Cover
Bacterium or noise?
Two-dimensional projections of three-dimensional light sheet fluorescence microscropy images of gut bacteria in larval zebrafish. The right half consists of images hand-labeled as bacteria, the left half as noise or non-bacterial objects. These and thousands of other datasets were used to train a convolutional neural network, which achieves human-level classfication accuracy.
Image Credit: Edouard A Hay and Raghuveer Parthasarathy, The University of Oregon
Editorials
Ten simple rules for documenting scientific software
PLOS Computational Biology: published December 20, 2018 | https://doi.org/10.1371/journal.pcbi.1006561
One thousand simple rules
PLOS Computational Biology: published December 20, 2018 | https://doi.org/10.1371/journal.pcbi.1006670
Education Articles
Eleven quick tips to build a usable REST API for life sciences
PLOS Computational Biology: published December 13, 2018 | https://doi.org/10.1371/journal.pcbi.1006542
Ten quick tips for sharing open genomic data
PLOS Computational Biology: published December 27, 2018 | https://doi.org/10.1371/journal.pcbi.1006472
Perspectives
Local epigenomic state cannot discriminate interacting and non-interacting enhancer–promoter pairs with high accuracy
PLOS Computational Biology: published December 18, 2018 | https://doi.org/10.1371/journal.pcbi.1006625
Harnessing formal concepts of biological mechanism to analyze human disease
PLOS Computational Biology: published December 26, 2018 | https://doi.org/10.1371/journal.pcbi.1006540
Research Articles
A comprehensive ensemble model for comparing the allosteric effect of ordered and disordered proteins
PLOS Computational Biology: published December 3, 2018 | https://doi.org/10.1371/journal.pcbi.1006393
Chain organization of human interphase chromosome determines the spatiotemporal dynamics of chromatin loci
PLOS Computational Biology: published December 3, 2018 | https://doi.org/10.1371/journal.pcbi.1006617
A stochastic framework to model axon interactions within growing neuronal populations
PLOS Computational Biology: published December 3, 2018 | https://doi.org/10.1371/journal.pcbi.1006627
Performance of convolutional neural networks for identification of bacteria in 3D microscopy datasets
PLOS Computational Biology: published December 3, 2018 | https://doi.org/10.1371/journal.pcbi.1006628
TAMMiCol: Tool for analysis of the morphology of microbial colonies
PLOS Computational Biology: published December 3, 2018 | https://doi.org/10.1371/journal.pcbi.1006629
Detection and analysis of spatiotemporal patterns in brain activity
PLOS Computational Biology: published December 3, 2018 | https://doi.org/10.1371/journal.pcbi.1006643
Regulation of harvester ant foraging as a closed-loop excitable system
PLOS Computational Biology: published December 4, 2018 | https://doi.org/10.1371/journal.pcbi.1006200
The empirical characteristics of human pattern vision defy theoretically-driven expectations
PLOS Computational Biology: published December 4, 2018 | https://doi.org/10.1371/journal.pcbi.1006585
Insights on the impact of mitochondrial organisation on bioenergetics in high-resolution computational models of cardiac cell architecture
PLOS Computational Biology: published December 5, 2018 | https://doi.org/10.1371/journal.pcbi.1006640
Bayesian adaptive dual control of deep brain stimulation in a computational model of Parkinson’s disease
PLOS Computational Biology: published December 6, 2018 | https://doi.org/10.1371/journal.pcbi.1006606
Function and energy consumption constrain neuronal biophysics in a canonical computation: Coincidence detection
PLOS Computational Biology: published December 6, 2018 | https://doi.org/10.1371/journal.pcbi.1006612
Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study
PLOS Computational Biology: published December 6, 2018 | https://doi.org/10.1371/journal.pcbi.1006642
Multi-scale computational study of the Warburg effect, reverse Warburg effect and glutamine addiction in solid tumors
PLOS Computational Biology: published December 7, 2018 | https://doi.org/10.1371/journal.pcbi.1006584
Deep convolutional networks do not classify based on global object shape
PLOS Computational Biology: published December 7, 2018 | https://doi.org/10.1371/journal.pcbi.1006613
PathFX provides mechanistic insights into drug efficacy and safety for regulatory review and therapeutic development
PLOS Computational Biology: published December 7, 2018 | https://doi.org/10.1371/journal.pcbi.1006614
Projecting social contact matrices to different demographic structures
PLOS Computational Biology: published December 7, 2018 | https://doi.org/10.1371/journal.pcbi.1006638
Predicting protein targets for drug-like compounds using transcriptomics
PLOS Computational Biology: published December 7, 2018 | https://doi.org/10.1371/journal.pcbi.1006651
Odorant mixtures elicit less variable and faster responses than pure odorants
PLOS Computational Biology: published December 10, 2018 | https://doi.org/10.1371/journal.pcbi.1006536
Coherency of circadian rhythms in the SCN is governed by the interplay of two coupling factors
PLOS Computational Biology: published December 10, 2018 | https://doi.org/10.1371/journal.pcbi.1006607
Identifying (un)controllable dynamical behavior in complex networks
PLOS Computational Biology: published December 10, 2018 | https://doi.org/10.1371/journal.pcbi.1006630
Enzymatic and non-enzymatic pathways of kynurenines' dimerization: the molecular factors for oxidative stress development
PLOS Computational Biology: published December 10, 2018 | https://doi.org/10.1371/journal.pcbi.1006672
PremPDI estimates and interprets the effects of missense mutations on protein-DNA interactions
PLOS Computational Biology: published December 11, 2018 | https://doi.org/10.1371/journal.pcbi.1006615
SFPEL-LPI: Sequence-based feature projection ensemble learning for predicting LncRNA-protein interactions
PLOS Computational Biology: published December 11, 2018 | https://doi.org/10.1371/journal.pcbi.1006616
Coherent chaos in a recurrent neural network with structured connectivity
PLOS Computational Biology: published December 13, 2018 | https://doi.org/10.1371/journal.pcbi.1006309
Full-Length Envelope Analyzer (FLEA): A tool for longitudinal analysis of viral amplicons
PLOS Computational Biology: published December 13, 2018 | https://doi.org/10.1371/journal.pcbi.1006498
G-quadruplex forming sequences in the genome of all known human viruses: A comprehensive guide
PLOS Computational Biology: published December 13, 2018 | https://doi.org/10.1371/journal.pcbi.1006675
Prediction of antibiotic resistance in Escherichia coli from large-scale pan-genome data
PLOS Computational Biology: published December 14, 2018 | https://doi.org/10.1371/journal.pcbi.1006258
Multiscale computational model of Achilles tendon wound healing: Untangling the effects of repair and loading
PLOS Computational Biology: published December 14, 2018 | https://doi.org/10.1371/journal.pcbi.1006652
A graph-based evidence synthesis approach to detecting outbreak clusters: An application to dog rabies
PLOS Computational Biology: published December 17, 2018 | https://doi.org/10.1371/journal.pcbi.1006554
Bayesian inference of protein conformational ensembles from limited structural data
PLOS Computational Biology: published December 17, 2018 | https://doi.org/10.1371/journal.pcbi.1006641
Determinants of drug-target interactions at the single cell level
PLOS Computational Biology: published December 20, 2018 | https://doi.org/10.1371/journal.pcbi.1006601
Dynamical anchoring of distant arrhythmia sources by fibrotic regions via restructuring of the activation pattern
PLOS Computational Biology: published December 20, 2018 | https://doi.org/10.1371/journal.pcbi.1006637
Movement and conformity interact to establish local behavioural traditions in animal populations
PLOS Computational Biology: published December 20, 2018 | https://doi.org/10.1371/journal.pcbi.1006647
Conventional analysis of trial-by-trial adaptation is biased: Empirical and theoretical support using a Bayesian estimator
PLOS Computational Biology: published December 26, 2018 | https://doi.org/10.1371/journal.pcbi.1006501
On variational solutions for whole brain serial-section histology using a Sobolev prior in the computational anatomy random orbit model
PLOS Computational Biology: published December 26, 2018 | https://doi.org/10.1371/journal.pcbi.1006610
Hosts mobility and spatial spread of Rickettsia rickettsii
PLOS Computational Biology: published December 26, 2018 | https://doi.org/10.1371/journal.pcbi.1006636
A likelihood approach to testing hypotheses on the co-evolution of epigenome and genome
PLOS Computational Biology: published December 26, 2018 | https://doi.org/10.1371/journal.pcbi.1006673
Accurate calculation of side chain packing and free energy with applications to protein molecular dynamics
PLOS Computational Biology: published December 27, 2018 | https://doi.org/10.1371/journal.pcbi.1006342
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Trajectory-based training enables protein simulations with accurate folding and Boltzmann ensembles in cpu-hours
PLOS Computational Biology: published December 27, 2018 | https://doi.org/10.1371/journal.pcbi.1006578
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Active degradation of MarA controls coordination of its downstream targets
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Chirality provides a direct fitness advantage and facilitates intermixing in cellular aggregates
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Chemogenomic model identifies synergistic drug combinations robust to the pathogen microenvironment
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Change, stability, and instability in the Pavlovian guidance of behaviour from adolescence to young adulthood
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Exploring chromatin hierarchical organization via Markov State Modelling
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Scene complexity modulates degree of feedback activity during object detection in natural scenes
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