statistical model

Deducing splicing events from transcript sets with splicelogic

splicelogic converts transcript-set comparisons into interpretable splicing events, enabling downstream analysis of isoform changes in RNA-seq data.

Contrasting Range and Demographic Histories in two Palearctic Dragonfly Species (Odonata: Anisoptera)

This study examines the relationship between climatic suitability and effective population size in two dragonfly species, finding they are not directly correlated.

Theoretical prediction of assembly contiguity

The paper derives a formula (Z-value) to predict contig length from read length, coverage, and genome properties, showing high accuracy and practical applications for assembler choice and experimental design.

Plate design confounds donor variation and model evaluation in single-cell perturbation screens

The paper shows that plate design confounds donor variation in single-cell perturbation screens and demonstrates how improved analysis methods can change interpretations of recent studies.

Bioprocess Modeling Made Easy With Hybrax

Hybrax simplifies hybrid bioprocess modeling by providing a framework that automates model setup and data handling, enabling reproducible and reusable models.

siRNA/mRNA payload of lipid nanoparticles quantified using fluorescence microscopy and correlation spectroscopy

The paper quantifies mRNA and siRNA payload in lipid nanoparticles using fluorescence microscopy and FCS, showing size-dependent payload and coencapsulation dynamics.

Genome-wide Analysis of the VQ Gene Family and Expression Profiling in Sorghum bicolor

This study identifies and characterizes VQ genes in sorghum, showing their differential expression and potential roles in salt stress tolerance.

Analysis of reproductive traits associated with lipoprotein(a) deficiency in participants from the Pakistan Genome Resource

The paper analyzes reproductive outcomes in individuals with LPA loss-of-function variants to assess the safety of Lp(a) lowering therapies.

Single-Cell Transcriptomics Reveals Tumorigenic Lineages and Interactions Persisting and Evolving From Premalignancy to Cancer in the Stomach

The paper uses single-cell transcriptomics to track molecular changes from premalignancy to cancer in gastric tissue, identifying persistent and evolving tumorigenic lineages and markers like EMB.

hAM-pe soluble extract increases human keratinocyte HaCaT cell-line mobility in scratch assays

The paper shows that hAM-pe extract accelerates wound closure in HaCaT cells by enhancing cellular motion persistence rather than individual speed.

TACO: An open, interpretable model for microsecond-scale TCR specificity prediction

TACO predicts TCR specificity against HLA-A*02:01-presented peptides using a statistical model, achieving AUROC 0.67 on held-out data and enabling efficient computational evaluation of TCR-peptide interactions.

Chemosensory receptor copy number evolution is not associated with host-plant specialization in butterflies

This study examines the relationship between host-plant specialization and chemosensory receptor copy numbers in butterflies, finding no significant association.

Sexing carnivores from faecal metagenomes: calibrating Rx for stone marten and red fox

The paper evaluates the use of the X-to-autosome ratio (Rx) for sexing carnivores from faecal metagenomes, finding it effective above a certain read depth.

Apparent sequential effects due to trial-to-trial fluctuations in decision criterion

This study shows that trial-to-trial fluctuations in decision criterion can explain sequential effects in decision making, challenging the assumption that these effects are caused by updates to decision parameters.

Compositional computations in the primate frontal cortex

The paper investigates how neural circuits in the primate frontal cortex support compositional generalization by separating computations into spatial and temporal components and identifying biases when these components are misaligned.

Metatranscriptomic Profiling of Viral Diversity in Aquatic Environments with a Focus on Microalgal Viruses

The paper uses metatranscriptomics to analyze viral diversity in freshwater and marine environments, identifying new RNA viruses associated with microalgae and proposing a new genus within Marnaviridae.

RoDPAA: A Robust Dissimilarity-Based Principal Angle Analysis Framework for Multi-View Microbiome Data Integration

RoDPAA integrates multi-view microbiome data using dissimilarity-based principal angle analysis, recovering shared structure in IBD cohorts where log-ratio methods failed.

Prenatal THC exposure alters metabolic gene expression and KEAP1 regulation in the mouse placental labyrinth

This study shows prenatal THC exposure reduces metabolic gene expression and KEAP1 in mouse placental labyrinth, while CBD has no significant effect.

Genomic evidence of a single domestication origin for modern cattle

The paper uses whole-genome analyses to challenge the two-domestication model of cattle, showing zebu originated from admixture between taurine cattle and Indian aurochs with introgression from gaur-like or banteng-like populations.

U-statistics-based Pairwise Discordance Regression for Joint Mean-Variability Inference in Longitudinal Studies with Missing Data

This paper introduces a semiparametric method for joint mean-variability inference in longitudinal studies with missing data, demonstrating robustness and reliability through simulations and a real-world application.

Geometric Morphometrics of Pistillate Flowers in Astrocaryum sect. Huicungo (Arecaceae): Taxonomic Implications for the Peruvian Species

This study uses geometric morphometrics to analyze pistillate flower shapes in Peruvian Astrocaryum species, revealing taxonomic insights through quantitative shape analysis.

Dopamine synthesis capacity and tau pathology differentially modulate rest-to-task functional network dynamics

This study examines how dopamine synthesis and tau pathology affect functional brain network dynamics during rest and task performance in young and older adults.

Microglial AhR Drives Sex-Biased Amyloid Pathology

This study identifies microglial AhR as a regulator of sex-biased amyloid pathology, showing that AhR activation exacerbates amyloid deposition and that AhR deficiency reduces amyloid burden.

Temporal stability for individual differences in both habit learning and expression

The paper examines the temporal stability of individual differences in habit learning and expression across two experiments with 313 participants.

High reproducibility demonstrated in a direct-to-consumer microbiome testing workflow under real-world conditions using fecal reference material

This study demonstrates high reproducibility in a DTC microbiome testing workflow using NIST fecal reference material across multiple processing steps and real-world conditions.

The C. elegans Connectome Toolbox: an open, extensible framework for multimodal connectomic data integration and analysis

The paper introduces the C. elegans Connectome Toolbox, a framework for integrating and analyzing multimodal connectomic data, enabling comparison across datasets and modalities.

Evaluating State-Transition Models in Short Resting-State fMRI with Continuous-Dynamics Controls

This study compares hidden Markov models (HMMs) and vector autoregressive (VAR) models in resting-state fMRI to determine if apparent state transitions reflect discrete dynamics or continuous activity, finding that VAR often outperforms HMMs in continuous cases.

40 Hz visual stimulation increases gamma-band functional connectivity between visual, parietal and frontal regions

This study shows that 40 Hz visual stimulation increases gamma-band functional connectivity between visual, parietal, and frontal regions, with the visual-parietal connection being most significant.

Genomic architecture of the major histocompatibility complex genes in the Neotropical Midas cichlid

This study characterizes the MHC genomic architecture in the Midas cichlid using integrated genomic and transcriptomic analyses, revealing gene diversity, evolutionary patterns, and tissue-specific expression.

Reconstruction of Cellular Trajectories with Biologically Interpretable States

The paper proposes a Latent Cell-State Model to reconstruct cellular trajectories by inferring hidden cell states and generating gene expression profiles at unobserved timepoints.