Jiangning Song

According to our database1, Jiangning Song authored at least 90 papers between 2006 and 2021.

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Bibliography

2021
A Deep Learning-Based Method for Identification of Bacteriophage-Host Interaction.
IEEE ACM Trans. Comput. Biol. Bioinform., 2021

Formator: Predicting Lysine Formylation Sites Based on the Most Distant Undersampling and Safe-Level Synthetic Minority Oversampling.
IEEE ACM Trans. Comput. Biol. Bioinform., 2021

BastionHub: a universal platform for integrating and analyzing substrates secreted by Gram-negative bacteria.
Nucleic Acids Res., 2021

Personalized On-Device E-health Analytics with Decentralized Block Coordinate Descent.
CoRR, 2021

Feature Erasing and Diffusion Network for Occluded Person Re-Identification.
CoRR, 2021

ReCGBM: a gradient boosting-based method for predicting human dicer cleavage sites.
BMC Bioinform., 2021

OCTID: a one-class learning-based Python package for tumor image detection.
Bioinform., 2021

XRRpred: accurate predictor of crystal structure quality from protein sequence.
Bioinform., 2021

Accurate multistage prediction of protein crystallization propensity using deep-cascade forest with sequence-based features.
Briefings Bioinform., 2021

Comprehensive assessment of machine learning-based methods for predicting antimicrobial peptides.
Briefings Bioinform., 2021

DeepVF: a deep learning-based hybrid framework for identifying virulence factors using the stacking strategy.
Briefings Bioinform., 2021

PScL-HDeep: image-based prediction of protein subcellular location in human tissue using ensemble learning of handcrafted and deep learned features with two-layer feature selection.
Briefings Bioinform., 2021

SAResNet: self-attention residual network for predicting DNA-protein binding.
Briefings Bioinform., 2021

Anthem: a user customised tool for fast and accurate prediction of binding between peptides and HLA class I molecules.
Briefings Bioinform., 2021

Why can deep convolutional neural networks improve protein fold recognition? A visual explanation by interpretation.
Briefings Bioinform., 2021

Improving protein fold recognition using triplet network and ensemble deep learning.
Briefings Bioinform., 2021

DeepTorrent: a deep learning-based approach for predicting DNA N4-methylcytosine sites.
Briefings Bioinform., 2021

Porpoise: a new approach for accurate prediction of RNA pseudouridine sites.
Briefings Bioinform., 2021

Computational prediction and interpretation of both general and specific types of promoters in Escherichia coli by exploiting a stacked ensemble-learning framework.
Briefings Bioinform., 2021

Assessing the performance of computational predictors for estimating protein stability changes upon missense mutations.
Briefings Bioinform., 2021

nhKcr: a new bioinformatics tool for predicting crotonylation sites on human nonhistone proteins based on deep learning.
Briefings Bioinform., 2021

Systematic evaluation of machine learning methods for identifying human-pathogen protein-protein interactions.
Briefings Bioinform., 2021

Leveraging the attention mechanism to improve the identification of DNA N6-methyladenine sites.
Briefings Bioinform., 2021

2020
Pippin: A random forest-based method for identifying presynaptic and postsynaptic neurotoxins.
J. Bioinform. Comput. Biol., 2020

PROSPECT: A web server for predicting protein histidine phosphorylation sites.
J. Bioinform. Comput. Biol., 2020

A framework towards data analytics on host-pathogen protein-protein interactions.
J. Ambient Intell. Humaniz. Comput., 2020

Procleave: Predicting Protease-specific Substrate Cleavage Sites by Combining Sequence and Structural Information.
Genom. Proteom. Bioinform., 2020

PeNGaRoo, a combined gradient boosting and ensemble learning framework for predicting non-classical secreted proteins.
Bioinform., 2020

DeepCleave: a deep learning predictor for caspase and matrix metalloprotease substrates and cleavage sites.
Bioinform., 2020

PASSION: an ensemble neural network approach for identifying the binding sites of RBPs on circRNAs.
Bioinform., 2020

Comparative analysis and prediction of quorum-sensing peptides using feature representation learning and machine learning algorithms.
Briefings Bioinform., 2020

A comprehensive review and performance evaluation of bioinformatics tools for HLA class I peptide-binding prediction.
Briefings Bioinform., 2020

PRISMOID: a comprehensive 3D structure database for post-translational modifications and mutations with functional impact.
Briefings Bioinform., 2020

Comprehensive review and assessment of computational methods for predicting RNA post-transcriptional modification sites from RNA sequences.
Briefings Bioinform., 2020

iLearn : an integrated platform and meta-learner for feature engineering, machine-learning analysis and modeling of DNA, RNA and protein sequence data.
Briefings Bioinform., 2020

PhosTransfer: A Deep Transfer Learning Framework for Kinase-Specific Phosphorylation Site Prediction in Hierarchy.
Proceedings of the Advances in Knowledge Discovery and Data Mining, 2020

Prediction of secondary structure population and intrinsic disorder of proteins using multitask deep learning.
Proceedings of the AMIA 2020, 2020

2019
Deep learning with evolutionary and genomic profiles for identifying cancer subtypes.
J. Bioinform. Comput. Biol., 2019

SIMLIN: a bioinformatics tool for prediction of S-sulphenylation in the human proteome based on multi-stage ensemble-learning models.
BMC Bioinform., 2019

Positive-unlabelled learning of glycosylation sites in the human proteome.
BMC Bioinform., 2019

MULTiPly: a novel multi-layer predictor for discovering general and specific types of promoters.
Bioinform., 2019

Bastion3: a two-layer ensemble predictor of type III secreted effectors.
Bioinform., 2019

Computational analysis and prediction of lysine malonylation sites by exploiting informative features in an integrative machine-learning framework.
Briefings Bioinform., 2019

Systematic analysis and prediction of type IV secreted effector proteins by machine learning approaches.
Briefings Bioinform., 2019

iProt-Sub: a comprehensive package for accurately mapping and predicting protease-specific substrates and cleavage sites.
Briefings Bioinform., 2019

Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods.
Briefings Bioinform., 2019

Large-scale comparative assessment of computational predictors for lysine post-translational modification sites.
Briefings Bioinform., 2019

Toward more accurate prediction of caspase cleavage sites: a comprehensive review of current methods, tools and features.
Briefings Bioinform., 2019

2018
Computing Minimum Reaction Modifications in a Boolean Metabolic Network.
IEEE ACM Trans. Comput. Biol. Bioinform., 2018

ProBAPred: Inferring protein-protein binding affinity by incorporating protein sequence and structural features.
J. Bioinform. Comput. Biol., 2018

ACPred-FL: a sequence-based predictor using effective feature representation to improve the prediction of anti-cancer peptides.
Bioinform., 2018

Bastion6: a bioinformatics approach for accurate prediction of type VI secreted effectors.
Bioinform., 2018

PROSPERous: high-throughput prediction of substrate cleavage sites for 90 proteases with improved accuracy.
Bioinform., 2018

Quokka: a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome.
Bioinform., 2018

iFeature: a Python package and web server for features extraction and selection from protein and peptide sequences.
Bioinform., 2018

Comprehensive assessment and performance improvement of effector protein predictors for bacterial secretion systems III, IV and VI.
Briefings Bioinform., 2018

Structural Principles Analysis of Host-Pathogen Protein-Protein Interactions: A Structural Bioinformatics Survey.
IEEE Access, 2018

2017
Staged heterogeneity learning to identify conformational B-cell epitopes from antigen sequences.
BMC Genom., 2017

POSSUM: a bioinformatics toolkit for generating numerical sequence feature descriptors based on PSSM profiles.
Bioinform., 2017

Critical evaluation of bioinformatics tools for the prediction of protein crystallization propensity.
Briefings Bioinform., 2017

Collaborative data analytics towards prediction on pathogen-host protein-protein interactions.
Proceedings of the 21st IEEE International Conference on Computer Supported Cooperative Work in Design, 2017

Leveraging Stacked Denoising Autoencoder in Prediction of Pathogen-Host Protein-Protein Interactions.
Proceedings of the 2017 IEEE International Congress on Big Data, 2017

Towards Elucidating the Structural Principles of Host-Pathogen Protein-Protein Interaction Networks: A Bioinformatics Survey.
Proceedings of the 2017 IEEE International Congress on Big Data, 2017

2016
PolyQ 2.0: an improved version of PolyQ, a database of human polyglutamine proteins.
Database J. Biol. Databases Curation, 2016

PolyQ 2.0: an improved version of PolyQ, a database of human polyglutamine proteins.
Database J. Biol. Databases Curation, 2016

KinetochoreDB: a comprehensive online resource for the kinetochore and its related proteins.
Database J. Biol. Databases Curation, 2016

Critical evaluation of <i>in silico</i> methods for prediction of coiled-coil domains in proteins.
Briefings Bioinform., 2016

Towards Data Analytics of Pathogen-Host Protein-Protein Interaction: A Survey.
Proceedings of the 2016 IEEE International Congress on Big Data, San Francisco, CA, USA, June 27, 2016

Preface.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016

Host-Pathogen Protein Interaction Prediction Based on Local Topology Structures of a Protein Interaction Network.
Proceedings of the 16th IEEE International Conference on Bioinformatics and Bioengineering, 2016

2015
Computing Smallest Intervention Strategies for Multiple Metabolic Networks in a Boolean Model.
J. Comput. Biol., 2015

GlycoMine: a machine learning-based approach for predicting N-, C- and O-linked glycosylation in the human proteome.
Bioinform., 2015

Towards more accurate prediction of ubiquitination sites: a comprehensive review of current methods, tools and features.
Briefings Bioinform., 2015

Towards more accurate prediction of protein folding rates: a review of the existing web-based bioinformatics approaches.
Briefings Bioinform., 2015

2014
Cascleave 2.0, a new approach for predicting caspase and granzyme cleavage targets.
Bioinform., 2014

Bioinformatics approaches for improved recombinant protein production in <i>Escherichia coli: </i> protein solubility prediction.
Briefings Bioinform., 2014

2013
Prediction of protein-RNA residue-base contacts using two-dimensional conditional random field with the lasso.
BMC Syst. Biol., 2013

2012
The drug cocktail network.
BMC Syst. Biol., 2012

Exploring drug combinations in genetic interaction network.
BMC Bioinform., 2012

Predicting protein-RNA residue-base contacts using two-dimensional conditional random field.
Proceedings of the 6th IEEE International Conference on Systems Biology, 2012

2011
Bioinformatic Approaches for Predicting substrates of Proteases.
J. Bioinform. Comput. Biol., 2011

Conditional random field approach to prediction of protein-protein interactions using domain information.
BMC Syst. Biol., 2011

2010
Improving the accuracy of predicting disulfide connectivity by feature selection.
J. Comput. Chem., 2010

APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility.
BMC Bioinform., 2010

Cascleave: towards more accurate prediction of caspase substrate cleavage sites.
Bioinform., 2010

EGM: encapsulated gene-by-gene matching to identify gene orthologs and homologous segments in genomes.
Bioinform., 2010

2008
HSEpred: predict half-sphere exposure from protein sequences.
Bioinform., 2008

2007
Predicting disulfide connectivity from protein sequence using multiple sequence feature vectors and secondary structure.
Bioinform., 2007

2006
Prediction of <i>cis</i>/<i>trans </i>isomerization in proteins using PSI-BLAST profiles and secondary structure information.
BMC Bioinform., 2006

Predicting residue-wise contact orders in proteins by support vector regression.
BMC Bioinform., 2006


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