6,276 results match your criteria PLoS Computational Biology [Journal]


SPINDLE: End-to-end learning from EEG/EMG to extrapolate animal sleep scoring across experimental settings, labs and species.

PLoS Comput Biol 2019 Apr 18;15(4):e1006968. Epub 2019 Apr 18.

Department of Computer Science, ETH Zurich, Zürich, Switzerland.

Understanding sleep and its perturbation by environment, mutation, or medication remains a central problem in biomedical research. Its examination in animal models rests on brain state analysis via classification of electroencephalographic (EEG) signatures. Traditionally, these states are classified by trained human experts by visual inspection of raw EEG recordings, which is a laborious task prone to inter-individual variability. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1006968DOI Listing

Bet-hedging strategies in expanding populations.

PLoS Comput Biol 2019 Apr 18;15(4):e1006529. Epub 2019 Apr 18.

Biological Complexity Unit, Okinawa Institute for Science and Technology and Graduate University, Onna, Okinawa 904-0495, Japan.

In ecology, species can mitigate their extinction risks in uncertain environments by diversifying individual phenotypes. This observation is quantified by the theory of bet-hedging, which provides a reason for the degree of phenotypic diversity observed even in clonal populations. Bet-hedging in well-mixed populations is rather well understood. Read More

View Article

Download full-text PDF

Source
http://dx.plos.org/10.1371/journal.pcbi.1006529
Publisher Site
http://dx.doi.org/10.1371/journal.pcbi.1006529DOI Listing
April 2019
1 Read

Imperfect Bayesian inference in visual perception.

PLoS Comput Biol 2019 Apr 18;15(4):e1006465. Epub 2019 Apr 18.

Department of Psychology, University of Uppsala, Uppsala, Sweden.

Optimal Bayesian models have been highly successful in describing human performance on perceptual decision-making tasks, such as cue combination and visual search. However, recent studies have argued that these models are often overly flexible and therefore lack explanatory power. Moreover, there are indications that neural computation is inherently imprecise, which makes it implausible that humans would perform optimally on any non-trivial task. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1006465DOI Listing

Toward a 3D model of phyllotaxis based on a biochemically plausible auxin-transport mechanism.

PLoS Comput Biol 2019 Apr 18;15(4):e1006896. Epub 2019 Apr 18.

Institute of Plant Sciences, University of Bern, Bern, Switzerland.

Polar auxin transport lies at the core of many self-organizing phenomena sustaining continuous plant organogenesis. In angiosperms, the shoot apical meristem is a potentially unique system in which the two main modes of auxin-driven patterning-convergence and canalization-co-occur in a coordinated manner and in a fully three-dimensional geometry. In the epidermal layer, convergence points form, from which auxin is canalized towards inner tissue. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1006896DOI Listing

Predicting synthetic lethal interactions using conserved patterns in protein interaction networks.

PLoS Comput Biol 2019 Apr 17;15(4):e1006888. Epub 2019 Apr 17.

Bioinformatics Lab, School of Life Sciences, University of Sussex, Falmer, Brighton, United Kingdom.

In response to a need for improved treatments, a number of promising novel targeted cancer therapies are being developed that exploit human synthetic lethal interactions. This is facilitating personalised medicine strategies in cancers where specific tumour suppressors have become inactivated. Mainly due to the constraints of the experimental procedures, relatively few human synthetic lethal interactions have been identified. Read More

View Article

Download full-text PDF

Source
http://dx.plos.org/10.1371/journal.pcbi.1006888
Publisher Site
http://dx.doi.org/10.1371/journal.pcbi.1006888DOI Listing
April 2019
1 Read

Learning and forgetting using reinforced Bayesian change detection.

PLoS Comput Biol 2019 Apr 17;15(4):e1006713. Epub 2019 Apr 17.

CoAction Lab, Institue of Neuroscience, Université Catholique de Louvain, Bruxelles, Belgium.

Agents living in volatile environments must be able to detect changes in contingencies while refraining to adapt to unexpected events that are caused by noise. In Reinforcement Learning (RL) frameworks, this requires learning rates that adapt to past reliability of the model. The observation that behavioural flexibility in animals tends to decrease following prolonged training in stable environment provides experimental evidence for such adaptive learning rates. Read More

View Article

Download full-text PDF

Source
http://dx.plos.org/10.1371/journal.pcbi.1006713
Publisher Site
http://dx.doi.org/10.1371/journal.pcbi.1006713DOI Listing
April 2019
1 Read

Neural control of body-plan axis in regenerating planaria.

PLoS Comput Biol 2019 Apr 16;15(4):e1006904. Epub 2019 Apr 16.

Allen Discovery Center, Tufts University, Medford, Massachusetts, United States of America.

Control of axial polarity during regeneration is a crucial open question. We developed a quantitative model of regenerating planaria, which elucidates self-assembly mechanisms of morphogen gradients required for robust body-plan control. The computational model has been developed to predict the fraction of heteromorphoses expected in a population of regenerating planaria fragments subjected to different treatments, and for fragments originating from different regions along the anterior-posterior and medio-lateral axis. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1006904DOI Listing

MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments.

PLoS Comput Biol 2019 Apr 15;15(4):e1006982. Epub 2019 Apr 15.

Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, United States of America.

Hi-C and chromatin immunoprecipitation (ChIP) have been combined to identify long-range chromatin interactions genome-wide at reduced cost and enhanced resolution, but extracting information from the resulting datasets has been challenging. Here we describe a computational method, MAPS, Model-based Analysis of PLAC-seq and HiChIP, to process the data from such experiments and identify long-range chromatin interactions. MAPS adopts a zero-truncated Poisson regression framework to explicitly remove systematic biases in the PLAC-seq and HiChIP datasets, and then uses the normalized chromatin contact frequencies to identify significant chromatin interactions anchored at genomic regions bound by the protein of interest. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1006982DOI Listing

Approximate Bayesian estimation of coevolutionary arms races.

PLoS Comput Biol 2019 Apr 15;15(4):e1006988. Epub 2019 Apr 15.

Bioinformatics and Computational Biology, University of Idaho, Moscow, Idaho, United States of America.

Exaggerated traits involved in species interactions have long captivated the imagination of evolutionary biologists and inspired the durable metaphor of the coevolutionary arms race. Despite decades of research, however, we have only a handful of examples where reciprocal coevolutionary change has been rigorously established as the cause of trait exaggeration. Support for a coevolutionary mechanism remains elusive because we lack generally applicable tools for quantifying the intensity of coevolutionary selection. Read More

View Article

Download full-text PDF

Source
http://dx.plos.org/10.1371/journal.pcbi.1006988
Publisher Site
http://dx.doi.org/10.1371/journal.pcbi.1006988DOI Listing
April 2019
1 Read

Passenger mutations accurately classify human tumors.

PLoS Comput Biol 2019 Apr 15;15(4):e1006953. Epub 2019 Apr 15.

Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, Barcelona, Spain.

Determining the cancer type and molecular subtype has important clinical implications. The primary site is however unknown for some malignancies discovered in the metastatic stage. Moreover liquid biopsies may be used to screen for tumoral DNA, which upon detection needs to be assigned to a site-of-origin. Read More

View Article

Download full-text PDF

Source
http://dx.plos.org/10.1371/journal.pcbi.1006953
Publisher Site
http://dx.doi.org/10.1371/journal.pcbi.1006953DOI Listing
April 2019
1 Read

Competing evolutionary paths in growing populations with applications to multidrug resistance.

PLoS Comput Biol 2019 Apr 15;15(4):e1006866. Epub 2019 Apr 15.

School of Mathematics, University of Edinburgh, Edinburgh, Scotland.

Investigating the emergence of a particular cell type is a recurring theme in models of growing cellular populations. The evolution of resistance to therapy is a classic example. Common questions are: when does the cell type first occur, and via which sequence of steps is it most likely to emerge? For growing populations, these questions can be formulated in a general framework of branching processes spreading through a graph from a root to a target vertex. Read More

View Article

Download full-text PDF

Source
http://dx.plos.org/10.1371/journal.pcbi.1006866
Publisher Site
http://dx.doi.org/10.1371/journal.pcbi.1006866DOI Listing
April 2019
1 Read

Increasing consensus of context-specific metabolic models by integrating data-inferred cell functions.

PLoS Comput Biol 2019 Apr 15;15(4):e1006867. Epub 2019 Apr 15.

Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, School of Medicine, La Jolla, CA, United States of America.

Genome-scale metabolic models provide a valuable context for analyzing data from diverse high-throughput experimental techniques. Models can quantify the activities of diverse pathways and cellular functions. Since some metabolic reactions are only catalyzed in specific environments, several algorithms exist that build context-specific models. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1006867DOI Listing

GOOGA: A platform to synthesize mapping experiments and identify genomic structural diversity.

PLoS Comput Biol 2019 Apr 15;15(4):e1006949. Epub 2019 Apr 15.

Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, United States of America.

Understanding genomic structural variation such as inversions and translocations is a key challenge in evolutionary genetics. We develop a novel statistical approach to comparative genetic mapping to detect large-scale structural mutations from low-level sequencing data. The procedure, called Genome Order Optimization by Genetic Algorithm (GOOGA), couples a Hidden Markov Model with a Genetic Algorithm to analyze data from genetic mapping populations. Read More

View Article

Download full-text PDF

Source
http://dx.plos.org/10.1371/journal.pcbi.1006949
Publisher Site
http://dx.doi.org/10.1371/journal.pcbi.1006949DOI Listing
April 2019
1 Read

The relative contribution of color and material in object selection.

PLoS Comput Biol 2019 Apr 12;15(4):e1006950. Epub 2019 Apr 12.

Department of Psychology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.

Object perception is inherently multidimensional: information about color, material, texture and shape all guide how we interact with objects. We developed a paradigm that quantifies how two object properties (color and material) combine in object selection. On each experimental trial, observers viewed three blob-shaped objects-the target and two tests-and selected the test that was more similar to the target. Read More

View Article

Download full-text PDF

Source
http://dx.plos.org/10.1371/journal.pcbi.1006950
Publisher Site
http://dx.doi.org/10.1371/journal.pcbi.1006950DOI Listing
April 2019
1 Read

Assessing intra-lab precision and inter-lab repeatability of outgrowth assays of HIV-1 latent reservoir size.

PLoS Comput Biol 2019 Apr 12;15(4):e1006849. Epub 2019 Apr 12.

Blood Systems Research Institute, San Francisco, California, United States of America.

Quantitative viral outgrowth assays (QVOA) use limiting dilutions of CD4+ T cells to measure the size of the latent HIV-1 reservoir, a major obstacle to curing HIV-1. Efforts to reduce the reservoir require assays that can reliably quantify its size in blood and tissues. Although QVOA is regarded as a "gold standard" for reservoir measurement, little is known about its accuracy and precision or about how cell storage conditions or laboratory-specific practices affect results. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1006849DOI Listing
April 2019
1 Read

A global map of the protein shape universe.

PLoS Comput Biol 2019 Apr 12;15(4):e1006969. Epub 2019 Apr 12.

Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America.

Proteins are involved in almost all functions in a living cell, and functions of proteins are realized by their tertiary structures. Obtaining a global perspective of the variety and distribution of protein structures lays a foundation for our understanding of the building principle of protein structures. In light of the rapid accumulation of low-resolution structure data from electron tomography and cryo-electron microscopy, here we map and classify three-dimensional (3D) surface shapes of proteins into a similarity space. Read More

View Article

Download full-text PDF

Source
http://dx.plos.org/10.1371/journal.pcbi.1006969
Publisher Site
http://dx.doi.org/10.1371/journal.pcbi.1006969DOI Listing
April 2019
2 Reads

Microstimulation in a spiking neural network model of the midbrain superior colliculus.

PLoS Comput Biol 2019 Apr 12;15(4):e1006522. Epub 2019 Apr 12.

Department of Biophysics, Donders Institute for Brain, Radboud University, Cognition and Behaviour, Nijmegen, the Netherlands.

The midbrain superior colliculus (SC) generates a rapid saccadic eye movement to a sensory stimulus by recruiting a population of cells in its topographically organized motor map. Supra-threshold electrical microstimulation in the SC reveals that the site of stimulation produces a normometric saccade vector with little effect of the stimulation parameters. Moreover, electrically evoked saccades (E-saccades) have kinematic properties that strongly resemble natural, visual-evoked saccades (V-saccades). Read More

View Article

Download full-text PDF

Source
http://dx.plos.org/10.1371/journal.pcbi.1006522
Publisher Site
http://dx.doi.org/10.1371/journal.pcbi.1006522DOI Listing
April 2019
1 Read

Ten quick tips for creating an effective lesson.

Authors:
Greg Wilson

PLoS Comput Biol 2019 Apr 11;15(4):e1006915. Epub 2019 Apr 11.

RStudio, Toronto, Ontario, Canada.

We present 10 tips for building effective lessons that are grounded in empirical research on pedagogy and cognitive psychology and that we have found to be practically useful in both classroom and free-range settings. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1006915DOI Listing

Model-based analysis of influenza A virus replication in genetically engineered cell lines elucidates the impact of host cell factors on key kinetic parameters of virus growth.

PLoS Comput Biol 2019 Apr 11;15(4):e1006944. Epub 2019 Apr 11.

Department of Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.

The best measure to limit spread of contagious diseases caused by influenza A viruses (IAVs) is annual vaccination. The growing global demand for low-cost vaccines requires the establishment of high-yield production processes. One possible option to address this challenge is the engineering of novel vaccine producer cell lines by manipulating gene expression of host cell factors relevant for virus replication. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1006944DOI Listing

Exon level machine learning analyses elucidate novel candidate miRNA targets in an avian model of fetal alcohol spectrum disorder.

PLoS Comput Biol 2019 Apr 11;15(4):e1006937. Epub 2019 Apr 11.

Nutrition Research Institute, Department of Nutrition, University of North Carolina at Chapel Hill, Kannapolis, North Carolina, United States of America.

Gestational alcohol exposure causes fetal alcohol spectrum disorder (FASD) and is a prominent cause of neurodevelopmental disability. Whole transcriptome sequencing (RNA-Seq) offer insights into mechanisms underlying FASD, but gene-level analysis provides limited information regarding complex transcriptional processes such as alternative splicing and non-coding RNAs. Moreover, traditional analytical approaches that use multiple hypothesis testing with a false discovery rate adjustment prioritize genes based on an adjusted p-value, which is not always biologically relevant. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1006937DOI Listing

Reconciling high-throughput gene essentiality data with metabolic network reconstructions.

PLoS Comput Biol 2019 Apr 11;15(4):e1006507. Epub 2019 Apr 11.

Biomedical Engineering, University of Virginia, Charlottesville, Virginia, United States of America.

The identification of genes essential for bacterial growth and survival represents a promising strategy for the discovery of antimicrobial targets. Essential genes can be identified on a genome-scale using transposon mutagenesis approaches; however, variability between screens and challenges with interpretation of essentiality data hinder the identification of both condition-independent and condition-dependent essential genes. To illustrate the scope of these challenges, we perform a large-scale comparison of multiple published Pseudomonas aeruginosa gene essentiality datasets, revealing substantial differences between the screens. Read More

View Article

Download full-text PDF

Source
http://dx.plos.org/10.1371/journal.pcbi.1006507
Publisher Site
http://dx.doi.org/10.1371/journal.pcbi.1006507DOI Listing
April 2019
2 Reads

Network motifs and their origins.

PLoS Comput Biol 2019 Apr 11;15(4):e1006749. Epub 2019 Apr 11.

Department of Theoretical and Computational Ecology, IBED, University of Amsterdam, Amsterdam, the Netherlands.

Modern network science is a new and exciting research field that has transformed the study of complex systems over the last 2 decades. Of particular interest is the identification of small "network motifs" that might be embedded in a larger network and that indicate the presence of evolutionary design principles or have an overly influential role on system-wide dynamics. Motifs are patterns of interconnections, or subgraphs, that appear in an observed network significantly more often than in compatible randomized networks. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1006749DOI Listing
April 2019
1 Read

Ten simple rules towards healthier research labs.

PLoS Comput Biol 2019 Apr 11;15(4):e1006914. Epub 2019 Apr 11.

Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, Móstoles, Spain.

The negative effects of extremely competitive academic and research environments on the performance and health of researchers are well known and common worldwide. The prevalence of these effects, particularly among early career researchers, calls for a more humane and people-centered way of working within research labs. Although there is growing concern about the urgent need for a better life-work balance when doing science, there are not many examples about how this could be achieved in practice. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1006914DOI Listing

Physical constraints on accuracy and persistence during breast cancer cell chemotaxis.

PLoS Comput Biol 2019 Apr 10;15(4):e1006961. Epub 2019 Apr 10.

School of Mechanical Engineering, Purdue University, West Lafayette Indiana, United States of America.

Directed cell motion in response to an external chemical gradient occurs in many biological phenomena such as wound healing, angiogenesis, and cancer metastasis. Chemotaxis is often characterized by the accuracy, persistence, and speed of cell motion, but whether any of these quantities is physically constrained by the others is poorly understood. Using a combination of theory, simulations, and 3D chemotaxis assays on single metastatic breast cancer cells, we investigate the links among these different aspects of chemotactic performance. Read More

View Article

Download full-text PDF

Source
http://dx.plos.org/10.1371/journal.pcbi.1006961
Publisher Site
http://dx.doi.org/10.1371/journal.pcbi.1006961DOI Listing
April 2019
2 Reads

Estimation of the breadth of CD4bs targeting HIV antibodies by molecular modeling and machine learning.

PLoS Comput Biol 2019 Apr 10;15(4):e1006954. Epub 2019 Apr 10.

Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, United States of America.

HIV is a highly mutable virus for which all attempts to develop a vaccine have been unsuccessful. Nevertheless, few long-infected patients develop antibodies, called broadly neutralizing antibodies (bnAbs), that have a high breadth and can neutralize multiple variants of the virus. This suggests that a universal HIV vaccine should be possible. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1006954DOI Listing

Confidence resets reveal hierarchical adaptive learning in humans.

PLoS Comput Biol 2019 Apr 9;15(4):e1006972. Epub 2019 Apr 9.

Cognitive Neuroimaging Unit / NeuroSpin center / Institute for Life Sciences Frédéric Joliot / Fundamental Research Division / Commissariat à l'Energie Atomique et aux énergies alternatives; INSERM, Université Paris-Sud; Université Paris-Saclay; Gif-sur-Yvette, France.

Hierarchical processing is pervasive in the brain, but its computational significance for learning under uncertainty is disputed. On the one hand, hierarchical models provide an optimal framework and are becoming increasingly popular to study cognition. On the other hand, non-hierarchical (flat) models remain influential and can learn efficiently, even in uncertain and changing environments. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1006972DOI Listing

Stytra: An open-source, integrated system for stimulation, tracking and closed-loop behavioral experiments.

PLoS Comput Biol 2019 Apr 8;15(4):e1006699. Epub 2019 Apr 8.

Research Group of Sensorimotor Control, Max Planck Institute of Neurobiology, Martinsried, Germany.

We present Stytra, a flexible, open-source software package, written in Python and designed to cover all the general requirements involved in larval zebrafish behavioral experiments. It provides timed stimulus presentation, interfacing with external devices and simultaneous real-time tracking of behavioral parameters such as position, orientation, tail and eye motion in both freely-swimming and head-restrained preparations. Stytra logs all recorded quantities, metadata, and code version in standardized formats to allow full provenance tracking, from data acquisition through analysis to publication. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1006699DOI Listing

Recentrifuge: Robust comparative analysis and contamination removal for metagenomics.

PLoS Comput Biol 2019 Apr 8;15(4):e1006967. Epub 2019 Apr 8.

Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain.

Metagenomic sequencing is becoming widespread in biomedical and environmental research, and the pace is increasing even more thanks to nanopore sequencing. With a rising number of samples and data per sample, the challenge of efficiently comparing results within a specimen and between specimens arises. Reagents, laboratory, and host related contaminants complicate such analysis. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1006967DOI Listing

Contextual influence on confidence judgments in human reinforcement learning.

PLoS Comput Biol 2019 Apr 8;15(4):e1006973. Epub 2019 Apr 8.

CREED, Amsterdam School of Economics (ASE), Universiteit van Amsterdam, Amsterdam, the Netherlands.

The ability to correctly estimate the probability of one's choices being correct is fundamental to optimally re-evaluate previous choices or to arbitrate between different decision strategies. Experimental evidence nonetheless suggests that this metacognitive process-confidence judgment- is susceptible to numerous biases. Here, we investigate the effect of outcome valence (gains or losses) on confidence while participants learned stimulus-outcome associations by trial-and-error. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1006973DOI Listing

The intrinsic dimension of protein sequence evolution.

PLoS Comput Biol 2019 Apr 8;15(4):e1006767. Epub 2019 Apr 8.

SISSA, Trieste, Italy.

It is well known that, in order to preserve its structure and function, a protein cannot change its sequence at random, but only by mutations occurring preferentially at specific locations. We here investigate quantitatively the amount of variability that is allowed in protein sequence evolution, by computing the intrinsic dimension (ID) of the sequences belonging to a selection of protein families. The ID is a measure of the number of independent directions that evolution can take starting from a given sequence. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1006767DOI Listing

Unsupervised extraction of epidemic syndromes from participatory influenza surveillance self-reported symptoms.

PLoS Comput Biol 2019 Apr 8;15(4):e1006173. Epub 2019 Apr 8.

ISI Foundation, Turin, Italy.

Seasonal influenza surveillance is usually carried out by sentinel general practitioners (GPs) who compile weekly reports based on the number of influenza-like illness (ILI) clinical cases observed among visited patients. This traditional practice for surveillance generally presents several issues, such as a delay of one week or more in releasing reports, population biases in the health-seeking behaviour, and the lack of a common definition of ILI case. On the other hand, the availability of novel data streams has recently led to the emergence of non-traditional approaches for disease surveillance that can alleviate these issues. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1006173DOI Listing

Dynamic filopodial forces induce accumulation, damage, and plastic remodeling of 3D extracellular matrices.

PLoS Comput Biol 2019 Apr 8;15(4):e1006684. Epub 2019 Apr 8.

Yale University, Biomedical Engineering Department, New Haven, Connecticut, United States of America.

The mechanical properties of the extracellular matrix (ECM)-a complex, 3D, fibrillar scaffold of cells in physiological environments-modulate cell behavior and can drive tissue morphogenesis, regeneration, and disease progression. For simplicity, it is often convenient to assume these properties to be time-invariant. In living systems, however, cells dynamically remodel the ECM and create time-dependent local microenvironments. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1006684DOI Listing

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis.

PLoS Comput Biol 2019 Apr 8;15(4):e1006650. Epub 2019 Apr 8.

Centre of Computational Evolution, University of Auckland, Auckland, New Zealand.

Elaboration of Bayesian phylogenetic inference methods has continued at pace in recent years with major new advances in nearly all aspects of the joint modelling of evolutionary data. It is increasingly appreciated that some evolutionary questions can only be adequately answered by combining evidence from multiple independent sources of data, including genome sequences, sampling dates, phenotypic data, radiocarbon dates, fossil occurrences, and biogeographic range information among others. Including all relevant data into a single joint model is very challenging both conceptually and computationally. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1006650DOI Listing

Multiple factors influence the morphology of the bipolar electrogram: An in silico modeling study.

PLoS Comput Biol 2019 Apr 5;15(4):e1006765. Epub 2019 Apr 5.

Division of Cardiology, Yonsei University Health System, Seoul, Republic of Korea.

Although bipolar electrograms (Bi-egms) are commonly used for catheter mapping and ablation of cardiac arrhythmias, the accuracy and reproducibility of Bi-egms have not been evaluated. We aimed to clarify the influence of the catheter orientation (CO), catheter contact angle (CA), local conduction velocity (CV), scar size, and catheter type on the Bi-egm morphology using an in silico 3-dimensional realistic model of atrial fibrillation. We constructed a 3-dimensional, realistic, in silico left atrial model with activation wave propagation including bipolar catheter models. Read More

View Article

Download full-text PDF

Source
http://dx.plos.org/10.1371/journal.pcbi.1006765
Publisher Site
http://dx.doi.org/10.1371/journal.pcbi.1006765DOI Listing
April 2019
4 Reads

Model diagnostics and refinement for phylodynamic models.

PLoS Comput Biol 2019 Apr 5;15(4):e1006955. Epub 2019 Apr 5.

Maxwell Institute for Mathematical Sciences, School of Mathematical and Computer Sciences, Heriot-Watt University, Edinburgh, EH14 4AS, UK.

Phylodynamic modelling, which studies the joint dynamics of epidemiological and evolutionary processes, has made significant progress in recent years due to increasingly available genomic data and advances in statistical modelling. These advances have greatly improved our understanding of transmission dynamics of many important pathogens. Nevertheless, there remains a lack of effective, targetted diagnostic tools for systematically detecting model mis-specification. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1006955DOI Listing
April 2019
1 Read

Modeling neuronal avalanches and long-range temporal correlations at the emergence of collective oscillations: Continuously varying exponents mimic M/EEG results.

PLoS Comput Biol 2019 Apr 5;15(4):e1006924. Epub 2019 Apr 5.

Departamento de Física, Universidade Federal de Pernambuco (UFPE), Recife, PE, Brazil.

We revisit the CROS ("CRitical OScillations") model which was recently proposed as an attempt to reproduce both scale-invariant neuronal avalanches and long-range temporal correlations. With excitatory and inhibitory stochastic neurons locally connected in a two-dimensional disordered network, the model exhibits a transition where alpha-band oscillations emerge. Precisely at the transition, the fluctuations of the network activity have nontrivial detrended fluctuation analysis (DFA) exponents, and avalanches (defined as supra-threshold activity) have power law distributions of size and duration. Read More

View Article

Download full-text PDF

Source
http://dx.plos.org/10.1371/journal.pcbi.1006924
Publisher Site
http://dx.doi.org/10.1371/journal.pcbi.1006924DOI Listing
April 2019
3 Reads

Conservation of conformational dynamics across prokaryotic actins.

PLoS Comput Biol 2019 Apr 5;15(4):e1006683. Epub 2019 Apr 5.

Department of Bioengineering, Stanford University, Stanford, CA, United States of America.

The actin family of cytoskeletal proteins is essential to the physiology of virtually all archaea, bacteria, and eukaryotes. While X-ray crystallography and electron microscopy have revealed structural homologies among actin-family proteins, these techniques cannot probe molecular-scale conformational dynamics. Here, we use all-atom molecular dynamic simulations to reveal conserved dynamical behaviors in four prokaryotic actin homologs: MreB, FtsA, ParM, and crenactin. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1006683DOI Listing
April 2019
2 Reads

Genotype-phenotype relations of the von Hippel-Lindau tumor suppressor inferred from a large-scale analysis of disease mutations and interactors.

PLoS Comput Biol 2019 Apr 3;15(4):e1006478. Epub 2019 Apr 3.

Department of Biomedical Sciences, University of Padova, Padova, Italy.

Familiar cancers represent a privileged point of view for studying the complex cellular events inducing tumor transformation. Von Hippel-Lindau syndrome, a familiar predisposition to develop cancer is a clear example. Here, we present our efforts to decipher the role of von Hippel-Lindau tumor suppressor protein (pVHL) in cancer insurgence. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1006478DOI Listing
April 2019
4 Reads

A quick guide for student-driven community genome annotation.

PLoS Comput Biol 2019 Apr 3;15(4):e1006682. Epub 2019 Apr 3.

Boyce Thompson Institute, Ithaca, New York.

High quality gene models are necessary to expand the molecular and genetic tools available for a target organism, but these are available for only a handful of model organisms that have undergone extensive curation and experimental validation over the course of many years. The majority of gene models present in biological databases today have been identified in draft genome assemblies using automated annotation pipelines that are frequently based on orthologs from distantly related model organisms and usually have minor or major errors. Manual curation is time consuming and often requires substantial expertise, but is instrumental in improving gene model structure and identification. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1006682DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6447164PMC
April 2019
2 Reads

Rich-club connectivity, diverse population coupling, and dynamical activity patterns emerging from local cortical circuits.

PLoS Comput Biol 2019 Apr 2;15(4):e1006902. Epub 2019 Apr 2.

School of Physics, University of Sydney, New South Wales, Australia.

Experimental studies have begun revealing essential properties of the structural connectivity and the spatiotemporal activity dynamics of cortical circuits. To integrate these properties from anatomy and physiology, and to elucidate the links between them, we develop a novel cortical circuit model that captures a range of realistic features of synaptic connectivity. We show that the model accounts for the emergence of higher-order connectivity structures, including highly connected hub neurons that form an interconnected rich-club. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1006902DOI Listing
April 2019
2 Reads

Gene set meta-analysis with Quantitative Set Analysis for Gene Expression (QuSAGE).

PLoS Comput Biol 2019 Apr 2;15(4):e1006899. Epub 2019 Apr 2.

Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America.

Small sample sizes combined with high person-to-person variability can make it difficult to detect significant gene expression changes from transcriptional profiling studies. Subtle, but coordinated, gene expression changes may be detected using gene set analysis approaches. Meta-analysis is another approach to increase the power to detect biologically relevant changes by integrating information from multiple studies. Read More

View Article

Download full-text PDF

Source
http://dx.plos.org/10.1371/journal.pcbi.1006899
Publisher Site
http://dx.doi.org/10.1371/journal.pcbi.1006899DOI Listing
April 2019
5 Reads

Structure, stability and specificity of the binding of ssDNA and ssRNA with proteins.

PLoS Comput Biol 2019 Apr 1;15(4):e1006768. Epub 2019 Apr 1.

Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel.

Recognition of single-stranded DNA (ssDNA) or single-stranded RNA (ssRNA) is important for many fundamental cellular functions. A variety of single-stranded DNA-binding proteins (ssDBPs) and single-stranded RNA-binding proteins (ssRBPs) have evolved that bind ssDNA and ssRNA, respectively, with varying degree of affinities and specificities to form complexes. Structural studies of these complexes provide key insights into their recognition mechanism. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1006768DOI Listing

Prediction of VRC01 neutralization sensitivity by HIV-1 gp160 sequence features.

PLoS Comput Biol 2019 Apr 1;15(4):e1006952. Epub 2019 Apr 1.

Vaccine and Infectious Disease Division and Statistical Center for HIV/AIDS Research and Prevention, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America.

The broadly neutralizing antibody (bnAb) VRC01 is being evaluated for its efficacy to prevent HIV-1 infection in the Antibody Mediated Prevention (AMP) trials. A secondary objective of AMP utilizes sieve analysis to investigate how VRC01 prevention efficacy (PE) varies with HIV-1 envelope (Env) amino acid (AA) sequence features. An exhaustive analysis that tests how PE depends on every AA feature with sufficient variation would have low statistical power. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1006952DOI Listing
April 2019
2 Reads

Ten simple rules for organizing a webinar series.

PLoS Comput Biol 2019 04 1;15(4):e1006671. Epub 2019 Apr 1.

Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1006671DOI Listing

Adaptive multi-view multi-label learning for identifying disease-associated candidate miRNAs.

PLoS Comput Biol 2019 Apr 1;15(4):e1006931. Epub 2019 Apr 1.

College of Computer Science and Electronic Engineering, Hunan University, Changsha, China.

Increasing evidence has indicated that microRNAs(miRNAs) play vital roles in various pathological processes and thus are closely related with many complex human diseases. The identification of potential disease-related miRNAs offers new opportunities to understand disease etiology and pathogenesis. Although there have been numerous computational methods proposed to predict reliable miRNA-disease associations, they suffer from various limitations that affect the prediction accuracy and their applicability. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1006931DOI Listing
April 2019
1 Read

Inferring rates of metastatic dissemination using stochastic network models.

PLoS Comput Biol 2019 Apr 1;15(4):e1006868. Epub 2019 Apr 1.

Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy at the University of Gothenburg, Sahlgrenska University Hospital, Gothenburg, Sweden.

The formation of metastases is driven by the ability of cancer cells to disseminate from the site of the primary tumour to target organs. The process of dissemination is constrained by anatomical features such as the flow of blood and lymph in the circulatory system. We exploit this fact in a stochastic network model of metastasis formation, in which only anatomically feasible routes of dissemination are considered. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1006868DOI Listing
April 2019
1 Read

Evolutionary multiplayer games on graphs with edge diversity.

PLoS Comput Biol 2019 Apr 1;15(4):e1006947. Epub 2019 Apr 1.

Center for Systems and Control, College of Engineering, Peking University, Beijing, China.

Evolutionary game dynamics in structured populations has been extensively explored in past decades. However, most previous studies assume that payoffs of individuals are fully determined by the strategic behaviors of interacting parties, and social ties between them only serve as the indicator of the existence of interactions. This assumption neglects important information carried by inter-personal social ties such as genetic similarity, geographic proximity, and social closeness, which may crucially affect the outcome of interactions. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1006947DOI Listing
April 2019
2 Reads

Bayesian inference of transmission chains using timing of symptoms, pathogen genomes and contact data.

PLoS Comput Biol 2019 Mar 29;15(3):e1006930. Epub 2019 Mar 29.

MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, United Kingdom.

There exists significant interest in developing statistical and computational tools for inferring 'who infected whom' in an infectious disease outbreak from densely sampled case data, with most recent studies focusing on the analysis of whole genome sequence data. However, genomic data can be poorly informative of transmission events if mutations accumulate too slowly to resolve individual transmission pairs or if there exist multiple pathogens lineages within-host, and there has been little focus on incorporating other types of outbreak data. We present here a methodology that uses contact data for the inference of transmission trees in a statistically rigorous manner, alongside genomic data and temporal data. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1006930DOI Listing
March 2019
3 Reads

Bayes-optimal estimation of overlap between populations of fixed size.

PLoS Comput Biol 2019 03 29;15(3):e1006898. Epub 2019 Mar 29.

Department of Computer Science, University of Colorado Boulder, Boulder, Colorado, United States of America.

Measuring the overlap between two populations is, in principle, straightforward. Upon fully sampling both populations, the number of shared objects-species, taxonomical units, or gene variants, depending on the context-can be directly counted. In practice, however, only a fraction of each population's objects are likely to be sampled due to stochastic data collection or sequencing techniques. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1006898DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6440621PMC
March 2019
1 Read

Synchrony is more than its top-down and climatic parts: interacting Moran effects on phytoplankton in British seas.

PLoS Comput Biol 2019 03 28;15(3):e1006744. Epub 2019 Mar 28.

Department of Ecology and Evolutionary Biology and Kansas Biological Survey, University of Kansas, Lawrence, Kansas, USA.

Large-scale spatial synchrony is ubiquitous in ecology. We examined 56 years of data representing chlorophyll density in 26 areas in British seas monitored by the Continuous Plankton Recorder survey. We used wavelet methods to disaggregate synchronous fluctuations by timescale and determine that drivers of synchrony include both biotic and abiotic variables. Read More

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1006744DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6438443PMC
March 2019
1 Read