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New Articles in PLOS Computational Biology

PUBLISHED: June 01, 2022 to June 30, 2022

Editorials

Advancing code sharing in the computational biology community

Ten simple rules for succeeding as an underrepresented STEM undergraduate

Ten simple rules for good research practice

Perspectives

Ten simple rules for good leadership

Ten simple rules for improving communication among scientists

Education

Ten simple rules for managing communications with a large number of coauthors

Research Articles

Developmental shifts in computations used to detect environmental controllability

Spatial modelling for population replacement of mosquito vectors at continental scale

Improved transcriptome assembly using a hybrid of long and short reads with StringTie

Role of water-bridged interactions in metal ion coupled protein allostery

Learning the statistics and landscape of somatic mutation-induced insertions and deletions in antibodies

Pulmonary drug delivery and retention: A computational study to identify plausible parameters based on a coupled airway-mucus flow model

Radical pairs may explain reactive oxygen species-mediated effects of hypomagnetic field on neurogenesis

fingeRNAt'A novel tool for high-throughput analysis of nucleic acid-ligand interactions

Priority-based transformations of stimulus representation in visual working memory

sumSTAAR: A flexible framework for gene-based association studies using GWAS summary statistics

A musculoskeletal finite element model of rat knee joint for evaluating cartilage biomechanics during gait

Strain design optimization using reinforcement learning

CellDynaMo'stochastic reaction-diffusion-dynamics model: Application to search-and-capture process of mitotic spindle assembly

scAmpi'A versatile pipeline for single-cell RNA-seq analysis from basics to clinics

Addressing delayed case reporting in infectious disease forecast modeling

From affinity selection to kinetic selection in Germinal Centre modelling

Quantifying the impact of ecological memory on the dynamics of interacting communities

Induced fit with replica exchange improves protein complex structure prediction

Finding landmarks - An investigation of viewing behavior during spatial navigation in VR using a graph-theoretical analysis approach

Nanoscale organization of ryanodine receptor distribution and phosphorylation pattern determines the dynamics of calcium sparks

Deciphering clock cell network morphology within the biological master clock, suprachiasmatic nucleus: From the perspective of circadian wave dynamics

Model-checking ecological state-transition graphs

Non-monotonic effects of GABAergic synaptic inputs on neuronal firing

Characterizing collaborative transcription regulation with a graph-based deep learning approach

Fluid mechanics of the zebrafish embryonic heart trabeculation

Whole community invasions and the integration of novel ecosystems

Identification of upstream transcription factor binding sites in orthologous genes using mixed Student's t-test statistics

An approximate stochastic optimal control framework to simulate nonlinear neuro-musculoskeletal models in the presence of noise

Data-dependent visualization of biological networks in the web-browser with NDExEdit

Cargo surface fluidity can reduce inter-motor mechanical interference, promote load-sharing and enhance processivity in teams of molecular motors

Annotation-free delineation of prokaryotic homology groups

Individual-based model highlights the importance of trade-offs for virus-host population dynamics and long-term co-existence

Inference and dynamic simulation of malaria using a simple climate-driven entomological model of malaria transmission

Contextual cues are not unique for motor learning: Task-dependant switching of feedback controllers

The lexical categorization model: A computational model of left ventral occipito-temporal cortex activation in visual word recognition

Analysis of emergent patterns in crossing flows of pedestrians reveals an invariant of stripe' formation in human data

Motor response vigour and visual fixation patterns reflect subjective valuation during intertemporal choice

Deriving time-concordant event cascades from gene expression data: A case study for Drug-Induced Liver Injury (DILI)

SALARECON connects the Atlantic salmon genome to growth and feed efficiency

cytoNet: Spatiotemporal network analysis of cell communities

Computational simulations and Ca2+ imaging reveal that slow synaptic depolarizations (slow EPSPs) inhibit fast EPSP evoked action potentials for most of their time course in enteric neurons

Discrete modeling for integration and analysis of large-scale signaling networks

Two types of critical cell density for mechanical elimination of abnormal cell clusters from epithelial tissue

HiCImpute: A Bayesian hierarchical model for identifying structural zeros and enhancing single cell Hi-C data

Design and execution of a verification, validation, and uncertainty quantification plan for a numerical model of left ventricular flow after LVAD implantation

A mechanism for punctuating equilibria during mammalian vocal development

Differential methods for assessing sensitivity in biological models

Modeling cell biological features of meiotic chromosome pairing to study interlock resolution

Direct reciprocity between individuals that use different strategy spaces

Pre- and postsynaptically expressed spike-timing-dependent plasticity contribute differentially to neuronal learning

SPF: A spatial and functional data analytic approach to cell imaging data

Explainable detection of adverse drug reaction with imbalanced data distribution

A weighted constraint satisfaction approach to human goal-directed decision making

Orchestrated neuronal migration and cortical folding: A computational and experimental study

Prediction and expression analysis of deleterious nonsynonymous SNPs of Arabidopsis ACD11 gene by combining computational algorithms and molecular docking approach

Active inference unifies intentional and conflict-resolution imperatives of motor control

Size regulation of multiple organelles competing for a limiting subunit pool

Systematic perturbation of an artificial neural network: A step towards quantifying causal contributions in the brain

Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues

Metastable spiking networks in the replica-mean-field limit

SCRaPL: A Bayesian hierarchical framework for detecting technical associates in single cell multiomics data

Error-based or target-based? A unified framework for learning in recurrent spiking networks

Combined computational modeling and experimental analysis integrating chemical and mechanical signals suggests possible mechanism of shoot meristem maintenance

Neural circuit mechanisms of hierarchical sequence learning tested on large-scale recording data

Towards a more general understanding of the algorithmic utility of recurrent connections

Efficient Bayesian inference for mechanistic modelling with high-throughput data

Sequence learning, prediction, and replay in networks of spiking neurons

Quantifying biochemical reaction rates from static population variability within incompletely observed complex networks

A method for the inference of cytokine interaction networks

Systematic inference of indirect transcriptional regulation by protein kinases and phosphatases

Topological Sholl descriptors for neuronal clustering and classification

Tracking the contribution of inductive bias to individualised internal models

Epidemic management and control through risk-dependent individual contact interventions

Modeling cortical synaptic effects of anesthesia and their cholinergic reversal

Interpretable pairwise distillations for generative protein sequence models

Image-based parameter inference for epithelial mechanics

Identifying control ensembles for information processing within the cortico-basal ganglia-thalamic circuit

LaDIVA: A neurocomputational model providing laryngeal motor control for speech acquisition and production

A pipeline for the reconstruction and evaluation of context-specific human metabolic models at a large-scale

Evidence for influenza and RSV interaction from 10 years of enhanced surveillance in Nha Trang, Vietnam, a modelling study

MaxHiC: A robust background correction model to identify biologically relevant chromatin interactions in Hi-C and capture Hi-C experiments

Data-based stochastic modeling reveals sources of activity bursts in single-cell TGF-beta signaling

Increasing reproducibility, robustness, and generalizability of biomarker selection from meta-analysis using Bayesian methodology

Inferring the effective reproductive number from deterministic and semi-deterministic compartmental models using incidence and mobility data

An ensemble forecast system for tracking dynamics of dengue outbreaks and its validation in China

Mathematical modeling of the microtubule detyrosination/tyrosination cycle for cell-based drug screening design

The topology of genome-scale metabolic reconstructions unravels independent modules and high network flexibility

Computational analysis of memory consolidation following inhibitory avoidance (IA) training in adult and infant rats: Critical roles of CaMKIIalpha and MeCP2

Ig-VAE: Generative modeling of protein structure by direct 3D coordinate generation

Characterizing superspreading potential of infectious disease: Decomposition of individual transmissibility

Covalent docking and molecular dynamics simulations reveal the specificity-shifting mutations Ala237Arg and Ala237Lys in TEM beta-lactamase

Discovering molecular features of intrinsically disordered regions by using evolution for contrastive learning

Corrections

Correction: Graph neural fields: A framework for spatiotemporal dynamical models on the human connectome

Correction: Modeling multi-sensory feedback control of zebrafish in a flow

Correction: A probabilistic model for the ultradian timing of REM sleep in mice

Correction: Stability of spontaneous, correlated activity in mouse auditory cortex

Correction: Novel comparison of evaluation metrics for gene ontology classifiers reveals drastic performance differences

Correction: Stress generation, relaxation and size control in confined tumor growth

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