Related papers: MicroRNAs -- targeting and target prediction
Selected ribonucleotide sequences bind well to zwitterionic phospholipid bilayer membranes, though randomized RNAs do not. There are no evident repeated sequences in selected membrane binding RNAs. This implies small and varied motifs…
Gene regulation is a series of processes that control gene expression and its extent. The connections among genes and their regulatory molecules, usually transcription factors, and a descriptive model of such connections, are known as gene…
In this paper we consider the problem of RNA folding with pseudoknots. We use a graphical representation in which the secondary structures are described by planar diagrams. Pseudoknots are identified as non-planar diagrams. We analyze the…
Living cells are the product of gene expression programs that involve the regulated transcription of thousands of genes. The elucidation of transcriptional regulatory networks in thus needed to understand the cell's working mechanism, and…
Competition to bind microRNAs induces an effective positive crosstalk between their targets, therefore known as `competing endogenous RNAs' or ceRNAs. While such an effect is known to play a significant role in specific conditions,…
The dysregulation of transcripts is characterized as one of the main mechanisms in tumor pathogenesis. The recent discovery developed a new hypothesis, competitive endogenous RNAs (ceRNAs), which could regulate other RNA transcripts via…
It has been well accepted that the RNA secondary structures of most functional non-coding RNAs (ncRNAs) are closely related to their functions and are conserved during evolution. Hence, prediction of conserved secondary structures from…
RNA velocity is an important model that combines cellular spliced and unspliced RNA counts to infer dynamical properties of various regulatory functions. Despite its wide applicability and many variants used in practice, the model has not…
The discovery of CRISPR-mediated gene activation (CRISPRa) has transformed the way in which we perform genetic screening, bioproduction and therapeutics through its ability to scale and multiplex. However, the emergence of loads on the key…
Many recent exciting discoveries have revealed the versatility of RNAs and their importance in a variety of cellular functions which are strongly coupled to RNA structures. To understand the functions of RNAs, some structure prediction…
Dysregulated microRNA (miRNA) expression is a well-established feature of human cancer. However, the role of specific miRNAs in determining cancer outcomes remains unclear. Using Level 3 expression data from the Cancer Genome Atlas (TCGA),…
Prions are misfolded proteins that transmit their structural arrangement to neighboring proteins. In biological systems, prion dynamics can produce a variety of complex functional outcomes. Yet, an understanding of prionic causes has been…
Genetic linkage may result in the expression of multiple products from a polycistronic transcript, under the control of a single promoter. In animals, protein-coding polycistronic transcripts are rare. However, microRNAs are frequently…
The revelation of the supreme authority of nucleic acids in the cellular landscape has precipitated the recognition of the versatility of RNAs in cells. The subsequent discovery of non-coding RNAs was a major breakthrough that revealed…
Formal methods have enabled breakthroughs in many fields, such as in hardware verification, machine learning and biological systems. The key object of interest in systems biology, synthetic biology, and molecular programming is chemical…
MicroRNAs (miRNAs) are an emerging class of biomarkers that are frequently deregulated in cancer cells and have shown a great promise for cancer classification and prognosis. In this work, we developed a three-way electrochemical sensor for…
mRNA editing of sequences of many species is analyzed. The nature of the inserted nucleotides and the position of the insertion sites, once fixed the edited peptide chain, are explained by introducing a minimum principle in the framework of…
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…
RNA function is tied to secondary structure, operating through dynamic and heterogeneous structural ensembles. While current analysis tools typically output single static structures or averaged contact maps, chemical probing methods like…
MicroRNAs play an indispensable role in numerous biological processes ranging from organismic development to tumor progression.In oncology,these microRNAs constitute a fundamental regulation role in the pathology of cancer that provides the…