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Spike Correlations in a Songbird Agree with a Simple Markov Population Model
(2007)PLoS Computational BiologyThe relationships between neural activity at the single-cell and the population levels are of central importance for understanding neural codes. In many sensory systems, collective behaviors in large cell groups can be described by pairwise spike correlations. Here, we test whether in a highly specialized premotor system of songbirds, pairwise spike correlations themselves can be seen as a simple corollary of an underlying random process. ...Journal Article -
Revisiting Estimates of CTL Killing Rates In Vivo
(2007)PLoS ONERecent experimental advances have allowed the estimation of the in vivo rates of killing of infected target cells by cytotoxic T lymphocytes (CTL). We present several refinements to a method applied previously to quantify killing of targets in the spleen using a dynamical model. We reanalyse data previously used to estimate killing rates of CTL specific for two epitopes of lymphocytic choriomeningitis virus (LCMV) in mice and show that, ...Journal Article -
Using Likelihood-Free Inference to Compare Evolutionary Dynamics of the Protein Networks of H. pylori and P. falciparum
(2007)PLoS Computational BiologyGene duplication with subsequent interaction divergence is one of the primary driving forces in the evolution of genetic systems. Yet little is known about the precise mechanisms and the role of duplication divergence in the evolution of protein networks from the prokaryote and eukaryote domains. We developed a novel, model-based approach for Bayesian inference on biological network data that centres on approximate Bayesian computation, ...Journal Article -
Genetic Progression and the Waiting Time to Cancer
(2007)PLoS Computational BiologyCancer results from genetic alterations that disturb the normal cooperative behavior of cells. Recent high-throughput genomic studies of cancer cells have shown that the mutational landscape of cancer is complex and that individual cancers may evolve through mutations in as many as 20 different cancer-associated genes. We use data published by Sjöblom et al. (2006) to develop a new mathematical model for the somatic evolution of colorectal ...Journal Article -
Force-induced unfolding of fibronectin in the extracellular matrix of living cells
(2007)PLoS BiologyWhether mechanically unfolded fibronectin (Fn) is present within native extracellular matrix fibrils is controversial. Fn extensibility under the influence of cell traction forces has been proposed to originate either from the force-induced lengthening of an initially compact, folded quaternary structure as is found in solution (quaternary structure model, where the dimeric arms of Fn cross each other), or from the force-induced unfolding ...Journal Article -
Cytogenetic mapping and STR polymorphism of thwo candidate genes (DRD2 and HTR1D) for behavioural traits in four canids
(2007)Archives of Animal BreedingThe dopamine D2 receptor (DRD2) and serotonin receptors 1D (HTR1D) are candidate genes for behavioural traits. In the present study, we show chromosomal location and polymorphism of these genes in four species from the family Canidae: dog (CFA), red fox (VVU), arctic fox (ALA) and the Chinese raccoon dog (NPP). Using fluorescence in situ hybridisation (FISH) the DRD2 gene was localized in the following chromosomes: CFA5q12-13, VVU12q21, ...Journal Article -
Salmonella enterica serovar typhimurium exploits inflammation to compete with the intestinal microbiota
(2007)PLoS BiologyMost mucosal surfaces of the mammalian body are colonized by microbial communities (“microbiota”). A high density of commensal microbiota inhabits the intestine and shields from infection (“colonization resistance”). The virulence strategies allowing enteropathogenic bacteria to successfully compete with the microbiota and overcome colonization resistance are poorly understood. Here, we investigated manipulation of the intestinal microbiota ...Journal Article -
New approaches to model and study social networks
(2007)New Journal of PhysicsWe describe and develop three recent novelties in network research which are particularly useful for studying social systems. The first one concerns the discovery of some basic dynamical laws that enable the emergence of the fundamental features observed in social networks, namely the nontrivial clustering properties, the existence of positive degree correlations and the subdivision into communities. To reproduce all these features, we ...Journal Article -
The generalized Lyapunov theorem and its application to quantum channels
(2007)New Journal of PhysicsWe give a simple and physically intuitive necessary and sufficient condition for a map acting on a compact metric space to be mixing (i.e. infinitely many applications of the map transfer any input into a fixed convergency point). This is a generalization of the 'Lyapunov direct method'. First we prove this theorem in topological spaces and for arbitrary continuous maps. Finally we apply our theorem to maps which are relevant in open ...Journal Article -
Interference in a quantum dot molecule embedded in a ring interferometer
(2007)New Journal of PhysicsInterference experiments are presented involving electronic quantum transport through an artificial quantum dot molecule in the Coulomb blockade regime embedded in a ring interferometer. Full tunability and the high stability of the structure allowed the transmission phase through this system, spin-related interference phenomena, and Fano-type interference to be studied. When a part of the interferometer is itself tuned into the Coulomb ...Journal Article