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Plos Computational Biology : Beauty is in the Eye of the Beholder ...

By: Martin Juliette
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Plos Computational Biology : Ten Simple Rules for Building and Mai...

By: Philip E. Bourne
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Plos Computational Biology : Recombination Rate and Selection Stre...

By: Richard A. Neher
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Plos Computational Biology : a Statistical Framework for Modeling ...

By: Philip E. Bourne

Description : The identification of T cell epitopes and their HLA (human leukocyte antigen) restrictions is important for applications such as the design of cellular vaccines for HIV. Traditional methods for such identification are costly and timeconsuming. Recently, a more expeditious laboratory technique using ELISpot assays has been developed that allows for rapid screening of specific responses. However, this assay does not directly provide information concerning the...

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Plos Computational Biology : an Allosteric Mechanism for Switching...

By: Daniel Segre

Description : Methionine (Met) is an essential amino acid that is needed for the synthesis of S-adenosylmethionine (AdoMet), the major biological methylating agent. Methionine used for AdoMet synthesis can be replenished via remethylation of homocysteine. Alternatively, homocysteine can be converted to cysteine via the transsulfuration pathway. Aberrations in methionine metabolism are associated with a number of complex diseases, including cancer, anemia, and neurodegene...

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Plos Computational Biology : Search Algorithms as a Framework for ...

By: Greg Tucker-kellogg

Description : Combination therapies are often needed for effective clinical outcomes in the management of complex diseases, but presently they are generally based on empirical clinical experience. Here we suggest a novel application of search algorithms—originally developed for digital communication—modified to optimize combinations of therapeutic interventions. In biological experiments measuring the restoration of the decline with age in heart function and exercise cap...

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Plos Computational Biology : Biomedical Cloud Computing with Amazo...

By: Vincent A. Fusaro
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Plos Computational Biology : Cellularly-driven Differences in Netw...

By: Christian G. Fink

Description : Spatiotemporal pattern formation in neuronal networks depends on the interplay between cellular and network synchronization properties. The neuronal phase response curve (PRC) is an experimentally obtainable measure that characterizes the cellular response to small perturbations, and can serve as an indicator of cellular propensity for synchronization. Two broad classes of PRCs have been identified for neurons : Type I, in which small excitatory perturbatio...

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Plos Computational Biology : Small Regulatory Rnas May Sharpen Spa...

By: Edmund John Crampin

Description : The precise establishment of gene expression patterns is a crucial step in development. Formation of a sharp boundary between high and low spatial expression domains requires a genetic mechanism that exhibits sensitivity, yet is robust to fluctuations, a demand that may not be easily achieved by morphogens alone. Recently, it has been demonstrated that small RNAs (and, in particular, microRNAs) play many roles in embryonic development. Whereas some RNAs are...

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Plos Computational Biology : Optimization of Muscle Activity for T...

By: J. Lucas McKay

Description : Optimality principles have been proposed as a general framework for understanding motor control in animals and humans largely based on their ability to predict general features movement in idealized motor tasks. However, generalizing these concepts past proof-of-principle to understand the neuromechanical transformation from task-level control to detailed execution-level muscle activity and forces during behaviorally-relevant motor tasks has proved difficul...

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Plos Computational Biology : Insights Into Protein–dna Interaction...

By: Ruth Nussinov

Description : Protein–DNA interactions are crucial for many cellular processes. Now with the increased availability of structures of protein–DNA complexes, gaining deeper insights into the nature of protein–DNA interactions has become possible. Earlier, investigations have characterized the interface properties by considering pairwise interactions. However, the information communicated along the interfaces is rarely a pairwise phenomenon, and we feel that a global pictur...

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Plos Computational Biology : Quantifying Intramolecular Binding in...

By: Anurag Sethi

Description : Numerous signaling proteins use multivalent binding to increase the specificity and affinity of their interactions within the cell. Enhancement arises because the effective binding constant for multivalent binding is larger than the binding constants for each individual interaction. We seek to gain both qualitative and quantitative understanding of the multivalent interactions of an adaptor protein, growth factor receptor bound protein-2 (Grb2), containing ...

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Plos Computational Biology : Predicting Spatial and Temporal Gene ...

By: Eran Segal

Description : Wilczynski B, Liu Y-H, Yeo ZX, Furlong EEM (2012) Predicting Spatial and Temporal Gene Expression Using an Integrative Model of Transcription Factor Occupancy and Chromatin State.

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Plos Computational Biology : Metabolic Regulation in Progression t...

By: Marko Sysi-aho

Description : Recent evidence from serum metabolomics indicates that specific metabolic disturbances precede b-cell autoimmunity in humans and can be used to identify those children who subsequently progress to type 1 diabetes. The mechanisms behind these disturbances are unknown. Here we show the specificity of the pre-autoimmune metabolic changes, as indicated by their conservation in a murine model of type 1 diabetes. We performed a study in non-obese prediabetic (NOD...

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Plos Computational Biology : Positive Evolutionary Selection of an...

By: Istvan Miklos
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Plos Computational Biology : a Single-rate Context-dependent Learn...

By: James N. Ingram

Description : Motor learning has been extensively studied using dynamic (force-field) perturbations. These induce movement errors that result in adaptive changes to the motor commands. Several state-space models have been developed to explain how trialby- trial errors drive the progressive adaptation observed in such studies. These models have been applied to adaptation involving novel dynamics, which typically occurs over tens to hundreds of trials, and which appears to...

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Plos Computational Biology : Modeling Boundary Vector Cell Firing ...

By: Florian Raudies

Description : Boundary vector cells in entorhinal cortex fire when a rat is in locations at a specific distance from walls of an environment. This firing may originate from memory of the barrier location combined with path integration, or the firing may depend upon the apparent visual input image stream. The modeling work presented here investigates the role of optic flow, the apparent change of patterns of light on the retina, as input for boundary vector cell firing. A...

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Plos Computational Biology : Ten Simple Rules for Teaching Bioinfo...

By: David Form
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Plos Computational Biology : Computational Resources in Infectious...

By: Ernest Fraenkel
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Plos Computational Biology : Are There Rearrangement Hotspots in t...

By: Daniel Huson

Description : In a landmark paper, Nadeau and Taylor [18] formulated the random breakage model (RBM) of chromosome evolution that postulates that there are no rearrangement hotspots in the human genome. In the next two decades, numerous studies with progressively increasing levels of resolution made RBM the de facto theory of chromosome evolution. Despite the fact that RBM had prophetic prediction power, it was recently refuted by Pevzner and Tesler [4], who introduced t...

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