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Author Details

Chen Li
Biomedicine Discovery Institute, Monash University
2015
41
15
PMIDPaper TitleJournal TitlePublished Year
36890882Immunolyser: A web-based computational pipeline for analysing and mining immunopeptidomic data.Comput Struct Biotechnol J2023
37886621DeepSecE: A Deep-Learning-Based Framework for Multiclass Prediction of Secreted Proteins in Gram-Negative Bacteria.Research (Wash D C)2023
37610353MULGA, a unified multi-view graph autoencoder-based approach for identifying drug-protein interaction and drug repositioning.Bioinformatics2023
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
37369638iAMPCN: a deep-learning approach for identifying antimicrobial peptides and their functional activities.Brief Bioinform2023
36732611Multi-modality data-driven analysis of diagnosis and treatment of psoriatic arthritis.NPJ Digit Med2023
36794913PFresGO: an attention mechanism-based deep-learning approach for protein annotation by integrating gene ontology inter-relationships.Bioinformatics2023
34798331MhcVizPipe: A Quality Control Software for Rapid Assessment of Small- to Large-Scale Immunopeptidome Datasets.Mol Cell Proteomics2022
34729589Positive-unlabeled learning in bioinformatics and computational biology: a brief review.Brief Bioinform2022
34745458ggVolcanoR: A Shiny app for customizable visualization of differential expression datasets.Comput Struct Biotechnol J2021
33811468Resourcing, annotating, and analysing synthetic peptides of SARS-CoV-2 for immunopeptidomics and other immunological studies.Proteomics2021
33859439PCprophet: a framework for protein complex prediction and differential analysis using proteomic data.Nat Methods2021
33660783iLearnPlus: a comprehensive and automated machine-learning platform for nucleic acid and protein sequence analysis, prediction and visualization.Nucleic Acids Res2021
34746858RHybridFinder: An R package to process immunopeptidomic data for putative hybrid peptide discovery.STAR Protoc2021
32469363Pan-transcriptomic analysis identified common differentially expressed genes of Acinetobacter baumannii in response to polymyxin treatments.Mol Omics2020
33338026Correction: ColistinDose, a Mobile App for Determining Intravenous Dosage Regimens of Colistimethate in Critically Ill Adult Patients: Clinician-Centered Design and Development Study.JMIR Mhealth Uhealth2020
33325835ColistinDose, a Mobile App for Determining Intravenous Dosage Regimens of Colistimethate in Critically Ill Adult Patients: Clinician-Centered Design and Development Study.JMIR Mhealth Uhealth2020
32938616Spliced Peptides and Cytokine-Driven Changes in the Immunopeptidome of Melanoma.Cancer Immunol Res2020
30285084Large-scale comparative assessment of computational predictors for lysine post-translational modification sites.Brief Bioinform2019
31752668SIMLIN: a bioinformatics tool for prediction of S-sulphenylation in the human proteome based on multi-stage ensemble-learning models.BMC Bioinformatics2019
30184176Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods.Brief Bioinform2019
31420321Response to Comment on "A subset of HLA-I peptides are not genomically templated: Evidence for cis- and trans-spliced peptide ligands".Sci Immunol2019
27777222Comprehensive assessment and performance improvement of effector protein predictors for bacterial secretion systems III, IV and VI.Brief Bioinform2018
29954286ProBAPred: Inferring protein-protein binding affinity by incorporating protein sequence and structural features.J Bioinform Comput Biol2018
30111491Structural Capacitance in Protein Evolution and Human Diseases.J Mol Biol2018
29947803Quokka: a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome.Bioinformatics2018
30315122A subset of HLA-I peptides are not genomically templated: Evidence for cis- and trans-spliced peptide ligands.Sci Immunol2018
29288722Comparative analysis of phosphoethanolamine transferases involved in polymyxin resistance across 10 clinically relevant Gram-negative bacteria.Int J Antimicrob Agents2018
28720874Knowledge-transfer learning for prediction of matrix metalloprotease substrate-cleavage sites.Sci Rep2017
28112271SecretEPDB: a comprehensive web-based resource for secreted effector proteins of the bacterial types III, IV and VI secretion systems.Sci Rep2017
28358052HIVed, a knowledgebase for differentially expressed human genes and proteins during HIV infection, replication and latency.Sci Rep2017
26177815Critical evaluation of in silico methods for prediction of coiled-coil domains in proteins.Brief Bioinform2016
27708373GlycoMine<sup>struct</sup>: a new bioinformatics tool for highly accurate mapping of the human N-linked and O-linked glycoproteomes by incorporating structural features.Sci Rep2016
27189606PolyQ 2.0: an improved version of PolyQ, a database of human polyglutamine proteins.Database (Oxford)2016
26989151KinetochoreDB: a comprehensive online resource for the kinetochore and its related proteins.Database (Oxford)2016
26980520PolyQ 2.0: an improved version of PolyQ, a database of human polyglutamine proteins.Database (Oxford)2016
26931649Periscope: quantitative prediction of soluble protein expression in the periplasm of Escherichia coli.Sci Rep2016
27074717SPAR: a random forest-based predictor for self-interacting proteins with fine-grained domain information.Amino Acids2016
25568279GlycoMine: a machine learning-based approach for predicting N-, C- and O-linked glycosylation in the human proteome.Bioinformatics2015
25435395Computational characterization of parallel dimeric and trimeric coiled-coils using effective amino acid indices.Mol Biosyst2015
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Collaborators

Monash Data Futures Institute, Monash University
Co-authored papers 33
Monash Biomedicine Discovery Institute, Monash University
Co-authored papers 13
Monash University
Co-authored papers 2
Human Genome Center, The Institute of Medical Science, The University of Tokyo
Co-authored papers 2
Henan Agricultural University
Co-authored papers 2
The Peter Doherty Institute for Infection and Immunity, The University of Melbourne
Co-authored papers 2
Institute of Molecular Systems Biology, ETH Zurich
Co-authored papers 1
King Abdullah University of Science and Technology (KAUST)
Co-authored papers 1
Co-authored papers 1
Co-authored papers 1
Institute of Computational Biology, University of Natural Resources and Life Sciences
Co-authored papers 1
ETH Zurich
Co-authored papers 1
Lund University
Co-authored papers 1
Co-authored papers 1
University of Bern
Co-authored papers 1
Australia Olivia Newton-John Cancer Research Institute, La Trobe University
Co-authored papers 1
Biomedicine Discovery Institute, Monash University
Co-authored papers 1
Institute of Translational Medicine, ETH Zurich
Co-authored papers 1
Max-Planck Institute of Biochemistry
Co-authored papers 1
J. David Gladstone Institutes
Co-authored papers 1
Institute of Biochemistry, ETH Zurich
Co-authored papers 1
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
Co-authored papers 1
Institute of Molecular Systems Biology, ETH Zurich
Co-authored papers 1