Tzong-Yi Lee
Orcid: 0000-0001-8475-7868
According to our database1,
Tzong-Yi Lee
authored at least 77 papers
between 2005 and 2023.
Collaborative distances:
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Bibliography
2023
Predicting Anti-inflammatory Peptides by Ensemble Machine Learning and Deep Learning.
J. Chem. Inf. Model., December, 2023
A risk assessment framework for multidrug-resistant <i>Staphylococcus aureus</i> using machine learning and mass spectrometry technology.
Briefings Bioinform., September, 2023
Identification of species-specific RNA N6-methyladinosine modification sites from RNA sequences.
Briefings Bioinform., March, 2023
Holistic similarity-based prediction of phosphorylation sites for understudied kinases.
Briefings Bioinform., March, 2023
Extraction of microRNA-target interaction sentences from biomedical literature by deep learning approach.
Briefings Bioinform., January, 2023
KinasePhos 3.0: Redesign and Expansion of the Prediction on Kinase-specific Phosphorylation Sites.
Genom. Proteom. Bioinform., 2023
2022
Integrating transformer and imbalanced multi-label learning to identify antimicrobial peptides and their functional activities.
Bioinform., December, 2022
dbPTM in 2022: an updated database for exploring regulatory networks and functional associations of protein post-translational modifications.
Nucleic Acids Res., 2022
dbAMP 2.0: updated resource for antimicrobial peptides with an enhanced scanning method for genomic and proteomic data.
Nucleic Acids Res., 2022
miRTarBase update 2022: an informative resource for experimentally validated miRNA-target interactions.
Nucleic Acids Res., 2022
CircNet 2.0: an updated database for exploring circular RNA regulatory networks in cancers.
Nucleic Acids Res., 2022
J. Comput. Aided Mol. Des., 2022
2021
Incorporating support vector machine with sequential minimal optimization to identify anticancer peptides.
BMC Bioinform., 2021
A representation and deep learning model for annotating ubiquitylation sentences stating E3 ligase - substrate interaction.
BMC Bioinform., 2021
UbiNet 2.0: a verified, classified, annotated and updated database of E3 ubiquitin ligase-substrate interactions.
Database J. Biol. Databases Curation, 2021
A large-scale investigation and identification of methicillin-resistant Staphylococcus aureus based on peaks binning of matrix-assisted laser desorption ionization-time of flight MS spectra.
Briefings Bioinform., 2021
AVPIden: a new scheme for identification and functional prediction of antiviral peptides based on machine learning approaches.
Briefings Bioinform., 2021
Identifying anti-coronavirus peptides by incorporating different negative datasets and imbalanced learning strategies.
Briefings Bioinform., 2021
2020
miRTarBase 2020: updates to the experimentally validated microRNA?target interaction database.
Nucleic Acids Res., 2020
SuccSite: Incorporating Amino Acid Composition and Informative <i>k</i>-spaced Amino Acid Pairs to Identify Protein Succinylation Sites.
Genom. Proteom. Bioinform., 2020
Incorporating deep learning and multi-omics autoencoding for analysis of lung adenocarcinoma prognostication.
Comput. Biol. Chem., 2020
Characterization and identification of antimicrobial peptides with different functional activities.
Briefings Bioinform., 2020
2019
Rapid classification of group B Streptococcus serotypes based on matrix-assisted laser desorption ionization-time of flight mass spectrometry and machine learning techniques.
BMC Bioinform., December, 2019
dbAMP: an integrated resource for exploring antimicrobial peptides with functional activities and physicochemical properties on transcriptome and proteome data.
Nucleic Acids Res., 2019
dbPTM in 2019: exploring disease association and cross-talk of post-translational modifications.
Nucleic Acids Res., 2019
PlantPAN3.0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants.
Nucleic Acids Res., 2019
Characterization and identification of lysine glutarylation based on intrinsic interdependence between positions in the substrate sites.
BMC Bioinform., 2019
2018
Machine Learning-Based Method for Obesity Risk Evaluation Using Single-Nucleotide Polymorphisms Derived from Next-Generation Sequencing.
J. Comput. Biol., 2018
Delineation of condition specific Cis- and Trans-acting elements in plant promoters under various Endo- and exogenous stimuli.
BMC Genom., 2018
Genome-wide discovery of viral microRNAs based on phylogenetic analysis and structural evolution of various human papillomavirus subtypes.
Briefings Bioinform., 2018
2017
IEEE ACM Trans. Comput. Biol. Bioinform., 2017
Investigation and identification of functional post-translational modification sites associated with drug binding and protein-protein interactions.
BMC Syst. Biol., 2017
MDD-carb: a combinatorial model for the identification of protein carbonylation sites with substrate motifs.
BMC Syst. Biol., 2017
Identification of natural antimicrobial peptides from bacteria through metagenomic and metatranscriptomic analysis of high-throughput transcriptome data of Taiwanese oolong teas.
BMC Syst. Biol., 2017
Investigation and identification of protein carbonylation sites based on position-specific amino acid composition and physicochemical features.
BMC Bioinform., 2017
2016
dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins.
Nucleic Acids Res., 2016
PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants.
Nucleic Acids Res., 2016
A new scheme to discover functional associations and regulatory networks of E3 ubiquitin ligases.
BMC Syst. Biol., 2016
UbiSite: incorporating two-layered machine learning method with substrate motifs to predict ubiquitin-conjugation site on lysines.
BMC Syst. Biol., 2016
SOHSite: incorporating evolutionary information and physicochemical properties to identify protein <i>S</i>-sulfenylation sites.
BMC Genom., 2016
Gene expression profiling identifies candidate biomarkers for active and latent tuberculosis.
BMC Bioinform., 2016
MDD-SOH: exploiting maximal dependence decomposition to identify <i>S</i>-sulfenylation sites with substrate motifs.
Bioinform., 2016
UbiNet: an online resource for exploring the functional associations and regulatory networks of protein ubiquitylation.
Database J. Biol. Databases Curation, 2016
2015
A two-layered machine learning method to identify protein O-GlcNAcylation sites with O-GlcNAc transferase substrate motifs.
BMC Bioinform., December, 2015
dbSNO 2.0: a resource for exploring structural environment, functional and disease association and regulatory network of protein <i>S</i>-nitrosylation.
Nucleic Acids Res., 2015
Characterization and identification of ubiquitin conjugation sites with E3 ligase recognition specificities.
BMC Bioinform., 2015
ViralmiR: a support-vector-machine-based method for predicting viral microRNA precursors.
BMC Bioinform., 2015
An interpretable rule-based diagnostic classification of diabetic nephropathy among type 2 diabetes patients.
BMC Bioinform., 2015
2014
topPTM: a new module of dbPTM for identifying functional post-translational modifications in transmembrane proteins.
Nucleic Acids Res., 2014
Incorporating significant amino acid pairs and protein domains to predict RNA splicing-related proteins with functional roles.
J. Comput. Aided Mol. Des., 2014
Identification and characterization of lysine-methylated sites on histones and non-histone proteins.
Comput. Biol. Chem., 2014
Characterization and identification of protein O-GlcNAcylation sites with substrate specificity.
BMC Bioinform., 2014
RegPhos 2.0: an updated resource to explore protein kinase-substrate phosphorylation networks in mammals.
Database J. Biol. Databases Curation, 2014
2013
dbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications.
Nucleic Acids Res., 2013
EuLoc: a web-server for accurately predict protein subcellular localization in eukaryotes by incorporating various features of sequence segments into the general form of Chou's PseAAC.
J. Comput. Aided Mol. Des., 2013
Incorporating substrate sequence motifs and spatial amino acid composition to identify kinase-specific phosphorylation sites on protein three-dimensional structures.
BMC Bioinform., 2013
ViralPhos: incorporating a recursively statistical method to predict phosphorylation sites on virus proteins.
BMC Bioinform., 2013
2012
GPMiner: an integrated system for mining combinatorial cis-regulatory elements in mammalian gene group.
BMC Genom., 2012
2011
RegPhos: a system to explore the protein kinase-substrate phosphorylation network in humans.
Nucleic Acids Res., 2011
Carboxylator: incorporating solvent-accessible surface area for identifying protein carboxylation sites.
J. Comput. Aided Mol. Des., 2011
BMC Bioinform., 2011
PlantPhos: using Maximal Dependence Decomposition to Identify Plant Phosphorylation Sites with Substrate Site Specificity.
BMC Bioinform., 2011
BMC Bioinform., 2011
Exploiting maximal dependence decomposition to identify conserved motifs from a group of aligned signal sequences.
Bioinform., 2011
Prediction of transporter targets using efficient RBF networks with PSSM profiles and biochemical properties.
Bioinform., 2011
2010
N-Ace: Using solvent accessibility and physicochemical properties to identify protein N-acetylation sites.
J. Comput. Chem., 2010
Incorporating significant amino acid pairs to identify O-linked glycosylation sites on transmembrane proteins and non-transmembrane proteins.
BMC Bioinform., 2010
2009
Incorporating structural characteristics for identification of protein methylation sites.
J. Comput. Chem., 2009
Incorporating support vector machine for identifying protein tyrosine sulfation sites.
J. Comput. Chem., 2009
2007
KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns.
Nucleic Acids Res., 2007
2006
Nucleic Acids Res., 2006
ProKware: integrated software for presenting protein structural properties in protein tertiary structures.
Nucleic Acids Res., 2006
An agent-based system to discover protein-protein interactions, identify protein complexes and proteins with multiple peptide mass fingerprints.
J. Comput. Chem., 2006
2005
KinasePhos: a web tool for identifying protein kinase-specific phosphorylation sites.
Nucleic Acids Res., 2005
Incorporating hidden Markov models for identifying protein kinase-specific phosphorylation sites.
J. Comput. Chem., 2005