Related papers: microRNAs may sharpen spatial expression patterns
Since microRNAs (miRNAs) play a crucial role in post-transcriptional gene regulation, miRNA identification is one of the most essential problems in computational biology. miRNAs are usually short in length ranging between 20 and 23 base…
Lung transplantation remains the only viable treatment option for the majority of patients with advanced lung diseases. However, 5-year post-transplant survival rates remain low primarily secondary to chronic rejection. Novel insights from…
Conformational dynamics is crucial for ribonucleic acid (RNA) function. Techniques such as nuclear magnetic resonance, cryo-electron microscopy, small- and wide-angle X-ray scattering, chemical probing, single-molecule F\"orster resonance…
The phenomenon of cell sorting/segregation, by which cells organise spatially into clusters of specific cell type or function, is essential for tissue morphogenesis. This self-organization process involves an interplay between mechanical,…
Motivation: Spatial pattern formation of the primary anterior-posterior morphogenetic gradient of the transcription factor Bicoid (Bcd) has been studied experimentally and computationally for many years. Bcd specifies positional information…
Rhizomes play fundamental roles in plant evolution, persistence, and environmental adaptation by enabling clonal propagation, resource storage, and stress resilience. Despite their ecological and agronomic importance across diverse plant…
Modelling gene regulatory networks not only requires a thorough understanding of the biological system depicted but also the ability to accurately represent this system from a mathematical perspective. Throughout this chapter, we aim to…
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…
Microarray data are often used to determine which genes are differentially expressed between groups, for example, between treatment and control groups. There are methods of determining which genes have a high probability of differential…
We propose a probabilistic model for interpreting gene expression levels that are observed through single-cell RNA sequencing. In the model, each cell has a low-dimensional latent representation. Additional latent variables account for…
MicroRNAs (miRNAs) are small RNA molecules composed of 19-22 nt, which play important regulatory roles in post-transcriptional gene regulation by inhibiting the translation of the mRNA into proteins or otherwise cleaving the target mRNA.…
The recent development of single-cell transcriptomics has enabled gene expression to be measured in individual cells instead of being population-averaged. Despite this considerable precision improvement, inferring regulatory networks…
Biological genotypes do not code directly for phenotypes; developmental physiology is the control layer that separates genomes from capacities ascertained by selection. A key aspect is competency, as cells are not a passive material but…
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…
Identifying subtle phenotypic variations in cellular images is critical for advancing biological research and accelerating drug discovery. These variations are often masked by the inherent cellular heterogeneity, making it challenging to…
Adaptation mechanism of cells on the basis of stochastic gene expression and epigenetic modification is proposed. From marginally stable states generated by epigenetic modification, a gene expression pattern that achieves greater cell…
MicroRNAs (miRNAs) are short sequences of ribonucleic acids that control the expression of target messenger RNAs (mRNAs) by binding them. Robust prediction of miRNA-mRNA pairs is of utmost importance in deciphering gene regulations but has…
It is well known that correlations in microarray data represent a serious nuisance deteriorating the performance of gene selection procedures. This paper is intended to demonstrate that the correlation structure of microarray data provides…
By analyzing the spacing of genes on chromosomes, we find that transcriptional and RNA-processing regulatory sequences outside coding regions leave footprints on the distribution of intergenic distances. Using analogies between genes on…
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…