Subject: PLOS Computational Biology Volume 15(9) September 2019 Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: 8bit

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New Articles in PLOS Computational Biology

PUBLISHED: September 01, 2019 to September 30, 2019

Editorial

Ten simple rules to create biological network figures for communication

Perspectives

Bioinformatics in Jordan: Status, challenges, and future directions

Perspective: Dimensions of the scientific method

Education

Ten simple rules for helping newcomers become contributors to open projects

Research Articles

The FACTS model of speech motor control: Fusing state estimation and task-based control

Benchmarking network propagation methods for disease gene identification

Learning unsupervised feature representations for single cell microscopy images with paired cell inpainting

Executable pathway analysis using ensemble discrete-state modeling for large-scale data

Estimating information in time-varying signals

Deconvolving multiplexed protease signatures with substrate reduction and activity clustering

Evaluation of parameters affecting performance and reliability of machine learning-based antibiotic susceptibility testing from whole genome sequencing data

Integrating thermodynamic and sequence contexts improves protein-RNA binding prediction

3D computational models explain muscle activation patterns and energetic functions of internal structures in fish swimming

Cost-benefit trade-offs in decision-making and learning

p13CMFA: Parsimonious 13C metabolic flux analysis

Learning the structure of the world: The adaptive nature of state-space and action representations in multi-stage decision-making

MHC binding affects the dynamics of different T-cell receptors in different ways

Prepaid parameter estimation without likelihoods

Designing combination therapies with modeling chaperoned machine learning

Systematically understanding the immunity leading to CRPC progression

From Escherichia coli mutant 13C labeling data to a core kinetic model: A kinetic model parameterization pipeline

Role of dynamic nuclear deformation on genomic architecture reorganization

Network trade-offs and homeostasis in Arabidopsis shoot architectures

Generation of Binary Tree-Child phylogenetic networks

Predicting gene expression in the human malaria parasite Plasmodium falciparum using histone modification, nucleosome positioning, and 3D localization features

Long-term dynamics of measles in London: Titrating the impact of wars, the 1918 pandemic, and vaccination

Characterizing and dissociating multiple time-varying modulatory computations influencing neuronal activity

Weak coupling between intracellular feedback loops explains dissociation of clock gene dynamics

Loop analysis of blood pressure/volume homeostasis

EMULSION: Transparent and flexible multiscale stochastic models in human, animal and plant epidemiology

Deep attention networks reveal the rules of collective motion in zebrafish

Close spatial arrangement of mutants favors and disfavors fixation

A flexible and generalizable model of online latent-state learning

Optimizing spatial allocation of seasonal influenza vaccine under temporal constraints

Deep learning as a tool for neural data analysis: Speech classification and cross-frequency coupling in human sensorimotor cortex

Fast and near-optimal monitoring for healthcare acquired infection outbreaks

Frequency spectrum of chemical fluctuation: A probe of reaction mechanism and dynamics

3D spatial organization and network-guided comparison of mutation profiles in Glioblastoma reveals similarities across patients

Unified feature association networks through integration of transcriptomic and proteomic data

Complex genetic and epigenetic regulation deviates gene expression from a unifying global transcriptional program

Predicting gene regulatory interactions based on spatial gene expression data and deep learning

Multi-Cell ECM compaction is predictable via superposition of nonlinear cell dynamics linearized in augmented state space

Why do G-quadruplexes dimerize through the 5'-ends? Driving forces for G4 DNA dimerization examined in atomic detail

Quantifying model evidence for yellow fever transmission routes in Africa

A scale-free analysis of the HIV-1 genome demonstrates multiple conserved regions of structural and functional importance

Dimensions of control for subthreshold oscillations and spontaneous firing in dopamine neurons

Time scales and wave formation in non-linear spatial public goods games

Heterogeneous responses to low level death receptor activation are explained by random molecular assembly of the Caspase-8 activation platform

On measuring selection in cancer from subclonal mutation frequencies

Invariant neural responses for sensory categories revealed by the time-varying information for communication calls

Telescope: Characterization of the retrotranscriptome by accurate estimation of transposable element expression

LOTUS: A single- and multitask machine learning algorithm for the prediction of cancer driver genes

Computational modelling predicts substantial carbon assimilation gains for C3 plants with a single-celled C4 biochemical pump

Corrections

Correction: Minimal model of interictal and ictal discharges "Epileptor-2"

Correction: Comprehensively benchmarking applications for detecting copy number variation

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