Related papers: Mathematical model for autoregulated miRNA biogene…
Signal duration (e.g. the time scales over which an active signaling intermediate persists) is a key regulator of biological decisions in myriad contexts such as cell growth, proliferation, and developmental lineage commitments.…
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…
Long noncoding RNAs (lncRNAs) are a recently discovered class of non-protein coding RNAs which have now increasingly been shown to be involved in a wide variety of biological processes as regulatory molecules. Little is known regarding the…
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…
We study several Fokker-Planck equations arising from a stochastic chemical kinetic system modeling a gene regulatory network in biology. The densities solving the Fokker-Planck equations describe the joint distribution of the messenger RNA…
Biomolecular condensates have been shown to play a fundamental role in localizing biochemistry in a cell. RNA is a common constituent of condensates, and can determine their biophysical properties. Functions of biomolecular condensates are…
Deprivation of essential nutrients can have stark consequences for many processes in a cell. We consider amino acid starvation, which can result in bottlenecks in mRNA translation when ribosomes stall due to lack of resources, i.e. tRNAs…
There is increasing evidence that protein binding to specific sites along DNA can activate the reading out of genetic information without coming into direct physical contact with the gene. There also is evidence that these distant but…
The ribosome is a macromolecular complex which is responsible for protein synthesis in all living cells according to their transcribed genetic information. Using X-ray crystallography and, more recently, cryo-electron microscopy (cryo-EM),…
mRNA translation is a crucial process that leads to protein synthesis in living cells. Therefore, it is a process that needs to work optimally for a cell to stay healthy and alive. With advancements in microscopy and novel experimental…
Bacteria reside in constantly changing environments and require rapid and precise adjustments of gene expression to ensure survival. Small regulatory RNAs (sRNAs) are a crucial element that bacteria utilize to achieve this. sRNAs are short…
MicroRNAs (miRNAs) are non-coding RNAs with approximately 22 nucleotides (nt) that are derived from precursor molecules. These precursor molecules or pre-miRNAs often fold into stem-loop hairpin structures. However, a large number of…
Transcriptional and post-transcriptional regulation shape tissue-type-specific proteomes, but their relative contributions remain contested. Estimates of the factors determining protein levels in human tissues do not distinguish between (i)…
In this work, we describe a computational framework for the genome-wide identification and characterization of mixed transcriptional/post-transcriptional regulatory circuits in humans. We concentrated in particular on feed-forward loops…
Length-regulation of microtubules (MTs) is essential for many cellular processes. Molecular motors like kinesin 8, which move along MTs and also act as depolymerases, are known as key players in MT dynamics. However, the regulatory…
Bone remodeling involves the coordinated removal of bone by osteoclasts and addition of bone by osteoblasts, a process that is modulated by the prevailing mechanical environment. In this paper a fully coupled model of bone remodeling is…
MicroRNAs play critical roles in many physiological processes. Their dysregulations are also closely related to the development and progression of various human diseases, including cancer. Therefore, identifying new microRNAs that are…
This limited review is intended as an introduction to the fast growing subject of mathematical modelling of cell metabolism and its biochemical pathways, and more precisely on pathways linked to apoptosis of cancerous cells. Some basic…
Translation is a key step in the synthesis of proteins. Accordingly, cells have evolved an intricate array of control mechanisms to regulate this process. By constructing a multi-component mathematical framework for translation we uncover…
The inherent probabilistic nature of the biochemical reactions, and low copy number of species can lead to stochasticity in gene expression across identical cells. As a result, after induction of gene expression, the time at which a…