A5030196668- Phosphodiesterase function and regulation
- Plant Molecular Biology Research
- Inflammatory mediators and NSAID effects
- Peptidase Inhibition and Analysis
- Plant Gene Expression Analysis
- Helicobacter pylori-related gastroenterology studies
- Photosynthetic Processes and Mechanisms
- Genetic factors in colorectal cancer
- Cancer, Lipids, and Metabolism
- Digestive system and related health
- Genomics and Phylogenetic Studies
- Estrogen and related hormone effects
- Virus-based gene therapy research
- Colorectal Cancer Treatments and Studies
- Cancer-related molecular mechanisms research
- Microbial Metabolic Engineering and Bioproduction
- RNA modifications and cancer
- Colorectal Cancer Screening and Detection
- Plant Reproductive Biology
- Cancer-related gene regulation
- Advanced ceramic materials synthesis
- RNA and protein synthesis mechanisms
- Machine Learning in Bioinformatics
- Herpesvirus Infections and Treatments
- Satellite Image Processing and Photogrammetry
National Cheng Kung University
2016-2025
Northwest A&F University
2022-2025
National Taiwan University
2010-2025
Ministry of Agriculture and Rural Affairs
2025
Fox Chase Cancer Center
2013-2024
National Taiwan University Hospital
2024
Academia Sinica
2018-2023
Taipei Veterans General Hospital
2007-2022
Feng Chia University
2016-2021
Chang Gung Memorial Hospital
2014-2018
High oil and protein content make tetraploid peanut a leading food legume. Here we report high-quality genome sequence, comprising 2.54 Gb with 20 pseudomolecules 83,709 protein-coding gene models. We characterize functional groups implicated in seed size evolution, content, disease resistance symbiotic nitrogen fixation. The B subgenome has more genes general expression dominance, temporally associated long-terminal-repeat expansion the A that also raises questions about A-genome...
The Plant Promoter Analysis Navigator (PlantPAN; http://PlantPAN.itps.ncku.edu.tw/) is an effective resource for predicting regulatory elements and reconstructing transcriptional networks plant genes. In this release (PlantPAN 3.0), 17 230 TFs were collected from 78 species. To explore landscapes, genomic locations of TFBSs have been captured 662 public ChIP-seq samples using standard data processing. A total 1 233 999 linkages identified 99 factors (TFs, histones other DNA-binding proteins)...
Transcription factors (TFs) are sequence-specific DNA-binding proteins acting as critical regulators of gene expression. The Plant Promoter Analysis Navigator (PlantPAN; http://PlantPAN2.itps.ncku.edu.tw) provides an informative resource for detecting transcription factor binding sites (TFBSs), corresponding TFs, and other important regulatory elements (CpG islands tandem repeats) in a promoter or set plant promoters. Additionally, TFBSs, CpG islands, repeats the conserve regions between...
Abstract Background The elucidation of transcriptional regulation in plant genes is important area research for scientists, following the mapping various genomes, such as A. thaliana , O. sativa and Z. mays . A variety bioinformatic servers or databases promoters have been established, although most focused only on annotating transcription factor binding sites a single gene neglected some regulatory elements (tandem repeats CpG/CpNpG islands) promoter regions. Additionally, combinatorial...
The dbPTM (http://dbPTM.mbc.nctu.edu.tw/) has been maintained for over 10 years with the aim to provide functional and structural analyses post-translational modifications (PTMs). In this update, not only integrates more experimentally validated PTMs from available databases through manual curation of literature but also provides PTM-disease associations based on non-synonymous single nucleotide polymorphisms (nsSNPs). high-throughput deep sequencing technology led a surge in data generated...
Protein post-translational modifications (PTMs) play an important role in different cellular processes. In view of the importance PTMs functions and massive data accumulated by rapid development mass spectrometry (MS)-based proteomics, this paper presents update dbPTM with over 2 777 000 PTM substrate sites obtained from existing databases manual curation literature, which more than 235 entries are experimentally verified. This has manually curated 42 new modification types that were not...
Protein modification is an extremely important post-translational regulation that adjusts the physical and chemical properties, conformation, stability activity of a protein; thus altering protein function. Due to high throughput mass spectrometry (MS)-based methods in identifying site-specific modifications (PTMs), dbPTM (http://dbPTM.mbc.nctu.edu.tw/) updated integrate experimental PTMs obtained from public resources as well manually curated MS/MS peptides associated with research...
Abstract Background MicroRNAs (miRNAs), small non-coding RNAs of 19 to 25 nt, play important roles in gene regulation both animals and plants. In the last few years, oligonucleotide microarray is one high-throughput robust method for detecting miRNA expression. However, approach restricted expression known miRNAs. Second-generation sequencing an inexpensive method. This new a promising tool with high sensitivity specificity can be used measure abundance small-RNA sequences sample. Hence,...
MicroRNAs (miRNAs) are critical small non-coding RNAs that regulate gene expression by hybridizing to the 3′-untranslated regions (3′-UTR) of target mRNAs, subsequently controlling diverse biological processes at post-transcriptional level. How miRNA genes regulated receives considerable attention because it directly affects miRNA-mediated regulatory networks. Although numerous prediction models were developed for identifying promoters or transcriptional start sites (TSSs), most them lack...
Abstract Nonsteroidal anti-inflammatory drugs (NSAID) display promising antineoplastic activity for colorectal and other cancers, but toxicity from COX inhibition limits their long-term use chemoprevention. Previous studies have concluded that the basis tumor cell growth inhibitory does not require inhibition, although underlying mechanism is poorly understood. Here, we report NSAID sulindac sulfide inhibits cyclic guanosine 3′,5′-monophosphate phosphodiesterase (cGMP PDE) to increase...
Abstract PlantPAN 4.0 (http://PlantPAN.itps.ncku.edu.tw/) is an integrative resource for constructing transcriptional regulatory networks diverse plant species. In this release, the gene annotation and promoter sequences were expanded to cover 115 can help users characterize evolutionary differences similarities among cis-regulatory elements; furthermore, system now in identification of conserved non-coding homologous genes. The updated transcription factor binding site repository contains...
Synthetic Biology, a multidisciplinary field, is growing rapidly. Improving the understanding of biological systems through mimicry and producing bio-orthogonal with new functions are two complementary pursuits in this field. A web server called FMM (From Metabolite to Metabolite) was developed for purpose. can reconstruct metabolic pathways form one metabolite another among different species, based mainly on Kyoto Encyclopedia Genes Genomes (KEGG) database other integrated databases. Novel...
Abstract Studies over the last few years have identified protein methylation on histones and other proteins that are involved in regulation of gene transcription. Several works developed approaches to identify computationally potential sites lysine arginine. tertiary structure demonstrated preferentially regions easily accessible. However, previous studies not taken into account solvent‐accessible surface area (ASA) surrounds sites. This work presents a method named MASA combines support...
Sequence features in promoter regions are involved regulating gene transcription initiation. Although numerous computational methods have been developed for predicting transcriptional start sites (TSSs) or factor (TF) binding (TFBSs), they lack annotations do not consider some important regulatory such as CpG islands, tandem repeats, the TATA box, CCAAT GC over-represented oligonucleotides, DNA stability, and content. Additionally, combinatorial interaction of TFs regulates group that is...
Mycoplasma synoviae ( MS ) is a primary avian pathogen prevalent worldwide that causes airsacculitis and synovitis in birds. Vaccination recommended as the most cost-effective strategy control of infection. Novel alternative vaccines are needed for eradicating controlling infection flocks. DnaK, enolase, elongation factor Tu (EF-Tu), MSPB, NADH oxidase LP78 major immunogenic antigens promising targets subunit vaccine candidates. In present study, genes encoding EF-Tu, LP78, were cloned...
Abstract Tyrosine sulfation is a post‐translational modification of many secreted and membrane‐bound proteins. It governs protein‐protein interactions that are involved in leukocyte adhesion, hemostasis, chemokine signaling. However, the intrinsic feature sulfated protein remains elusive to be delineated. This investigation presents SulfoSite, which computational method based on support vector machine (SVM) for predicting sulfotyrosine sites. The approach was developed consider structural...
Protein phosphorylation catalyzed by kinases plays crucial regulatory roles in intracellular signal transduction. With the increasing number of experimental sites that has been identified mass spectrometry-based proteomics, desire to explore networks protein and substrates is motivated. Manning et al. have 518 human kinase genes, which provide a starting point for comprehensive analysis networks. In this study, knowledgebase developed integrate experimentally verified data protein–protein...
Peripheral nerve conduits were fabricated from biodegradable polyurethane (PU) which was synthesized by a waterborne process. The PU based on poly(ε-caprolactone) diol and polyethylene butylene adipate (2:3 molar ratio) as the soft segment. Conduits formed freeze-drying process had asymmetric microporous structure. used to bridge 10-mm gap in rat sciatic nerve. Nerve regeneration evaluated walking track analysis, magnetic resonance imaging (MRI), electrophysiological, histological analyses....
Mycoplasma synoviae ( M. ) is one of the major poultry pathogens causing infectious synovitis, airsacculitis, a high incidence shell breakage, and egg production loss. However, pathogenesis remains unclear. Adhesion mycoplasmas to host cells crucial step in infection colonization. The purpose this study was determine adhesive function putative P80 family lipoprotein (LP78) evaluate its application detection antibodies against . Recombinant LP78 (rLP78) expressed supernatant component...