-Noghabi et al.   BIOINFORMATICS

Clinical-grade computational pathology using weakly supervised deep learning on whole slide images

(2019) Gabriele Campanella et al.   NATURE MEDICINE

DeepCleave: a deep learning predictor for caspase and matrix metalloprotease substrates and cleavage sites

(2019) Fuyi Li et al.   BIOINFORMATICS

A survey on ensemble learning

(2019) Xibin Dong et al.   Frontiers of Computer Science

SIMLIN: a bioinformatics tool for prediction of S-sulphenylation in the human proteome based on multi-stage ensemble-learning models

(2019) Xiaochuan Wang et al.   BMC BIOINFORMATICS

Comprehensive review and assessment of computational methods for predicting RNA post-transcriptional modification sites from RNA sequences

(2019) Zhen Chen et al.   BRIEFINGS IN BIOINFORMATICS

Predicting disease-associated circular RNAs using deep forests combined with positive-unlabeled learning methods

(2019) Xiangxiang Zeng et al.   BRIEFINGS IN BIOINFORMATICS

A survey on semi-supervised learning

(2019) Jesper E. van Engelen et al.   MACHINE LEARNING

Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs

(2019) Tristan Bepler et al.   NATURE METHODS

Quokka: a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome

(2018) Fuyi Li et al.   BIOINFORMATICS

iFeature: a Python package and web server for features extraction and selection from protein and peptide sequences

(2018) Zhen Chen et al.   BIOINFORMATICS

DeepGSR: an optimized deep-learning structure for the recognition of genomic signals and regions

(2018) Manal Kalkatawi et al.   BIOINFORMATICS

Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods

(2018) Fuyi Li et al.   BRIEFINGS IN BIOINFORMATICS

Promoter analysis and prediction in the human genome using sequence-based deep learning models

(2018) Ramzan Umarov et al.   BIOINFORMATICS

Deep forest

(2018) Zhi-Hua Zhou et al.   National Science Review

EPuL: An Enhanced Positive-Unlabeled Learning Algorithm for the Prediction of Pupylation Sites

(2017) Xuanguo Nan et al.   MOLECULES

Predicting drug–target interaction using positive-unlabeled learning

(2016) Wei Lan et al.   NEUROCOMPUTING

Compact Integration of Multi-Network Topology for Functional Analysis of Genes

(2016) Hyunghoon Cho et al.   Cell Systems

GlycoMine struct : a new bioinformatics tool for highly accurate mapping of the human N-linked and O-linked glycoproteomes by incorporating structural features

(2016) Fuyi Li et al.   Scientific Reports

GlycoMine: a machine learning-based approach for predicting N-, C- and O-linked glycosylation in the human proteome

(2015) Fuyi Li et al.   BIOINFORMATICS

Positive-unlabeled learning for the prediction of conformational B-cell epitopes

(2015) Jing Ren et al.   BMC BIOINFORMATICS

Computationally predicting protein-RNA interactions using only positive and unlabeled examples

(2015) Zhanzhan Cheng et al.   Journal of Bioinformatics and Computational Biology

Integrating microRNA target predictions for the discovery of gene regulatory networks: a semi-supervised ensemble learning approach

(2014) Gianvito Pio et al.   BMC BIOINFORMATICS

One-class classification: taxonomy of study and review of techniques

(2014) Shehroz S. Khan et al.   KNOWLEDGE ENGINEERING REVIEW

iPro54-PseKNC: a sequence-based predictor for identifying sigma-54 promoters in prokaryote with pseudo k-tuple nucleotide composition

(2014) Hao Lin et al.   NUCLEIC ACIDS RESEARCH

Multi-class AdaBoost

(2013) Trevor Hastie et al.   Statistics and Its Interface

Positive-unlabeled learning for disease gene identification

(2012) Peng Yang et al.   BIOINFORMATICS

Structure-based prediction of protein–protein interactions on a genome-wide scale

(2012) Qiangfeng Cliff Zhang et al.   NATURE

ProDiGe: Prioritization Of Disease Genes with multitask machine learning from positive and unlabeled examples

(2011) Fantine Mordelet et al.   BMC BIOINFORMATICS

Learning gene regulatory networks from only positive and unlabeled data

(2010) Luigi Cerulo et al.   BMC BIOINFORMATICS

Genome-wide sequence-based prediction of peripheral proteins using a novel semi-supervised learning technique

(2010) Nitin Bhardwaj et al.   BMC BIOINFORMATICS

Predicting gene function using few positive examples and unlabeled ones

(2010) Yiming Chen et al.   BMC GENOMICS

Genome-wide association analysis by lasso penalized logistic regression

(2009) Tong Tong Wu et al.   BIOINFORMATICS

Biological sequence classification utilizing positive and unlabeled data

(2008) Yuanyuan Xiao et al.   BIOINFORMATICS