Publications by authors named "Hsi-Yuan Huang"
MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression by binding to the 3'-untranslated regions of target mRNAs, influencing various biological processes at the post-transcriptional level. Identifying miRNA transcription start sites (TSSs) and transcription factors' (TFs) regulatory roles is crucial for elucidating miRNA function and transcriptional regulation. miRStart 2.
View Article and Find Full Text PDFMicroRNAs (miRNAs) are small non-coding RNAs (18-26 nucleotides) that regulate gene expression by interacting with target mRNAs, affecting various physiological and pathological processes. miRTarBase, a database of experimentally validated miRNA-target interactions (MTIs), now features over 3 817 550 validated MTIs from 13 690 articles, significantly expanding its previous version. The updated database includes miRNA interactions with therapeutic agents, revealing roles in drug resistance and therapeutic strategies.
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- Drug repositioning offers a quicker and cheaper way to find new uses for existing drugs, but current databases have limitations like inadequate data and poor organization.
- The new DrugRepoBank database includes a 'Literature' module with extensive drug repositioning studies, and a 'Prediction' module that uses various algorithms to suggest new drug candidates.
- DrugRepoBank provides an easy-to-use web interface, allowing users to input drugs or diseases to receive new target suggestions and access related information, potentially speeding up the drug repositioning process.
Article Synopsis
- Time-series experiments help us understand biological processes over time, but identifying causal mechanisms can be challenging.
- This study introduces a new algorithm that combines known biological networks with gene expression data to map out signaling pathways during the transition from aerobic to anaerobic conditions.
- The research identifies a novel regulatory network involving environmentally responsive genes that influence nitrogen metabolism regulators, ultimately affecting cell motility, enhancing our understanding of microbial physiology and its potential biotechnological applications.
Article Synopsis
- * Research indicates that once absorbed, these miRNAs can regulate gene expression in the infant's gastrointestinal system, suggesting their potential as functional regulators.
- * This review summarizes the evidence of BM miRNA absorption, evaluates past studies' strengths and weaknesses, and explores implications for improving infant formula and drug delivery methods.
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- Ferroptosis is a specific type of cell death linked to the build-up of iron-dependent lipid peroxides and is regulated by both enzymatic and non-enzymatic processes.
- * Natural compounds can affect various enzymes that play key roles in oxidative stress and lipid metabolism, which are crucial in the regulation of ferroptosis.
- * While much research has focused on how natural products influence the expression of these enzymes, there is a significant gap in exploring how they affect enzyme activity, highlighting an area for future investigation.*
Drug-target interactions (DTIs) are considered a crucial component of drug design and drug discovery. To date, many computational methods were developed for drug-target interactions, but they are insufficiently informative for accurately predicting DTIs due to the lack of experimentally verified negative datasets, inaccurate molecular feature representation, and ineffective DTI classifiers. Therefore, we address the limitations of randomly selecting negative DTI data from unknown drug-target pairs by establishing two experimentally validated datasets and propose a capsule network-based framework called CapBM-DTI to capture hierarchical relationships of drugs and targets, which adopts pre-trained bidirectional encoder representations from transformers (BERT) for contextual sequence feature extraction from target proteins through transfer learning and the message-passing neural network (MPNN) for the 2-D graph feature extraction of compounds to accurately and robustly identify drug-target interactions.
View Article and Find Full Text PDFEthnopharmacological Relevance: Sophorae Flavescentis Radix (Kushen) is the primary herb component of Compound Kushen Injection (CKI), an approved clinical treatment for tumors. Despite CKI's widespread use, the underlying mechanisms of Kushen regarding microRNA-target and pathway remain unclear in non-small cell lung cancer (NSCLC).
Aim Of The Study: This study aimed to elucidate the crucial miRNAs-targets and pathways responsible for the Kushen's impact on NSCLC.
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- Herbal medicine Sanqi (SQ), derived from Panax notoginseng (PNS), shows promise in combating diabetes and obesity, but detailed studies on its signaling networks are limited.
- Researchers used a systems biology approach with RNA and miRNA sequencing to identify key pathways and genes related to metabolic disorders like insulin resistance.
- The study found that PNS treatment increased levels of certain protective proteins while decreasing harmful microRNAs, suggesting a mechanism for how PNS helps regulate cellular functions in metabolic issues.
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- Cyclic AMP receptor proteins (CRPs) are crucial for regulating gene expression in various species, and traditional methods for predicting their binding sites are limited to known motifs.
- A new model called CRPBSFinder was created, incorporating advanced techniques like hidden Markov models and binding affinity matrices, leading to better prediction accuracy and ranking of binding sites based on their strength.
- The model not only identified 1089 new CRP-regulated genes but also categorized CRP functions into four main classes, revealing novel roles in metabolism and cellular response, and can be applied to study CRPs in 35 other species, with results available online.
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- This study explores the anti-cancer effects of a traditional Chinese medicine (CR) by analyzing how various cancer cell lines respond to different concentrations of CR treatment through mRNA sequencing.
- Using differential expression (DE) and gene set enrichment analysis (GSEA), researchers identified that the Cell cycle pathway was significantly disturbed by CR treatment, particularly the G2/M phase-related genes.
- Experimental validation showed that CR inhibits cancer cell growth by targeting the PLK1/CDK1/Cyclin B pathway, indicating that down-regulation of these genes correlates with better overall survival in cancer patients.
MicroRNA (miRNA)-target interaction (MTI) plays a substantial role in various cell activities, molecular regulations and physiological processes. Published biomedical literature is the carrier of high-confidence MTI knowledge. However, digging out this knowledge in an efficient manner from large-scale published articles remains challenging.
View Article and Find Full Text PDFBackground: Dysregulated BMP (bone morphogenetic protein) or TGF-β (transforming growth factor beta) signaling pathways are imperative in idiopathic and familial pulmonary arterial hypertension (PAH) as well as experimental pulmonary hypertension (PH) in rodent models. MED1 (mediator complex subunit 1) is a key transcriptional co-activator and KLF4 (Krüppel-like factor 4) is a master transcription factor in endothelium. However, MED1 and KLF4 epigenetic and transcriptional regulations of the BMP/TGF-β axes in pulmonary endothelium and their dysregulations leading to PAH remain elusive.
View Article and Find Full Text PDFBackground: Air pollution is known to have notable negative effects on human health. Recently, the effect of air pollution on blood pressure among the elderly has attracted researchers' attention. However, the existing evidence is not consistent, given that positive, null, and negative outcomes are presented in the literature.
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- - Head and neck cancer patients often face a higher risk of developing second primary tumors, contributing to a lower survival rate compared to other cancers.
- - The study utilized next-generation sequencing on tumor samples from 13 patients to compare mutations between their first and second oral cancer diagnoses.
- - Results revealed that some patients misdiagnosed as having recurrent cancer actually had primary tumors, emphasizing the potential of genetic testing to improve diagnostic accuracy.
Drug-metabolizing enzymes, particularly the cytochrome P450 (CYP450) monooxygenases, play a pivotal role in pharmacokinetics. CYP450 enzymes can be affected by various xenobiotic substrates, which will eventually be responsible for most metabolism-based herb-herb or herb-drug interactions, usually involving competition with another drug for the same enzyme binding site. Compounds from herbal or natural products are involved in many scenarios in the context of such interactions.
View Article and Find Full Text PDFMicroRNAs (miRNAs) are noncoding RNAs with 18-26 nucleotides; they pair with target mRNAs to regulate gene expression and produce significant changes in various physiological and pathological processes. In recent years, the interaction between miRNAs and their target genes has become one of the mainstream directions for drug development. As a large-scale biological database that mainly provides miRNA-target interactions (MTIs) verified by biological experiments, miRTarBase has undergone five revisions and enhancements.
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- Circular RNAs (circRNAs) are looped RNA molecules that regulate gene expression by acting as sponges for microRNAs and are gaining recognition as potential cancer biomarkers.
- The newly updated CircNet 2.0 integrates circRNAs from various databases, analyzing 2732 samples from 37 cancer types and predicting target microRNAs using reliable computational tools.
- This version of CircNet enhances user experience with an interactive web interface and offers a comprehensive resource for constructing circRNA-miRNA-gene regulatory networks in biomedical research.
Idiopathic pulmonary fibrosis (IPF) is a progressive lung disease with limited treatment options. Despite endothelial cells (ECs) comprising 30% of the lung cellular composition, the role of EC dysfunction in pulmonary fibrosis (PF) remains unclear. We hypothesize that sterol regulatory element-binding protein 2 (SREBP2) plays a critical role in the pathogenesis of PF via EC phenotypic modifications.
View Article and Find Full Text PDFBackground: The soil quality and health of the tea plantations are dependent on agriculture management practices, and long-term chemical fertilizer use is implicated in soil decline. Hence, several sustainable practices are used to improve and maintain the soil quality. Here, in this study, changes in soil properties, enzymatic activity, and dysbiosis in bacterial community composition were compared using three agricultural management practices, namely conventional (CA), sustainable (SA), and transformational agriculture (TA) in the tea plantation during 2016 and 2017 period.
View Article and Find Full Text PDFDNA methylation is an important epigenetic regulator in gene expression and has several roles in cancer and disease progression. MethHC version 2.0 (MethHC 2.
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- * Deletion mutations in the pre-S1 and pre-S2 gene segments of the hepatitis B virus (HBV) have been linked to this recurrence, prompting a study using next-generation sequencing.
- * The study found that the pre-S2 deletion (nucleotide 1 to 54) is the most common in HBV-related HCC patients and serves as a strong predictor of recurrence, suggesting its use as a noninvasive biomarker for high-risk patients post-surgery.
Background: MicroRNAs (miRNAs) play a key role in mediating the action of insulin on cell growth and the development of diabetes. However, few studies have been conducted to provide a comprehensive overview of the miRNA-mediated signaling network in response to glucose in pancreatic beta cells. In our study, we established a computational framework integrating multi-omics profiles analyses, including RNA sequencing (RNA-seq) and small RNA sequencing (sRNA-seq) data analysis, inverse expression pattern analysis, public data integration, and miRNA targets prediction to illustrate the miRNA-mediated regulatory network at different glucose concentrations in INS-1 pancreatic beta cells (INS-1), which display important characteristics of the pancreatic beta cells.
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