A5102816014- Reproductive tract infections research
- Genomics and Phylogenetic Studies
- Cancer Genomics and Diagnostics
- Genomics and Rare Diseases
- RNA and protein synthesis mechanisms
- Parasitic Infections and Diagnostics
- Bacteriophages and microbial interactions
- Preterm Birth and Chorioamnionitis
- Reproductive System and Pregnancy
- Neuroendocrine regulation and behavior
- Advanced Proteomics Techniques and Applications
- Gut microbiota and health
- Reproductive Physiology in Livestock
- Hepatitis B Virus Studies
- RNA modifications and cancer
- Gene expression and cancer classification
- Hepatitis C virus research
- Bioinformatics and Genomic Networks
- Machine Learning in Bioinformatics
- Listeria monocytogenes in Food Safety
- Cancer-related molecular mechanisms research
- Plant and fungal interactions
- Microbial Metabolic Engineering and Bioproduction
- Virology and Viral Diseases
- Amoebic Infections and Treatments
Chang Gung Memorial Hospital
2017-2024
Chang Gung University
2015-2024
Memorial Hospital of South Bend
2020-2023
Bridge University
2020-2023
National Defense Medical Center
2020
National Tsing Hua University
2010-2013
National Taipei University of Technology
2011
Oral squamous cell carcinoma is a prominent cancer worldwide, particularly in Taiwan. By integrating omics analyses 50 matched samples, we uncover Taiwanese patients predominant mutation signature associated with cytidine deaminase APOBEC, which correlates the upregulation of APOBEC3A expression APOBEC3 gene cluster at 22q13. significantly higher tumors carrying APOBEC3B-deletion allele(s). High-level better overall survival, especially among alleles, as examined second cohort (n = 188; p...
DSAP is an automated multiple-task web service designed to provide a total solution analyzing deep-sequencing small RNA datasets generated by next-generation sequencing technology. uses tab-delimited file as input format, which holds the unique sequence reads (tags) and their corresponding number of copies Solexa platform. The data will go through four analysis steps in DSAP: (i) cleanup: removal adaptors poly-A/T/C/G/N nucleotides; (ii) clustering: grouping cleaned tags into clusters; (iii)...
Despite their lack of protein-coding potential, long noncoding RNAs (lncRNAs) and circular (circRNAs) have emerged as key determinants in gene regulation, acting to fine-tune transcriptional signaling output. These RNA transcripts are known affect expression messenger (mRNAs) via epigenetic post-transcriptional regulation. Given widespread target spectrum, well extensive modes action, a complete understanding biological relevance will depend on integrative analyses systems data at various...
Chronic obstructive pulmonary disease (COPD) is a progressive, life-threatening lung with increasing prevalence and incidence worldwide. Increasing evidence suggests that microbiomes might play physiological role in acute exacerbations of COPD. The objective this study was to characterize the association microbiota exacerbation risk or airflow limitation stable COPD patients.The sputum from 78 outpatients during periods clinical stability investigated using 16S rRNA V3-V4 amplicon...
Trichomonas vaginalis is parasitic protozoan that causes human urogenital infections. Accumulated reports indicated exosomes released by this parasite play a crucial role in transmitting information and substances between cells during host-parasite interactions. Current knowledge on the protein contents T. exosome mainly generated from three previous studies used different isolates as an experimental model. Whether comprise common set of proteins (core proteome) still unclear. To explore...
Chromatin is a dynamic but highly regulated structure. DNA-binding proteins such as transcription factors, epigenetic and chromatin modifiers are responsible for regulating specific gene expression pattern may result in different phenotypes. To reveal the identity of associated with region on DNA, immunoprecipitation (ChIP) most widely used technique. ChIP assay followed by next generation sequencing (ChIP-seq) or microarray (ChIP-chip) often to study patterns protein-binding profiles cell...
Trichomonas vaginalis, the most common nonviral sexually transmitted parasite, causes ∼283 million trichomoniasis infections annually and is associated with pregnancy complications increased risk of HIV-1 acquisition. The antimicrobial drug metronidazole used for treatment, but in a fraction clinical cases, parasites can become resistant to this drug. We undertook sequencing multiple isolates lab derived lines identify genetic markers mechanisms resistance. Reduced representation genome ∼100...
Cancer is a genetic disease caused by somatic mutations; however, the understanding of causative biological processes generating these mutations limited. A cancer genome bears cumulative effects mutational during tumor development. Deciphering signatures in new topic research. The Wellcome Trust Sanger Institute (WTSI) has categorized 30 reference COSMIC database based on analyses ∼10 000 sequencing datasets from TCGA and ICGC. Large cohorts bioinformatics skills are required to perform same...
Trichomonasvirus (TVV) is a double-stranded RNA virus from the Pseudototiviridae family that exclusively infects Trichomonas vaginalis , protozoan responsible for most common non-viral sexually transmitted infection. Within genus, five distinct viral species have been identified, and intriguingly, single T. isolate can simultaneously harbor multiple TVV species. Previous studies explored impact of infection on physiology virulence yet findings remain inconsistent often contradictory. We...
The three most common sexually transmitted infections (STIs) are Chlamydia trachomatis (CT), Neisseria gonorrhoeae (GC) and Trichomonas vaginalis (TV). prevalence of these STIs in Taiwan remains largely unknown the risk STI acquisition affected by vaginal microbiota is also elusive. In this study, a total 327 swabs collected from women with vaginitis were analyzed to determine presence associated microorganisms using BD Max CT/GC/TV molecular assay, microbial cultures, 16S rRNA sequencing....
Accumulated evidence suggests that the endosymbiotic Trichomonasvirus (TVV) may play a role in pathogenesis and drug susceptibility of Trichomonas vaginalis. Several reports have shown extracellular vesicles (EVs) released from TVV-positive (TVV+) trichomonads can modulate immune response human vaginal epithelial cells animal models. These results prompted us to examine whether EVs TVV+ isolates contained TVV. We isolated small (sEVs) six T. vaginalis were either TVV free (ATCC 50143),...
Millions of people throughout the world suffer from parasite infections. Traditionally, technicians use manual eye inspection microscopic specimens to perform a examination. However, operations have limitations that hinder ability obtain precise egg counts and cause inefficient identification infected parasites on co-infections. The technician requirements for handling large number examinations in countries limited medical resources are substantial. We developed helminth analysis platform...
Hepatitis delta virus (HDV) is the only animal RNA that has an unbranched rod-like genome with ribozyme activity. It replicates in nucleus by host polymerase via a rolling circle mechanism. Similar to many viruses encoding their own RNA-dependent polymerases, homologous recombination of HDV occurs mixed-genotype infections and cultured cells cotransfected two sequences, as demonstrated molecular analyses.Among 237 published complete genomic 34 sequences were reported from small isolated...
Whole-exome sequencing, which centres on the protein coding regions of disease/cancer associated genes, represents most cost-effective method to-date for deciphering association between genetic alterations and diseases. Large-scale whole exome/genome sequencing projects have been launched by various institutions, such as NCI, Broad Institute TCGA, to provide a comprehensive catalogue variants in diverse tissue samples cell lines. Further functional clinical interrogation these sequence...
Trichomonas vaginalis is the causative agent of trichomoniasis, most prevalent non-viral sexually transmitted infection worldwide. Metronidazole (MTZ) mainstay anti-trichomonal chemotherapy; however, drug resistance has become an increasingly worrying issue. Additionally, molecular events MTZ-induced cell death in T. remain elusive. To gain insight into differential expression genes related to MTZ and death, we conducted RNA-sequencing three paired MTZ-resistant (MTZ-R) MTZ-sensitive (MTZ-S)...
Iron is an essential element for cellular functions, such as energy metabolism. Trichomonas vaginalis, a human urogenital tract pathogen, capable of surviving in the environment without sufficient iron supplementation. Pseudocysts (cyst-like structures) are environmentally tolerated stage this parasite while encountering undesired conditions, including deficiency. We previously demonstrated that deficiency induces more active glycolysis but drastic downregulation hydrogenosomal metabolic...
Whole genome sequence construction is becoming increasingly feasible because of advances in next generation sequencing (NGS), including increasing throughput and read length. By simply overlapping paired-end reads, we can obtain longer reads with higher accuracy, which facilitate the assembly process. However, influences different library sizes methods on sequencing-based de novo remain poorly understood. We used 250 bp Illumina Miseq generated from genomic DNA Escherichia coli DH1...
Trichomonas vaginalis colonizes the human urogenital tract and causes trichomoniasis, most common nonviral sexually transmitted disease. Currently, 5-nitroimidazoles are only recommended drugs for treating trichomoniasis. However, increased resistance of parasite to has emerged as a highly problematic public health issue. Hence, it is essential identify alternative chemotherapeutic agents against refractory Tetracycline (TET) broad-spectrum antibiotic with activity several protozoan...
Acinetobacter baumannii has emerged recently as a major cause of health care-associated infections due to the extent its antimicrobial resistance and propensity large nosocomial outbreaks. Here we report genome sequence TYTH-1 isolated in Taiwan during 2008.
The initial step to interpreting putative biological functions from comparative multi-omics studies usually starts a differential expressed gene list followed by functional enrichment analysis (FEA). However, most FEA packages are designed exclusively for humans and model organisms. Although parasitic protozoan is the important pathogen in tropics, no package available (ProFun) analysis. To speed up research on protozoans, we constructed ProFun, web-based, user-friendly platform community....
Abstract Trichomonas vaginalis is the causative agent of venereal disease trichomoniasis which infects men and women globally associated with serious outcomes during pregnancy cancers human reproductive tract. Trichomonads parasitize a range hosts in addition to humans including birds, livestock, domesticated animals. Recent genetic analysis trichomonads recovered from columbid birds has provided evidence that these parasite species undergo frequent host-switching, current epoch spillover...
Abstract Background In the last decade, a considerable amount of research has been devoted to investigating phylogenetic properties organisms from systems-level perspective. Most studies have focused on classification based structural comparison and local alignment metabolic pathways. contrast, global multiple networks complements sequence-based analyses provides more comprehensive information. Results We explored relationships between microorganisms through networks. The proposed approach...
γ-Carboxymuconolactone decarboxylase (CMD) participates in the β-ketoadipate pathway, which catalyzes aromatic compounds to produce acetyl- or succinyl-CoA, prokaryotes and yeast. Our previous study demonstrated that expression of a CMD homologue contains two signatures (dualCMD) is negatively regulated by iron Trichomonas vaginalis. However, we were not able identify components pathway parasite's genome. These observations prompted us investigate biological functions this novel T. The...
Recently, the deep learning (DL) dimension of artificial intelligence has received much attention from biochemical researchers and thus gradually become key approach adopted in area biosensing applications. Studies have shown that use DL techniques for sensing can not only shorten time data analysis but also significantly increase accuracy prediction, resulting performance improvement systems comparison to conventional methods. However, obtaining reliable equilibrium rate constants...