Related papers: Quantitative transcriptional analysis of aging C. …
Molecular dynamics simulations hold great promise for providing insight into the microscopic behavior of complex molecular systems. However, their effectiveness is often constrained by long timescales associated with rare events. Enhanced…
Identity, response to external stimuli, and spatial architecture of a living system are central topics of molecular biology. Presently, they are largely seen as a result of the interplay between a gene repertoire and the regulatory…
Investigation of age-related genes is of great importance for multiple purposes, for instance, improving our understanding of the mechanism of ageing, increasing life expectancy, age prediction, and other healthcare applications. In his…
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…
Genetic Regulatory Networks (GRNs) plays a vital role in the understanding of complex biological processes. Modeling GRNs is significantly important in order to reveal fundamental cellular processes, examine gene functions and understanding…
Diseases involve complex processes and modifications to the cellular machinery. The gene expression profile of the affected cells contains characteristic patterns linked to a disease. Hence, biological knowledge pertaining to a disease can…
Transcriptomic data is a treasure-trove in modern molecular biology, as it offers a comprehensive viewpoint into the intricate nuances of gene expression dynamics underlying biological systems. This genetic information must be utilised to…
The processes taking place inside the living cell are now understood to the point where predictive computational models can be used to gain detailed understanding of important biological phenomena. A key challenge is to extrapolate this…
Aging, as defined in terms of the slope of the probability of death versus time (hazard curve), is a generic phenomenon observed in nearly all complex systems. Theoretical models of aging predict hazard curves that monotonically increase in…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
DNA microarray experiments, a well-established experimental technique, aim at understanding the function of genes in some biological processes. One of the most common experiments in functional genomics research is to compare two groups of…
By creating networks of biochemical pathways, communities of micro-organisms are able to modulate the properties of their environment and even the metabolic processes within their hosts. Next-generation high-throughput sequencing has led to…
In the last years, tens of thousands gene expression profiles for cells of several organisms have been monitored. Gene expression is a complex transcriptional process where mRNA molecules are translated into proteins, which control most of…
The evolutionary biology of aging is fundamental to understanding the mechanisms of aging and how to develop anti-aging treatments. Thus far most evolutionary theory concerns the genetics of aging with limited physiological integration.…
Gene expression is a central process to any form of life. It involves multiple temporal and functional scales that extend from specific protein-DNA interactions to the coordinated regulation of multiple genes in response to intracellular…
A simple mathematical model of the aging process for long-lived organisms is considered. The key point in this model is the assumption that the body does not have internal clocks that count out the chronological time at scales of decades.…
Genetic data are often used to infer demographic history and changes or detect genes under selection. Inferential methods are commonly based on models making various strong assumptions: demography and population structures are supposed…
The paper discusses a connection between asymmetric reproduction -- that is reproduction in a parent-child relationship where the parent does not mutate during reproduction --, the fact that all non-viral lifeforms bear genes of their…
We apply topological data analysis to the behavior of C. elegans, a widely-studied model organism in biology. In particular, we use topology to produce a quantitative summary of complex behavior which may be applied to high-throughput data.…
We describe a percolation-type approach to modeling of the processes of aging and certain other properties of tissues analyzed as systems consisting of interacting cells. Tissues are considered as structures made of regular healthy,…