Related papers: MicroRNAs -- targeting and target prediction
While RNA has recently been recognized as an interesting small-molecule drug target, many challenges remain to be addressed before we take full advantage of it. This emphasizes the necessity to improve our understanding of its structures…
Background: Small interfering RNA (siRNA) is a promising therapeutic agent due to its ability to silence disease-related genes via RNA interference. While traditional machine learning and early deep learning methods have made progress in…
miRNA and gene expression profiles have been proved useful for classifying cancer samples. Efficient classifiers have been recently sought and developed. A number of attempts to classify cancer samples using miRNA/gene expression profiles…
Machine learning is a field which studies how machines can alter and adapt their behavior, improving their actions according to the information they are given. This field is subdivided into multiple areas, among which the best known are…
MicroRNAs can affect the protein translation using nine mechanistically different mechanisms, including repression of initiation and degradation of the transcript. There is a hot debate in the current literature about which mechanism and in…
This methods paper presents computational protocols for the identification of non-coding RNA genes or RNA motifs within genomic sequences. An application to bacterial small RNA is proposed.
Understanding the connection between complex structural features of RNA and biological function is a fundamental challenge in evolutionary studies and in RNA design. However, building datasets of RNA 3D structures and making appropriate…
In recent studies, non-coding protein RNAs have been identified as microRNA that can be used as biomarkers for early diagnosis and treatment of cancer, that decrease mortality in cancer. A microRNA may target hundreds or thousands of genes…
Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) associated with trait diversity and disease susceptibility, yet the functional properties of many genetic variants and their molecular…
Deep networks trained on large-scale data can learn transferable features to promote learning multiple tasks. Since deep features eventually transition from general to specific along deep networks, a fundamental problem of multi-task…
Single-cell RNA sequencing (scRNA-seq) provides a high throughput, quantitative and unbiased framework for scientists in many research fields to identify and characterize cell types within heterogeneous cell populations from various…
RNA secondary structure prediction and classification are two important problems in the field of RNA biology. Here, we propose a new permutation based approach to create logical non-disjoint clusters of different secondary structures of a…
Protein translation is a multistep process which can be represented as a cascade of biochemical reactions (initiation, ribosome assembly, elongation, etc.), the rate of which can be regulated by small non-coding microRNAs through multiple…
The evolution of the genome has led to very sophisticated and complex regulation. Because of the abundance of non-coding RNA (ncRNA) in the cell, different species will promiscuously associate with each other, suggesting collective dynamics…
Small open reading frames are understudied as they have been historically excluded from genome annotations. However, evidence for the functional significance of small proteins in various cellular processes accumulates. Proteins with less…
Isoforms are mRNAs produced from the same gene site in the phenomenon called Alternative Splicing. Studies have shown that more than 95% of human multi-exon genes have undergone alternative splicing. Although there are few changes in mRNA…
Regulation of mRNA decay is a critical component of global cellular adaptation to changing environments. The corresponding changes in mRNA lifetimes can be coordinated with changes in mRNA transcription rates to fine-tune gene expression.…
Long non-coding RNAs (lncRNAs) are important regulators to modulate gene expression and cell proliferation in the developing human brain. Previous methods mainly use bulk lncRNA and mRNA expression data to study lncRNA regulation. However,…
Functional or non-coding RNAs are attracting more attention as they are now potentially considered valuable resources in the development of new drugs intended to cure several human diseases. The identification of drugs targeting the…
Gene expression is a fundamental process in a living system. The small RNAs (sRNAs) is widely observed as a global regulator in gene expression. The inherent nonlinearity in this regulatory process together with the bursty production of…