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

By: Will Fischer
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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 : Regulatory Control and the Costs and ...

By: Aviv Regev

Description : Experiments in recent years have vividly demonstrated that gene expression can be highly stochastic. How protein concentration fluctuations affect the growth rate of a population of cells is, however, a wide-open question. We present a mathematical model that makes it possible to quantify the effect of protein concentration fluctuations on the growth rate of a population of genetically identical cells. The model predicts that the population’s growth rate de...

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Plos Computational Biology : Drug-induced Regulation of Target Exp...

By: Murat Iskar
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Plos Computational Biology : Optforce ; an Optimization Procedure ...

By: Sridhar Ranganathan
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Plos Computational Biology : an Automated Phenotype-driven Approac...

By: Dipak Barua
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Plos Computational Biology : Lipid Exchange Mechanism of the Chole...

By: Artturi Koivuniemi

Description : Cholesteryl ester transfer protein (CETP) transports cholesteryl esters, triglycerides, and phospholipids between different lipoprotein fractions in blood plasma. The inhibition of CETP has been shown to be a sound strategy to prevent and treat the development of coronary heart disease. We employed molecular dynamics simulations to unravel the mechanisms associated with the CETP-mediated lipid exchange. To this end we used both atomistic and coarse-grained ...

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Plos Computational Biology : Probing the Energy Landscape of Activ...

By: Tobias Linder

Description : The bacterial potassium channel KcsA, which has been crystallized in several conformations, offers an ideal model to investigate activation gating of ion channels. In this study, essential dynamics simulations are applied to obtain insights into the transition pathways and the energy profile of KcsA pore gating. In agreement with previous hypotheses, our simulations reveal a two phasic activation gating process. In the first phase, local structural rearrang...

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Plos Computational Biology : Evolutionary Modeling of Rate Shifts ...

By: Rob J. De Boer

Description : A hallmark of the human immunodeficiency virus 1 (HIV-1) is its rapid rate of evolution within and among its various subtypes. Two complementary hypotheses are suggested to explain the sequence variability among HIV-1 subtypes. The first suggests that the functional constraints at each site remain the same across all subtypes, and the differences among subtypes are a direct reflection of random substitutions, which have occurred during the time elapsed sinc...

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Plos Computational Biology : Detecting Coevolution in and Among Pr...

By: Andrey Rzhetsky

Description : Correlated changes of nucleic or amino acids have provided strong information about the structures and interactions of molecules. Despite the rich literature in coevolutionary sequence analysis, previous methods often have to trade off between generality, simplicity, phylogenetic information, and specific knowledge about interactions. Furthermore, despite the evidence of coevolution in selected protein families, a comprehensive screening of coevolution amon...

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Plos Computational Biology : a Survey of Genomic Properties for th...

By: Yitzhak Pilpel

Description : Advances in the computational identification of functional noncoding polymorphisms will aid in cataloging novel determinants of health and identifying genetic variants that explain human evolution. To date, however, the development and evaluation of such techniques has been limited by the availability of known regulatory polymorphisms. We have attempted to address this by assembling, from the literature, a computationally tractable set of regulatory polymor...

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Plos Computational Biology : Bang-bang Control of Feeding ; Role o...

By: Karl J. Friston

Description : Rats, people, and many other omnivores eat in meals rather than continuously. We show by experimental test that eating in meals is regulated by a simple bang-bang control system, an idea foreshadowed by Le Magnen and many others, shown by us to account for a wide range of behavioral data, but never explicitly tested or tied to neurophysiological facts. The hypothesis is simply that the tendency to eat rises with time at a rate determined by satiety signals....

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Plos Computational Biology : Nonlinear Muscles, Passive Viscoelast...

By: Tom Daniel

Description : Locomotion provides superb examples of cooperation among neuromuscular systems, environmental reaction forces, and sensory feedback. As part of a program to understand the neuromechanics of locomotion, here we construct a model of anguilliform (eel-like) swimming in slender fishes. Building on a continuum mechanical representation of the body as an viscoelastic rod, actuated by a traveling wave of preferred curvature and subject to hydrodynamic reaction for...

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Plos Computational Biology : Functional Analysis of Metabolic Chan...

By: Yun Lee

Description : Lignin is a polymer in secondary cell walls of plants that is known to have negative impacts on forage digestibility, pulping efficiency, and sugar release from cellulosic biomass. While targeted modifications of different lignin biosynthetic enzymes have permitted the generation of transgenic plants with desirable traits, such as improved digestibility or reduced recalcitrance to saccharification, some of the engineered plants exhibit monomer compositions ...

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Plos Computational Biology : What is Stochastic Resonance Definiti...

By: Karl J. Friston

Description : Stochastic resonance is said to be observed when increases in levels of unpredictable fluctuations— e.g., random noise—cause an increase in a metric of the quality of signal transmission or detection performance, rather than a decrease. This counterintuitive effect relies on system nonlinearities and on some parameter ranges being ‘‘suboptimal’’. Stochastic resonance has been observed, quantified, and described in a plethora of physical and biological syste...

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Plos Computational Biology : Using Likelihood-free Inference to Co...

By: Sebastian Bonhoeffer

Description : Gene 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, or likelihood-free i...

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Plos Computational Biology : Chaste ; an Open Source C++ Library f...

By: Gary R. Mirams

Description : Chaste — Cancer, Heart And Soft Tissue Environment — is an open source C++ library for the computational simulation of mathematical models developed for physiology and biology. Code development has been driven by two initial applications : cardiac electrophysiology and cancer development. A large number of cardiac electrophysiology studies have been enabled and performed, including high-performance computational investigations of defibrillation on realistic...

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Plos Computational Biology : How Recent History Affects Perception...

By: Ofri Raviv

Description : There is accumulating evidence that prior knowledge about expectations plays an important role in perception. The Bayesian framework is the standard computational approach to explain how prior knowledge about the distribution of expected stimuli is incorporated with noisy observations in order to improve performance. However, it is unclear what information about the prior distribution is acquired by the perceptual system over short periods of time and how t...

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Plos Computational Biology : Rocky Mountain Conference on Bioinfor...

By: Lawrence E. Hunter
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Plos Computational Biology : Structural Reorganisation and Potenti...

By: Eugene I. Shakhnovich

Description : Increasing evidence indicates that oligomeric protein assemblies may represent the molecular species responsible for cytotoxicity in a range of neurological disorders including Alzheimer and Parkinson diseases. We use all-atom computer simulations to reveal that the process of oligomerization can be divided into two steps. The first is characterised by a hydrophobic coalescence resulting in the formation of molten oligomers in which hydrophobic residues are...

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