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AI-powered Immune Repertoire Analysis: Enhancing Diagnostic Precision and Unveiling Disease Insights
Integrating AI with next-generation sequencing (NGS) of human immune repertoires has transformative potential for clinical diagnostics. By leveraging machine learning, AI improves diagnostic precision through accurate disease classification, subtype identification, and discovery of immune markers, paving the way for personalized treatment strategies.
Image Credit: Paul Schmidt-Barbo
Education Articles
Ten simple rules for building and maintaining a responsible data science workflow
PLOS Computational Biology: published July 18, 2024 | https://doi.org/10.1371/journal.pcbi.1012232
Nine quick tips for open meta-analyses
PLOS Computational Biology: published July 25, 2024 | https://doi.org/10.1371/journal.pcbi.1012252
Research Articles
Model-based analysis of the acute effects of transcutaneous magnetic spinal cord stimulation on micturition after spinal cord injury in humans
PLOS Computational Biology: published July 1, 2024 | https://doi.org/10.1371/journal.pcbi.1012237
Co-existence of synaptic plasticity and metastable dynamics in a spiking model of cortical circuits
PLOS Computational Biology: published July 1, 2024 | https://doi.org/10.1371/journal.pcbi.1012220
Compressive instabilities enable cell-induced extreme densification patterns in the fibrous extracellular matrix: Discrete model predictions
PLOS Computational Biology: published July 1, 2024 | https://doi.org/10.1371/journal.pcbi.1012238
Detection of disease-specific signatures in B cell repertoires of lymphomas using machine learning
PLOS Computational Biology: published July 2, 2024 | https://doi.org/10.1371/journal.pcbi.1011570
A variational autoencoder trained with priors from canonical pathways increases the interpretability of transcriptome data
PLOS Computational Biology: published July 3, 2024 | https://doi.org/10.1371/journal.pcbi.1011198
Modeling the impact of neuromorphological alterations in Down syndrome on fast neural oscillations
PLOS Computational Biology: published July 5, 2024 | https://doi.org/10.1371/journal.pcbi.1012259
Joint modeling of choices and reaction times based on Bayesian contextual behavioral control
PLOS Computational Biology: published July 5, 2024 | https://doi.org/10.1371/journal.pcbi.1012228
Nonlinear fusion is optimal for a wide class of multisensory tasks
PLOS Computational Biology: published July 5, 2024 | https://doi.org/10.1371/journal.pcbi.1012246
scBoolSeq: Linking scRNA-seq statistics and Boolean dynamics
PLOS Computational Biology: published July 8, 2024 | https://doi.org/10.1371/journal.pcbi.1011620
Elucidating the complex membrane binding of a protein with multiple anchoring domains using extHMMM
PLOS Computational Biology: published July 8, 2024 | https://doi.org/10.1371/journal.pcbi.1011421
Phenotypic memory in quorum sensing
PLOS Computational Biology: published July 8, 2024 | https://doi.org/10.1371/journal.pcbi.1011696
Kernel Bayesian logistic tensor decomposition with automatic rank determination for predicting multiple types of miRNA-disease associations
PLOS Computational Biology: published July 8, 2024 | https://doi.org/10.1371/journal.pcbi.1012287
Competitive advantages of T-even phage lysis inhibition in response to secondary infection
PLOS Computational Biology: published July 8, 2024 | https://doi.org/10.1371/journal.pcbi.1012242
Synaptic reorganization of synchronized neuronal networks with synaptic weight and structural plasticity
PLOS Computational Biology: published July 9, 2024 | https://doi.org/10.1371/journal.pcbi.1012261
Jointly efficient encoding and decoding in neural populations
PLOS Computational Biology: published July 10, 2024 | https://doi.org/10.1371/journal.pcbi.1012240
PARE: A framework for removal of confounding effects from any distance-based dimension reduction method
PLOS Computational Biology: published July 10, 2024 | https://doi.org/10.1371/journal.pcbi.1012241
Reinforcement learning of altruistic punishment differs between cultures and across the lifespan
PLOS Computational Biology: published July 11, 2024 | https://doi.org/10.1371/journal.pcbi.1012274
An integrative approach to protein sequence design through multiobjective optimization
PLOS Computational Biology: published July 11, 2024 | https://doi.org/10.1371/journal.pcbi.1011953
Role of diffusion and reaction of the constituents in spreading of histone modification marks
PLOS Computational Biology: published July 11, 2024 | https://doi.org/10.1371/journal.pcbi.1012235
Parameter estimation in a whole-brain network model of epilepsy: Comparison of parallel global optimization solvers
PLOS Computational Biology: published July 11, 2024 | https://doi.org/10.1371/journal.pcbi.1011642
Identifying cell states in single-cell RNA-seq data at statistically maximal resolution
PLOS Computational Biology: published July 12, 2024 | https://doi.org/10.1371/journal.pcbi.1012224
Epidemiological modeling of SARS-CoV-2 in white-tailed deer (Odocoileus virginianus) reveals conditions for introduction and widespread transmission
PLOS Computational Biology: published July 12, 2024 | https://doi.org/10.1371/journal.pcbi.1012263
Agent-based model predicts that layered structure and 3D movement work synergistically to reduce bacterial load in 3D in vitro models of tuberculosis granuloma
PLOS Computational Biology: published July 12, 2024 | https://doi.org/10.1371/journal.pcbi.1012266
Identifying topologically associating domains using differential kernels
PLOS Computational Biology: published July 15, 2024 | https://doi.org/10.1371/journal.pcbi.1012221
Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference
PLOS Computational Biology: published July 15, 2024 | https://doi.org/10.1371/journal.pcbi.1012180
Convergence, sampling and total order estimator effects on parameter orthogonality in global sensitivity analysis
PLOS Computational Biology: published July 17, 2024 | https://doi.org/10.1371/journal.pcbi.1011946
When should lockdown be implemented? Devising cost-effective strategies for managing epidemics amid vaccine uncertainty
PLOS Computational Biology: published July 18, 2024 | https://doi.org/10.1371/journal.pcbi.1012010
Fixation times on directed graphs
PLOS Computational Biology: published July 18, 2024 | https://doi.org/10.1371/journal.pcbi.1012299
Emergent effects of synaptic connectivity on the dynamics of global and local slow waves in a large-scale thalamocortical network model of the human brain
PLOS Computational Biology: published July 19, 2024 | https://doi.org/10.1371/journal.pcbi.1012245
Simulation of Soluble and Bound VEGF-stimulated in vitro Capillary-like Network Formation on Deformed Substrate
PLOS Computational Biology: published July 22, 2024 | https://doi.org/10.1371/journal.pcbi.1012281
Protein stability prediction by fine-tuning a protein language model on a mega-scale dataset
PLOS Computational Biology: published July 22, 2024 | https://doi.org/10.1371/journal.pcbi.1012248
Quantifying massively parallel microbial growth with spatially mediated interactions
PLOS Computational Biology: published July 22, 2024 | https://doi.org/10.1371/journal.pcbi.1011585
Spatial information allows inference of the prevalence of direct cell–to–cell viral infection
PLOS Computational Biology: published July 23, 2024 | https://doi.org/10.1371/journal.pcbi.1012264
Generating information-dense promoter sequences with optimal string packing
PLOS Computational Biology: published July 24, 2024 | https://doi.org/10.1371/journal.pcbi.1012276
A comprehensive exploration of the druggable conformational space of protein kinases using AI-predicted structures
PLOS Computational Biology: published July 24, 2024 | https://doi.org/10.1371/journal.pcbi.1012302
A low-dimensional approximation of optimal confidence
PLOS Computational Biology: published July 24, 2024 | https://doi.org/10.1371/journal.pcbi.1012273
FedGMMAT: Federated generalized linear mixed model association tests
PLOS Computational Biology: published July 24, 2024 | https://doi.org/10.1371/journal.pcbi.1012142
Improved protein complex prediction with AlphaFold-multimer by denoising the MSA profile
PLOS Computational Biology: published July 25, 2024 | https://doi.org/10.1371/journal.pcbi.1012253
Spatial inequities in access to medications for treatment of opioid use disorder highlight scarcity of methadone providers under counterfactual scenarios
PLOS Computational Biology: published July 26, 2024 | https://doi.org/10.1371/journal.pcbi.1012307
A rule-based multiscale model of hepatic stellate cell plasticity: Critical role of the inactivation loop in fibrosis progression
PLOS Computational Biology: published July 29, 2024 | https://doi.org/10.1371/journal.pcbi.1011858
Reassessing the modularity of gene co-expression networks using the Stochastic Block Model
PLOS Computational Biology: published July 29, 2024 | https://doi.org/10.1371/journal.pcbi.1012300
Derivation and simulation of a computational model of active cell populations: How overlap avoidance, deformability, cell-cell junctions and cytoskeletal forces affect alignment
PLOS Computational Biology: published July 29, 2024 | https://doi.org/10.1371/journal.pcbi.1011879
Using deep learning to decipher the impact of telomerase promoter mutations on the dynamic metastatic morpholome
PLOS Computational Biology: published July 30, 2024 | https://doi.org/10.1371/journal.pcbi.1012271
Population bursts in a modular neural network as a mechanism for synchronized activity in KNDy neurons
PLOS Computational Biology: published July 31, 2024 | https://doi.org/10.1371/journal.pcbi.1011820
Forecasting of influenza activity and associated hospital admission burden and estimating the impact of COVID-19 pandemic on 2019/20 winter season in Hong Kong
PLOS Computational Biology: published July 31, 2024 | https://doi.org/10.1371/journal.pcbi.1012311
Multitask learning of a biophysically-detailed neuron model
PLOS Computational Biology: published July 31, 2024 | https://doi.org/10.1371/journal.pcbi.1011728
Probabilistic neural transfer function estimation with Bayesian system identification
PLOS Computational Biology: published July 31, 2024 | https://doi.org/10.1371/journal.pcbi.1012354
Methods
NeuroMotion: Open-source platform with neuromechanical and deep network modules to generate surface EMG signals during voluntary movement
PLOS Computational Biology: published July 3, 2024 | https://doi.org/10.1371/journal.pcbi.1012257
Estimating error rates for single molecule protein sequencing experiments
PLOS Computational Biology: published July 5, 2024 | https://doi.org/10.1371/journal.pcbi.1012258
Modeling soybean growth: A mixed model approach
PLOS Computational Biology: published July 11, 2024 | https://doi.org/10.1371/journal.pcbi.1011258
Achieving Occam’s razor: Deep learning for optimal model reduction
PLOS Computational Biology: published July 18, 2024 | https://doi.org/10.1371/journal.pcbi.1012283
Detecting and quantifying heterogeneity in susceptibility using contact tracing data
PLOS Computational Biology: published July 29, 2024 | https://doi.org/10.1371/journal.pcbi.1012310
Software
ArborSim: Articulated, branching, OpenSim routing for constructing models of multi-jointed appendages with complex muscle-tendon architecture
PLOS Computational Biology: published July 5, 2024 | https://doi.org/10.1371/journal.pcbi.1012243
HPVsim: An agent-based model of HPV transmission and cervical disease
PLOS Computational Biology: published July 5, 2024 | https://doi.org/10.1371/journal.pcbi.1012181
BCI Toolbox: An open-source python package for the Bayesian causal inference model
PLOS Computational Biology: published July 8, 2024 | https://doi.org/10.1371/journal.pcbi.1011791
NRV: An open framework for in silico evaluation of peripheral nerve electrical stimulation strategies
PLOS Computational Biology: published July 12, 2024 | https://doi.org/10.1371/journal.pcbi.1011826
nf-core/airrflow: An adaptive immune receptor repertoire analysis workflow employing the Immcantation framework
PLOS Computational Biology: published July 26, 2024 | https://doi.org/10.1371/journal.pcbi.1012265