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Plos Computational Biology : Influence of Low-level Stimulus Featu...

By: Kollmorge Sepp
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Plos Computational Biology : Computational Biology in Argentina, V...

By: Philip E. Bourne
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Plos Computational Biology : Welcome to Plos Computational Biology...

By: Lewitter F.
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Plos Computational Biology : Bioinformatics Meets User-centred Des...

By: Katrina Pavelin

Description : Designers have a saying that β€˜β€˜the joy of an early release lasts but a short time. The bitterness of an unusable system lasts for years.’’ It is indeed disappointing to discover that your data resources are not being used to their full potential. Not only have you invested your time, effort, and research grant on the project, but you may face costly redesigns if you want to improve the system later. This scenario would be less likely if the product was desi...

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Plos Computational Biology : Dynamic Correlation Between Intrahost...

By: Rob J. De Boer

Description : Quantifying the dynamics of intrahost HIV-1 sequence evolution is one means of uncovering information about the interaction between HIV-1 and the host immune system. In the chronic phase of infection, common dynamics of sequence divergence and diversity have been reported. We developed an HIV-1 sequence evolution model that simulated the effects of mutation and fitness of sequence variants. The amount of evolution was described by the distance from the foun...

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Plos Computational Biology : Noise Contributions in an Inducible G...

By: Elijah Roberts

Description : Stochastic expression of genes produces heterogeneity in clonal populations of bacteria under identical conditions. We analyze and compare the behavior of the inducible lac genetic switch using well-stirred and spatially resolved simulations for Escherichia coli cells modeled under fast and slow-growth conditions. Our new kinetic model describing the switching of the lac operon from one phenotype to the other incorporates parameters obtained from recently p...

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Plos Computational Biology : Dynamic Changes in Protein Functional...

By: Luhua Lai

Description : Response of cells to changing environmental conditions is governed by the dynamics of intricate biomolecular interactions. It may be reasonable to assume, proteins being the dominant macromolecules that carry out routine cellular functions, that understanding the dynamics of protein:protein interactions might yield useful insights into the cellular responses. The largescale protein interaction data sets are, however, unable to capture the changes in the pro...

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Plos Computational Biology : Blockade of Neuronal A7-nachr by A-co...

By: Kaas Quentin

Description : a-Conotoxins potently inhibit isoforms of nicotinic acetylcholine receptors (nAChRs), which are essential for neuronal and neuromuscular transmission. They are also used as neurochemical tools to study nAChR physiology and are being evaluated as drug leads to treat various neuronal disorders. A number of experimental studies have been performed to investigate the structure-activity relationships of conotoxin/nAChR complexes. However, the structural determin...

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Plos Computational Biology : Chapter 15 ; Disease Gene Prioritizat...

By: Yana Bromberg

Description : Disease-causing aberrations in the normal function of a gene define that gene as a disease gene. Proving a causal link between a gene and a disease experimentally is expensive and timeconsuming. Comprehensive prioritization of candidate genes prior to experimental testing drastically reduces the associated costs. Computational gene prioritization is based on various pieces of correlative evidence that associate each gene with the given disease and suggest p...

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Plos Computational Biology : Genetic Signatures in the Envelope Gl...

By: S. Gnanakaran
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Plos Computational Biology : a Structure-based Approach for Detect...

By: Jacquelyn S. Fetrow

Description : Cysteine (Cys) residues often play critical roles in proteins, for example, in the formation of structural disulfide bonds, metal binding, targeting proteins to the membranes, and various catalytic functions. However, the structural determinants for various Cys functions are not clear. Thiol oxidoreductases, which are enzymes containing catalytic redox-active Cys residues, have been extensively studied, but even for these proteins there is little understand...

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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 : Using Phylogeny to Improve Genome-wid...

By: Philip E. Bourne

Description : The gap between the number of known protein sequences and structures continues to widen, particularly as a result of sequencing projects for entire genomes. Recently there have been many attempts to generate structural assignments to all genes on sets of completed genomes using fold-recognition methods. We developed a method that detects false positives made by these genome-wide structural assignment experiments by identifying isolated occurrences. The meth...

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Plos Computational Biology : Dynamics of Immune Escape During Hiv,...

By: Mercedes Pascual

Description : Several studies have shown that cytotoxic T lymphocytes (CTLs) play an important role in controlling HIV/SIV infection. Notably, the observation of escape mutants suggests a selective pressure induced by the CTL response. However, it remains difficult to assess the definite role of the cellular immune response. We devise a computational model of HIV/SIV infection having a broad cellular immune response targeting different viral epitopes. The CTL clones are ...

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Plos Computational Biology : Inferring Dynamic Signatures of Micro...

By: Georg K. Gerber

Description : The human gut microbiota comprise a complex and dynamic ecosystem that profoundly affects host development and physiology. Standard approaches for analyzing time-series data of the microbiota involve computation of measures of ecological community diversity at each time-point, or measures of dissimilarity between pairs of time-points. Although these approaches, which treat data as static snapshots of microbial communities, can identify shifts in overall com...

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

By: Lawrence E. Hunter
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Plos Computational Biology : Identifying Drug Effects Via Pathway ...

By: Philip E. Bourne

Description : Understanding the mechanisms of cell function and drug action is a major endeavor in the pharmaceutical industry. Drug effects are governed by the intrinsic properties of the drug (i.e., selectivity and potency) and the specific signaling transduction network of the host (i.e., normal vs. diseased cells). Here, we describe an unbiased, phosphoproteomic-based approach to identify drug effects by monitoring drug-induced topology alterations. With our proposed...

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Plos Computational Biology : a Variant of Tnfr2-fc Fusion Protein ...

By: Tong Yang
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Plos Computational Biology : Gemini ; Integrative Exploration of G...

By: Umadevi Paila

Description : Modern DNA sequencing technologies enable geneticists to rapidly identify genetic variation among many human genomes. However, isolating the minority of variants underlying disease remains an important, yet formidable challenge for medical genetics. We have developed GEMINI (GEnome MINIng), a flexible software package for exploring all forms of human genetic variation. Unlike existing tools, GEMINI integrates genetic variation with a diverse and adaptable s...

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Plos Computational Biology : a Differentiation-based Phylogeny of ...

By: Riester Markus
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