Overview of cell nuclei in a pluripotent zebrafish embryo, illustrating the variety of patterns formed by DNA in different cells. These patterns were mapped to multiplicative cascades, capturing DNA distribution across length scales. This mapping also relates the DNA distribution in these cells to a wider class of multi-fractal systems, including, for example, clouds in the sky or cracks in the soil. The image shows an optical section through a sphere stage embryo acquired by STimulated Emission Depletion (STED) microscopy, field of view 155-by-155 micrometers.
Image Credit: Amra Noa Lennart Hilbert, Karlsruhe Institute of Technology, Institute of Biological and Chemical System; image acquired at Karlsruhe Center for Optics and Photonics; 2021
Editorials
Ten simple rules to cultivate transdisciplinary collaboration in data science
PLOS Computational Biology: published May 13, 2021 | https://doi.org/10.1371/journal.pcbi.1008879
Ten simple rules to make your publication look better
PLOS Computational Biology: published May 20, 2021 | https://doi.org/10.1371/journal.pcbi.1008938
Ten simple rules for productive lab meetings
PLOS Computational Biology: published May 27, 2021 | https://doi.org/10.1371/journal.pcbi.1008953
Education Articles
Ten steps to investigate a cellular system with mathematical modeling
PLOS Computational Biology: published May 13, 2021 | https://doi.org/10.1371/journal.pcbi.1008921
A constructivist-based proposal for bioinformatics teaching practices during lockdown
PLOS Computational Biology: published May 13, 2021 | https://doi.org/10.1371/journal.pcbi.1008922
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Fostering accessible online education using Galaxy as an e-learning platform
PLOS Computational Biology: published May 13, 2021 | https://doi.org/10.1371/journal.pcbi.1008923
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What do Eulerian and Hamiltonian cycles have to do with genome assembly?
PLOS Computational Biology: published May 20, 2021 | https://doi.org/10.1371/journal.pcbi.1008928
Research Articles
Signaling through polymerization and degradation: Analysis and simulations of T cell activation mediated by Bcl10
PLOS Computational Biology: published May 20, 2021 | https://doi.org/10.1371/journal.pcbi.1007986
Pseudocell Tracer—A method for inferring dynamic trajectories using scRNAseq and its application to B cells undergoing immunoglobulin class switch recombination
PLOS Computational Biology: published May 3, 2021 | https://doi.org/10.1371/journal.pcbi.1008094
A first-takes-all model of centriole copy number control based on cartwheel elongation
PLOS Computational Biology: published May 10, 2021 | https://doi.org/10.1371/journal.pcbi.1008359
Activity-mediated accumulation of potassium induces a switch in firing pattern and neuronal excitability type
PLOS Computational Biology: published May 27, 2021 | https://doi.org/10.1371/journal.pcbi.1008510
Genome-scale metabolic modelling when changes in environmental conditions affect biomass composition
PLOS Computational Biology: published May 24, 2021 | https://doi.org/10.1371/journal.pcbi.1008528
Calculation of the force field required for nucleus deformation during cell migration through constrictions
PLOS Computational Biology: published May 24, 2021 | https://doi.org/10.1371/journal.pcbi.1008592
Conformational plasticity and dynamic interactions of the N-terminal domain of the chemokine receptor CXCR1
PLOS Computational Biology: published May 20, 2021 | https://doi.org/10.1371/journal.pcbi.1008593
Sensory modulation of gait characteristics in human locomotion: A neuromusculoskeletal modeling study
PLOS Computational Biology: published May 19, 2021 | https://doi.org/10.1371/journal.pcbi.1008594
What we can and what we cannot see with extracellular multielectrodes
PLOS Computational Biology: published May 14, 2021 | https://doi.org/10.1371/journal.pcbi.1008615
Patterns of selection against centrosome amplification in human cell lines
PLOS Computational Biology: published May 12, 2021 | https://doi.org/10.1371/journal.pcbi.1008765
Numerical analysis of the impact of cytoskeletal actin filament density alterations onto the diffusive vesicle-mediated cell transport
PLOS Computational Biology: published May 3, 2021 | https://doi.org/10.1371/journal.pcbi.1008784
Extracting representations of cognition across neuroimaging studies improves brain decoding
PLOS Computational Biology: published May 3, 2021 | https://doi.org/10.1371/journal.pcbi.1008795
Modelling optimal vaccination strategy for SARS-CoV-2 in the UK
PLOS Computational Biology: published May 6, 2021 | https://doi.org/10.1371/journal.pcbi.1008849
Hierarchical semantic composition of biosimulation models using bond graphs
PLOS Computational Biology: published May 13, 2021 | https://doi.org/10.1371/journal.pcbi.1008859
Hypoxic pulmonary vasoconstriction as a regulator of alveolar-capillary oxygen flux: A computational model of ventilation-perfusion matching
PLOS Computational Biology: published May 6, 2021 | https://doi.org/10.1371/journal.pcbi.1008861
CRIMSON: An open-source software framework for cardiovascular integrated modelling and simulation
PLOS Computational Biology: published May 10, 2021 | https://doi.org/10.1371/journal.pcbi.1008881
Leveraging eQTLs to identify individual-level tissue of interest for a complex trait
PLOS Computational Biology: published May 21, 2021 | https://doi.org/10.1371/journal.pcbi.1008915
Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions
PLOS Computational Biology: published May 4, 2021 | https://doi.org/10.1371/journal.pcbi.1008920
Incorporating the speciation process into species delimitation
PLOS Computational Biology: published May 13, 2021 | https://doi.org/10.1371/journal.pcbi.1008924
Global importance analysis: An interpretability method to quantify importance of genomic features in deep neural networks
PLOS Computational Biology: published May 13, 2021 | https://doi.org/10.1371/journal.pcbi.1008925
Red blood cell phenotyping from 3D confocal images using artificial neural networks
PLOS Computational Biology: published May 13, 2021 | https://doi.org/10.1371/journal.pcbi.1008934
Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models?
PLOS Computational Biology: published May 13, 2021 | https://doi.org/10.1371/journal.pcbi.1008936
Agent-based model provides insight into the mechanisms behind failed regeneration following volumetric muscle loss injury
PLOS Computational Biology: published May 10, 2021 | https://doi.org/10.1371/journal.pcbi.1008937
How multisite phosphorylation impacts the conformations of intrinsically disordered proteins
PLOS Computational Biology: published May 4, 2021 | https://doi.org/10.1371/journal.pcbi.1008939
Effects of incomplete inter-hospital network data on the assessment of transmission dynamics of hospital-acquired infections
PLOS Computational Biology: published May 6, 2021 | https://doi.org/10.1371/journal.pcbi.1008941
Small subpopulations of β-cells do not drive islet oscillatory [Ca2+] dynamics via gap junction communication
PLOS Computational Biology: published May 3, 2021 | https://doi.org/10.1371/journal.pcbi.1008948
Deep template-based protein structure prediction
PLOS Computational Biology: published May 3, 2021 | https://doi.org/10.1371/journal.pcbi.1008954
Computational phenotyping of brain-behavior dynamics underlying approach-avoidance conflict in major depressive disorder
PLOS Computational Biology: published May 10, 2021 | https://doi.org/10.1371/journal.pcbi.1008955
A model of dopamine and serotonin-kynurenine metabolism in cortisolemia: Implications for depression
PLOS Computational Biology: published May 10, 2021 | https://doi.org/10.1371/journal.pcbi.1008956
On the effect of phylogenetic correlations in coevolution-based contact prediction in proteins
PLOS Computational Biology: published May 24, 2021 | https://doi.org/10.1371/journal.pcbi.1008957
Balanced networks under spike-time dependent plasticity
PLOS Computational Biology: published May 12, 2021 | https://doi.org/10.1371/journal.pcbi.1008958
Estimating direct and spill-over impacts of political elections on COVID-19 transmission using synthetic control methods
PLOS Computational Biology: published May 27, 2021 | https://doi.org/10.1371/journal.pcbi.1008959
Model guided trait-specific co-expression network estimation as a new perspective for identifying molecular interactions and pathways
PLOS Computational Biology: published May 3, 2021 | https://doi.org/10.1371/journal.pcbi.1008960
Modeling historic incidence trends implies early field cancerization in esophageal squamous cell carcinoma
PLOS Computational Biology: published May 3, 2021 | https://doi.org/10.1371/journal.pcbi.1008961
Performance assessment of sample-specific network control methods for bulk and single-cell biological data analysis
PLOS Computational Biology: published May 6, 2021 | https://doi.org/10.1371/journal.pcbi.1008962
Cortical propagation tracks functional recovery after stroke
PLOS Computational Biology: published May 17, 2021 | https://doi.org/10.1371/journal.pcbi.1008963
Maximally efficient prediction in the early fly visual system may support evasive flight maneuvers
PLOS Computational Biology: published May 20, 2021 | https://doi.org/10.1371/journal.pcbi.1008965
Antibody Watch: Text mining antibody specificity from the literature
PLOS Computational Biology: published May 27, 2021 | https://doi.org/10.1371/journal.pcbi.1008967
Sequence learning recodes cortical representations instead of strengthening initial ones
PLOS Computational Biology: published May 24, 2021 | https://doi.org/10.1371/journal.pcbi.1008969
Mathematical modeling of multiple pathways in colorectal carcinogenesis using dynamical systems with Kronecker structure
PLOS Computational Biology: published May 18, 2021 | https://doi.org/10.1371/journal.pcbi.1008970
A method for achieving complete microbial genomes and improving bins from metagenomics data
PLOS Computational Biology: published May 7, 2021 | https://doi.org/10.1371/journal.pcbi.1008972
Active head rolls enhance sonar-based auditory localization performance
PLOS Computational Biology: published May 10, 2021 | https://doi.org/10.1371/journal.pcbi.1008973
The hierarchical packing of euchromatin domains can be described as multiplicative cascades
PLOS Computational Biology: published May 5, 2021 | https://doi.org/10.1371/journal.pcbi.1008974
Modelling 3D saccade generation by feedforward optimal control
PLOS Computational Biology: published May 24, 2021 | https://doi.org/10.1371/journal.pcbi.1008975
MetaGSCA: A tool for meta-analysis of gene set differential coexpression
PLOS Computational Biology: published May 4, 2021 | https://doi.org/10.1371/journal.pcbi.1008976
Swarm: A federated cloud framework for large-scale variant analysis
PLOS Computational Biology: published May 12, 2021 | https://doi.org/10.1371/journal.pcbi.1008977
scHiCTools: A computational toolbox for analyzing single-cell Hi-C data
PLOS Computational Biology: published May 18, 2021 | https://doi.org/10.1371/journal.pcbi.1008978
VCF2CAPS–A high-throughput CAPS marker design from VCF files and its test-use on a genotyping-by-sequencing (GBS) dataset
PLOS Computational Biology: published May 20, 2021 | https://doi.org/10.1371/journal.pcbi.1008980
Predicting mean ribosome load for 5’UTR of any length using deep learning
PLOS Computational Biology: published May 10, 2021 | https://doi.org/10.1371/journal.pcbi.1008982
Elucidation of trophic interactions in an unusual single-cell nitrogen-fixing symbiosis using metabolic modeling
PLOS Computational Biology: published May 7, 2021 | https://doi.org/10.1371/journal.pcbi.1008983
Global disruption in excitation-inhibition balance can cause localized network dysfunction and Schizophrenia-like context-integration deficits
PLOS Computational Biology: published May 25, 2021 | https://doi.org/10.1371/journal.pcbi.1008985
Targeted modification of the Per2 clock gene alters circadian function in mPer2luciferase (mPer2Luc) mice
PLOS Computational Biology: published May 28, 2021 | https://doi.org/10.1371/journal.pcbi.1008987
Molecular dynamics shows complex interplay and long-range effects of post-translational modifications in yeast protein interactions
PLOS Computational Biology: published May 12, 2021 | https://doi.org/10.1371/journal.pcbi.1008988
Finding recurrent RNA structural networks with fast maximal common subgraphs of edge-colored graphs
PLOS Computational Biology: published May 28, 2021 | https://doi.org/10.1371/journal.pcbi.1008990
Robust switches in thalamic network activity require a timescale separation between sodium and T-type calcium channel activations
PLOS Computational Biology: published May 18, 2021 | https://doi.org/10.1371/journal.pcbi.1008997
PRER: A patient representation with pairwise relative expression of proteins on biological networks
PLOS Computational Biology: published May 26, 2021 | https://doi.org/10.1371/journal.pcbi.1008998
Real-time single-cell characterization of the eukaryotic transcription cycle reveals correlations between RNA initiation, elongation, and cleavage
PLOS Computational Biology: published May 18, 2021 | https://doi.org/10.1371/journal.pcbi.1008999
NMDA receptor inhibition increases, synchronizes, and stabilizes the collective pancreatic beta cell activity: Insights through multilayer network analysis
PLOS Computational Biology: published May 11, 2021 | https://doi.org/10.1371/journal.pcbi.1009002
Effects of subclinical depression on prefrontal–striatal model-based and model-free learning
PLOS Computational Biology: published May 14, 2021 | https://doi.org/10.1371/journal.pcbi.1009003
Secondary indoor air pollution and passive smoking associated with cannabis smoking using electric cigarette device–demonstrative in silico study
PLOS Computational Biology: published May 13, 2021 | https://doi.org/10.1371/journal.pcbi.1009004
The gradient clusteron: A model neuron that learns to solve classification tasks via dendritic nonlinearities, structural plasticity, and gradient descent
PLOS Computational Biology: published May 24, 2021 | https://doi.org/10.1371/journal.pcbi.1009015
MiMeNet: Exploring microbiome-metabolome relationships using neural networks
PLOS Computational Biology: published May 17, 2021 | https://doi.org/10.1371/journal.pcbi.1009021
Mechanistic model of nutrient uptake explains dichotomy between marine oligotrophic and copiotrophic bacteria
PLOS Computational Biology: published May 19, 2021 | https://doi.org/10.1371/journal.pcbi.1009023
Evaluation of residue-residue contact prediction methods: From retrospective to prospective
PLOS Computational Biology: published May 24, 2021 | https://doi.org/10.1371/journal.pcbi.1009027
G2S3: A gene graph-based imputation method for single-cell RNA sequencing data
PLOS Computational Biology: published May 18, 2021 | https://doi.org/10.1371/journal.pcbi.1009029
MGDrivE 2: A simulation framework for gene drive systems incorporating seasonality and epidemiological dynamics
PLOS Computational Biology: published May 21, 2021 | https://doi.org/10.1371/journal.pcbi.1009030
A reaction-diffusion network model predicts a dual role of Cactus/IκB to regulate Dorsal/NFκB nuclear translocation in Drosophila
PLOS Computational Biology: published May 27, 2021 | https://doi.org/10.1371/journal.pcbi.1009040
A deep learning algorithm for 3D cell detection in whole mouse brain image datasets
PLOS Computational Biology: published May 28, 2021 | https://doi.org/10.1371/journal.pcbi.1009074
Corrections
Correction: PPM-Decay: A computational model of auditory prediction with memory decay
PLOS Computational Biology: published May 26, 2021 | https://doi.org/10.1371/journal.pcbi.1008995
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Correction: Critical role of deadenylation in regulating poly(A) rhythms and circadian gene expression
PLOS Computational Biology: published May 26, 2021 | https://doi.org/10.1371/journal.pcbi.1009065