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List of works by Jiangning Song

A highly Conserved Aspartic Acid Residue of the Chitosanase from Bacillus Sp. TS Is Involved in the Substrate Binding.

scientific article published on 18 June 2016

A polytherapy based approach to combat antimicrobial resistance using cubosomes

scientific article published in 2022

A subset of HLA-I peptides are not genomically templated: Evidence for cis- and trans-spliced peptide ligands

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

scientific article published on 01 December 2018

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

scientific article

ASPIRER: a new computational approach for identifying non-classical secreted proteins based on deep learning

scientific article published in 2022

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

scientific article

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

scientific article published on 20 May 2020

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

scientific article published on 25 August 2020

An Overview of Bioinformatics Methods for Analyzing Autism Spectrum Disorders

scientific article published on 01 January 2020

An integrative computational framework based on a two-step random forest algorithm improves prediction of zinc-binding sites in proteins

scientific article

Anthelmintic closantel enhances bacterial killing of polymyxin B against multidrug-resistant Acinetobacter baumannii

scientific article published on 16 December 2015

Antimicrobial susceptibility and mechanisms of fosfomycin resistance in extended-spectrum β-lactamase-producing Escherichia coli strains from urinary tract infections in Wenzhou, China.

scientific article published on 26 April 2017

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

scientific article published on 01 June 2019

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

scientific article published on 14 March 2018

Bioinformatic approaches for predicting substrates of proteases

scientific article published on February 2011

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

scientific article published on 07 August 2013

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

scientific article

Cascleave: towards more accurate prediction of caspase substrate cleavage sites

scientific article published on 3 February 2010

Cell graph neural networks enable the precise prediction of patient survival in gastric cancer

scientific article published in 2022

Characteristic and mechanism of immobilization effect of Staphylococcus aureus on human spermatozoa

scientific article published on 27 March 2018

Characterization of the ERG-regulated Kinome in Prostate Cancer Identifies TNIK as a Potential Therapeutic Target

scientific article published on 20 March 2019

Characterization of the Src-regulated kinome identifies SGK1 as a key mediator of Src-induced transformation

scientific article published in Nature Communications

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

scientific article

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

scientific article published on 16 December 2015

ColistinDose, a Mobile App for Determining Intravenous Dosage Regimens of Colistimethate in Critically Ill Adult Patients: Clinician-Centered Design and Development Study

scientific article published on 16 December 2020

Comparative analysis of phosphoethanolamine transferases involved in polymyxin resistance across ten clinically relevant gram-negative bacteria

scientific article

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

scientific article

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

scientific article published on 11 November 2019

Computational Identification of Protein Pupylation Sites by Using Profile-Based Composition of k-Spaced Amino Acid Pairs

scientific article published on 16 June 2015

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

scientific article published in December 2014

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

scientific article

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

scientific article published on 24 November 2020

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

scientific article published on 04 May 2020

Computing Minimum Reaction Modifications in a Boolean Metabolic Network

scientific article published on 24 November 2017

Computing smallest intervention strategies for multiple metabolic networks in a boolean model

scientific article

Correction: ColistinDose, a Mobile App for Determining Intravenous Dosage Regimens of Colistimethate in Critically Ill Adult Patients: Clinician-Centered Design and Development Study

scientific article published on 18 December 2020

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

scientific article published on 27 February 2017

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

scientific article published on 22 June 2017

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

scientific article published on 15 July 2015

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

scientific article

DEMoS: a deep learning-based ensemble approach for predicting the molecular subtypes of gastric adenocarcinomas from histopathological images

scientific article published in 2022

Deep Ensemble Machine Learning Framework for the Estimation of PM2.5 Concentrations

scientific article published in 2022

Deep learning with evolutionary and genomic profiles for identifying cancer subtypes

scientific article published on 01 June 2019

DeepGenGrep: a general deep learning-based predictor for multiple genomic signals and regions

scientific article published in 2022

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

scientific article published on 22 March 2016

Development of thermodynamic optimum searching (TOS) to improve the prediction accuracy of flux balance analysis

scientific article published on 18 October 2012

Draft Genome Sequence of Lysinibacillus fusiformis Strain SW-B9, a Novel Strain for Biotransformation of Isoeugenol to Vanillin

scientific article published on 16 April 2015

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

scientific article published on 27 June 2010

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

scientific article published on December 30, 2011

Exploring drug combinations in genetic interaction network

scientific article

Exploring synonymous codon usage preferences of disulfide-bonded and non-disulfide bonded cysteines in the E. coli genome.

scientific article published on 19 January 2006

Extracellular overexpression of chitosanase from Bacillus sp. TS in Escherichia coli

scientific article published on 31 January 2015

FunSAV: predicting the functional effect of single amino acid variants using a two-stage random forest model

scientific article

FusC, a member of the M16 protease family acquired by bacteria for iron piracy against plants

article

Genome-Wide Analysis of Haemonchus contortus Proteases and Protease Inhibitors Using Advanced Informatics Provides Insights into Parasite Biology and Host–Parasite Interactions

scientific article published in 2023

Genome-scale metabolic modeling of responses to polymyxins in Pseudomonas aeruginosa.

scientific article published in April 2018

Global metabolic analyses identify key differences in metabolite levels between polymyxin-susceptible and polymyxin-resistant Acinetobacter baumannii

scientific article published on 29 February 2016

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

scientific article published on 06 October 2016

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

scientific article published on 6 January 2015

GraphormerDTI: A graph transformer-based approach for drug-target interaction prediction

scientific article published in 2024

HIVed, a knowledgebase for differentially expressed human genes and proteins during HIV infection, replication and latency

scientific article

Identification of WD40 repeats by secondary structure-aided profile-profile alignment

scientific article

Identification of catalytic residues using a novel feature that integrates the microenvironment and geometrical location properties of residues

scientific article

Immunopeptidomic analysis reveals that deamidated HLA-bound peptides arise predominantly from deglycosylated precursors

scientific article published on 01 May 2020

Increased production of alkaline polygalacturonate lyase in the recombinant Pichia pastoris by controlling cell concentration during continuous culture

article

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

scientific article published in January 2017

Inference of Essential Genes of the Parasite Haemonchus contortus via Machine Learning

scientific article published on 27 June 2024

Integer programming-based method for designing synthetic metabolic networks by Minimum Reaction Insertion in a Boolean model

scientific article

Integrated Analysis of Multiscale Large-Scale Biological Data for Investigating Human Disease 2016

scientific article

Integrated analysis of multiscale large-scale biological data for investigating human disease.

scientific article published on 20 April 2015

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

scientific article published on 17 March 2016

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

scientific article

MERITS: a web-based integrated <i>Mycobacterial</i> PE/PPE protein database

scientific article published in 2024

MSNet-4mC: learning effective multi-scale representations for identifying DNA N4-methylcytosine sites

scientific article published in 2022

Mathematical Modelling of the MAP Kinase Pathway Using Proteomic Datasets ⬇️

scientific article published on August 8, 2012

Metabolic changes in Klebsiella oxytoca in response to low oxidoreduction potential, as revealed by comparative proteomic profiling integrated with flux balance analysis

scientific article (publication date: May 2014)

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

scientific article published in 2021

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

scientific article published in September 2017

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

scientific article published on 30 January 2018

PROSPECT: A web server for predicting protein histidine phosphorylation sites

scientific article published on 05 June 2020

PROSPER: an integrated feature-based tool for predicting protease substrate cleavage sites

scientific article

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

scientific article

PScL-DDCFPred: an ensemble deep learning-based approach for characterizing multiclass subcellular localization of human proteins from bioimage data

scientific article published in 2022

Pan-transcriptomic analysis identified common differentially expressed genes of Acinetobacter baumannii in response to polymyxin treatments

scientific article published on 29 May 2020

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

scientific article published on 2 March 2016

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

scientific article

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

scientific article

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

scientific article published on 05 May 2020

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

scientific article published on 15 March 2016

Post-translational modification (PTM) bioinformatics in China: progresses and perspectives

scientific article

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

scientific article published in March 2011

PredPPCrys: accurate prediction of sequence cloning, protein production, purification and crystallization propensity from protein sequences using multi-step heterogeneous feature fusion and selection

scientific article

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

scientific article published on 17 October 2007

Predicting residue-residue contacts and helix-helix interactions in transmembrane proteins using an integrative feature-based random forest approach

scientific article

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

scientific article

Predicting serpin/protease interactions

scientific article

Prediction of Multiple Types of RNA Modifications via Biological Language Model

scientific article published on 08 June 2023

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

scientific article

Preterm birth and term low birth weight associated with wildfire-specific PM2.5: A cohort study in New South Wales, Australia during 2016–2019

scientific article published in 2023

Prodepth: predict residue depth by support vector regression approach from protein sequences only

scientific article

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

scientific article published on 01 December 2018

RBP-TSTL is a two-stage transfer learning framework for genome-scale prediction of RNA-binding proteins

scientific article published in 2022

ReCGBM: a gradient boosting-based method for predicting human dicer cleavage sites

scientific article published on 10 February 2021

Reductive evolution in outer membrane protein biogenesis has not compromised cell surface complexity in Helicobacter pylori

scientific article published on 21 October 2017

Resolvins E1 and D1 inhibit interstitial fibrosis in the obstructed kidney via inhibition of local fibroblast proliferation.

scientific article published on 6 November 2012

Response to Comment on "A subset of HLA-I peptides are not genomically templated: Evidence for cis- and trans-spliced peptide ligands"

scientific article published on 01 August 2019

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

scientific article published on 21 November 2019

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

scientific article published on July 2016

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

scientific article

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

scientific article published on 23 January 2017

Significantly improving the yield of recombinant proteins in Bacillus subtilis by a novel powerful mutagenesis tool (ARTP): Alkaline α-amylase as a case study

scientific article published on 29 June 2015

Staged heterogeneity learning to identify conformational B-cell epitopes from antigen sequences

scientific article

Structural Capacitance in Protein Evolution and Human Diseases

scientific article published on 03 July 2018

Structural propensities of human ubiquitination sites: accessibility, centrality and local conformation.

scientific article published on 11 December 2013

Structure-based engineering of a pectate lyase with improved specific activity for ramie degumming.

scientific article published on 27 December 2016

Survey of predictors of propensity for protein production and crystallization with application to predict resolution of crystal structures

scientific article published on 20 September 2017

Synergistic Combination of Polymyxin B and Enrofloxacin Induced Metabolic Perturbations in Extensive Drug-Resistant Pseudomonas aeruginosa

scientific article published on 03 October 2019

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

scientific article published on 27 November 2017

TANGLE: two-level support vector regression approach for protein backbone torsion angle prediction from primary sequences

scientific article

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

scientific article published on 08 October 2018

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

scientific article published on 8 February 2016

The flagellotropic bacteriophage YSD1 targets Salmonella Typhi with a Chi-like protein tail fibre

scientific article published on 09 October 2019

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

scientific article published on 01 September 2019

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

scientific article published on 11 March 2014

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

scientific article published on 10 September 2014

TransC-ac4C: Identification of N4-Acetylcytidine (ac4C) Sites in mRNA Using Deep Learning

scientific article published on 12 April 2024

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

scientific article published on 12 February 2016

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

scientific article published in September 2013

csORF-finder: an effective ensemble learning framework for accurate identification of multi-species coding short open reading frames

scientific article published in 2022

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

scientific article published on 8 March 2018

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

scientific article published on 01 June 2021

nhKcr: a new bioinformatics tool for predicting crotonylation sites on human nonhistone proteins based on deep learning

scientific article published on 01 November 2021

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