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Author Details

Jiangning Song
Monash Data Futures Institute, Monash University
2004
228
42
PMIDPaper TitleJournal TitlePublished Year
36413068PScL-2LSAESM: bioimage-based prediction of protein subcellular localization by integrating heterogeneous features with the two-level SAE-SM and mean ensemble method.Bioinformatics2023
37995291Interpretable prediction models for widespread m6A RNA modification across cell lines and tissues.Bioinformatics2023
37507781Smad7 in the hippocampus contributes to memory impairment in aged mice after anesthesia and surgery.J Neuroinflammation2023
37610353MULGA, a unified multi-view graph autoencoder-based approach for identifying drug-protein interaction and drug repositioning.Bioinformatics2023
37874948ProsperousPlus: a one-stop and comprehensive platform for accurate protease-specific substrate cleavage prediction and machine-learning model construction.Brief Bioinform2023
37572513Surformer: An interpretable pattern-perceptive survival transformer for cancer survival prediction from histopathology whole slide images.Comput Methods Programs Biomed2023
37569696Genome-Wide Analysis of <i>Haemonchus contortus</i> Proteases and Protease Inhibitors Using Advanced Informatics Provides Insights into Parasite Biology and Host-Parasite Interactions.Int J Mol Sci2023
36958111Preterm birth and term low birth weight associated with wildfire-specific PM<sub>2.5</sub>: A cohort study in New South Wales, Australia during 2016-2019.Environ Int2023
37291763TIMER is a Siamese neural network-based framework for identifying both general and species-specific bacterial promoters.Brief Bioinform2023
37289599Prediction of Multiple Types of RNA Modifications via Biological Language Model.IEEE/ACM Trans Comput Biol Bioinform2023
37150785ATTIC is an integrated approach for predicting A-to-I RNA editing sites in three species.Brief Bioinform2023
37080771TripletCell: a deep metric learning framework for accurate annotation of cell types at the single-cell level.Brief Bioinform2023
37410078The evolutionary mechanism of non-carbapenemase carbapenem-resistant phenotypes in <i>Klebsiella</i> spp.Elife2023
37143762An informatic workflow for the enhanced annotation of excretory/secretory proteins of <i>Haemonchus contortus</i>.Comput Struct Biotechnol J2023
37307727Association between long-term exposure to wildfire-related PM<sub>2.5</sub> and mortality: A longitudinal analysis of the UK Biobank.J Hazard Mater2023
37369638iAMPCN: a deep-learning approach for identifying antimicrobial peptides and their functional activities.Brief Bioinform2023
37031189Genetic algorithm-based feature selection with manifold learning for cancer classification using microarray data.BMC Bioinformatics2023
37356289Digerati - A multipath parallel hybrid deep learning framework for the identification of mycobacterial PE/PPE proteins.Comput Biol Med2023
36889862Global estimates of daily ambient fine particulate matter concentrations and unequal spatiotemporal distribution of population exposure: a machine learning modelling study.Lancet Planet Health2023
36723814Predicting Pseudouridine Sites with Porpoise.Methods Mol Biol2023
36880172ResNetKhib: a novel cell type-specific tool for predicting lysine 2-hydroxyisobutylation sites via transfer learning.Brief Bioinform2023
36567255Interpretable artificial intelligence model for accurate identification of medical conditions using immune repertoire.Brief Bioinform2023
36528813COPPER: an ensemble deep-learning approach for identifying exclusive virus-derived small interfering RNAs in plants.Brief Funct Genomics2023
36528806VPatho: a deep learning-based two-stage approach for accurate prediction of gain-of-function and loss-of-function variants.Brief Bioinform2023
36864612Targeting tumor heterogeneity: multiplex-detection-based multiple instance learning for whole slide image classification.Bioinformatics2023
36794913PFresGO: an attention mechanism-based deep-learning approach for protein annotation by integrating gene ontology inter-relationships.Bioinformatics2023
34657153T4SEfinder: a bioinformatics tool for genome-scale prediction of bacterial type IV secreted effectors using pre-trained protein language model.Brief Bioinform2022
35353532Enhancing Characteristic Gene Selection and Tumor Classification by the Robust Laplacian Supervised Discriminative Sparse PCA.J Chem Inf Model2022
35739342Cell graph neural networks enable the precise prediction of patient survival in gastric cancer.NPJ Precis Oncol2022
35652827Response to "Comment on 'Deep Ensemble Machine Learning Framework for the Estimation of <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:msub><mml:mrow><mml:mrow><mml:mi>PM</mml:mi></mml:mrow></mml:mrow><mml:mrow><mml:mrow><mml:mn>2.5</mml:mn></mml:mrow></mml:mrow></mml:msub></mml:mrow></mml:math> Concentrations'".Environ Health Perspect2022
35771606PScL-DDCFPred: an ensemble deep learning-based approach for characterizing multiclass subcellular localization of human proteins from bioimage data.Bioinformatics2022
35649392RBP-TSTL is a two-stage transfer learning framework for genome-scale prediction of RNA-binding proteins.Brief Bioinform2022
35801909DEMoS: a deep learning-based ensemble approach for predicting the molecular subtypes of gastric adenocarcinomas from histopathological images.Bioinformatics2022
35799358DeepGenGrep: a general deep learning-based predictor for multiple genomic signals and regions.Bioinformatics2022
35765650PERISCOPE-Opt: Machine learning-based prediction of optimal fermentation conditions and yields of recombinant periplasmic protein expressed in <i>Escherichia coli</i>.Comput Struct Biotechnol J2022
35724564PCfun: a hybrid computational framework for systematic characterization of protein complex function.Brief Bioinform2022
35696083Systematic Characterization of Lysine Post-translational Modification Sites Using MUscADEL.Methods Mol Biol2022
35853501Ubiquitination pathway model for the barber's pole worm - Haemonchus contortus.Int J Parasitol2022
35524557iFeatureOmega: an integrative platform for engineering, visualization and analysis of features from molecular sequences, structural and ligand data sets.Nucleic Acids Res2022
35487269Performing protein fold recognition by exploiting a stack convolutional neural network with the attention mechanism.Anal Biochem2022
35973091PROST: AlphaFold2-aware Sequence-Based Predictor to Estimate Protein Stability Changes upon Missense Mutations.J Chem Inf Model2022
36341591Clarion is a multi-label problem transformation method for identifying mRNA subcellular localizations.Brief Bioinform2022
36205602MSNet-4mC: learning effective multi-scale representations for identifying DNA N4-methylcytosine sites.Bioinformatics2022
36094083csORF-finder: an effective ensemble learning framework for accurate identification of multi-species coding short open reading frames.Brief Bioinform2022
35985185A multi-channel deep convolutional neural network for multi-classifying thyroid diseases.Comput Biol Med2022
35951370Coassembled Nitric Oxide-Releasing Nanoparticles with Potent Antimicrobial Efficacy against Methicillin-Resistant <i>Staphylococcus aureus</i> (MRSA) Strains.ACS Appl Mater Interfaces2022
36284264PreAcrs: a machine learning framework for identifying anti-CRISPR proteins.BMC Bioinformatics2022
36049552Improving the prediction of DNA-protein binding by integrating multi-scale dense convolutional network with fault-tolerant coding.Anal Biochem2022
34953462Prediction of disease-associated nsSNPs by integrating multi-scale ResNet models with deep feature fusion.Brief Bioinform2022
35254864Deep Ensemble Machine Learning Framework for the Estimation of <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi>P</mml:mi><mml:msub><mml:mrow><mml:mi>M</mml:mi></mml:mrow><mml:mrow><mml:mrow><mml:mn>2.5</mml:mn></mml:mrow></mml:mrow></mml:msub></mml:mrow></mml:math> Concentrations.Environ Health Perspect2022
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Collaborators

Chen Li
Biomedicine Discovery Institute, Monash University
Co-authored papers 33
Anthony W Purcell
Monash Biomedicine Discovery Institute, Monash University
Co-authored papers 14
James C Whisstock
Monash University
Co-authored papers 12
Zhen Chen
Henan Agricultural University
Co-authored papers 11
Lachlan J M Coin
The Peter Doherty Institute for Infection and Immunity, The University of Melbourne
Co-authored papers 8
Seiya Imoto
Human Genome Center, The Institute of Medical Science, The University of Tokyo
Co-authored papers 5
David R Powell
Biomedicine Discovery Institute, Monash University
Co-authored papers 3
Ruedi Aebersold
Institute of Molecular Systems Biology, ETH Zurich
Co-authored papers 2
Andrea Fossati
J. David Gladstone Institutes
Co-authored papers 2
Alex Boussioutas
Royal Melbourne Hospital, University of Melbourne
Co-authored papers 2
Neil D Rawlings
Co-authored papers 2
Pietro Li??
University of Cambridge
Co-authored papers 1
Mitchell G Lawrence
Biomedicine Discovery Institute, Monash University
Co-authored papers 1
Hsien-Da Huang
Co-authored papers 1
Fei He
Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
Co-authored papers 1
Rodolfo Ciuffa
Institute of Molecular Systems Biology, ETH Zurich
Co-authored papers 1
David S Rickman
Meyer Cancer Center
Co-authored papers 1
Vladimir N Uversky
Morsani College of Medicine, University of South Florida
Co-authored papers 1
Peter Sykacek
Institute of Computational Biology, University of Natural Resources and Life Sciences
Co-authored papers 1
Zhenguo Zhang
Co-authored papers 1
Bernd Wollscheid
ETH Zurich
Co-authored papers 1
Peer Bork
University of Wurzburg
Co-authored papers 1
Wenguang Shao
Institute of Molecular Systems Biology, ETH Zurich
Co-authored papers 1
Evan G Williams
University of Luxembourg
Co-authored papers 1
Andrzej Joachimiak
Center for Structural Biology of Infectious Diseases, University of Chicago
Co-authored papers 1
Mar??a Rodr??guez Mart??nez
Herbert Irving Cancer Research Center, Columbia University Medical Center
Co-authored papers 1
Mark A Rubin
University of Bern
Co-authored papers 1
Patrick G A Pedrioli
Institute of Translational Medicine, Swiss Federal Institute of Technology/ETH Zurich
Co-authored papers 1
Moritz Heusel
Lund University
Co-authored papers 1
Varun S Sharma
Institute of Molecular Systems Biology, ETH Zurich
Co-authored papers 1
Release 1.2