A mosaic image of an anopheles mosquito was created by representing each pixel of the template with a deep ultraviolet microscopy image of an individual red blood cell. The red blood cell images were drawn from a pool containing healthy cells and P.falciparum-infected cells. Red blood cell images were adjusted in their mean intensity values to reflect template pixel intensities. Lebel et al 2021
Image Credit: The template anopheles mosquito image was modified from a BioRender.com icon (Anopheles mosquito, 2020). The mosaic was created using custom software written by Paul Lebel and is being shared under the creative commons license (CC BY 4.0).
Editorials
Ten simple rules for teaching applied programming in an authentic and immersive online environment
PLOS Computational Biology: published August 5, 2021 | https://doi.org/10.1371/journal.pcbi.1009184
Ten simple rules for organizing a bioinformatics training course in low- and middle-income countries
PLOS Computational Biology: published August 19, 2021 | https://doi.org/10.1371/journal.pcbi.1009218
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Ten simple rules for creating reusable pathway models for computational analysis and visualization
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Ten simple rules for aspiring graduate students
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Ten simple rules for Global North researchers to stop perpetuating helicopter research in the Global South
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Education
Fifteen quick tips for success with HPC, i.e., responsibly BASHing that Linux cluster
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Review
Review of machine learning methods for RNA secondary structure prediction
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Research Articles
Large-scale simulations of biological cell sorting driven by differential adhesion follow diffusion-limited domain coalescence regime
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Circadian rhythm shows potential for mRNA efficiency and self-organized division of labor in multinucleate cells
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PPIDomainMiner: Inferring domain-domain interactions from multiple sources of protein-protein interactions
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Using machine learning and big data to explore the drug resistance landscape in HIV
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Critical behaviour of the stochastic Wilson-Cowan model
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High-throughput Interpretation of Killer-cell Immunoglobulin-like Receptor Short-read Sequencing Data with PING
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Identification of structures for ion channel kinetic models
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A strategy for mapping biophysical to abstract neuronal network models applied to primary visual cortex
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A modular approach for modeling the cell cycle based on functional response curves
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Integration of a physiologically-based pharmacokinetic model with a whole-body, organ-resolved genome-scale model for characterization of ethanol and acetaldehyde metabolism
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Trip duration drives shift in travel network structure with implications for the predictability of spatial disease spread
PLOS Computational Biology: published August 10, 2021 | https://doi.org/10.1371/journal.pcbi.1009127
An uncertainty-based model of the effects of fixation on choice
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Wing structure and neural encoding jointly determine sensing strategies in insect flight
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Dendritic normalisation improves learning in sparsely connected artificial neural networks
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Models of heterogeneous dopamine signaling in an insect learning and memory center
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A multi-approach and multi-scale platform to model CD4+ T cells responding to infections
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The unbiased estimation of the fraction of variance explained by a model
PLOS Computational Biology: published August 4, 2021 | https://doi.org/10.1371/journal.pcbi.1009212
Topology-preserving smoothing of retinotopic maps
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Evaluation and comparison of multi-omics data integration methods for cancer subtyping
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Relating simulation studies by provenance—Developing a family of Wnt signaling models
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A computational method for identifying an optimal combination of existing drugs to repair the action potentials of SQT1 ventricular myocytes
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Using mobility data in the design of optimal lockdown strategies for the COVID-19 pandemic
PLOS Computational Biology: published August 12, 2021 | https://doi.org/10.1371/journal.pcbi.1009236
Comparative mapping of crawling-cell morphodynamics in deep learning-based feature space
PLOS Computational Biology: published August 12, 2021 | https://doi.org/10.1371/journal.pcbi.1009237
Improving the understanding of cytoneme-mediated morphogen gradients by in silico modeling
PLOS Computational Biology: published August 3, 2021 | https://doi.org/10.1371/journal.pcbi.1009245
A novel artificial intelligence-based approach for identification of deoxynucleotide aptamers
PLOS Computational Biology: published August 3, 2021 | https://doi.org/10.1371/journal.pcbi.1009247
IUSMMT: Survival mediation analysis of gene expression with multiple DNA methylation exposures and its application to cancers of TCGA
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Mathematical framework for place coding in the auditory system
PLOS Computational Biology: published August 2, 2021 | https://doi.org/10.1371/journal.pcbi.1009251
A large-scale brain network mechanism for increased seizure propensity in Alzheimer’s disease
PLOS Computational Biology: published August 11, 2021 | https://doi.org/10.1371/journal.pcbi.1009252
Using de novo assembly to identify structural variation of eight complex immune system gene regions
PLOS Computational Biology: published August 3, 2021 | https://doi.org/10.1371/journal.pcbi.1009254
Computational identification and experimental characterization of preferred downstream positions in human core promoters
PLOS Computational Biology: published August 12, 2021 | https://doi.org/10.1371/journal.pcbi.1009256
Label-free imaging and classification of live P. falciparum enables high performance parasitemia quantification without fixation or staining
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Bistability in fatty-acid oxidation resulting from substrate inhibition
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Interspike interval correlations in neuron models with adaptation and correlated noise
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A multi-objective genetic algorithm to find active modules in multiplex biological networks
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Mitigating COVID-19 outbreaks in workplaces and schools by hybrid telecommuting
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Model checking via testing for direct effects in Mendelian Randomization and transcriptome-wide association studies
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Unveiling functions of the visual cortex using task-specific deep neural networks
PLOS Computational Biology: published August 13, 2021 | https://doi.org/10.1371/journal.pcbi.1009267
Analysis of protrusion dynamics in amoeboid cell motility by means of regularized contour flows
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Validation and tuning of in situ transcriptomics image processing workflows with crowdsourced annotations
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SiGMoiD: A super-statistical generative model for binary data
PLOS Computational Biology: published August 6, 2021 | https://doi.org/10.1371/journal.pcbi.1009275
The evolutionary history of topological variations in the CPA/AT transporters
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A hidden Markov model reliably characterizes ketamine-induced spectral dynamics in macaque local field potentials and human electroencephalograms
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Optimal closed-loop deep brain stimulation using multiple independently controlled contacts
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Discovering differential genome sequence activity with interpretable and efficient deep learning
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Diffusion enables integration of heterogeneous data and user-driven learning in a desktop knowledge-base
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Deep geometric representations for modeling effects of mutations on protein-protein binding affinity
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Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants
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Elucidating relationships between P.falciparum prevalence and measures of genetic diversity with a combined genetic-epidemiological model of malaria
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Estimating the conditional probability of developing human papilloma virus related oropharyngeal cancer by combining machine learning and inverse Bayesian modelling
PLOS Computational Biology: published August 20, 2021 | https://doi.org/10.1371/journal.pcbi.1009289
miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data
PLOS Computational Biology: published August 24, 2021 | https://doi.org/10.1371/journal.pcbi.1009290
Multiscale representations of community structures in attractor neural networks
PLOS Computational Biology: published August 23, 2021 | https://doi.org/10.1371/journal.pcbi.1009296
Enhancing oscillations in intracranial electrophysiological recordings with data-driven spatial filters
PLOS Computational Biology: published August 19, 2021 | https://doi.org/10.1371/journal.pcbi.1009298
Quantifying dose-, strain-, and tissue-specific kinetics of parainfluenza virus infection
PLOS Computational Biology: published August 12, 2021 | https://doi.org/10.1371/journal.pcbi.1009299
Bayesian structural time series for biomedical sensor data: A flexible modeling framework for evaluating interventions
PLOS Computational Biology: published August 23, 2021 | https://doi.org/10.1371/journal.pcbi.1009303
ZWA: Viral genome assembly and characterization hindrances from virus-host chimeric reads; a refining approach
PLOS Computational Biology: published August 9, 2021 | https://doi.org/10.1371/journal.pcbi.1009304
The impact of local assembly rules on RNA packaging in a T = 1 satellite plant virus
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Epigenetic instability may alter cell state transitions and anticancer drug resistance
PLOS Computational Biology: published August 23, 2021 | https://doi.org/10.1371/journal.pcbi.1009307
DeepG4: A deep learning approach to predict cell-type specific active G-quadruplex regions
PLOS Computational Biology: published August 12, 2021 | https://doi.org/10.1371/journal.pcbi.1009308
A probabilistic model for the ultradian timing of REM sleep in mice
PLOS Computational Biology: published August 25, 2021 | https://doi.org/10.1371/journal.pcbi.1009316
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Targeted modulation of protein liquid–liquid phase separation by evolution of amino-acid sequence
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The role of memory in non-genetic inheritance and its impact on cancer treatment resistance
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Targeted pandemic containment through identifying local contact network bottlenecks
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AIM: A network model of attention in auditory cortex
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Corrections
Correction: Bayesian inference and comparison of stochastic transcription elongation models
PLOS Computational Biology: published August 11, 2021 | https://doi.org/10.1371/journal.pcbi.1009314
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Correction: Estimation of the dispersal distances of an aphid-borne virus in a patchy landscape
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