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Discrimination of Membrane Antigen Affinity by B cells Requires Dominance of Kinetic Proofreading over Serial Triggering
Membrane Antigen Affinity B cells Requires Dominance
2011/1/5
B cells receptor (BCR) signaling in response to membrane-bound antigen increases with antigen affinity, a process known as affinity discrimination. We use computational modeling to show that B cell af...
Optimal atomic-resolution structures of prion AGAAAAGA amyloid fibrils
Optimal atomic-resolution structures prion AGAAAAGA amyloid fibrils
2011/1/5
To date, there is little structural data available on the AGAAAAGA palindrome in the hydrophobic region (113-120) of prion proteins, although many experimental studies have shown that this region has ...
Weighted genomic distance can hardly impose a bound on the proportion of transpositions
Weighted genomic distance the proportion of transpositions
2011/1/5
Genomic distance between two genomes, i.e., the smallest number of genome rearrangements required to transform one genome into the other, is often used as a measure of evolutionary closeness of the ge...
Deterministic and stochastic aspects of VEGF-A production and the cooperative behavior of tumoral cell colony
Deterministic stochastic aspects VEGF-A production
2011/1/5
A model is proposed to study the process of hypoxia-induced angiogenesis in cancer cells. The model accounts for the role played by the vascular endothelial growth factor (VEGF)-A in regulating the ox...
Many of life's most fascinating phenomena emerge from interactions among many elements--many amino acids determine the structure of a single protein, many genes determine the fate of a cell, many neur...
Large-scale interval and point estimates from an empirical Bayes extension of confidence posteriors
Large-scale interval point estimates empirical Bayes extension
2011/1/6
The proposed approach extends the confidence posterior distribution to the semi-parametric empirical Bayes setting. Whereas the Bayesian posterior is defined in terms of a prior distribution condition...
Computational challenges of tumor spheroid modeling
Computational challenges tumor spheroid modeling
2011/1/5
The speed and the versatility of today's computers open up new opportunities to simulate complex biological systems. Here we review a computational approach recently proposed by us to model large tumo...
Chem2Bio2RDF: A Linked Open Data Portal for Chemical Biology
Chem2Bio2RDF Linked Open Data Portal
2011/1/6
The Chem2Bio2RDF portal is a Linked Open Data (LOD) portal for systems chemical biology aiming for facilitating drug discovery. It converts around 25 different datasets on genes, compounds, drugs, pat...
A robust two-gene oscillator at the core of Ostreococcus tauri circadian clock
two-gene oscillator Ostreococcus tauri circadian clock
2011/1/5
The microscopic green alga Ostreococcus tauri is rapidly emerging as a promising model organism in the green lineage. In particular, recent results by Corellou et al. [Plant Cell, 21, 3436 (2009)] and...
Some thoughts on the ontogenesis in B-cell immune networks
Some thoughts the ontogenesis B-cell immune networks
2011/1/5
We are interested in modeling theoretical immunology within a statistical mechanics flavor: focusing on the antigen-independent maturation process of B-cells, in this paper we try to revise the proble...
Role of water in the enzymatic catalysis: study of ATP + AMP -> 2ADP conversion by adenylate kinase
enzymatic catalysis ATP + AMP -> 2ADP conversion
2011/1/6
The catalytic conversion ATP + AMP -> 2ADP by the enzyme adenylate kinase (ADK) involves the binding of one ATP molecule to the LID domain and one AMP molecule to the NMP domain. The latter is followe...
Epidemic prediction and control in clustered populations
Epidemic prediction control clustered populations
2011/1/5
There has been much recent interest in modelling epidemics on networks, particularly in the presence of substantial clustering. Here, we develop pairwise methods to answer questions that are often add...
Rare events and stochastic tunneling in a two-locus system with recombination
Rare events stochastic tunneling two-locus system
2011/1/5
We study the evolution of a population in a two-locus genotype space, in which the negative effects of two single mutations are overcompensated in a high fitness double mutant. We discuss how the inte...
A Network-Based Meta-Population Approach to Model Rift Valley Fever Epidemics
Network-Based Meta-Population Rift Valley Fever Epidemics
2011/1/5
Rift Valley Fever virus (RVFv) has been expanding its geographical distribution with important implications for both human and animal health. The emergence of Rift Valley Fever (RVF) in the Middle Eas...
Robust entrainment of circadian oscillators requires specific phase response curves
Robust entrainment circadian oscillators
2011/1/5
The circadian clocks keeping time of day in many living organisms rely on self-sustained biochemical oscillations which can be entrained by external cues, such as light, to the 24-hour cycle induced b...