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Plos Computational Biology : is Protein Folding Sub-diffusive, Vol...

By: Sergei V. Krivov*
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Plos Computational Biology : Integrin Clustering is Driven by Mech...

By: Douglas Lauffenberger

Description : Integrins have emerged as key sensory molecules that translate chemical and physical cues from the extracellular matrix (ECM) into biochemical signals that regulate cell behavior. Integrins function by clustering into adhesion plaques, but the molecular mechanisms that drive integrin clustering in response to interaction with the ECM remain unclear. To explore how deformations in the cell-ECM interface influence integrin clustering, we developed a spatial-t...

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Plos Computational Biology : Coping with Viral Diversity in Hiv Va...

By: Sebastian Bonhoeffer

Description : The ability of human immunodeficiency virus type 1 (HIV-1) to develop high levels of genetic diversity, and thereby acquire mutations to escape immune pressures, contributes to the difficulties in producing a vaccine. Possibly no single HIV-1 sequence can induce sufficiently broad immunity to protect against a wide variety of infectious strains, or block mutational escape pathways available to the virus after infection. The authors describe the generation o...

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Plos Computational Biology : Stochastic Modeling of Expression Kin...

By: Filippo Cacace

Description : The transcriptome in a cell is finely regulated by a large number of molecular mechanisms able to control the balance between mRNA production and degradation. Recent experimental findings have evidenced that fine and specific regulation of degradation is needed for proper orchestration of a global cell response to environmental conditions. We developed a computational technique based on stochastic modeling, to infer condition-specific individual mRNA half-l...

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Plos Computational Biology : Spectral Analysis of Input Spike Trai...

By: Matthieu Gilson

Description : Spike-timing-dependent plasticity (STDP) has been observed in many brain areas such as sensory cortices, where it is hypothesized to structure synaptic connections between neurons. Previous studies have demonstrated how STDP can capture spiking information at short timescales using specific input configurations, such as coincident spiking, spike patterns and oscillatory spike trains. However, the corresponding computation in the case of arbitrary input sign...

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Plos Computational Biology : Genome-wide Association Between Branc...

By: Martina Hallegger
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Plos Computational Biology : Optimal Balance of the Striatal Mediu...

By: Adam Ponzi

Description : Slowly varying activity in the striatum, the main Basal Ganglia input structure, is important for the learning and execution of movement sequences. Striatal medium spiny neurons (MSNs) form cell assemblies whose population firing rates vary coherently on slow behaviourally relevant timescales. It has been shown that such activity emerges in a model of a local MSN network but only at realistic connectivities of 10*20% and only when MSN generated inhibitory p...

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Plos Computational Biology : Self-assembly and Dna Binding of the ...

By: Michele Caselle

Description : X chromosome inactivation (XCI) is the phenomenon occurring in female mammals whereby dosage compensation of X-linked genes is obtained by transcriptional silencing of one of their two X chromosomes, randomly chosen during early embryo development. The earliest steps of random X-inactivation, involving counting of the X chromosomes and choice of the active and inactive X, are still not understood. To explain ‘‘counting and choice,’’ the longstanding hypothe...

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Plos Computational Biology : Inferring Visuomotor Priors for Senso...

By: Daniel M. Wolpert

Description : Sensorimotor learning has been shown to depend on both prior expectations and sensory evidence in a way that is consistent with Bayesian integration. Thus, prior beliefs play a key role during the learning process, especially when only ambiguous sensory information is available. Here we develop a novel technique to estimate the covariance structure of the prior over visuomotor transformations – the mapping between actual and visual location of the hand – du...

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Plos Computational Biology : Exploration of Multi-state Conformati...

By: Yong Wang

Description : An increasing number of biological machines have been revealed to have more than two macroscopic states. Quantifying the underlying multiple-basin functional landscape is essential for understanding their functions. However, the present models seem to be insufficient to describe such multiple-state systems. To meet this challenge, we have developed a coarse grained triple-basin structure-based model with implicit ligand. Based on our model, the constructed ...

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Plos Computational Biology : Scientific Software Development is No...

By: Johanna McEntyre

Description : ‘‘Many scientists and engineers spend much of their lives writing, debugging, and maintaining software, but only a handful have ever been taught how to do this effectively : after a couple of introductory courses, they are left to rediscover (or reinvent) the rest of programming on their own. The result? Most spend far too much time wrestling with software, instead of doing research, but have no idea how reliable or efficient their programs are.’’ —Greg Wilson [1]

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Plos Computational Biology : Analyzing Short-term Noise Dependenci...

By: Arno Onken

Description : Simultaneous spike-counts of neural populations are typically modeled by a Gaussian distribution. On short time scales, however, this distribution is too restrictive to describe and analyze multivariate distributions of discrete spike-counts. We present an alternative that is based on copulas and can account for arbitrary marginal distributions, including Poisson and negative binomial distributions as well as second and higher-order interactions. We describ...

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Plos Computational Biology : a Model-based Bayesian Estimation of ...

By: R. Zachariah Aandahl

Description : Variable numbers of tandem repeats (VNTR) typing is widely used for studying the bacterial cause of tuberculosis. Knowledge of the rate of mutation of VNTR loci facilitates the study of the evolution and epidemiology of Mycobacterium tuberculosis. Previous studies have applied population genetic models to estimate the mutation rate, leading to estimates varying widely from around 10{5 to 10{2 per locus per year. Resolving this issue using more detailed mode...

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Plos Computational Biology : Efficiency and Cost of Economical Bra...

By: Karl J. Friston

Description : Brain anatomical networks are sparse, complex, and have economical small-world properties. We investigated the efficiency and cost of human brain functional networks measured using functional magnetic resonance imaging (fMRI) in a factorial design : two groups of healthy old (N¼11: mean age¼66.5 years) and healthy young (N¼15: mean age¼ 24.7 years) volunteers were each scanned twice in a no-task or ‘‘resting’’ state following placebo or a single dose of a d...

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Plos Computational Biology : Quantitative Test of the Barrier Nucl...

By: Wolfram Möbius
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Plos Computational Biology : Systems Analysis of Bioenergetics and...

By: Reinhard Hensel

Description : Halobacterium salinarum is a bioenergetically flexible, halophilic microorganism that can generate energy by respiration, photosynthesis, and the fermentation of arginine. In a previous study, using a genome-scale metabolic model, we have shown that the archaeon unexpectedly degrades essential amino acids under aerobic conditions, a behavior that can lead to the termination of growth earlier than necessary. Here, we further integratively investigate energy ...

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Plos Computational Biology : How Informative Are Spatial CA3 Repre...

By: Erika Cerasti
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Plos Computational Biology : Evolutionary Accessibility of Mutatio...

By: Jasper Franke

Description : Functional effects of different mutations are known to combine to the total effect in highly nontrivial ways. For the trait under evolutionary selection (‘fitness’), measured values over all possible combinations of a set of mutations yield a fitness landscape that determines which mutational states can be reached from a given initial genotype. Understanding the accessibility properties of fitness landscapes is conceptually important in answering questions ...

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Plos Computational Biology : Mathematical Descrption of Bacterial ...

By: Jonathan Saragosti
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Plos Computational Biology : Global Entrainment of Transcriptional...

By: Giovanni Russo
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