Subject: PLOS Computational Biology Volume 14(12) December 2018 Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: 8bit

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New Articles in PLOS Computational Biology

PUBLISHED: December 01, 2018 to December 31, 2018

Editorials

Ten simple rules for documenting scientific software

One thousand simple rules

Perspectives

Local epigenomic state cannot discriminate interacting and non-interacting enhancer'promoter pairs with high accuracy

Harnessing formal concepts of biological mechanism to analyze human disease

Education

Eleven quick tips to build a usable REST API for life sciences

Ten quick tips for sharing open genomic data

Research Articles

A stochastic framework to model axon interactions within growing neuronal populations

TAMMiCol: Tool for analysis of the morphology of microbial colonies

Detection and analysis of spatiotemporal patterns in brain activity

Chain organization of human interphase chromosome determines the spatiotemporal dynamics of chromatin loci

Performance of convolutional neural networks for identification of bacteria in 3D microscopy datasets

A comprehensive ensemble model for comparing the allosteric effect of ordered and disordered proteins

Regulation of harvester ant foraging as a closed-loop excitable system

The empirical characteristics of human pattern vision defy theoretically-driven expectations

Insights on the impact of mitochondrial organisation on bioenergetics in high-resolution computational models of cardiac cell architecture

Bayesian adaptive dual control of deep brain stimulation in a computational model of Parkinson's disease

Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study

Function and energy consumption constrain neuronal biophysics in a canonical computation: Coincidence detection

PathFX provides mechanistic insights into drug efficacy and safety for regulatory review and therapeutic development

Multi-scale computational study of the Warburg effect, reverse Warburg effect and glutamine addiction in solid tumors

Projecting social contact matrices to different demographic structures

Predicting protein targets for drug-like compounds using transcriptomics

Deep convolutional networks do not classify based on global object shape

Odorant mixtures elicit less variable and faster responses than pure odorants

Coherency of circadian rhythms in the SCN is governed by the interplay of two coupling factors

Enzymatic and non-enzymatic pathways of kynurenines' dimerization: the molecular factors for oxidative stress development

Identifying (un)controllable dynamical behavior in complex networks

SFPEL-LPI: Sequence-based feature projection ensemble learning for predicting LncRNA-protein interactions

PremPDI estimates and interprets the effects of missense mutations on protein-DNA interactions

Full-Length Envelope Analyzer (FLEA): A tool for longitudinal analysis of viral amplicons

Coherent chaos in a recurrent neural network with structured connectivity

G-quadruplex forming sequences in the genome of all known human viruses: A comprehensive guide

Prediction of antibiotic resistance in Escherichia coli from large-scale pan-genome data

Multiscale computational model of Achilles tendon wound healing: Untangling the effects of repair and loading

Bayesian inference of protein conformational ensembles from limited structural data

A graph-based evidence synthesis approach to detecting outbreak clusters: An application to dog rabies

Dynamical anchoring of distant arrhythmia sources by fibrotic regions via restructuring of the activation pattern

Determinants of drug-target interactions at the single cell level

Movement and conformity interact to establish local behavioural traditions in animal populations

Conventional analysis of trial-by-trial adaptation is biased: Empirical and theoretical support using a Bayesian estimator

On variational solutions for whole brain serial-section histology using a Sobolev prior in the computational anatomy random orbit model

A likelihood approach to testing hypotheses on the co-evolution of epigenome and genome

Hosts mobility and spatial spread of Rickettsia rickettsii

Active degradation of MarA controls coordination of its downstream targets

Trajectory-based training enables protein simulations with accurate folding and Boltzmann ensembles in cpu-hours

Chirality provides a direct fitness advantage and facilitates intermixing in cellular aggregates

Accurate calculation of side chain packing and free energy with applications to protein molecular dynamics

Statistical investigations of protein residue direct couplings

Scene complexity modulates degree of feedback activity during object detection in natural scenes

Chemogenomic model identifies synergistic drug combinations robust to the pathogen microenvironment

Change, stability, and instability in the Pavlovian guidance of behaviour from adolescence to young adulthood

Exploring chromatin hierarchical organization via Markov State Modelling

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