Representative fields of view show the trajectories of individual cells tracked from Control keratinocytes (left) and keratinocytes with enhanced PIEZO1 activity (right) during collective cell migration. Each color-coded trajectory delineates the path of an individual cell. Chen & Holt et al 2024
Image Credit: Jesse R. Holt and Medha M. Pathak
Education
Ten simple rules for leading a successful undergraduate-intensive research lab
PLOS Computational Biology: published April 11, 2024 | https://doi.org/10.1371/journal.pcbi.1011994
Research Articles
The mechanical influence of densification on epithelial architecture
PLOS Computational Biology: published April 1, 2024 | https://doi.org/10.1371/journal.pcbi.1012001
Predictive coding networks for temporal prediction
PLOS Computational Biology: published April 1, 2024 | https://doi.org/10.1371/journal.pcbi.1011183
Comparison of stochastic and deterministic models for gambiense sleeping sickness at different spatial scales: A health area analysis in the DRC
PLOS Computational Biology: published April 1, 2024 | https://doi.org/10.1371/journal.pcbi.1011993
Modelling cell shape in 3D structured environments: A quantitative comparison with experiments
PLOS Computational Biology: published April 4, 2024 | https://doi.org/10.1371/journal.pcbi.1011412
Mesoscale simulations predict the role of synergistic cerebellar plasticity during classical eyeblink conditioning
PLOS Computational Biology: published April 4, 2024 | https://doi.org/10.1371/journal.pcbi.1011277
DBDNMF: A Dual Branch Deep Neural Matrix Factorization method for drug response prediction
PLOS Computational Biology: published April 4, 2024 | https://doi.org/10.1371/journal.pcbi.1012012
A probabilistic knowledge graph for target identification
PLOS Computational Biology: published April 5, 2024 | https://doi.org/10.1371/journal.pcbi.1011945
Partial label learning for automated classification of single-cell transcriptomic profiles
PLOS Computational Biology: published April 5, 2024 | https://doi.org/10.1371/journal.pcbi.1012006
PIEZO1 regulates leader cell formation and cellular coordination during collective keratinocyte migration
PLOS Computational Biology: published April 5, 2024 | https://doi.org/10.1371/journal.pcbi.1011855
DeepDynaForecast: Phylogenetic-informed graph deep learning for epidemic transmission dynamic prediction
PLOS Computational Biology: published April 10, 2024 | https://doi.org/10.1371/journal.pcbi.1011351
Mathematical model for the role of multiple pericentromeric repeats on heterochromatin assembly
PLOS Computational Biology: published April 10, 2024 | https://doi.org/10.1371/journal.pcbi.1012027
Perturbation Variability Does Not Influence Implicit Sensorimotor Adaptation
PLOS Computational Biology: published April 10, 2024 | https://doi.org/10.1371/journal.pcbi.1011951
Benchmarking multi-ancestry prostate cancer polygenic risk scores in a real-world cohort
PLOS Computational Biology: published April 10, 2024 | https://doi.org/10.1371/journal.pcbi.1011990
Modeling single cell trajectory using forward-backward stochastic differential equations
PLOS Computational Biology: published April 15, 2024 | https://doi.org/10.1371/journal.pcbi.1012015
Dopamine encoding of novelty facilitates efficient uncertainty-driven exploration
PLOS Computational Biology: published April 16, 2024 | https://doi.org/10.1371/journal.pcbi.1011516
Gradient boosted decision trees reveal nuances of auditory discrimination behavior
PLOS Computational Biology: published April 16, 2024 | https://doi.org/10.1371/journal.pcbi.1011985
Spatio-temporal spread of artemisinin resistance in Southeast Asia
PLOS Computational Biology: published April 16, 2024 | https://doi.org/10.1371/journal.pcbi.1012017
How robust are estimates of key parameters in standard viral dynamic models?
PLOS Computational Biology: published April 16, 2024 | https://doi.org/10.1371/journal.pcbi.1011437
Network-neuron interactions underlying sensory responses of layer 5 pyramidal tract neurons in barrel cortex
PLOS Computational Biology: published April 16, 2024 | https://doi.org/10.1371/journal.pcbi.1011468
SubGE-DDI: A new prediction model for drug-drug interaction established through biomedical texts and drug-pairs knowledge subgraph enhancement
PLOS Computational Biology: published April 16, 2024 | https://doi.org/10.1371/journal.pcbi.1011989
Precise cortical contributions to sensorimotor feedback control during reactive balance
PLOS Computational Biology: published April 17, 2024 | https://doi.org/10.1371/journal.pcbi.1011562
CoVar: A generalizable machine learning approach to identify the coordinated regulators driving variational gene expression
PLOS Computational Biology: published April 17, 2024 | https://doi.org/10.1371/journal.pcbi.1012016
Encoding surprise by retinal ganglion cells
PLOS Computational Biology: published April 17, 2024 | https://doi.org/10.1371/journal.pcbi.1011965
Mathematical analysis of left ventricular elastance with respect to afterload change during ejection phase
PLOS Computational Biology: published April 18, 2024 | https://doi.org/10.1371/journal.pcbi.1011974
Ranking of cell clusters in a single-cell RNA-sequencing analysis framework using prior knowledge
PLOS Computational Biology: published April 18, 2024 | https://doi.org/10.1371/journal.pcbi.1011550
Non-invasive assessment of stroke volume and cardiovascular parameters based on peripheral pressure waveform
PLOS Computational Biology: published April 18, 2024 | https://doi.org/10.1371/journal.pcbi.1012013
What does the mean mean? A simple test for neuroscience
PLOS Computational Biology: published April 19, 2024 | https://doi.org/10.1371/journal.pcbi.1012000
Locations and structures of influenza A virus packaging-associated signals and other functional elements via an in silico pipeline for predicting constrained features in RNA viruses
PLOS Computational Biology: published April 22, 2024 | https://doi.org/10.1371/journal.pcbi.1012009
Temperature-driven coordination of circadian transcriptional regulation
PLOS Computational Biology: published April 22, 2024 | https://doi.org/10.1371/journal.pcbi.1012029
Neutral competition explains the clonal composition of neural organoids
PLOS Computational Biology: published April 22, 2024 | https://doi.org/10.1371/journal.pcbi.1012054
Validity conditions of approximations for a target-mediated drug disposition model: A novel first-order approximation and its comparison to other approximations
PLOS Computational Biology: published April 24, 2024 | https://doi.org/10.1371/journal.pcbi.1012066
A phylogenetic method linking nucleotide substitution rates to rates of continuous trait evolution
PLOS Computational Biology: published April 24, 2024 | https://doi.org/10.1371/journal.pcbi.1011995
Indirect reciprocity with Bayesian reasoning and biases
PLOS Computational Biology: published April 25, 2024 | https://doi.org/10.1371/journal.pcbi.1011979
Method for cycle detection in sparse, irregularly sampled, long-term neuro-behavioral timeseries: Basis pursuit denoising with polynomial detrending of long-term, inter-ictal epileptiform activity
PLOS Computational Biology: published April 25, 2024 | https://doi.org/10.1371/journal.pcbi.1011152
A weak coupling mechanism for the early steps of the recovery stroke of myosin VI: A free energy simulation and string method analysis
PLOS Computational Biology: published April 25, 2024 | https://doi.org/10.1371/journal.pcbi.1012005
Evolutionary analyses of intrinsically disordered regions reveal widespread signals of conservation
PLOS Computational Biology: published April 25, 2024 | https://doi.org/10.1371/journal.pcbi.1012028
Emergent neural dynamics and geometry for generalization in a transitive inference task
PLOS Computational Biology: published April 25, 2024 | https://doi.org/10.1371/journal.pcbi.1011954
Spatial transcriptome-guided multi-scale framework connects P. aeruginosa metabolic states to oxidative stress biofilm microenvironment
PLOS Computational Biology: published April 26, 2024 | https://doi.org/10.1371/journal.pcbi.1012031
Bayesian inference of structured latent spaces from neural population activity with the orthogonal stochastic linear mixing model
PLOS Computational Biology: published April 26, 2024 | https://doi.org/10.1371/journal.pcbi.1011975
Human decision making balances reward maximization and policy compression
PLOS Computational Biology: published April 26, 2024 | https://doi.org/10.1371/journal.pcbi.1012057
Wagers for work: Decomposing the costs of cognitive effort
PLOS Computational Biology: published April 29, 2024 | https://doi.org/10.1371/journal.pcbi.1012060
Informing policy via dynamic models: Cholera in Haiti
PLOS Computational Biology: published April 29, 2024 | https://doi.org/10.1371/journal.pcbi.1012032
A novel hypergraph model for identifying and prioritizing personalized drivers in cancer
PLOS Computational Biology: published April 29, 2024 | https://doi.org/10.1371/journal.pcbi.1012068
Recurrent neural networks that learn multi-step visual routines with reinforcement learning
PLOS Computational Biology: published April 29, 2024 | https://doi.org/10.1371/journal.pcbi.1012030
Bayesian workflow for time-varying transmission in stratified compartmental infectious disease transmission models
PLOS Computational Biology: published April 29, 2024 | https://doi.org/10.1371/journal.pcbi.1011575
Reconstruction Set Test (RESET): A computationally efficient method for single sample gene set testing based on randomized reduced rank reconstruction error
PLOS Computational Biology: published April 29, 2024 | https://doi.org/10.1371/journal.pcbi.1012084
Synergistic epistasis among cancer drivers can rescue early tumors from the accumulation of deleterious passengers
PLOS Computational Biology: published April 30, 2024 | https://doi.org/10.1371/journal.pcbi.1012081
Methods
TPMA: A two pointers meta-alignment tool to ensemble different multiple nucleic acid sequence alignments
PLOS Computational Biology: published April 1, 2024 | https://doi.org/10.1371/journal.pcbi.1011988
Optimizing strategies for slowing the spread of invasive species
PLOS Computational Biology: published April 3, 2024 | https://doi.org/10.1371/journal.pcbi.1011996
StellarPath: Hierarchical-vertical multi-omics classifier synergizes stable markers and interpretable similarity networks for patient profiling
PLOS Computational Biology: published April 12, 2024 | https://doi.org/10.1371/journal.pcbi.1012022
Generative Bayesian modeling to nowcast the effective reproduction number from line list data with missing symptom onset dates
PLOS Computational Biology: published April 16, 2024 | https://doi.org/10.1371/journal.pcbi.1012021
HGCLAMIR: Hypergraph contrastive learning with attention mechanism and integrated multi-view representation for predicting miRNA-disease associations
PLOS Computational Biology: published April 23, 2024 | https://doi.org/10.1371/journal.pcbi.1011927
Combined multiplex panel test results are a poor estimate of disease prevalence without adjustment for test error
PLOS Computational Biology: published April 26, 2024 | https://doi.org/10.1371/journal.pcbi.1012062
Learning spatio-temporal patterns with Neural Cellular Automata
PLOS Computational Biology: published April 26, 2024 | https://doi.org/10.1371/journal.pcbi.1011589
Ensemble learning and ground-truth validation of synaptic connectivity inferred from spike trains
PLOS Computational Biology: published April 29, 2024 | https://doi.org/10.1371/journal.pcbi.1011964
Software
MCell4 with BioNetGen: A Monte Carlo simulator of rule-based reaction-diffusion systems with Python interface
PLOS Computational Biology: published April 24, 2024 | https://doi.org/10.1371/journal.pcbi.1011800
UNNT: A novel Utility for comparing Neural Net and Tree-based models
PLOS Computational Biology: published April 29, 2024 | https://doi.org/10.1371/journal.pcbi.1011504