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Plos Computational Biology : Electron Transfer Interactome of Cyto...

By: Dennis R. Livesay

Description : Volkov AN, van Nuland NAJ (2012) Electron Transfer Interactome of Cytochrome c

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Plos Computational Biology : a Compact Representation of Drawing M...

By: Felix Polyakov

Description : Some studies suggest that complex arm movements in humans and monkeys may optimize several objective functions, while others claim that arm movements satisfy geometric constraints and are composed of elementary components. However, the ability to unify different constraints has remained an open question. The criterion for a maximally smooth (minimizing jerk) motion is satisfied for parabolic trajectories having constant equi-affine speed, which thus comply ...

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Plos Computational Biology : Protein Molecular Function Prediction...

By: Jonathan Eisen

Description : We present a statistical graphical model to infer specific molecular function for unannotated protein sequences using homology. Based on phylogenomic principles, SIFTER (Statistical Inference of Function Through Evolutionary Relationships) accurately predicts molecular function for members of a protein family given a reconciled phylogeny and available function annotations, even when the data are sparse or noisy. Our method produced specific and consistent m...

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Plos Computational Biology : Classifying Rna-binding Proteins Base...

By: Uwe Ohler

Description : Protein structure can provide new insight into the biological function of a protein and can enable the design of better experiments to learn its biological roles. Moreover, deciphering the interactions of a protein with other molecules can contribute to the understanding of the protein’s function within cellular processes. In this study, we apply a machine learning approach for classifying RNA-binding proteins based on their three-dimensional structures. Th...

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Plos Computational Biology : Vulnerabilities in the Tau Network an...

By: Theresa M. Yuraszeck
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Plos Computational Biology : Self-organized Criticality in Develop...

By: Christian Tetzlaff
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Plos Computational Biology : a Hidden Markov Model for Single Part...

By: Raibatak Das

Description : The extraction of hidden information from complex trajectories is a continuing problem in single-particle and single-molecule experiments. Particle trajectories are the result of multiple phenomena, and new methods for revealing changes in molecular processes are needed. We have developed a practical technique that is capable of identifying multiple states of diffusion within experimental trajectories. We model single particle tracks for a membrane-associat...

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Plos Computational Biology : Bridging the Resolution Gap in Struct...

By: Marc A. Marti-renom

Description : Over the last decade, and especially after the advent of fluorescent in situ hybridization imaging and chromosome conformation capture methods, the availability of experimental data on genome three-dimensional organization has dramatically increased. We now have access to unprecedented details of how genomes organize within the interphase nucleus. Development of new computational approaches to leverage this data has already resulted in the first three-dimen...

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Plos Computational Biology : a Two-dimensional Model of the Coloni...

By: Sara-jane Dunn
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Plos Computational Biology : Sequence Motifs in Mads Transcription...

By: Aalt D. J. Van Dijk
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Plos Computational Biology : Evolution of Networks for Body Plan P...

By: Paulien Hogeweg

Description : A major goal of evolutionary developmental biology (evo-devo) is to understand how multicellular body plans of increasing complexity have evolved, and how the corresponding developmental programs are genetically encoded. It has been repeatedly argued that key to the evolution of increased body plan complexity is the modularity of the underlying developmental gene regulatory networks (GRNs). This modularity is considered essential for network robustness and ...

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Plos Computational Biology : a Range-normalization Model of Contex...

By: Alireza Soltani

Description : Most utility theories of choice assume that the introduction of an irrelevant option (called the decoy) to a choice set does not change the preference between existing options. On the contrary, a wealth of behavioral data demonstrates the dependence of preference on the decoy and on the context in which the options are presented. Nevertheless, neural mechanisms underlying context-dependent preference are poorly understood. In order to shed light on these me...

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Plos Computational Biology : Computational Biology in Brazil, Volume 3

By: Philip E. Bourne
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Plos Computational Biology : the Rna Silencing Pathway ; the Bits ...

By: Simon Levin

Description : Cellular pathways are generally proposed on the basis of available experimental knowledge. The proposed pathways, however, may be inadequate to describe the phenomena they are supposed to explain. For instance, by means of concise mathematical models we are able to reveal shortcomings in the current description of the pathway of RNA silencing. The silencing pathway operates by cleaving siRNAs from dsRNA. siRNAs can associate with RISC, leading to the degrad...

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Plos Computational Biology : MacHine Learning and Its Applications...

By: Fran Lewitter
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Plos Computational Biology : Genome Comparison of Human and Non-hu...

By: Christian Frech

Description : Genes underlying important phenotypic differences between Plasmodium species, the causative agents of malaria, are frequently found in only a subset of species and cluster at dynamically evolving subtelomeric regions of chromosomes. We hypothesized that chromosome-internal regions of Plasmodium genomes harbour additional species subset-specific genes that underlie differences in human pathogenicity, human-to-human transmissibility, and human virulence. We c...

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Plos Computational Biology : Sarcomere Lattice Geometry Influences...

By: Carl T. Bergstrom

Description : In muscle, force emerges from myosin binding with actin (forming a cross-bridge). This actomyosin binding depends upon myofilament geometry, kinetics of thin-filament Ca2þ activation, and kinetics of cross-bridge cycling. Binding occurs within a compliant network of protein filaments where there is mechanical coupling between myosins along the thick-filament backbone and between actin monomers along the thin filament. Such mechanical coupling precludes usin...

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Plos Computational Biology : Effects of Electrical and Structural ...

By: Trine Krogh-madsen
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Plos Computational Biology : Modeling and Inferring Cleavage Patte...

By: Jeffrey Axelrod

Description : The regulation of cleavage plane orientation is one of the key mechanisms driving epithelial morphogenesis. Still, many aspects of the relationship between local cleavage patterns and tissue-level properties remain poorly understood. Here we develop a topological model that simulates the dynamics of a 2D proliferating epithelium from generation to generation, enabling the exploration of a wide variety of biologically plausible cleavage patterns. We investig...

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Plos Computational Biology : Convergent Transmission of Rnai Guide...

By: Thomas T. Joseph

Description : In RNA interference, a guide strand derived from a short dsRNA such as a microRNA (miRNA) is loaded into Argonaute, the central protein in the RNA Induced Silencing Complex (RISC) that silences messenger RNAs on a sequence-specific basis. The positions of any mismatched base pairs in an miRNA determine which Argonaute subtype is used. Subsequently, the Argonaute-guide complex binds and silences complementary target mRNAs: certain Argonautes cleave the targe...

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