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Plos Computational Biology : Heat Shock Partially Dissociates the ...

By: Peter Csermely

Description : Network analysis became a powerful tool giving new insights to the understanding of cellular behavior. Heat shock, the archetype of stress responses, is a well-characterized and simple model of cellular dynamics. S. cerevisiae is an appropriate model organism, since both its protein-protein interaction network (interactome) and stress response at the gene expression level have been well characterized. However, the analysis of the reorganization of the yeast...

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Plos Computational Biology : Mdck Cystogenesis Driven by Cell Stab...

By: Jesse A. Engelberg

Description : The study of epithelial morphogenesis is fundamental to increasing our understanding of organ function and disease. Great progress has been made through study of culture systems such as Madin-Darby canine kidney (MDCK) cells, but many aspects of even simple morphogenesis remain unclear. For example, are specific cell actions tightly coupled to the characteristics of the cell’s environment or are they more often cell state dependent? How does the single lume...

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Plos Computational Biology : Automated Protein Subfamily Identific...

By: Jonathan A. Eisen

Description : Function prediction by homology is widely used to provide preliminary functional annotations for genes for which experimental evidence of function is unavailable or limited. This approach has been shown to be prone to systematic error, including percolation of annotation errors through sequence databases. Phylogenomic analysis avoids these errors in function prediction but has been difficult to automate for high-throughput application. To address this limit...

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Plos Computational Biology : Blurring of High-resolution Data Show...

By: Wee Siong Goh
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Plos Computational Biology : Integrating Flux Balance Analysis Int...

By: Xueyang Feng
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Plos Computational Biology : Dynamic Modeling of Vaccinating Behav...

By: Flavio Codeco Coelho

Description : Individual perception of vaccine safety is an important factor in determining a person’s adherence to a vaccination program and its consequences for disease control. This perception, or belief, about the safety of a given vaccine is not a static parameter but a variable subject to environmental influence. To complicate matters, perception of risk (or safety) does not correspond to actual risk. In this paper we propose a way to include the dynamics of such b...

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Plos Computational Biology : Testing Whether Humans Have an Accura...

By: Hang Zhang

Description : In many motor tasks, optimal performance presupposes that human movement planning is based on an accurate internal model of the subject’s own motor error. We developed a motor choice task that allowed us to test whether the internal model implicit in a subject’s choices differed from the actual in isotropy (elongation) and variance. Subjects were first trained to hit a circular target on a touch screen within a time limit. After training, subjects were repe...

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Plos Computational Biology : from Functional Genomics to Functiona...

By: Rolf Kötter

Description : The development of DNA microarray technology a decade ago led to the establishment of functional genomics as one of the most active and successful scientific disciplines today. With the ongoing development of immunomic microarray technology—a spatially addressable, large-scale technology for measurement of specific immunological response—the new challenge of functional immunomics is emerging, which bears similarities to but is also significantly different from...

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Plos Computational Biology : Emergent Dynamics of Thymocyte Develo...

By: Howard Petrie

Description : Experiments have generated a plethora of data about the genes, molecules, and cells involved in thymocyte development. Here, we use a computer-driven simulation that uses data about thymocyte development to generate an integrated dynamic representation—a novel technology we have termed reactive animation (RA). RA reveals emergent properties in complex dynamic biological systems. We apply RA to thymocyte development by reproducing and extending the effects o...

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Plos Computational Biology : Removal of Au Bias from Microarray Mr...

By: Yitzhak Pilpel

Description : Elucidation of regulatory roles played by microRNAs (miRs) in various biological networks is one of the greatest challenges of present molecular and computational biology. The integrated analysis of gene expression data and 39-UTR sequences holds great promise for being an effective means to systematically delineate active miRs in different biological processes. Applying such an integrated analysis, we uncovered a striking relationship between 39-UTR AU con...

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Plos Computational Biology : a Model of Reward- and Effort-based O...

By: Lionel Rigoux

Description : Costs (e.g. energetic expenditure) and benefits (e.g. food) are central determinants of behavior. In ecology and economics, they are combined to form a utility function which is maximized to guide choices. This principle is widely used in neuroscience as a normative model of decision and action, but current versions of this model fail to consider how decisions are actually converted into actions (i.e. the formation of trajectories). Here, we describe an app...

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Plos Computational Biology : Self Containment, a Property of Modul...

By: Lauren Ancel Meyers

Description : RNA molecules will tend to adopt a folded conformation through the pairing of bases on a single strand: the resulting socalled secondary structure is critical to the function of many types of RNA. The secondary structure of a particular substring of functional RNA may depend on its surrounding sequence. Yet, some RNAs such as microRNAs retain their specific structures during biogenesis, which involves extraction of the substructure from a larger structural ...

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Plos Computational Biology : Spontaneous Reaction Silencing in Met...

By: Herbert M. Sauro

Description : Metabolic reactions of single-cell organisms are routinely observed to become dispensable or even incapable of carrying activity under certain circumstances. Yet, the mechanisms as well as the range of conditions and phenotypes associated with this behavior remain very poorly understood. Here we predict computationally and analytically that any organism evolving to maximize growth rate, ATP production, or any other linear function of metabolic fluxes tends ...

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Plos Computational Biology : Numerical Modelling of the V-j Combin...

By: Florence Thuderoz
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Plos Computational Biology : Dynamically-driven Inactivation of th...

By: Jiahai Shi

Description : Despite utilizing the same chymotrypsin fold to host the catalytic machinery, coronavirus 3C-like proteases (3CLpro) noticeably differ from picornavirus 3C proteases in acquiring an extra helical domain in evolution. Previously, the extra domain was demonstrated to regulate the catalysis of the SARS-CoV 3CLpro by controlling its dimerization. Here, we studied N214A, another mutant with only a doubled dissociation constant but significantly abolished activit...

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Plos Computational Biology : Robustness in Glyoxylate Bypass Regul...

By: Jason A. Papin

Description : The glyoxylate bypass allows Escherichia coli to grow on carbon sources with only two carbons by bypassing the loss of carbons as CO2 in the tricarboxylic acid cycle. The flux toward this bypass is regulated by the phosphorylation of the enzyme isocitrate dehydrogenase (IDH) by a bifunctional kinase–phosphatase called IDHKP. In this system, IDH activity has been found to be remarkably robust with respect to wide variations in the total IDH protein concentra...

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Plos Computational Biology : Neighbor-dependent Ramachandran Proba...

By: Daniel Ting
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Plos Computational Biology : Restricted N-glycan Conformational Sp...

By: Sunhwan Jo

Description : Understanding glycan structure and dynamics is central to understanding protein-carbohydrate recognition and its role in protein-protein interactions. Given the difficulties in obtaining the glycan’s crystal structure in glycoconjugates due to its flexibility and heterogeneity, computational modeling could play an important role in providing glycosylated protein structure models. To address if glycan structures available in the PDB can be used as templates ...

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Plos Computational Biology : Accurate Structural Correlations from...

By: Roland Dunbrack

Description : The cores of globular proteins are densely packed, resulting in complicated networks of structural interactions. These interactions in turn give rise to dynamic structural correlations over a wide range of time scales. Accurate analysis of these complex correlations is crucial for understanding biomolecular mechanisms and for relating structure to function. Here we report a highly accurate technique for inferring the major modes of structural correlation in...

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Plos Computational Biology : Modeling the Violation of Reward Maxi...

By: Karl J. Friston

Description : It is often assumed that animals and people adjust their behavior to maximize reward acquisition. In visually cued reinforcement schedules, monkeys make errors in trials that are not immediately rewarded, despite having to repeat error trials. Here we show that error rates are typically smaller in trials equally distant from reward but belonging to longer schedules (referred to as ‘‘schedule length effect’’). This violates the principles of reward maximizat...

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