Publications by authors named "Shidong Cui"
MicroRNAs (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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- 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.
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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.
MicroRNAs (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.
MicroRNAs (miRNAs) are small non-coding RNAs (typically consisting of 18-25 nucleotides) that negatively control expression of target genes at the post-transcriptional level. Owing to the biological significance of miRNAs, miRTarBase was developed to provide comprehensive information on experimentally validated miRNA-target interactions (MTIs). To date, the database has accumulated >13,404 validated MTIs from 11,021 articles from manual curations.
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