Jiangning Song

发表

Improving the accuracy of predicting disulfide connectivity by feature selection

Jiangning Song, Lin Zhu, Jie Yang, 2010, J. Comput. Chem..

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

Geoffrey I. Webb, Jiangning Song, Tatsuya Akutsu, 2019, Bioinform..

PredCSF: an integrated feature-based approach for predicting conotoxin superfamily.

Jiangning Song, Hong-Bin Shen, Yong-Xian Fan, 2011, Protein and peptide letters.

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

Geoffrey I. Webb, Jiangning Song, Yang Zhang, 2016, Scientific Reports.

Pippin: A random forest-based method for identifying presynaptic and postsynaptic neurotoxins

Jiangning Song, Pengyu Li, He Zhang, 2020, J. Bioinform. Comput. Biol..

Bioinformatic Approaches for Predicting substrates of Proteases

Geoffrey I. Webb, Jiangning Song, Tatsuya Akutsu, 2011, J. Bioinform. Comput. Biol..

Bioinformatics approaches for improved recombinant protein production in Escherichia coli: protein solubility prediction

Jiangning Song, Catherine Ching Han Chang, Beng Ti Tey, 2014, Briefings Bioinform..

Towards Data Analytics of Pathogen-Host Protein-Protein Interaction: A Survey

Jiangning Song, Lei Wang, Jun Shen, 2016, 2016 IEEE International Congress on Big Data (BigData Congress).

Bastion3: a two-layer ensemble predictor of type III secreted effectors

Jiangning Song, Tatsuya Akutsu, Jiawei Wang, 2018, Bioinform..

Formator: predicting lysine formylation sites based on the most distant undersampling and safe-level synthetic minority oversampling.

Meng Zhang, Jiangning Song, Cangzhi Jia, 2019, IEEE/ACM transactions on computational biology and bioinformatics.

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

Jiangning Song, Tatsuya Akutsu, Tatiana T. Marquez-Lago, 2018, Bioinform..

A framework towards data analytics on host–pathogen protein–protein interactions

Jiangning Song, Huaming Chen, Jun Shen, 2020, Journal of Ambient Intelligence and Humanized Computing.

Systematic analysis and prediction of type IV secreted effector proteins by machine learning approaches

Geoffrey I. Webb, Jiangning Song, Qingyang Hong, 2017, Briefings Bioinform..

APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility

Xing-Ming Zhao, Jiangning Song, De-Shuang Huang, 2010, BMC Bioinformatics.

Prediction of protein folding rates from primary sequence by fusing multiple sequential features

Jiangning Song, Kuo-Chen Chou, Hong-Bin Shen, 2009 .

Structural Principles Analysis of Host-Pathogen Protein-Protein Interactions: A Structural Bioinformatics Survey

Jiangning Song, Lei Wang, Jun Shen, 2018, IEEE Access.

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

Jiangning Song, Jinxiang Chen, André Leier, 2020, Bioinform..

Towards more accurate prediction of protein folding rates: a review of the existing web-based bioinformatics approaches

Jiangning Song, Catherine Ching Han Chang, Beng Ti Tey, 2015, Briefings Bioinform..

Prediction of cis/trans isomerization in proteins using PSI-BLAST profiles and secondary structure information

Jiangning Song, Zheng Yuan, Kevin Burrage, 2006, BMC Bioinformatics.

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

Jiangning Song, Jian Li, Fuyi Li, 2019, Briefings in bioinformatics.

Host-Pathogen Protein Interaction Prediction Based on Local Topology Structures of a Protein Interaction Network

Jiangning Song, Tatsuya Akutsu, Morihiro Hayashida, 2016, 2016 IEEE 16th International Conference on Bioinformatics and Bioengineering (BIBE).

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

Jiangning Song, Tatsuya Akutsu, Jiawei Wang, 2019, Bioinform..

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

Jiangning Song, Yuan Zhou, Zhen Chen, 2015, Briefings Bioinform..

Conditional random field approach to prediction of protein-protein interactions using domain information

Jiangning Song, Tatsuya Akutsu, Morihiro Hayashida, 2011, BMC Systems Biology.

Critical evaluation of bioinformatics tools for the prediction of protein crystallization propensity

Huilin Wang, Liubin Feng, Geoffrey I. Webb, 2017, Briefings Bioinform..

Bastion6: a bioinformatics approach for accurate prediction of type VI secreted effectors

Jiangning Song, Tatsuya Akutsu, Jiawei Wang, 2018, Bioinform..

Inference Method for Developing Mathematical Models of Cell Signaling Pathways Using Proteomic Datasets.

Jiangning Song, Tianhai Tian, 2017, Methods in molecular biology.

Positive-unlabelled learning of glycosylation sites in the human proteome

Geoffrey I. Webb, Jiangning Song, Chen Li, 2019, BMC Bioinformatics.

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

Jiangning Song, Zhen Chen, Yanan Wang, 2019, Briefings Bioinform..

A neural network learning approach for improving the prediction of residue depth based on sequence-derived features

Jiangning Song, Xiaofeng Wang, Jian Li, 2016 .

Knowledge-transfer learning for prediction of matrix metalloprotease substrate-cleavage sites

Geoffrey I. Webb, Jiangning Song, Hong-Bin Shen, 2017, Scientific Reports.

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

Gholamreza Haffari, Geoffrey I. Webb, Jiangning Song, 2018, Bioinform..

Deep learning with evolutionary and genomic profiles for identifying cancer subtypes

Jiangning Song, Simon See, Jinn-Moon Yang, 2019, J. Bioinform. Comput. Biol..

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

Geoffrey I. Webb, Jiangning Song, Jiawei Wang, 2016, Briefings Bioinform..

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

Gholamreza Haffari, Geoffrey I. Webb, Jiangning Song, 2018, Briefings Bioinform..

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

Jiangning Song, Tatsuya Akutsu, Cangzhi Jia, 2020, Briefings Bioinform..

Computing Smallest Intervention Strategies for Multiple Metabolic Networks in a Boolean Model

Jiangning Song, Tatsuya Akutsu, Takeyuki Tamura, 2015, J. Comput. Biol..

ProBAPred: Inferring protein-protein binding affinity by incorporating protein sequence and structural features

Jiangning Song, Qingfeng Chen, Chen Li, 2018, J. Bioinform. Comput. Biol..

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

Geoffrey I. Webb, Jiangning Song, Tatsuya Akutsu, 2019, Briefings Bioinform..

POSSUM: a bioinformatics toolkit for generating numerical sequence feature descriptors based on PSSM profiles

Geoffrey I. Webb, Jiangning Song, Jiawei Wang, 2017, Bioinform..

The drug cocktail network

Xing-Ming Zhao, Jiangning Song, Ke-Jia Xu, 2012, BMC Systems Biology.

Systematic evaluation of machine learning methods for identifying human-pathogen protein-protein interactions

Jiangning Song, Lei Wang, Lukasz Kurgan, 2020, Briefings Bioinform..

Prediction of protein-RNA residue-base contacts using two-dimensional conditional random field with the lasso

Jiangning Song, Tatsuya Akutsu, Morihiro Hayashida, 2013, BMC Systems Biology.

KinetochoreDB: a comprehensive online resource for the kinetochore and its related proteins

Jiangning Song, Chen Li, Ashley M. Buckle, 2016, Database J. Biol. Databases Curation.

MetalExplorer, a Bioinformatics Tool for the Improved Prediction of Eight Types of Metal-Binding Sites Using a Random Forest Algorithm with Two- Step Feature Selection

Geoffrey I. Webb, Jiangning Song, Chen Li, 2017 .

A Short Review on Protein Secondary Structure Prediction Methods

Jiangning Song, Renxiang Yan, Weiwen Cai, 2015 .

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

Geoffrey I. Webb, Jiangning Song, Tatsuya Akutsu, 2020, Genom. Proteom. Bioinform..

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

Jiangning Song, Zongyuan Ge, Jinxiang Chen, 2020, Briefings Bioinform..

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

Geoffrey I. Webb, Jiangning Song, Zhen Chen, 2018, Bioinform..

PolyQ 2.0: an improved version of PolyQ, a database of human polyglutamine proteins

Jiangning Song, Chen Li, Ashley M. Buckle, 2016, Database J. Biol. Databases Curation.

iProt-Sub: a comprehensive package for accurately mapping and predicting protease-specific substrates and cleavage sites

Geoffrey I. Webb, Jiangning Song, Tatsuya Akutsu, 2018, Briefings Bioinform..

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

Jiangning Song, Tatsuya Akutsu, Takeyuki Tamura, 2018, Briefings Bioinform..

SPAR: a random forest-based predictor for self-interacting proteins with fine-grained domain information

Jiangning Song, Chen Li, Shiping Yang, 2016, Amino Acids.

PhosContext2vec: a distributed representation of residue-level sequence contexts and its application to general and kinase-specific phosphorylation site prediction

Jiangning Song, Campbell Wilson, Ying Xu, 2018, Scientific Reports.

A Deep Learning-Based Method for Identification of Bacteriophage-Host Interaction

Geoffrey I. Webb, Jiangning Song, Junfeng Xia, 2020, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

EGM: encapsulated gene-by-gene matching to identify gene orthologs and homologous segments in genomes

Geoffrey I. Webb, Jiangning Song, Arun Siddharth Konagurthu, 2010, Bioinform..

An Interpretable Prediction Model for Identifying N7-Methylguanosine Sites Based on XGBoost and SHAP

Jiangning Song, Cangzhi Jia, Fuyi Li, 2020, Molecular therapy. Nucleic acids.

Integer Programming-Based Method for Designing Synthetic Metabolic Networks by Minimum Reaction Insertion in a Boolean Model

Jiangning Song, Tatsuya Akutsu, Takeyuki Tamura, 2014, PloS one.

Using contrast patterns between true complexes and random subgraphs in PPI networks to predict unknown protein complexes

Jiangning Song, Jinyan Li, Quanzhong Liu, 2016, Scientific Reports.

Computational analysis and prediction of lysine malonylation sites by exploiting informative features in an integrative machine-learning framework

Geoffrey I. Webb, Jiangning Song, Tatsuya Akutsu, 2018, Briefings Bioinform..

DeepVF: a deep learning-based hybrid framework for identifying virulence factors using the stacking strategy

Jiangning Song, Jiawei Wang, Tatiana T Marquez-Lago, 2020, Briefings Bioinform..

Exploring drug combinations in a drug-cocktail network

Xing-Ming Zhao, Jiangning Song, Ke-Jia Xu, 2011, 2011 IEEE International Conference on Systems Biology (ISB).

Cascleave: towards more accurate prediction of caspase substrate cleavage sites

Geoffrey I. Webb, Jiangning Song, Tatsuya Akutsu, 2010, Bioinform..

An Overview of Bioinformatics Methods for Analyzing Autism Spectrum Disorders.

Jiangning Song, Tatsuya Akutsu, Jose C Nacher, 2019, Current pharmaceutical design.

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

Xing-Ming Zhao, Jiangning Song, Tatsuya Akutsu, 2014, Bioinform..

Predicting disulfide connectivity from protein sequence using multiple sequence feature vectors and secondary structure

Jiangning Song, Hao Tan, Zheng Yuan, 2007, Bioinform..

HSEpred: predict half-sphere exposure from protein sequences

Jiangning Song, Tatsuya Akutsu, Hao Tan, 2008, Bioinform..

DeepBL: a deep learning-based approach for in silico discovery of beta-lactamases.

Jiangning Song, Tatiana T Marquez-Lago, Yanan Wang, 2020, Briefings in bioinformatics.

Survey of Predictors of Propensity for Protein Production and Crystallization with Application to Predict Resolution of Crystal Structures.

Jiangning Song, Kui Wang, Zhonghua Wu, 2017, Current protein & peptide science.

Computing Minimum Reaction Modifications in a Boolean Metabolic Network

Jiangning Song, Tatsuya Akutsu, Takeyuki Tamura, 2018, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

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

Jiangning Song, Chen Zhou, Ran Su, 2018, Bioinform..

Large-scale comparative assessment of computational predictors for lysine post-translational modification sites

Geoffrey I. Webb, Jiangning Song, Tatsuya Akutsu, 2018, Briefings Bioinform..

Collaborative data analytics towards prediction on pathogen-host protein-protein interactions

Jiangning Song, Lei Wang, Jun Shen, 2017, 2017 IEEE 21st International Conference on Computer Supported Cooperative Work in Design (CSCWD).

Predicting protein-RNA residue-base contacts using two-dimensional conditional random field

Jiangning Song, Tatsuya Akutsu, Morihiro Hayashida, 2012, 2012 IEEE 6th International Conference on Systems Biology (ISB).

Leveraging Stacked Denoising Autoencoder in Prediction of Pathogen-Host Protein-Protein Interactions

Jiangning Song, Lei Wang, Jun Shen, 2017, 2017 IEEE International Congress on Big Data (BigData Congress).

Exploring drug combinations in genetic interaction network

Xing-Ming Zhao, Jiangning Song, Yin-Ying Wang, 2012, BMC Bioinformatics.

PRISMOID: a comprehensive 3D structure database for post-translational modifications and mutations with functional impact

Geoffrey I. Webb, Jiangning Song, Jian Li, 2019, bioRxiv.

Comparative analysis and prediction of quorum-sensing peptides using feature representation learning and machine learning algorithms

Jiangning Song, Fuyi Li, Jie Hu, 2018, Briefings Bioinform..

A comprehensive review and performance evaluation of bioinformatics tools for HLA class I peptide-binding prediction

Jiangning Song, Tatsuya Akutsu, Tatiana T Marquez-Lago, 2020, Briefings Bioinform..

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

Jiangning Song, Chee Keong Kwoh, Meng Zhang, 2019, Bioinform..

A Comparison Study for Supervised Machine Learning Models in Cancer Classification

Jiangning Song, Hong Zhao, Lei Wang, 2017 .

Critical evaluation of in silico methods for prediction of coiled-coil domains in proteins

Jiangning Song, Tatsuya Akutsu, Chen Li, 2016, Briefings Bioinform..

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

Geoffrey I. Webb, Jiangning Song, Fuyi Li, 2019, BMC Bioinformatics.

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

Geoffrey I. Webb, Jiangning Song, James C. Whisstock, 2015, Bioinform..

Predicting residue-wise contact orders in proteins by support vector regression

Jiangning Song, Kevin Burrage, K. Burrage, 2006, BMC Bioinformatics.

Towards Elucidating the Structural Principles of Host-Pathogen Protein-Protein Interaction Networks: A Bioinformatics Survey

Jiangning Song, Lei Wang, Jun Shen, 2017, 2017 IEEE International Congress on Big Data (BigData Congress).

DeepTorrent: a deep learning-based approach for predicting DNA N4-methylcytosine sites

Jiangning Song, Shuqin Li, Jinxiang Chen, 2020, Briefings Bioinform..

Crysalis: an integrated server for computational analysis and design of protein crystallization

Liubin Feng, Geoffrey I. Webb, Jiangning Song, 2016, Scientific Reports.

Why can deep convolutional neural networks improve protein fold recognition? A visual explanation by interpretation

Jiangning Song, Yan Liu, Dong-Jun Yu, 2021, Briefings Bioinform..

SAResNet: self-attention residual network for predicting DNA-protein binding

Jiangning Song, Dong-Jun Yu, Yan Liu, 2021, Briefings Bioinform..

Comprehensive assessment of machine learning-based methods for predicting antimicrobial peptides

Jiangning Song, Dong-Jun Yu, Fuyi Li, 2021, Briefings Bioinform..

BastionHub: a universal platform for integrating and analyzing substrates secreted by Gram-negative bacteria

Jiangning Song, Tatiana T Marquez-Lago, Trevor Lithgow, 2020, Nucleic Acids Res..

Towards a systematic characterization of protein complex function: a natural language processing and machine-learning framework

Jiangning Song, Ruedi Aebersold, Matteo Manica, 2021, bioRxiv.

OCTID: a one-class learning-based Python package for tumor image detection

Jiangning Song, Zongyuan Ge, Litao Yang, 2021, Bioinform..

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

Geoffrey I. Webb, Jiangning Song, Tatsuya Akutsu, 2021, Briefings Bioinform..

Accurate multistage prediction of protein crystallization propensity using deep-cascade forest with sequence-based features

Jiangning Song, Yang Zhang, Dong-Jun Yu, 2020, Briefings Bioinform..

hCKSAAP_UbSite: improved prediction of human ubiquitination sites by exploiting amino acid pattern and properties.

Jiangning Song, Ziding Zhang, Ziding Zhang, 2013, Biochimica et biophysica acta.

Cloning, expression and characterization of a pectate lyase from Paenibacillus sp. 0602 in recombinant Escherichia coli

Jiangning Song, Jian Li, Yanhe Ma, 2014, BMC Biotechnology.

SecretEPDB: a comprehensive web-based resource for secreted effector proteins of the bacterial types III, IV and VI secretion systems

Geoffrey I. Webb, Jiangning Song, Tatsuya Akutsu, 2017, Scientific Reports.

Efficient large-scale protein sequence comparison and gene matching to identify orthologs and co-orthologs

Geoffrey I. Webb, Jiangning Song, James C. Whisstock, 2011, Nucleic acids research.

Computational enzyme design approaches with significant biological outcomes: progress and challenges

Jiangning Song, Xiaoman Li, Ziding Zhang, 2012, Computational and structural biotechnology journal.

The exploration of network motifs as potential drug targets from post-translational regulatory networks

Xing-Ming Zhao, Jiangning Song, Peer Bork, 2016, Scientific Reports.

An Integrative Computational Framework Based on a Two-Step Random Forest Algorithm Improves Prediction of Zinc-Binding Sites in Proteins

Jiangning Song, Tatsuya Akutsu, Kazuhiro Takemoto, 2012, PloS one.

Can simple codon pair usage predict protein-protein interaction?

Jiangning Song, Ziding Zhang, Ziding Zhang, 2012, Molecular bioSystems.

PredPPCrys: Accurate Prediction of Sequence Cloning, Protein Production, Purification and Crystallization Propensity from Protein Sequences Using Multi-Step Heterogeneous Feature Fusion and Selection

Jiangning Song, Huilin Wang, Mingjun Wang, 2014, PloS one.

FunSAV: Predicting the Functional Effect of Single Amino Acid Variants Using a Two-Stage Random Forest Model

Xing-Ming Zhao, Jiangning Song, Tatsuya Akutsu, 2012, PloS one.

Taxonomic Landscape of the Dark Proteomes: Whole‐Proteome Scale Interplay Between Structural Darkness, Intrinsic Disorder, and Crystallization Propensity

Jiangning Song, Lukasz Kurgan, Vladimir N Uversky, 2018, Proteomics.

PAnDE : AVERAGED n-DEPENDENCE ESTIMATORS FOR POSITIVE UNLABELED LEARNING

Jiangning Song, Tatsuya Akutsu, Fuyi Li, 2017 .

Accurate in silico identification of species-specific acetylation sites by integrating protein sequence-derived and functional features

Geoffrey I. Webb, Jiangning Song, Huilin Wang, 2014, Scientific Reports.

Prodepth: Predict Residue Depth by Support Vector Regression Approach from Protein Sequences Only

Geoffrey I. Webb, Jiangning Song, Tatsuya Akutsu, 2009, PloS one.

Mathematical Modelling of the MAP Kinase Pathway Using Proteomic Datasets

Jiangning Song, Tianhai Tian, T. Tian, 2012, PloS one.

DephosSite: a machine learning approach for discovering phosphotase-specific dephosphorylation sites

Jiangning Song, Renxiang Yan, Renxiang Yan, 2016, Scientific Reports.

Predicting Protein N-Terminal Signal Peptides Using Position-Specific Amino Acid Propensities and Conditional Random Fields

Jiangning Song, Chen Xu, Hong-Bin Shen, 2013 .

Computational characterization of parallel dimeric and trimeric coiled-coils using effective amino acid indices.

Jiangning Song, Ziding Zhang, Chen Li, 2015, Molecular bioSystems.

SOHPRED: a new bioinformatics tool for the characterization and prediction of human S-sulfenylation sites.

Jiangning Song, Jinyan Li, Renxiang Yan, 2016, Molecular bioSystems.

PhosphoPredict: A bioinformatics tool for prediction of human kinase-specific phosphorylation substrates and sites by integrating heterogeneous feature selection

Geoffrey I. Webb, Jiangning Song, Tatsuya Akutsu, 2017, Scientific Reports.

TANGLE: Two-Level Support Vector Regression Approach for Protein Backbone Torsion Angle Prediction from Primary Sequences

Geoffrey I. Webb, Jiangning Song, Tatsuya Akutsu, 2012, PloS one.

Identifying Coevolution Between Amino Acid Residues in Protein Families: Advances in the Improvement and Evaluation of Correlated Mutation Algorithms

Jiangning Song, Xiaoqin Li, Ziding Zhang, 2013 .

Co-Occurring Atomic Contacts for the Characterization of Protein Binding Hot Spots

Jiangning Song, Qian Liu, Jinyan Li, 2015, PloS one.

PREvaIL, an integrative approach for inferring catalytic residues using sequence, structural, and network features in a machine-learning framework.

Gholamreza Haffari, Geoffrey I. Webb, Jiangning Song, 2018, Journal of theoretical biology.

Periscope: quantitative prediction of soluble protein expression in the periplasm of Escherichia coli

Geoffrey I. Webb, Jiangning Song, Geoffrey I Webb, 2016, Scientific reports.

ZincExplorer: an accurate hybrid method to improve the prediction of zinc-binding sites from protein sequences.

Jiangning Song, Ziding Zhang, Ziding Zhang, 2013, Molecular bioSystems.

Structural Propensities of Human Ubiquitination Sites: Accessibility, Centrality and Local Conformation

Jiangning Song, Sixue Liu, Ziding Zhang, 2013, PloS one.