Hsien-Da Huang
Orcid: 0000-0003-2857-7023
According to our database1,
Hsien-Da Huang
authored at least 94 papers
between 2001 and 2023.
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Bibliography
2023
Quantitative model for genome-wide cyclic AMP receptor protein binding site identification and characteristic analysis.
Briefings Bioinform., May, 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
dbPTM in 2022: an updated database for exploring regulatory networks and functional associations of protein post-translational modifications.
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
MethHC 2.0: information repository of DNA methylation and gene expression in human cancer.
Nucleic Acids Res., 2021
2020
miRTarBase 2020: updates to the experimentally validated microRNA?target interaction database.
Nucleic Acids Res., 2020
BMC Bioinform., 2020
2019
dbPTM in 2019: exploring disease association and cross-talk of post-translational modifications.
Nucleic Acids Res., 2019
Biogenesis mechanisms of circular RNA can be categorized through feature extraction of a machine learning model.
Bioinform., 2019
2018
miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions.
Nucleic Acids Res., 2018
Integrated microRNA and mRNA expression profile analysis of tumor-associated macrophages after exposure to single-dose irradiation.
Comput. Biol. Chem., 2018
Ouroboros resembling competitive endogenous loop (ORCEL) in circular RNAs revealed through transcriptome sequencing dataset analysis.
BMC Genom., 2018
BMC Genom., 2018
2017
Gene expression profiling of tumor-associated macrophages after exposure to single-dose irradiation.
Comput. Biol. Chem., 2017
Plant miRNAs found in human circulating system provide evidences of cross kingdom RNAi.
BMC Genom., 2017
2016
Nucleic Acids Res., 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
miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database.
Nucleic Acids Res., 2016
Transcriptome sequencing based annotation and homologous evidence based scaffolding of <i>Anguilla japonica</i> draft genome.
BMC Genom., 2016
PARRoT- a homology-based strategy to quantify and compare RNA-sequencing from non-model organisms.
BMC Bioinform., 2016
2015
IEEE ACM Trans. Comput. Biol. Bioinform., 2015
Nucleic Acids Res., 2015
GeNOSA: inferring and experimentally supporting quantitative gene regulatory networks in prokaryotes.
Bioinform., 2015
2014
miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions.
Nucleic Acids Res., 2014
Clinical detection of human probiotics and human pathogenic bacteria by using a novel high-throughput platform based on next generation sequencing.
J. Clin. Bioinform., 2014
lncRNAMap: A map of putative regulatory functions in the long non-coding transcriptome.
Comput. Biol. Chem., 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
A computational approach for identifying microRNA-target interactions using high-throughput CLIP and PAR-CLIP sequencing.
BMC Genom., 2013
An enhanced computational platform for investigating the roles of regulatory RNA and for identifying functional RNA motifs.
BMC Bioinform., 2013
pseudoMap: an innovative and comprehensive resource for identification of siRNA-mediated mechanisms in human transcribed pseudogenes.
Database J. Biol. Databases Curation, 2013
Clinical detection of human probiotics and human pathogenic bacteria by using a novel high-throughput platform based on next generation sequencing.
Proceedings of the International Work-Conference on Bioinformatics and Biomedical Engineering, 2013
2012
Int. J. Bioinform. Res. Appl., 2012
2011
RegPhos: a system to explore the protein kinase-substrate phosphorylation network in humans.
Nucleic Acids Res., 2011
miRTarBase: a database curates experimentally validated microRNA-target interactions.
Nucleic Acids Res., 2011
Medical Biol. Eng. Comput., 2011
BMC Bioinform., 2011
2010
N-Ace: Using solvent accessibility and physicochemical properties to identify protein N-acetylation sites.
J. Comput. Chem., 2010
An expert system to identify co-regulated gene groups from time-lagged gene clusters using cell cycle expression data.
Expert Syst. Appl., 2010
Prediction of small non-coding RNA in bacterial genomes using support vector machines.
Expert Syst. Appl., 2010
2009
sRNAMap: genomic maps for small non-coding RNAs, their regulators and their targets in microbial genomes.
Nucleic Acids Res., 2009
Nucleic Acids Res., 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
Expert Syst. Appl., 2009
Detecting LTR structures in human genomic sequences using profile hidden Markov models.
Expert Syst. Appl., 2009
miRExpress: Analyzing high-throughput sequencing data for profiling microRNA expression.
BMC Bioinform., 2009
Proceedings of the Ninth IEEE International Conference on Bioinformatics and Bioengineering, 2009
Proceedings of the Ninth IEEE International Conference on Bioinformatics and Bioengineering, 2009
2008
Identifying Discriminative Amino Acids Within the Hemagglutinin of Human Influenza A H5N1 Virus Using a Decision Tree.
IEEE Trans. Inf. Technol. Biomed., 2008
Nucleic Acids Res., 2008
Nucleic Acids Res., 2008
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
Biological Data Warehousing System for Identifying Transcriptional Regulatory Sites From Gene Expressions of Microarray Data.
IEEE Trans. Inf. Technol. Biomed., 2006
IEEE Trans. Inf. Technol. Biomed., 2006
Nucleic Acids Res., 2006
ProKware: integrated software for presenting protein structural properties in protein tertiary structures.
Nucleic Acids Res., 2006
Nucleic Acids Res., 2006
miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes.
Nucleic Acids Res., 2006
Nucleic Acids Res., 2006
Detection of discriminative sequence motifs in proteins obtained from prokaryotes grown at various temperatures.
J. Comput. Chem., 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
Nucleic Acids Res., 2005
Incorporating hidden Markov models for identifying protein kinase-specific phosphorylation sites.
J. Comput. Chem., 2005
Discovering Common Structural Motifs of Ribosomal Rna Secondary Structures in Prokaryotes.
Int. J. Artif. Intell. Tools, 2005
Proceedings of the Genetic and Evolutionary Computation Conference, 2005
Proceedings of 3rd Asia-Pacific Bioinformatics Conference, 17-21 January 2005, Singapore, 2005
2004
Identifying the combination of genetic factors that determine susceptibility to cervical cancer.
IEEE Trans. Inf. Technol. Biomed., 2004
A Computational Approach to Discover Differential Cooperation of Regulartory Sites in Functionally Related Genes in Yeast Genome.
J. Inf. Sci. Eng., 2004
Identifying Transcriptional Regulatory Sites in the Human Genome Using an Integrated Computation.
Proceedings of the 7th International Symposium on Parallel Architectures, 2004
RgS-Miner: A Biological Data Warehousing, Analyzing and Mining System for Identifying Transcriptional Regulatory Sites in Human Genome.
Proceedings of the Database and Expert Systems Applications, 15th International Conference, 2004
Identifying the Combination of Genetic Factors that Determine Susceptibility to Cervical Cancer.
Proceedings of the 4th IEEE International Symposium on BioInformatics and BioEngineering (BIBE 2004), 2004
2003
Database of repetitive elements in complete genomes and data mining using transcription factor binding sites.
IEEE Trans. Inf. Technol. Biomed., 2003
A Data Mining Method to Predict Transcriptional Regulatory Sites Based Based on Differentially Expressed Genes in Human Genome.
J. Inf. Sci. Eng., 2003
A Data Mining Method to Predict Transcriptional Regulatory Sites Based on Differentially Expressed Genes in Human Genome.
Proceedings of the 3rd IEEE International Symposium on BioInformatics and BioEngineering (BIBE 2003), 2003
2002
The Repetitive Sequence Database and Mining Putative Regulatory Elements in Gene Promoter Regions.
J. Comput. Biol., 2002
Mining putative regulatory elements in gene promoter regions of Saccharomyces cerevisiae.
Silico Biol., 2002
Proceedings of the 2002 Congress on Evolutionary Computation, 2002
2001
Mining Combinations of Structural Motif from SSU 16 S Ribosomal RNA Secondary Structures.
Proceedings of the Computer science and biology: Proceedings of the German Conference on Bioinformatics, 2001
Mining Putative Regulatory Elements in Gene Promoter Regions.
Proceedings of the Computer science and biology: Proceedings of the German Conference on Bioinformatics, 2001
Discovering Common Structural Motifs from SSU 16 S Ribosomal RNA Secondary Structures.
Proceedings of the 2nd IEEE International Symposium on Bioinformatics and Bioengineering, 2001