mixed model

Elevated conformational dynamics makes ACKR3 activation-prone and G protein-incompetent

This study compares the conformational dynamics of ACKR3 and CXCR4 using MD simulations and BRET assays, revealing that ACKR3's dynamic behavior leads to activation-proneness and G protein-incompetence.

Computational drug repurposing identified Artemisinin and Mebendazole as potential inhibitors of virulence-associated proteins SKSR and essential kinases CpCDPK1 of Cryptosporidium parvum

This paper identifies Artemisinin and Mebendazole as potential inhibitors of Cryptosporidium parvum virulence factors through molecular docking and MD simulations.

Ligandability Assessment of the LAG-3 D1 Domain Enables Discovery of a Small-Molecule Inhibitor

The paper assesses the ligandability of the LAG-3 D1 domain using molecular dynamics, virtual screening, and biochemical assays, identifying a small-molecule inhibitor with micromolar affinity.

Structure-Guided Biochemical Design of DNA Tweezers As A Dual Target of the Primary Glioblastoma Biomarkers S100A4 and Midkine

This study designs DNA tweezers that selectively bind S100A4 and midkine, biomarkers of glioblastoma invasiveness, using computational methods and molecular docking.

Predator-prey scaling laws support a suspension-feeding lifestyle in Cambrian luolishaniid lobopodians

Cambrian luolishaniid lobopodian appendage mesh spacing scales sublinearly with body length, and their predator-prey size ratios match modern suspension feeders rather than raptorial chaetognaths.

Ancient regulatory evolution shapes individual language abilities in present-day humans

Polygenic score variants in HAQERs (Human Ancestor Quickly Evolved Regions, <0.1% of the genome) predict spoken language but not nonverbal IQ; language associations replicate in SPARK, ABCD and UK Biobank.

A Mixed Effect Similarity Matrix Regression Model (SMRmix) for Integrating Multiple Microbiome Datasets at Community Level

This paper introduces SMRmix, a mixed effect model for integrating multiple microbiome datasets to identify consistent community-level associations with outcomes.

Wildlife trade drives animal-to-human pathogen transmission over 40 years

Legally traded wild mammals have higher odds (OR 2.72) of sharing pathogens with humans, and each 9 years in global trade adds roughly one human-shared pathogen.

Cross-species transmission of human hepatitis B virus to wild Neotropical primates

Sequenced HBV from wild Amazonian primates in a deforested, densely settled region matched human genotypes A and D, while pristine-forest monkeys were all negative, consistent with human-to-primate spillover.

dreampy: Pseudobulk mixed-model differential expression for single-cell RNA-seq in Python

dreampy implements the dreamlet framework for pseudobulk differential expression analysis in single-cell RNA-seq using Python.

Computational Prediction of Plasmodium falciparum Antigen-T-cell Receptor Interactions via Molecular Docking: Implications for Malaria Vaccine Design

This study uses molecular docking to predict Plasmodium falciparum antigen-T-cell receptor interactions, identifying three antigens as potential vaccine candidates.

Subjective and psychophysiological response to pictures of ancestral and modern threats: not all evolutionary threats are alike

Skin resistance responses in 119 non-phobic adults were most frequent and largest for height images; venomous snakes and firearms did not differ in response probability.

Cross-species meta-analysis reveals determinants of homing gene drive performance

Across nearly one million progeny from 10 species, species best predicts homing drive inheritance, while promoter, parent sex and maternal deposition each explain little of the inheritance variation.

Viruses and vectors tied to honey bee colony losses

During early-2025 US honey bee collapses (>60% losses), dying bees carried high loads of infectious DWV-A, DWV-B, and ABPV, and 100% of screened Varroa mites carried the amitraz-resistance allele.

Functional response predicts invasiveness but not trophic impact

Across 269 functional responses from 45 freshwater fish species, invasive species exceed non-invasive species only when sampled in their native range; introduced populations match non-invasive species.

Molecular dynamics of the pathogenic KCNQ2 variant G256W reveal mechanisms of channel dysfunction in epileptic encephalopathy

The paper uses molecular dynamics simulations to analyze the KCNQ2 G256W variant, revealing structural changes in the pore domain that disrupt ion selectivity and contribute to epileptic encephalopathy.

Uncertainty and reward histories have distinct effects on decisions after wins and losses

In 14 rats doing probabilistic reversal learning, model-derived uncertainty (unsigned average prediction error) and recency-weighted reward history distinctly and sex-specifically shaped win-stay versus lose-shift choices.

Heavy Resistance Exercise Training in Older Men: A Responder and Inter-individual Variability Analysis

Sixteen weeks of heavy resistance exercise in older men produces true inter-individual variability, yet multi-outcome classification shows 82% respond robustly or excellently and only 5% respond poorly.

Conformational State of Myosins Disordered Loop 2 Structure Mediates Actomyosin Association During Crossbridge Formation

The paper uses molecular dynamics simulations to show how conformational changes in loop 2 of myosin affect actomyosin association strength through electrostatic interactions.

Beyond species means - the intraspecific contribution to global wood density variation

Across 109,626 wood density records from 16,829 plant species (GWDD v.2), intraspecific variation explains 15% of global variance, tracks interspecific environmental gradients at 20-30% magnitude, and limits single-plant predictability.

MaAsLin 3: Refining and extending generalized multivariable linear models for meta-omic association discovery

MaAsLin 3 fits hurdle models separating microbial prevalence (augmented logistic) and abundance (median-adjusted log-linear) associations, improving precision over existing differential abundance tools and showing 77% of IBD associations are prevalence-driven.

Warm and cool temperatures decrease early-life telomere length in wild pied flycatchers

Both experimental nestbox heating (+2.83°C) and cooling (-1.72°C) during early postnatal development significantly shorten day-13 relative telomere length in wild pied flycatcher nestlings without altering body mass.

A multi-flow approach for binning circular plasmids from short-reads assembly graphs

The paper introduces PlasBin-HMF, a method for plasmid binning from short-read assemblies, which outperforms existing methods by preserving explainability.

A Federated and Privacy-Preserving Framework for Large-Scale Genome-Wide Association Studies with Mixed-Effects Models

This paper develops a federated framework for GWAS using mixed-effects models to enable privacy-preserving analysis across distributed datasets while maintaining statistical accuracy.

React-to-Me: A Conversational Interface for Interactive Exploration of the Reactome Pathway Knowledgebase.

React-to-Me, a retrieval-augmented chatbot grounding GPT-4o-mini in curated Reactome pathways with hyperlinked citations, earned higher blinded expert ratings than ungrounded GPT-4o-mini (odds ratio 2.01).

Exploring the potential value of aloe active components in inhibiting non-small cell lung cancer through network pharmacology

This study uses network pharmacology to identify Aloe vera compounds that target NSCLC through multiple pathways and proteins, suggesting potential for new anticancer therapies.

Land-use change undermines the stability of avian functional diversity

Across 1281 bird assemblages and 3696 species, land-use change lowers functional redundancy and resistance to simulated extinctions despite lower vulnerability, hitting frugivores and invertivores hardest.

Long-term evaluation of the association between dominance, bib size, sex and age

Across eleven years and more than 1,800 sociable weavers, black bib size grew with age but did not predict dominance; age predicted dominance in males only.

Partitioning Genotypic and Environmental Variance of Fresh Root Yield in Provitamin A Cassava Genotypes Using Mixed Models

This study uses mixed models to partition variance in cassava root yield, finding that environmental factors like rainfall and seasonality have a greater impact than genotype alone.

Elucidating the conformational dynamics of the mitochondrial localization signal, M3, of TDP-43 and accessing potential inhibitors using molecular docking and simulation

This study identifies vitamin D3 as a potential inhibitor of TDP-43's mitochondrial mis-localization through molecular docking and simulation of the M3 region.