Related papers: Competing endogenous RNA crosstalk at system level
Connectivity networks have recently become widely used in biology due to increasing amounts of information on the physical and functional links between individual proteins. This connectivity data provides valuable material for expanding our…
Cytoskeletal crowding plays a key role in the diffusion of DNA molecules through the cell, acting as a barrier to effective intracellular transport and conformational stability required for such processes as transfection, viral infection,…
Early sensory systems in the brain rapidly adapt to fluctuating input statistics, which requires recurrent communication between neurons. Mechanistically, such recurrent communication is often indirect and mediated by local interneurons. In…
Multicellular organisms comprise a diverse collection of stable tissues built from different cell types. It remains unclear how large numbers of interacting cells can precisely coordinate their gene expression during tissue…
The ribosomal density along the coding region of the mRNA molecule affect various fundamental intracellular phenomena including: protein production rates, organismal fitness, ribosomal drop off, and co-translational protein folding. Thus,…
Living cells must control the reading out or "expression" of information encoded in their genomes, and this regulation often is mediated by transcription factors--proteins that bind to DNA and either enhance or repress the expression of…
Intrinsic transcriptional noise induced by operator fluctuations is investigated with a simple spin like stochastic model. The effects of transcriptional fluctuations in protein synthesis is probed by coupling transcription and translation…
Emerging evidence suggests that the introns and intergenic sequences of the genomes of higher eukaryotes (the ``junk'' DNA) codes for a vast, RNA-based, genetic regulatory network. It is believed that this network is responsible for the…
This paper presents an intracellular feedback control strategy, to regulate the gene expression process dynamics. For this purpose, two types of genetic circuits are designed in order to compare concentrations of the input transcription…
Pre-mRNA splicing relies on the poorly understood dynamic interplay between >150 protein components of the spliceosome. The steps at which splicing can be regulated remain largely unknown. We systematically analyzed the effect of knocking…
Small regulatory RNAs (sRNAs) are short non-coding RNAs in bacteria capable of post-transcriptional regulation. sRNAs have recently gained attention as tools in basic and applied sciences for example to fine-tune genetic circuits or…
Mixed feedback loops combining transcriptional and post-transcriptional regulations are common in cellular regulatory networks. They consist of two genes, encoding a transcription factor and a small non-coding RNA (sRNA), which mutually…
Cells need to reliably sense external ligand concentrations to achieve various biological functions such as chemotaxis or signaling. The molecular recognition of ligands by surface receptors is degenerate in many systems leading to…
Eukaryotic cells transmit information by signaling through complex networks of interacting proteins. Here we develop a theoretical and computational framework that relates the biophysics of protein-protein interactions (PPIs) within a…
MicroRNAs (miRs) are robust regulators of gene expression, implicated in most biological processes. microRNAs predominantly downregulate the expression of genes post-transcriptionally and each miR is predicted to target several hundred…
Signal transduction within biological cells is governed by networks of interacting proteins. Communication between these proteins is mediated by signaling molecules which bind to receptors and induce stochastic transitions between different…
We introduce a random bit-string model of post-transcriptional genetic regulation based on sequence matching. The model spontaneously yields a scale free network with power law scaling with $ \gamma=-1$ and also exhibits log-periodic…
Biomolecular communication demands that interactions between parts of a molecular system act as scaffolds for message transmission. It also requires an evolving and organized system of signs - a communicative agency - for creating and…
Genetic oscillators are present in the cells of many organisms and control several biological processes. The common feature of such oscillators is the presence of a protein which represses the transcription of its own gene. Recently, it has…
Due to the stochastic nature of biochemical processes, the copy number of any given type of molecule inside a living cell often exhibits large temporal fluctuations. Here, we develop analytic methods to investigate how the noise arising…