statistical model

RNA accessibility sequencing reveals transcriptome-wide RBP binding and RNA structure

This paper introduces RAD-seq, a method to quantify RNA accessibility by protein binding, and shows it can detect RBP footprints and RNA structure changes under stress.

Diagnose Harmonisation (DHARM): An open-source tool for the harmonisation and analysis of batch effects in MRI-derived measures.

DHARM is an open-source tool that diagnoses, harmonizes, and evaluates batch effects in MRI data using standardized workflows and multivariate diagnostics.

Knockdown of fibrillarin reveals cell- and virus- dependent restriction of henipavirus replication and enhanced antiviral immune signalling

This study shows that fibrillarin depletion affects henipavirus replication differently across cell types and viruses, and enhances antiviral immune signaling.

Proteomic signatures of cold adaptation and sponge host adaptation in marine Archaea

The paper evaluates amino acid compositional indices for detecting cold adaptation in marine Archaea and finds no evidence of cold adaptation but identifies proteomic signatures linked to sponge host adaptation.

Donor Aware Reanalysis of Neuronal Nuclei Supports STMN2 Depletion Associated with Nuclear TDP 43 loss in FTD and ALS

The paper reanalyzes RNA-seq data from neuronal nuclei to identify gene expression changes associated with nuclear TDP-43 loss in FTD and ALS, finding STMN2 depletion and other transcriptomic variations.

Dissociable norepinephrine and dopamine representations during strategic decision-making and reward learning

This study investigates how norepinephrine and dopamine contribute to strategic decision-making and reward learning in mice, finding distinct roles for each in tracking immediate rewards and longer-timescale strategies.

Mixing, competence, and commitment set the stability of cell identity

The paper models cell identity stability using a Markov framework, showing how mixing, competence, and commitment influence transition rates and proposes experiments to test these mechanisms.

Tandem repeats in methanogenic archaea and their viruses reveal a shared potential for rapid genomic diversification

The paper identifies tandem repeats in methanogenic archaea and their viruses, showing they contribute to genomic diversity and adaptation potential.

Whole methylome changes in Barrett's metaplasia, dysplasia, and cancer

The paper identifies methylation changes associated with dysplasia and cancer progression in Barrett's esophagus using whole-genome methylation profiles.

Genetic diversity and population structure of Ethiopian taro Colocasia esculenta (L.) Schott) as revealed by SSR markers

This study assesses genetic diversity and population structure of Ethiopian taro using SSR markers, finding low diversity at individual loci but high multilocus genotypic diversity and weak genetic differentiation among populations.

A Comparison and Validation of BIDS Apps for Preprocessing of UCB-J PET data

This study compares and validates two BIDS Apps, PETPrep and PICNIC, against in-house software for preprocessing UCB-J PET data, finding high consistency but region-dependent bias.

Bridging Bibliometrics and Biology: A Framework for the Relevance Scoring and Biological Stratification of Scalable MeSH Co-occurrence Networks

This paper introduces a framework to score and stratify MeSH co-occurrence networks for systematic literature reviews, improving the identification of relevant biological concepts.

An RNA-centric atlas of human cell cycle regulation

The paper defines an RNA-centric landscape of human cell cycle control by profiling various RNA features and identifies key RNA elements involved in cell cycle regulation.

Resolving Gene-Metabolism Links through Multi-Metabolite mQTL Commonality Analysis

The paper develops a method to link genes to metabolism by analyzing commonality in metabolite features associated with mQTLs, demonstrating its effectiveness through three case studies.

Dissecting Genetic Variability and Multi-Trait Performance in Cucumber

This study evaluates 18 cucumber genotypes across two seasons for multiple traits to identify high-performing varieties with stable multi-trait performance.

Coupled Modeling of Tumor Volume and ctDNA Dynamics in HPV-Associated Anal Squamous Cell Carcinoma

The paper models tumor volume and ctDNA dynamics in HPV-associated anal cancer to predict immunotherapy response using patient-specific parameters.

Long-range allosteric restraint by the Spiral-Pincer scaffold gates oxidative activation of the ATM kinase

The paper investigates how the Spiral-Pincer scaffold regulates ATM kinase activation by oxidative stress, showing it restricts access to an oxidation-competent conformation.

A comparative analysis of BrdU and EdU genotoxicity shows that trypanosomatids exhibit unique responses to the presence of these thymidine analogs in their DNA

This study compares the genotoxic effects of BrdU and EdU in trypanosomatids, finding EdU more genotoxic and revealing species-specific responses to DNA damage.

CNVision: a computational framework for functional interpretation of intragenic copy number variants

CNVision is a computational framework that automates the interpretation of intragenic copy number variants by standardizing input parsing, transcript mapping, and reading-frame classification.

Multi-scale place fields provide a predictive basis for hierarchical control

This paper introduces a predictive map model that explains multi-scale place field activity in hippocampal neurons and validates its predictions with experimental data.

Circadian feeding rhythm loss drives sex-specific β-cell dysfunction in diet-induced obesity

This study shows that diet-induced obesity disrupts circadian β-cell function more in male mice than females, with time-restricted feeding partially restoring these effects.

Embodied Dynamic Causal Modelling: Brain and Cardiac Effective Connectivity

This paper introduces Embodied Dynamic Causal Modelling to estimate effective connectivity across the brain-heart axis using multimodal data from an auditory Go/No-Go task.

GxE and changes to the genetic architecture of flowering time in an overwintering environment

This study examines how genetic architecture of flowering time in Arabidopsis thaliana changes between overwintering environments and growth chambers, finding extensive gene-by-environment interaction and environment-specific genetic effects.

Unravelling the mechanisms of clozapine-induced neutropenia in treatment-resistant schizophrenia using cellular genomics

This study investigates clozapine-induced neutropenia in treatment-resistant schizophrenia using single nucleus RNA sequencing to identify cell type-specific transcriptional changes and cell-cell communication patterns.

Loss of cell-identity DNA methylation tracks division history, not DNA damage

The paper tests whether DNA damage drives aging by analyzing cell-identity DNA methylation changes in human fibroblasts and finds that division history, not DNA damage, correlates with loss of identity information.

PHASOR: An Open-Source Pipeline for Hidden Markov Model Analysis of Stimulus-Locked Retinal Multielectrode-Array Population Activity

PHASOR is a pipeline that analyzes retinal multielectrode-array data using hidden Markov models to link stimulus timing with population activity states.

Self-Other Neural Representational Distinction is Associated with Distorted Social Predictions in Social Anxiety

This study investigates how social anxiety affects self-other neural distinctions and social predictions, finding that higher SA correlates with greater self-other representational separation in the pgACC and altered prediction tracking in the precuneus.

HYphlow: bringing end-to-end flow to HyPhy selection analyses, from taxon reconciliation to trait-based foreground assignment

HYphlow streamlines phylogenetic selection analyses by integrating data preparation, foreground assignment, HyPhy execution, and result extraction into a single workflow, improving precision and reproducibility.

Integrative taxonomy of the North American pink flat-backed millipedes (Polydesmidae: Pseudopolydesmus Attems, 1898)

This study integrates genetic and morphological data to delimit species in the millipede genus Pseudopolydesmus, finding congruence between genitalic morphology and molecular phylogeny.

CardioShift: Resolving cell-to-cell functional heterogeneity in hiPSC-derived cardiomyocytes from high-throughput single-cell imaging

CardioShift resolves cell-to-cell functional heterogeneity in hiPSC-derived cardiomyocytes by accounting for nested variance, revealing hidden subpopulations and condition-dependent phenotypes.