420 results
Search Results
Now showing 1 - 10 of 420
Publication Metadata only Meta-iavp: A sequence-based meta-predictor for improving the prediction of antiviral peptides using effective feature representation(2019-11-02) Nalini Schaduangrat; Chanin Nantasenamat; Virapong Prachayasittikul; Watshara Shoombuatong; Mahidol University(AVPs) has become an influential antiviral agent due to their extraordinary advantages. With the avalanche of newly-found peptide sequences in the post-genomic era, there is a great demand to develop a sequence-based predictor for timely identifying AVPs... as this information is very useful for both basic research and drug development. In this study, we propose a novel sequence-based meta-predictor with an effective feature representation, called Meta-iAVP, for the accurate prediction of AVPs from given peptideItem Metadata only GPApred: The first computational predictor for identifying proteins with LPXTG-like motif using sequence-based optimal features(2023-02-28) Malik A.; Shoombuatong W.; Kim C.B.; Manavalan B.; Mahidol Universitythe first machine learning-based predictor called GPApred, which can identify LPXTG-like proteins from their primary sequences. Using a newly constructed benchmark dataset, we explored different classifiers and five feature encodings and their hybrids... (GPApred) was selected based on consistency during cross-validation and independent assessment. GPApred can be an effective tool for predicting LPXTG-like sequences and can be further employed for functional characterization or drug targeting. AvailabilityPublication Metadata only Genetic variation of kaempferia (zingiberaceae) in thailand based on chloroplast dna (psba-trnh and peta-psbj) sequences(2010-11-17) J. Techaprasan; S. Klinbunga; C. Ngamriabsakul; T. Jenjittikul; Thailand National Center for Genetic Engineering and Biotechnology; Walailak University; Mahidol University. filifolia, K. elegans, K. pulchra, K. rotunda, K. marginata, K. parviflora, K. larsenii, K. roscoeana, K. siamensis, and G. godefroyi A strict consensus tree based on combined psbA-trnH and partial petApsbJ sequences revealed four major groups of Kaempferia...J spacer sequences. Ten closely related species (Boesenbergia rotunda, Gagnepainia godefroyi, G. thoreliana, Globba substrigosa, Smithatris myanmarensis, S. supraneanae, Scaphochlamys biloba, S. minutiflora, S. rubescens, and Stahlianthus sp) were alsoPublication Metadata only Reagent and laboratory contamination can critically impact sequence-based microbiome analyses(2014-11-12) Susannah J. Salter; Michael J. Cox; Elena M. Turek; Szymon T. Calus; William O. Cookson; Miriam F. Moffatt; Paul Turner; Julian Parkhill; Nicholas J. Loman; Alan W. Walker; Wellcome Trust Sanger Institute; National Heart and Lung Institute; University of Birmingham; Mahidol University; Nuffield Department of Clinical Medicine; University of Aberdeenconfounder of these sequence-based approaches is the presence of contamination in DNA extraction kits and other laboratory reagents. Results: In this study we demonstrate that contaminating DNA is ubiquitous in commonly used DNA extraction kits and other... surveys and shotgun metagenomics. We provide an extensive list of potential contaminating genera, and guidelines on how to mitigate the effects of contamination. Conclusions: These results suggest that caution should be advised when applying sequence-basedItem Metadata only Multiplex polymerase chain reaction (PCR) with Nanopore sequencing for sequence-based detection of four tilapia pathogens(2025-01-01) Delamare-Deboutteville J.; Meemetta W.; Pimsannil K.; Gan H.M.; Khor L.; Chadag M.; Dong H.T.; Senapin S.; Delamare-Deboutteville J.; Mahidol UniversityNanopore sequencing, enabling the one-tube simultaneous detection and one-reaction Nanopore sequencing-based validation of four pathogens. Results. Our one-tube multiplex assay exhibits a detection limit of 1,000 copies per reaction for TiLV, ISKNV.... Integrating multiplex PCR and Nanopore sequencing provides an alternative approach platform for fast and precise diagnostics of major tilapia pathogens in clinically sick animals, adding to the available toolbox for disease diagnostics.Item Metadata only Detection of Genetic Variants in Thai Population by Trio-Based Whole-Genome Sequencing Study(2025-03-01) Boonin P.; Klumsathian S.; Iemwimangsa N.; Sensorn I.; Charoenyingwatana A.; Chantratita W.; Chareonsirisuthigul T.; Boonin P.; Mahidol UniversityThis trio-based whole-genome sequencing (WGS) study enhances the accuracy of variant detection by leveraging parental genotypes, which facilitates the identification of de novo mutations and population-specific variants. Nonetheless... pathogenic variant linked to a de novo mutation is found in the SF3B2 gene, which is associated with craniofacial microsomia. With its innovative methodology and comprehensive dataset, our trio-based whole-genome sequencing study provides an invaluablePublication Metadata only Is amplification bias consequential in transposon sequencing (Tnseq) assays? a case study with a staphylococcus aureus tnseq library subjected to pcr-based and amplification-free enrichment methods(2021-01-01) Duah Alkam; Thidathip Wongsurawat; Intawat Nookaew; Anthony R. Richardson; David Ussery; Mark S. Smeltzer; Piroon Jenjaroenpun; Siriraj Hospital; University of Arkansas for Medical Sciences; University of Pittsburgh School of Medicineemployed in their library preparation protocols. In addition, nCATRAs is comparable to traditional PCR-based methods (Kendall’s correlation=0.896–0.897) although the latter remain superior owing to their accessibility and high sequencing depth....As transposon sequencing (TnSeq) assays have become prolific in the microbiology field, it is of interest to scrutinize their potential drawbacks. TnSeq data consist of millions of nucleotide sequence reads that are generated by PCR amplificationItem Metadata only Ultrarapid and high-resolution HLA class I typing using transposase-based nanopore sequencing applied in pharmacogenetic testing(2023-01-01) Anukul N.; Jenjaroenpun P.; Sirikul C.; Wankaew N.; Nimsamer P.; Roothumnong E.; Pithukpakorn M.; Leetrakool N.; Wongsurawat T.; Mahidol UniversityNanopore sequencing has been examined as a method for rapid and high-resolution human leukocyte antigen (HLA) typing in recent years. We aimed to apply ultrarapid nanopore-based HLA typing for HLA class I alleles associated with drug..., an imbalance in the PCR amplification of different haplotypes could affect the accuracy of typing results. This work demonstrates the ability of transposase-based sequencing to report 3-field HLA alleles and its potential for race- and population-independentPublication Metadata only Amplicon-based next generation sequencing for rapid identification of rickettsia and ectoparasite species from entomological surveillance in thailand(2021-02-01) Suwanna Chaorattanakawee; Achareeya Korkusol; Bousaraporn Tippayachai; Sommai Promsathaporn; Betty K. Poole-Smith; Ratree Takhampunya; Armed Forces Research Institute of Medical Sciences, Thailand; Mahidol UniversityBackground: Next generation sequencing (NGS) technology has been used for a wide range of epidemiological and surveillance studies. Here, we used amplicon-based NGS to species identify Rickettsia and their arthropod hosts from entomological... to species, while the Cytochrome Oxidase subunit I (COI) and subunit II (COII) genes were used as target genes for ectoparasite identification. All target gene amplicons were pooled for library preparation and sequenced with Illumina MiSeq platform. ResultPublication Metadata only IQSP: A sequence-based tool for the prediction and analysis of quorum sensing peptides via chou’s 5-steps rule and informative physicochemical properties(2020-01-01) Phasit Charoenkwan; Nalini Schaduangrat; Chanin Nantasenamat; Theeraphon Piacham; Watshara Shoombuatong; Mahidol University; Chiang Mai University. With the avalanche of the newly available peptide sequences in the post-genomic age, it is highly desirable to develop a computational model for efficient, rapid and high-throughput QSP identification purely based on the peptide sequence information alone. Although..., few methods have been developed for predicting QSPs, their prediction accuracy and interpretability still requires further improvements. Thus, in this work, we proposed an accurate sequence-based predictor (called iQSP) and a set of interpretable rules