statistical model

Stochastic gene expression drives state switching and phenotypic heterogeneity in RNA repair

The paper shows stochastic RNA repair in E. coli leads to phenotypic heterogeneity and state switching in antibiotic responses.

Aging activates latent enhancers that can be reversed withexercise

This study identifies age-acquired enhancers in mouse hearts and shows that exercise can reverse their activation.

COSMOS: integrated vector-pathogen metagenomics for mosquito-borne disease

COSMOS integrates vector-pathogen metagenomics to monitor mosquito-borne diseases, detecting pathogens and mosquito communities in field samples with high accuracy.

Polygenic polymorphisms cooperate to drive expansion of HCMV adaptive NK cell and NK-like T cell populations

This study identifies genetic polymorphisms in NKG2C, CD16a, and HLA-E that influence NKG2C expression and ADCC capacity in HCMV-infected individuals.

Deterministic DNA-first discovery reveals recurrent genomic architectures

The paper introduces a DNA-first framework to detect genomic architectures by analyzing raw DNA sequences, identifying potential RNA-to-DNA systems without prior protein knowledge.

A Saliva-Inspired Model of Enzymatic Starch Hydrolysis by Alpha Amylase

This paper demonstrates how alpha-amylase hydrolyzes starch to generate reducing sugars, causing osmotic stress that remodels giant unilamellar vesicles.

Genome-scale metabolic models reveal phylogenetic conservation of amino acid fermentation-linked metabolic traits in soil bacteria

The paper constructs genome-scale metabolic models for soil bacteria to identify phylogenetically conserved fermentation traits and their metabolic fluxes.

Massively parallel quantification and prediction of monomeric protein yield in Escherichia coli

The paper develops a scalable assay and a protein language model to predict monomeric yield of proteins in E. coli, showing it can be learned and designed.

Interpretable Machine Learning Links Group-Specific Plasma Proteomics to Regional Structural Neuroimaging in Alzheimer's Disease

The paper identifies group-specific plasma proteomic signatures in Alzheimer's disease stages and links them to regional brain structural changes using machine learning and neuroimaging.

Immersion as inference: An active inference account of induced realities and its relation to the two-competitor model

This paper develops an active inference framework to explain immersion in virtual and augmented realities by modeling induced realities as competing generative models.

brisc: a multithreaded CPU toolkit for single-cell analysis

brisc is a multithreaded CPU toolkit for single-cell analysis that is faster and more reproducible than existing tools like Scanpy and Seurat.

Computational Analysis of Antioxidant Effects on Stress Response Mechanisms in Candida albicans

The paper uses computational methods to analyze antioxidant effects on stress response mechanisms in Candida albicans, identifying naringenin and quercetin as potential modulators of Sir2/SIRT3 pathways.

Chronic Sleep Disruption Activates the Transcriptional Unfolded Protein Response and Induces Compartment-Specific Proteomic Changes in Mice

This study shows chronic sleep disruption causes distinct transcriptional and proteomic changes in brain compartments, particularly affecting synaptic function and potentially contributing to Alzheimer's risk.

SQANTI-evidence: isoform-resolved, evidence-tiered structural annotation of unannotated genomes from long-read RNA-seq

SQANTI-evidence annotates genomes from long-read RNA-seq without a reference, achieving high precision in gene and isoform prediction across species.

Comparative Transcriptomic Analysis of Gene Expression Patterns in Neutrophils from Rheumatoid Arthritis and COVID-19

This paper compares neutrophil transcriptomic profiles in rheumatoid arthritis and COVID-19 to identify shared immune pathways and disease-specific features.

Integrative Transcriptomic Meta-Analysis Reveals SIRT1-SNCA Correlation in Parkinson's Disease

This study identifies a context-dependent resveratrol-SIRT1 axis in Parkinson's disease through integrative transcriptomic analysis across multiple models.

Hazard Structure and Repair Kinetics: A 2x2 Classification that Resolves the Stochastic-Death / Individual-Tolerance Dilemma

The paper classifies hazard structures in toxicology models and identifies peak-based hazard as the appropriate default for certain toxicants.

Connectivity of Implicit Statistical Learning Networks is Associated with Language Impairment Severity in Post-Stroke Aphasia

This study examines how implicit statistical learning networks' connectivity relates to aphasia severity in post-stroke patients, finding stronger connectivity correlates with milder aphasia.

Clustering instantaneous phase-locking states with a rank-two Bures-Wasserstein distance

This paper introduces a method to cluster instantaneous phase-locking states using the Bures-Wasserstein distance, improving sensitivity to phase-lag size and spatial patterns in EEG data.

Marker-specific pixel attribution for single-cell protein quantification with PixAQ

PixAQ improves single-cell protein quantification in imaging mass cytometry by assigning pixel signals to specific markers using spatial and intensity models.

NORMA 3.0: aesthetic and group-aware visualization and analysis of annotated biological networks

NORMA 3.0 provides enhanced visualization and analysis of annotated biological networks with improved group representation and layout algorithms.

TensorPLS: an R package for exploring molecular and temporal patterns in longitudinal omics data using PLS-DA

TensorPLS is an R package for analyzing longitudinal omics data using PLS-DA, handling missing data and providing temporal insights through VIP scores and cross-validation.

An end-to-end in silico framework for truth-based validation and regression testing of clinical genome sequencing pipelines, from simulated reads to reportable findings

This paper introduces an end-to-end in silico framework to validate and test clinical genome sequencing pipelines from simulated reads to reportable findings using a fixed truth set.

Inosine Triphosphate Pyrophosphatase as a Candidate Associated with White Matter Abnormalities in Chronic Heart Failure

This study identifies inosine triphosphate pyrophosphatase (ITPA) as a candidate factor linking chronic heart failure and white matter abnormalities through human, animal, and cellular analyses.

Social copying drives spatial allocation in gregarious herbivores

The paper investigates resting patch selection in cattle using GPS data and a model showing social copying drives spatial allocation.

Sourmash accurately profiles strains from long-read metagenomes preserving gene content

This study evaluates Sourmash's ability to profile microbial strains from long-read metagenomes, showing accurate gene content recovery and abundance estimation.

Intra-individual changes to peak alpha frequency map to pain perception following high frequency sensitisation of central nociceptive pathways: A test-retest reliability study

This study examines intra-individual changes in peak alpha frequency and -band power in EEG data following high-frequency sensitisation of central nociceptive pathways, assessing test-retest reliability and their relation to pain perception.

Life on leaves left a lasting mark on the Methylobacterium core genome

The study examines the core genome evolution of Methylobacterium to show that genes related to phyllosphere adaptation show greater evolutionary discordance, suggesting horizontal gene transfer.

A fibroblast-CD8+ T cell circuit drives a Type 1 shift in allergic inflammatory memory

This study identifies a fibroblast-CD8+ T cell circuit that drives a Type 1 immune shift in allergic inflammatory memory through mechanistic and translational analysis in murine and human models.

High-fat diet promotes exhaustion-associated T-cell remodeling across vascular and lymphoid tissues in atherosclerosis-prone mice

This study shows that a high-fat diet causes T-cell exhaustion in multiple tissues of atherosclerosis-prone mice, which partially reverses with dietary changes.