Terkko Navigator / PLoS Computational Biology

Aggregative cycles evolve as a solution to conflicts in social investment

Estimating and interpreting secondary attack risk: Binomial considered biased

Real-time resolution of short-read assembly graph using ONT long reads

Zika virus dynamics: Effects of inoculum dose, the innate immune response and viral interference

Disease-driven reduction in human mobility influences human-mosquito contacts and dengue transmission dynamics

Modeling the structure of the frameshift-stimulatory pseudoknot in SARS-CoV-2 reveals multiple possible conformers

A theory of memory for binary sequences: Evidence for a mental compression algorithm in humans

Bacterial fitness landscapes stratify based on proteome allocation associated with discrete aero-types

Four different mechanisms for switching cell polarity

Coincident glutamatergic depolarizations enhance GABA_A receptor-dependent Cl^- influx in mature and suppress Cl^- efflux in immature neurons

Reconciling kinetic and thermodynamic models of bacterial transcription

Rosetta design with co-evolutionary information retains protein function

Selection for rapid uptake of scarce or fluctuating resource explains vulnerability of glycolysis to imbalance

Breast cancer is marked by specific, Public T-cell receptor CDR3 regions shared by mice and humans

Reconstructing tumor evolutionary histories and clone trees in polynomial-time with SubMARine

Genome-wide prediction of topoisomerase II<i>β</i> binding by architectural factors and chromatin accessibility

Ten simple rules for tackling your first mathematical models: A guide for graduate students by graduate students

Probabilistic transmission models incorporating sequencing data for healthcare-associated <i>Clostridioides difficile</i> outperform heuristic rules and identify strain-specific differences in transmission

Investigating the mitochondrial genomic landscape of <i>Arabidopsis thaliana</i> by long-read sequencing

Preprocessing choices affect RNA velocity results for droplet scRNA-seq data

Thermodynamic modeling of genome-wide nucleosome depleted regions in yeast

Machine learning based CRISPR gRNA design for therapeutic exon skipping

On the role of transcription in positioning nucleosomes

Dissecting the links between reward and loss, decision-making, and self-reported affect using a computational approach

The complexity of protein interactions unravelled from structural disorder

Persistent thermal input controls steering behavior in <i>Caenorhabditis elegans</i>

Optimal tuning of weighted kNN- and diffusion-based methods for denoising single cell genomics data

Model based planners reflect on their model-free propensities

Lassa viral dynamics in non-human primates treated with favipiravir or ribavirin

Minimal biophysical model of combined antibiotic action

Network propagation of rare variants in Alzheimer’s disease reveals tissue-specific hub genes and communities

The value of decreasing the duration of the infectious period of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection

Dynamic bistable switches enhance robustness and accuracy of cell cycle transitions

Structural determination of <i>Streptococcus pyogenes</i> M1 protein interactions with human immunoglobulin G using integrative structural biology

A multiscale model of complex endothelial cell dynamics in early angiogenesis

Structured environments foster competitor coexistence by manipulating interspecies interfaces

The risks of using the chi-square periodogram to estimate the period of biological rhythms

Sampling bias and model choice in continuous phylogeography: Getting lost on a random walk

MetGEMs Toolbox: Metagenome-scale models as integrative toolbox for uncovering metabolic functions and routes of human gut microbiome

Computational modeling suggests binding-induced expansion of Epsin disordered regions upon association with AP2

Improving probabilistic infectious disease forecasting through coherence

Chemical graph generators

Overlaid positive and negative feedback loops shape dynamical properties of PhoPQ two-component system

A novel virtual screening procedure identifies Pralatrexate as inhibitor of SARS-CoV-2 RdRp and it reduces viral replication <i>in vitro</i>

Ten quick tips for making things findable

Ten simple rules for typographically appealing scientific texts

PremPS: Predicting the impact of missense mutations on protein stability

NGS-PrimerPlex: High-throughput primer design for multiplex polymerase chain reactions

Cerebellar Golgi cell models predict dendritic processing and mechanisms of synaptic plasticity

Modeling habitat connectivity in support of multiobjective species movement: An application to amphibian habitat systems