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Twelve quick tips for deploying a Beacon.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011817
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Ten simple rules for pushing boundaries of inclusion at academic events.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011797
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When do stereotypes undermine indirect reciprocity?
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011862
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A multiscale computational framework for the development of spines in molluscan shells.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011835
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Computational models of compound nerve action potentials: Efficient filter-based methods to quantify effects of tissue conductivities, conduction distance, and nerve fiber parameters.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011833
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Ten simple rules to leverage large language models for getting grants.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011863
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Dose optimization of an adjuvanted peptide-based personalized neoantigen melanoma vaccine.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011247
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Is it selfish to be filamentous in biofilms? Individual-based modeling links microbial growth strategies with morphology using the new and modular iDynoMiCS 2.0.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011303
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Identifying metabolic adaptations characteristic of cardiotoxicity using paired transcriptomics and metabolomics data integrated with a computational model of heart metabolism.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011919
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DeepD3, an open framework for automated quantification of dendritic spines.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011774
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Developmental hourglass: Verification by numerical evolution and elucidation by dynamical-systems theory.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011867
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TimeTeller: A tool to probe the circadian clock as a multigene dynamical system.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011779
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HormoneBayes: A novel Bayesian framework for the analysis of pulsatile hormone dynamics.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011928
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Bidirectional de novo peptide sequencing using a transformer model.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011892
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Quantifying the clusterness and trajectoriness of single-cell RNA-seq data.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011866
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ECOD domain classification of 48 whole proteomes from AlphaFold Structure Database using DPAM2.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011586
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Dissecting the roles of calcium cycling and its coupling with voltage in the genesis of early afterdepolarizations in cardiac myocyte models.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011930
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STGIC: A graph and image convolution-based method for spatial transcriptomic clustering.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011935
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Circadian regulation of sinoatrial nodal cell pacemaking function: Dissecting the roles of autonomic control, body temperature, and local circadian rhythmicity.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011907
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Disentangled deep generative models reveal coding principles of the human face processing network.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011887
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Methods and considerations for estimating parameters in biophysically detailed neural models with simulation based inference.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011108
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Shared input and recurrency in neural networks for metabolically efficient information transmission.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011896
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A biologically inspired repair mechanism for neuronal reconstructions with a focus on human dendrites.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011267
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A simulation framework to determine optimal strength training and musculoskeletal geometry for sprinting and distance running.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011410
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Genome scale metabolic network modelling for metabolic profile predictions.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011381
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Age-dependent ventilator-induced lung injury: Mathematical modeling, experimental data, and statistical analysis.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011113
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Diverse mutant selection windows shape spatial heterogeneity in evolving populations.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011878
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A novel batch-effect correction method for scRNA-seq data based on Adversarial Information Factorization.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011880
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EPINEST, an agent-based model to simulate epidemic dynamics in large-scale poultry production and distribution networks.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011375
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Fast adaptation to rule switching using neuronal surprise.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011839
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Robust and consistent measures of pattern separation based on information theory and demonstrated in the dentate gyrus.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1010706
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Connectivity Matrix Seriation via Relaxation.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011904
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Denoising diffusion probabilistic models for generation of realistic fully-annotated microscopy image datasets.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011890
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Ecological and evolutionary dynamics of cell-virus-virophage systems.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1010925
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Intra-ripple frequency accommodation in an inhibitory network model for hippocampal ripple oscillations.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011886
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Inference of annealed protein fitness landscapes with AnnealDCA.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011812
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The successor representation subserves hierarchical abstraction for goal-directed behavior.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011312
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Studentsourcing—Aggregating and reusing data from a practical cell biology course.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011836
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Enhancing predictive performance for spectroscopic studies in wildlife science through a multi-model approach: A case study for species classification of live amphibians.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011876
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Differential allelic representation (DAR) identifies candidate eQTLs and improves transcriptome analysis.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011868
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Learning what matters: Synaptic plasticity with invariance to second-order input correlations.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011844
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magpie: A power evaluation method for differential RNA methylation analysis in N6-methyladenosine sequencing.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011875
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Accounting for isoform expression increases power to identify genetic regulation of gene expression.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011857
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StressME: Unified computing framework of Escherichia coli metabolism, gene expression, and stress responses.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011865
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Generating synthetic population for simulating the spatiotemporal dynamics of epidemics.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011810
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Mathematical model of oxygen, nutrient, and drug transport in Tuberculosis Granulomas.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011847
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An Epigenomic fingerprint of human cancers by landscape interrogation of super enhancers at the constituent level.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011873
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CLAW: An automated Snakemake workflow for the assembly of chloroplast genomes from long-read data.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011870
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Intracellular signaling in proto-eukaryotes evolves to alleviate regulatory conflicts of endosymbiosis.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011860
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Emergent competition shapes top-down versus bottom-up control in multi-trophic ecosystems.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011675
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