Related papers: MicroRNAs Implicated in Dysregulation of Gene Expr…

Gene Regulatory Networks (GRNs) consisting of combinations of transcription factors (TFs) and their cis promoters are assumed to be sufficient to direct the development of organisms. Mutations in GRNs are assumed to be the primary drivers…

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…

A simple stochastic model of a self regulating gene that displays bistable switching is analyzed. While on, a gene transcribes mRNA at a constant rate. Transcription factors can bind to the DNA and affect the gene's transcription rate.…

Recent studies reported complex post-transcriptional interplay among targets of a common pool of microRNAs, a class of small non-coding downregulators of gene expression. Behaving as microRNA-sponges, distinct RNA species may compete for…

The Cancer Genome Atlas (TCGA) provides researchers with clinicopathological data and genomic characterizations of various carcinomas. These data sets include expression microarrays for genes and microRNAs -- short, non-coding strands of…

Gene regulatory networks (GRNs) represent the causal relationships between transcription factors (TFs) and target genes in single-cell RNA sequencing (scRNA-seq) data. Understanding these networks is crucial for uncovering disease…

Lung cancer is a condition where there is abnormal growth of malignant cells that spread in an uncontrollable fashion in the lungs. Some common treatment strategies are surgery, chemotherapy, and radiation which aren't the best options due…

In tumoral cells, gene regulation mechanisms are severely altered, and these modifications in the regulations may be characteristic of different subtypes of cancer. However, these alterations do not necessarily induce differential…

Tight regulation of messenger RNA (mRNA) stability is essential to ensure accurate gene expression in response to developmental and environmental cues. mRNA stability is controlled by mRNA decay pathways, which have traditionally been…

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…

It has recently been suggested that the competition for a finite pool of microRNAs (miRNA) gives rise to effective interactions among their common targets (competing endogenous RNAs or ceRNAs) that could prove to be crucial for…

Cellular phenotypes are determined by the dynamical activity of networks of co-regulated genes. Elucidating such networks is crucial for the understanding of normal cell physiology as well as for the dissection of complex pathologic…

A mutation in a protein-coding gene in DNA can alter the protein structure coded by the same gene. Structurally altered proteins usually lose their functions and sometimes gain an undesirable function instead. These types of mutations and…

Nowadays, the screening methods for the early detection of lung cancer struggle with several limitations such as many false positive results and low sensitivity. The detection of specific biomarkers is of high interest to complement these…

The maintainance of a stable periodicity during the yeast metabolic cycle involving approximately half of the genome requires a very strict and efficient control of gene expression. For this reason, the metabolic cycle is a very good…

With the advent of Information technology, the Bioinformatics research field is becoming increasingly attractive to researchers and academicians. The recent development of various Bioinformatics toolkits has facilitated the rapid processing…

We train a neural network to predict distributional responses in gene expression following genetic perturbations. This is an essential task in early-stage drug discovery, where such responses can offer insights into gene function and inform…

Some genes can promote or repress their own expressions, which is called autoregulation. Although gene regulation is a central topic in biology, autoregulation is much less studied. In general, it is extremely difficult to determine the…

We discuss recent developments in the modeling of negative autoregulated genetic networks. In particular, we consider the temporal evolution of the population of mRNA and proteins in simple networks using rate equations. In the limit of low…

Gene regulatory networks typically have low in-degrees, whereby any given gene is regulated by few of the genes in the network. They also tend to have broad distributions for the out-degree. What mechanisms might be responsible for these…