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New Articles in PLOS Computational Biology

PUBLISHED: January 01, 2017 to January 31, 2017

Editorials

Ten Simple Rules for Developing Usable Software in Computational Biology

Computing the Dynamic Supramolecular Structural Proteome

Ten Simple Rules to Enable Multi-site Collaborations through Data Sharing

Perspective

Efficient Switches in Biology and Computer Science

Review

Pain: A Statistical Account

Research Articles

Suboptimal Criterion Learning in Static and Dynamic Environments

Transcriptional and Post-Transcriptional Regulation of Thrombospondin-1 Expression: A Computational Model

Structure-Function Network Mapping and Its Assessment via Persistent Homology

FIJI Macro 3D ART VeSElecT: 3D Automated Reconstruction Tool for Vesicle Structures of Electron Tomograms

Functionality and Robustness of Injured Connectomic Dynamics in C. elegans: Linking Behavioral Deficits to Neural Circuit Damage

Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model

Using Chemical Reaction Kinetics to Predict Optimal Antibiotic Treatment Strategies

Customized Regulation of Diverse Stress Response Genes by the Multiple Antibiotic Resistance Activator MarA

Spikelets in Pyramidal Neurons: Action Potentials Initiated in the Axon Initial Segment That Do Not Activate the Soma

Modelling Systemic Iron Regulation during Dietary Iron Overload and Acute Inflammation: Role of Hepcidin-Independent Mechanisms

A Network Model of Local Field Potential Activity in Essential Tremor and the Impact of Deep Brain Stimulation

Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast

Spatiotemporal Feedback and Network Structure Drive and Encode Caenorhabditis elegans Locomotion

Multiple Choice Neurodynamical Model of the Uncertain Option Task

A Topological Criterion for Filtering Information in Complex Brain Networks

The Power of Malaria Vaccine Trials Using Controlled Human Malaria Infection

Could a Neuroscientist Understand a Microprocessor?

A Computational Approach for Identifying Synergistic Drug Combinations

Is the Conformational Ensemble of Alzheimer’s Aβ10-40 Peptide Force Field Dependent?

Inference of Transmission Network Structure from HIV Phylogenetic Trees

A Looping-Based Model for Quenching Repression

Computational Analysis of Residue Interaction Networks and Coevolutionary Relationships in the Hsp70 Chaperones: A Community-Hopping Model of Allosteric Regulation and Communication

A General Shear-Dependent Model for Thrombus Formation

A Likelihood Approach for Real-Time Calibration of Stochastic Compartmental Epidemic Models

A Two-Locus Model of the Evolution of Insecticide Resistance to Inform and Optimise Public Health Insecticide Deployment Strategies

Approximate Inference for Time-Varying Interactions and Macroscopic Dynamics of Neural Populations

Entropy Transfer between Residue Pairs and Allostery in Proteins: Quantifying Allosteric Communication in Ubiquitin

A New Approach to Model Pitch Perception Using Sparse Coding

Real Time Multiplicative Memory Amplification Mediated by Whole-Cell Scaling of Synaptic Response in Key Neurons

Effect of the Latent Reservoir on the Evolution of HIV at the Within- and Between-Host Levels

Identifying T Cell Receptors from High-Throughput Sequencing: Dealing with Promiscuity in TCRα and TCRβ Pairing

Contextual Refinement of Regulatory Targets Reveals Effects on Breast Cancer Prognosis of the Regulome

Complex Dynamics of Virus Spread from Low Infection Multiplicities: Implications for the Spread of Oncolytic Viruses

Psychotic Experiences and Overhasty Inferences Are Related to Maladaptive Learning

Modeling an Excitable Biosynthetic Tissue with Inherent Variability for Paired Computational-Experimental Studies

High Affinity vs. Native Fibronectin in the Modulation of αvβ3 Integrin Conformational Dynamics: Insights from Computational Analyses and Implications for Molecular Design

Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks

Inferring the Chemotactic Strategy of P. putida and E. coli Using Modified Kramers-Moyal Coefficients

Morphological Transformation and Force Generation of Active Cytoskeletal Networks

Computational Account of Spontaneous Activity as a Signature of Predictive Coding

Quantitative Comparison of Abundance Structures of Generalized Communities: From B-Cell Receptor Repertoires to Microbiomes

Gene Expression Noise Enhances Robust Organization of the Early Mammalian Blastocyst

Optogenetic Stimulation Shifts the Excitability of Cerebral Cortex from Type I to Type II: Oscillation Onset and Wave Propagation

Genome-Wide Association between Transcription Factor Expression and Chromatin Accessibility Reveals Regulators of Chromatin Accessibility

The Flash-Lag Effect as a Motion-Based Predictive Shift

The Potential Role of Direct and Indirect Contacts on Infection Spread in Dairy Farm Networks

A Validated Multiscale In-Silico Model for Mechano-sensitive Tumour Angiogenesis and Growth

The language of geometry: Fast comprehension of geometrical primitives and rules in human adults and preschoolers

THE REAL McCOIL: A method for the concurrent estimation of the complexity of infection and SNP allele frequency for malaria parasites

Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks

Identification of Entry Factors Involved in Hepatitis C Virus Infection Based on Host-Mimicking Short Linear Motifs

An Asymmetrically Balanced Organization of Kinases versus Phosphatases across Eukaryotes Determines Their Distinct Impacts

Cell Sorting and Noise-Induced Cell Plasticity Coordinate to Sharpen Boundaries between Gene Expression Domains

Optimal Sequential Immunization Can Focus Antibody Responses against Diversity Loss and Distraction

Exploring the inhibitory effect of membrane tension on cell polarization

Memory replay in balanced recurrent networks

Binding of DNA-bending non-histone proteins destabilizes regular 30-nm chromatin structure

Effect of mutation mechanisms on variant composition and distribution in Caenorhabditis elegans

Use of chiral cell shape to ensure highly directional swimming in trypanosomes

Iterative sure independence screening EM-Bayesian LASSO algorithm for multi-locus genome-wide association studies

Coevolutionary dynamics of phenotypic diversity and contingent cooperation

The missing link: Predicting connectomes from noisy and partially observed tract tracing data

Self-organised criticality in the evolution of a thermodynamic model of rodent thermoregulatory huddling

Corrections

Correction: Large-Scale Off-Target Identification Using Fast and Accurate Dual Regularized One-Class Collaborative Filtering and Its Application to Drug Repurposing

Correction: A Stochastic Model of the Yeast Cell Cycle Reveals Roles for Feedback Regulation in Limiting Cellular Variability

Correction: Suppressed Expression of T-Box Transcription Factors Is Involved in Senescence in Chronic Obstructive Pulmonary Disease

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