statistical model

Relaxation kinetics controls cell transport in crowded active monolayers

The paper shows that relaxation kinetics, not just cell stiffness, controls transport in crowded active monolayers, with slower relaxation increasing cell movement.

vafSOMA: Detecting cell-layer-fixed somatic mutations in plants

vafSOMA detects cell-layer-fixed somatic mutations in plants using tissue composition, improving mutation detection and rate estimation in bulk sequencing data.

SeCAT (Sequence Consensus Amplicon Trimming): a simulation-informed Nextflow pipeline for cross-study harmonisation of 16S rRNA metabarcoding datasets

SeCAT is a Nextflow pipeline that harmonizes 16S rRNA metabarcoding datasets by identifying a consensus sequence window and testing its impact on community structure before merging datasets.

MET inhibition exploits conserved regulatory dependencies in malignant rhabdoid tumors

This study identifies MET signaling as a targetable vulnerability in rhabdoid tumors through integrated single-cell multi-omic and spatial transcriptomics analyses.

Cellular composition and the interpretation of candidate RNA readouts of trogocytosis in colorectal cancer

The paper evaluates an eight-gene module associated with trogocytosis in CRC, finding its correlation with T-cell fraction is typical of random modules, suggesting it reflects cellular composition rather than trogocytosis.

Layer-Specific Source-Anchored Transfer Learning for Multi-Omics Survival Prediction in Younger Breast Cancer Patients

This paper introduces LSAT-EN, a transfer learning method that improves survival prediction for younger breast cancer patients using multi-omics data from older patients.

Naturalistic recall preserves temporal specificity despite cortical feature reorganization

The paper analyzes fMRI data to show that temporal specificity in recall is preserved despite reorganization of feature representations across the cortex during recall of a narrative episode.

Multispecies transport shapes electrochemical environments in perforated cells

The paper models multispecies transport through gasdermin pores to explain how pore formation leads to cell swelling and osmotic changes.

Rhizobia transform legume nodules via native T-DNA transfer systems

The paper identifies native T-DNA transfer systems in rhizobia that deliver cargo genes into legume nodules, showing they share similarities with Agrobacteria-mediated transformation but have distinct regulatory mechanisms.

Electrostatic control of conformational dynamics drives proton translocation in respiratory Complex I

The paper investigates how electrostatic interactions control conformational changes and proton translocation in Complex I using a combination of experimental and computational methods.

A subtype-specific gene regulatory program controls differential circuit integration of deep CA3 pyramidal neurons

The paper identifies ST18 as a regulator of deep CA3 pyramidal neuron identity, showing its role in restricting a superficial-like program and shaping circuit integration through molecular and electrophysiological changes.

The behaviour bends, the code holds: working-memory category information in the multiple-demand network across graded interruption

This study investigates how the multiple-demand network maintains working memory during task interruptions, finding that neural representations of category information remain stable despite behavioral costs.

Monoaminergic changes are associated with impaired neurogenesis along the longitudinal axis of the hippocampus in ageing and dementia

The paper examines monoaminergic changes and their association with impaired neurogenesis in the hippocampus across aging and Parkinson disease dementia.

Context, not contradiction: a pan-cancer framework for conforming and nonconforming co-expression programmes

The paper introduces a framework to analyze pan-cancer co-expression programs by addressing artifacts in existing methods, showing that gene expression patterns differ between cancer types.

Photographic age gap is associated with frailty and predicts survival in laboratory mice

This paper uses photographs of mice to predict biological age and finds that older appearance correlates with frailty and shorter survival.

Discovering compositional, interpretable structure in social behavior

This paper introduces a method to model social behavior using decomposed linear dynamical systems, showing it captures complex, compositional actions more effectively than existing methods.

Transmural Single-Nucleus Transcriptomics Nominates Candidate Disease Programs in Human Necrotizing Enterocolitis

The paper uses single-nucleus RNA sequencing to analyze intestinal tissues from NEC patients and controls, identifying disease-specific gene expression programs across multiple cell types.

Error-Controlled Discovery of Protein Interactions via Conformal Calibration

PPI-Caliper controls false discovery rate in protein interaction prediction using conformal calibration without retraining models.

Atmospheric pollution contributed to destabilizing a small mammal community amid four decades of environmental changes

The paper uses Empirical Dynamic Modelling to show atmospheric pollution destabilized a small mammal community over 39 years in the Black Triangle of Europe.

Leveraging short and long-read sequencing to comprehensively characterize alternatively polyadenylated and alternatively spliced transcripts

The paper uses short and long-read sequencing to identify alternatively spliced and polyadenylated transcripts in mantle cell lymphoma, revealing novel splice variants and polyadenylation signals.

Habitat degradation destabilizes complex metacommunities by disrupting dispersal

This study shows habitat degradation shifts metacommunities from stable to unstable regimes, increasing extinction risk, and highlights dispersal's role in stabilizing ecosystems.

Particle-Associated Prokaryotic Community Structures in the Bering and Chukchi Seas

The paper examines particle-associated prokaryotic communities in the Bering and Chukchi Seas, finding that lifestyle and water-mass origin, not depth, structure these communities.

Explainable Multimodal Prognostic Modeling Uncovers New Clinically Relevant Pathological Features in a Multi-Institutional Pancreatic Neuroendocrine Tumor Cohort

This paper develops a multimodal prognostic model for pancreatic neuroendocrine tumors using clinicopathologic data and histology images, finding that stromal features are as prognostic as tumor cells.

Ecology of gene drives: Organism fitness under larval competition determines gene drive performance

This study investigates how larval competition affects gene drive performance in Aedes aegypti mosquitoes using agent-based models and Bayesian optimization.

MULTI-COHORT TRANSCRIPTOMIC ANALYSIS REVEALS SHARED INFLAMMATORY SIGNALING AND UROTHELIAL DYSFUNCTION ACROSS IC/BPS PHENOTYPES

This study identifies shared molecular signatures of inflammation and urothelial dysfunction across different IC/BPS phenotypes using multi-cohort transcriptomic analysis.

PLATE: a global atlas of food metaplasmidomes

PLATE provides a global resource of food metaplasmidomes, offering curated catalogs and annotations for studying plasmid diversity and function in food ecosystems.

Plant-plant communication in tomato: mechanisms underpinning information transfer between plants

This study investigates plant-plant communication in tomato by analyzing metabolomic and volatile emissions changes in response to herbivory, showing mirror effects in immune system reprogramming between sender and receiver plants.

Platelet-endothelial crosstalk drives distinct endothelial dysfunction in bicuspid aortic valve disease

This study shows that platelet-derived signals cause distinct endothelial dysfunction in bicuspid aortic valve disease, leading to mitochondrial dysfunction and immune cell recruitment.

Linking dynamic photosynthetic traits to biomass: a functional data framework that pinpoints when photosynthesis limits growth

The paper models genotype-specific photosynthetic trait trajectories using functional data analysis to predict biomass, finding that early growth period traits most strongly influence final dry weight.

Model-Agnostic Decomposition of the Difference in Mean Response Between Two Groups via Game-Theoretic Attribution with Minimum-Switching-Distortion Coupling

This paper introduces a model-agnostic decomposition method to analyze differences in mean response between groups, using game-theoretic attribution and optimal transport coupling.