Search results for "computational"
showing 10 items of 5884 documents
One is not enough: On the effects of reference genome for the mapping and subsequent analyses of short-reads.
2020
Mapping of high-throughput sequencing (HTS) reads to a single arbitrary reference genome is a frequently used approach in microbial genomics. However, the choice of a reference may represent a source of errors that may affect subsequent analyses such as the detection of single nucleotide polymorphisms (SNPs) and phylogenetic inference. In this work, we evaluated the effect of reference choice on short-read sequence data from five clinically and epidemiologically relevant bacteria (Klebsiella pneumoniae, Legionella pneumophila, Neisseria gonorrhoeae, Pseudomonas aeruginosa and Serratia marcescens). Publicly available whole-genome assemblies encompassing the genomic diversity of these species…
Seven Mathematical Models of Hemorrhagic Shock
2021
Although mathematical modelling of pressure-flow dynamics in the cardiocirculatory system has a lengthy history, readily finding the appropriate model for the experimental situation at hand is often a challenge in and of itself. An ideal model would be relatively easy to use and reliable, besides being ethically acceptable. Furthermore, it would address the pathogenic features of the cardiovascular disease that one seeks to investigate. No universally valid model has been identified, even though a host of models have been developed. The object of this review is to describe several of the most relevant mathematical models of the cardiovascular system: the physiological features of circulator…
Translocation Biosensors – Cellular System Integrators to Dissect CRM1-Dependent Nuclear Export by Chemicogenomics
2009
Fluorescent protein biosensors are powerful cellular systems biology tools for dissecting the complexity of cellular processes with high spatial and temporal resolution. As regulated nucleo-cytoplasmic transport is crucial for the modulation of numerous (patho)physiological cellular responses, a detailed understanding of its molecular mechanism would open up novel options for a rational manipulation of the cell. In contrast to genetic approaches, we here established and employed high-content cellular translocation biosensors applicable for dissecting nuclear export by chemicogenomics. A431 cell lines, stably expressing a translocation biosensor composed of glutathione S-transferase, GFP and…
SYSCILIA, “A systems biology approach to dissect cilia function and its disruption in human genetic disease”
2012
Primary cilia are basically signaling hubs, harboring amongst others the noncanonical WNT, Hedgehog,and PDGF signaling systems, and their disruption leads to striking developmental defects. Some ciliopathy-associated proteins have recently been revealed to be physically or functionally associated in several distinct groupings, with limited connections to other crucial biological processes. Early proteomics studies have also suggested a discrete repertoire of about 1000 proteins within the organelle (i.e. <5% of the proteome) that are still in need of organisation into pathways and networks. Small, relatively isolated systems are often targeted by systems biology approaches under the assumpt…
Modular organization in the reductive evolution of protein-protein interaction networks
2006
Analysis of the reduction in genome size of Buchnera aphidicola from its common ancestor E. coli shows that the organization of networks into modules is the property that seems to be directly related with the evolutionary process of genome reduction.
Reverse-engineering post-transcriptional regulation of gap genes in Drosophila melanogaster
2013
16 páginas, 6 figuras, 1 tabla
THE INFLUENCE OF CONTRARIANS AND OPPORTUNISTS ON THE STABILITY OF A DEMOCRACY IN THE SZNAJD MODEL
2004
Sznajd-Weron and Sznajd introduced a model investigating the democratic development in a closed community. This model is based on the USDF-principle ("united we stand, divided we fall"). However, it faces the problem that the system tends either to a dictatorship (i.e., 100% pro or 100% contra) or to a stalemate state (i.e., exactly 50% pro, 50% contra). Based on their model, I will show that a democratic system keeps alive due to the existence of both opportunists and persons in opposition.
Design procedure for prestressed concrete beams
2014
Abstract. The theoretical basis and the main results of a design procedure, which attempts to provide the optimal layout of ordinary reinforcement in prestressed concrete beams, subjected to bending moment and shear force are presented. The difficulties encountered in simulating the actual behaviour of prestressed concrete beam in presence of coupled forces bending moment - shear force are discussed; particular emphasis is put on plastic models and stress fields approaches. A unified model for reinforced and prestressed concrete beams under axial force - bending moment - shear force interaction is provided. This analytical model is validated against both experimental results collected in li…
A contribution to the mathematical modeling of immune-cancer competition
2018
Abstract This paper deals with the modeling of interactions between the immune system and cancer cells, in the framework of the mathematical kinetic theory for active particles. The work deepens a previous paper of Belloquid et al. that assumes spatial homogeneity and discrete values of the activity of cancer and immune cells. A number of simulations are made with the aim to investigate how the state of the various cell populations evolves in time depending on the choice of the free parameters.
Discontinuous Galerkin semi-Lagrangian method for Vlasov-Poisson
2011
We present a discontinuous Galerkin scheme for the numerical approximation of the one-dimensional periodic Vlasov-Poisson equation. The scheme is based on a Galerkin-characteristics method in which the distribution function is projected onto a space of discontinuous functions. We present comparisons with a semi-Lagrangian method to emphasize the good behavior of this scheme when applied to Vlasov-Poisson test cases. Une méthode de Galerkin discontinu est proposée pour l’approximation numérique de l’équation de Vlasov-Poisson 1D. L’approche est basée sur une méthode Galerkin-caractéristiques où la fonction de distribution est projetée sur un espace de fonctions discontinues. En particulier, …