PCA visualization of LSTM hidden layer activity of an example 7-hidden-unit RNN while performing a 2-back working memory task. Visualized are the representations of different input stimuli (each represented with a different color) when in an unprioritized state in working memory. Solid gray arrow denotes the stimulus coding axis, which will rotate counterclockwise in the image plane (defined by the 1st and 2nd PCs) as the stimulus transitions to a prioritized state (indicated by the dashed gray arrow).
Image Credit: Quan Wan, Po'stl'ab, University of Wisconsin-Madison
Editorials
Advancing code sharing in the computational biology community
PLOS Computational Biology: published June 2, 2022 | https://doi.org/10.1371/journal.pcbi.1010193
Ten simple rules for succeeding as an underrepresented STEM undergraduate
PLOS Computational Biology: published June 9, 2022 | https://doi.org/10.1371/journal.pcbi.1010101
Ten simple rules for good research practice
PLOS Computational Biology: published June 23, 2022 | https://doi.org/10.1371/journal.pcbi.1010139
Education
Ten simple rules for managing communications with a large number of coauthors
PLOS Computational Biology: published June 30, 2022 | https://doi.org/10.1371/journal.pcbi.1010185
Perspectives
Ten simple rules for good leadership
PLOS Computational Biology: published June 9, 2022 | https://doi.org/10.1371/journal.pcbi.1010133
Ten simple rules for improving communication among scientists
PLOS Computational Biology: published June 23, 2022 | https://doi.org/10.1371/journal.pcbi.1010130
Research Articles
Developmental shifts in computations used to detect environmental controllability
PLOS Computational Biology: published June 1, 2022 | https://doi.org/10.1371/journal.pcbi.1010120
Improved transcriptome assembly using a hybrid of long and short reads with StringTie
PLOS Computational Biology: published June 1, 2022 | https://doi.org/10.1371/journal.pcbi.1009730
Spatial modelling for population replacement of mosquito vectors at continental scale
PLOS Computational Biology: published June 1, 2022 | https://doi.org/10.1371/journal.pcbi.1009526
Role of water-bridged interactions in metal ion coupled protein allostery
PLOS Computational Biology: published June 2, 2022 | https://doi.org/10.1371/journal.pcbi.1010195
sumSTAAR: A flexible framework for gene-based association studies using GWAS summary statistics
PLOS Computational Biology: published June 2, 2022 | https://doi.org/10.1371/journal.pcbi.1010172
fingeRNAt—A novel tool for high-throughput analysis of nucleic acid-ligand interactions
PLOS Computational Biology: published June 2, 2022 | https://doi.org/10.1371/journal.pcbi.1009783
Priority-based transformations of stimulus representation in visual working memory
PLOS Computational Biology: published June 2, 2022 | https://doi.org/10.1371/journal.pcbi.1009062
Pulmonary drug delivery and retention: A computational study to identify plausible parameters based on a coupled airway-mucus flow model
PLOS Computational Biology: published June 2, 2022 | https://doi.org/10.1371/journal.pcbi.1010143
Radical pairs may explain reactive oxygen species-mediated effects of hypomagnetic field on neurogenesis
PLOS Computational Biology: published June 2, 2022 | https://doi.org/10.1371/journal.pcbi.1010198
Learning the statistics and landscape of somatic mutation-induced insertions and deletions in antibodies
PLOS Computational Biology: published June 2, 2022 | https://doi.org/10.1371/journal.pcbi.1010167
scAmpi—A versatile pipeline for single-cell RNA-seq analysis from basics to clinics
PLOS Computational Biology: published June 3, 2022 | https://doi.org/10.1371/journal.pcbi.1010097
CellDynaMo–stochastic reaction-diffusion-dynamics model: Application to search-and-capture process of mitotic spindle assembly
PLOS Computational Biology: published June 3, 2022 | https://doi.org/10.1371/journal.pcbi.1010165
Addressing delayed case reporting in infectious disease forecast modeling
PLOS Computational Biology: published June 3, 2022 | https://doi.org/10.1371/journal.pcbi.1010115
From affinity selection to kinetic selection in Germinal Centre modelling
PLOS Computational Biology: published June 3, 2022 | https://doi.org/10.1371/journal.pcbi.1010168
A musculoskeletal finite element model of rat knee joint for evaluating cartilage biomechanics during gait
PLOS Computational Biology: published June 3, 2022 | https://doi.org/10.1371/journal.pcbi.1009398
Strain design optimization using reinforcement learning
PLOS Computational Biology: published June 3, 2022 | https://doi.org/10.1371/journal.pcbi.1010177
Quantifying the impact of ecological memory on the dynamics of interacting communities
PLOS Computational Biology: published June 3, 2022 | https://doi.org/10.1371/journal.pcbi.1009396
Induced fit with replica exchange improves protein complex structure prediction
PLOS Computational Biology: published June 3, 2022 | https://doi.org/10.1371/journal.pcbi.1010124
Fluid mechanics of the zebrafish embryonic heart trabeculation
PLOS Computational Biology: published June 6, 2022 | https://doi.org/10.1371/journal.pcbi.1010142
Characterizing collaborative transcription regulation with a graph-based deep learning approach
PLOS Computational Biology: published June 6, 2022 | https://doi.org/10.1371/journal.pcbi.1010162
Finding landmarks - An investigation of viewing behavior during spatial navigation in VR using a graph-theoretical analysis approach
PLOS Computational Biology: published June 6, 2022 | https://doi.org/10.1371/journal.pcbi.1009485
Non-monotonic effects of GABAergic synaptic inputs on neuronal firing
PLOS Computational Biology: published June 6, 2022 | https://doi.org/10.1371/journal.pcbi.1010226
Deciphering clock cell network morphology within the biological master clock, suprachiasmatic nucleus: From the perspective of circadian wave dynamics
PLOS Computational Biology: published June 6, 2022 | https://doi.org/10.1371/journal.pcbi.1010213
Nanoscale organization of ryanodine receptor distribution and phosphorylation pattern determines the dynamics of calcium sparks
PLOS Computational Biology: published June 6, 2022 | https://doi.org/10.1371/journal.pcbi.1010126
Model-checking ecological state-transition graphs
PLOS Computational Biology: published June 6, 2022 | https://doi.org/10.1371/journal.pcbi.1009657
Whole community invasions and the integration of novel ecosystems
PLOS Computational Biology: published June 7, 2022 | https://doi.org/10.1371/journal.pcbi.1010151
Identification of upstream transcription factor binding sites in orthologous genes using mixed Student’s t-test statistics
PLOS Computational Biology: published June 7, 2022 | https://doi.org/10.1371/journal.pcbi.1009773
An approximate stochastic optimal control framework to simulate nonlinear neuro-musculoskeletal models in the presence of noise
PLOS Computational Biology: published June 8, 2022 | https://doi.org/10.1371/journal.pcbi.1009338
Data-dependent visualization of biological networks in the web-browser with NDExEdit
PLOS Computational Biology: published June 8, 2022 | https://doi.org/10.1371/journal.pcbi.1010205
Annotation-free delineation of prokaryotic homology groups
PLOS Computational Biology: published June 8, 2022 | https://doi.org/10.1371/journal.pcbi.1010216
Cargo surface fluidity can reduce inter-motor mechanical interference, promote load-sharing and enhance processivity in teams of molecular motors
PLOS Computational Biology: published June 8, 2022 | https://doi.org/10.1371/journal.pcbi.1010217
Individual-based model highlights the importance of trade-offs for virus-host population dynamics and long-term co-existence
PLOS Computational Biology: published June 8, 2022 | https://doi.org/10.1371/journal.pcbi.1010228
Inference and dynamic simulation of malaria using a simple climate-driven entomological model of malaria transmission
PLOS Computational Biology: published June 9, 2022 | https://doi.org/10.1371/journal.pcbi.1010161
The lexical categorization model: A computational model of left ventral occipito-temporal cortex activation in visual word recognition
PLOS Computational Biology: published June 9, 2022 | https://doi.org/10.1371/journal.pcbi.1009995
Analysis of emergent patterns in crossing flows of pedestrians reveals an invariant of ‘stripe’ formation in human data
PLOS Computational Biology: published June 9, 2022 | https://doi.org/10.1371/journal.pcbi.1010210
Contextual cues are not unique for motor learning: Task-dependant switching of feedback controllers
PLOS Computational Biology: published June 9, 2022 | https://doi.org/10.1371/journal.pcbi.1010192
Motor response vigour and visual fixation patterns reflect subjective valuation during intertemporal choice
PLOS Computational Biology: published June 10, 2022 | https://doi.org/10.1371/journal.pcbi.1010096
SALARECON connects the Atlantic salmon genome to growth and feed efficiency
PLOS Computational Biology: published June 10, 2022 | https://doi.org/10.1371/journal.pcbi.1010194
Deriving time-concordant event cascades from gene expression data: A case study for Drug-Induced Liver Injury (DILI)
PLOS Computational Biology: published June 10, 2022 | https://doi.org/10.1371/journal.pcbi.1010148
HiCImpute: A Bayesian hierarchical model for identifying structural zeros and enhancing single cell Hi-C data
PLOS Computational Biology: published June 13, 2022 | https://doi.org/10.1371/journal.pcbi.1010129
Design and execution of a verification, validation, and uncertainty quantification plan for a numerical model of left ventricular flow after LVAD implantation
PLOS Computational Biology: published June 13, 2022 | https://doi.org/10.1371/journal.pcbi.1010141
Two types of critical cell density for mechanical elimination of abnormal cell clusters from epithelial tissue
PLOS Computational Biology: published June 13, 2022 | https://doi.org/10.1371/journal.pcbi.1010178
Differential methods for assessing sensitivity in biological models
PLOS Computational Biology: published June 13, 2022 | https://doi.org/10.1371/journal.pcbi.1009598
cytoNet: Spatiotemporal network analysis of cell communities
PLOS Computational Biology: published June 13, 2022 | https://doi.org/10.1371/journal.pcbi.1009846
Discrete modeling for integration and analysis of large-scale signaling networks
PLOS Computational Biology: published June 13, 2022 | https://doi.org/10.1371/journal.pcbi.1010175
A mechanism for punctuating equilibria during mammalian vocal development
PLOS Computational Biology: published June 13, 2022 | https://doi.org/10.1371/journal.pcbi.1010173
Modeling cell biological features of meiotic chromosome pairing to study interlock resolution
PLOS Computational Biology: published June 13, 2022 | https://doi.org/10.1371/journal.pcbi.1010252
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
PLOS Computational Biology: published June 13, 2022 | https://doi.org/10.1371/journal.pcbi.1009717
Direct reciprocity between individuals that use different strategy spaces
PLOS Computational Biology: published June 14, 2022 | https://doi.org/10.1371/journal.pcbi.1010149
Pre- and postsynaptically expressed spike-timing-dependent plasticity contribute differentially to neuronal learning
PLOS Computational Biology: published June 14, 2022 | https://doi.org/10.1371/journal.pcbi.1009409
Explainable detection of adverse drug reaction with imbalanced data distribution
PLOS Computational Biology: published June 15, 2022 | https://doi.org/10.1371/journal.pcbi.1010144
SPF: A spatial and functional data analytic approach to cell imaging data
PLOS Computational Biology: published June 15, 2022 | https://doi.org/10.1371/journal.pcbi.1009486
Orchestrated neuronal migration and cortical folding: A computational and experimental study
PLOS Computational Biology: published June 16, 2022 | https://doi.org/10.1371/journal.pcbi.1010190
Prediction and expression analysis of deleterious nonsynonymous SNPs of Arabidopsis ACD11 gene by combining computational algorithms and molecular docking approach
PLOS Computational Biology: published June 16, 2022 | https://doi.org/10.1371/journal.pcbi.1009539
A weighted constraint satisfaction approach to human goal-directed decision making
PLOS Computational Biology: published June 16, 2022 | https://doi.org/10.1371/journal.pcbi.1009553
Active inference unifies intentional and conflict-resolution imperatives of motor control
PLOS Computational Biology: published June 17, 2022 | https://doi.org/10.1371/journal.pcbi.1010095
Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues
PLOS Computational Biology: published June 17, 2022 | https://doi.org/10.1371/journal.pcbi.1010174
Size regulation of multiple organelles competing for a limiting subunit pool
PLOS Computational Biology: published June 17, 2022 | https://doi.org/10.1371/journal.pcbi.1010253
Metastable spiking networks in the replica-mean-field limit
PLOS Computational Biology: published June 17, 2022 | https://doi.org/10.1371/journal.pcbi.1010215
Systematic perturbation of an artificial neural network: A step towards quantifying causal contributions in the brain
PLOS Computational Biology: published June 17, 2022 | https://doi.org/10.1371/journal.pcbi.1010250
Efficient Bayesian inference for mechanistic modelling with high-throughput data
PLOS Computational Biology: published June 21, 2022 | https://doi.org/10.1371/journal.pcbi.1010191
Neural circuit mechanisms of hierarchical sequence learning tested on large-scale recording data
PLOS Computational Biology: published June 21, 2022 | https://doi.org/10.1371/journal.pcbi.1010214
Towards a more general understanding of the algorithmic utility of recurrent connections
PLOS Computational Biology: published June 21, 2022 | https://doi.org/10.1371/journal.pcbi.1010227
Combined computational modeling and experimental analysis integrating chemical and mechanical signals suggests possible mechanism of shoot meristem maintenance
PLOS Computational Biology: published June 21, 2022 | https://doi.org/10.1371/journal.pcbi.1010199
Error-based or target-based? A unified framework for learning in recurrent spiking networks
PLOS Computational Biology: published June 21, 2022 | https://doi.org/10.1371/journal.pcbi.1010221
SCRaPL: A Bayesian hierarchical framework for detecting technical associates in single cell multiomics data
PLOS Computational Biology: published June 21, 2022 | https://doi.org/10.1371/journal.pcbi.1010163
Sequence learning, prediction, and replay in networks of spiking neurons
PLOS Computational Biology: published June 21, 2022 | https://doi.org/10.1371/journal.pcbi.1010233
Quantifying biochemical reaction rates from static population variability within incompletely observed complex networks
PLOS Computational Biology: published June 22, 2022 | https://doi.org/10.1371/journal.pcbi.1010183
A method for the inference of cytokine interaction networks
PLOS Computational Biology: published June 22, 2022 | https://doi.org/10.1371/journal.pcbi.1010112
Systematic inference of indirect transcriptional regulation by protein kinases and phosphatases
PLOS Computational Biology: published June 22, 2022 | https://doi.org/10.1371/journal.pcbi.1009414
Topological Sholl descriptors for neuronal clustering and classification
PLOS Computational Biology: published June 22, 2022 | https://doi.org/10.1371/journal.pcbi.1010229
Tracking the contribution of inductive bias to individualised internal models
PLOS Computational Biology: published June 22, 2022 | https://doi.org/10.1371/journal.pcbi.1010182
Epidemic management and control through risk-dependent individual contact interventions
PLOS Computational Biology: published June 23, 2022 | https://doi.org/10.1371/journal.pcbi.1010171
Image-based parameter inference for epithelial mechanics
PLOS Computational Biology: published June 23, 2022 | https://doi.org/10.1371/journal.pcbi.1010209
Interpretable pairwise distillations for generative protein sequence models
PLOS Computational Biology: published June 23, 2022 | https://doi.org/10.1371/journal.pcbi.1010219
Modeling cortical synaptic effects of anesthesia and their cholinergic reversal
PLOS Computational Biology: published June 23, 2022 | https://doi.org/10.1371/journal.pcbi.1009743
LaDIVA: A neurocomputational model providing laryngeal motor control for speech acquisition and production
PLOS Computational Biology: published June 23, 2022 | https://doi.org/10.1371/journal.pcbi.1010159
Identifying control ensembles for information processing within the cortico-basal ganglia-thalamic circuit
PLOS Computational Biology: published June 23, 2022 | https://doi.org/10.1371/journal.pcbi.1010255
Evidence for influenza and RSV interaction from 10 years of enhanced surveillance in Nha Trang, Vietnam, a modelling study
PLOS Computational Biology: published June 24, 2022 | https://doi.org/10.1371/journal.pcbi.1010234
MaxHiC: A robust background correction model to identify biologically relevant chromatin interactions in Hi-C and capture Hi-C experiments
PLOS Computational Biology: published June 24, 2022 | https://doi.org/10.1371/journal.pcbi.1010241
A pipeline for the reconstruction and evaluation of context-specific human metabolic models at a large-scale
PLOS Computational Biology: published June 24, 2022 | https://doi.org/10.1371/journal.pcbi.1009294
Mathematical modeling of the microtubule detyrosination/tyrosination cycle for cell-based drug screening design
PLOS Computational Biology: published June 27, 2022 | https://doi.org/10.1371/journal.pcbi.1010236
Data-based stochastic modeling reveals sources of activity bursts in single-cell TGF-β signaling
PLOS Computational Biology: published June 27, 2022 | https://doi.org/10.1371/journal.pcbi.1010266
Inferring the effective reproductive number from deterministic and semi-deterministic compartmental models using incidence and mobility data
PLOS Computational Biology: published June 27, 2022 | https://doi.org/10.1371/journal.pcbi.1010206
An ensemble forecast system for tracking dynamics of dengue outbreaks and its validation in China
PLOS Computational Biology: published June 27, 2022 | https://doi.org/10.1371/journal.pcbi.1010218
Increasing reproducibility, robustness, and generalizability of biomarker selection from meta-analysis using Bayesian methodology
PLOS Computational Biology: published June 27, 2022 | https://doi.org/10.1371/journal.pcbi.1010260
Computational analysis of memory consolidation following inhibitory avoidance (IA) training in adult and infant rats: Critical roles of CaMKIIα and MeCP2
PLOS Computational Biology: published June 27, 2022 | https://doi.org/10.1371/journal.pcbi.1010239
Ig-VAE: Generative modeling of protein structure by direct 3D coordinate generation
PLOS Computational Biology: published June 27, 2022 | https://doi.org/10.1371/journal.pcbi.1010271
Covalent docking and molecular dynamics simulations reveal the specificity-shifting mutations Ala237Arg and Ala237Lys in TEM beta-lactamase
PLOS Computational Biology: published June 27, 2022 | https://doi.org/10.1371/journal.pcbi.1009944
Characterizing superspreading potential of infectious disease: Decomposition of individual transmissibility
PLOS Computational Biology: published June 27, 2022 | https://doi.org/10.1371/journal.pcbi.1010281
The topology of genome-scale metabolic reconstructions unravels independent modules and high network flexibility
PLOS Computational Biology: published June 27, 2022 | https://doi.org/10.1371/journal.pcbi.1010203
Discovering molecular features of intrinsically disordered regions by using evolution for contrastive learning
PLOS Computational Biology: published June 29, 2022 | https://doi.org/10.1371/journal.pcbi.1010238
Corrections
Correction: Graph neural fields: A framework for spatiotemporal dynamical models on the human connectome
PLOS Computational Biology: published June 1, 2022 | https://doi.org/10.1371/journal.pcbi.1010224
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Correction: Modeling multi-sensory feedback control of zebrafish in a flow
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Correction: A probabilistic model for the ultradian timing of REM sleep in mice
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Correction: Novel comparison of evaluation metrics for gene ontology classifiers reveals drastic performance differences
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