matrix factorization

Long-term biodiversity responses to anthropogenic change are spatially and taxonomically heterogeneous across coastal wetlands

The paper examines long-term biodiversity responses to human activity in coastal wetlands using sedimentary DNA and environmental data, finding context-dependent relationships between enrichment and biodiversity.

Genome-wide meta-analysis of pilonidal sinus disease and its genetic overlap with hidradenitis suppurativa, hair patterning and adiposity

This study identifies genetic risk loci for pilonidal sinus disease and finds strong genetic overlap with hidradenitis suppurativa and hair patterning, but not obesity.

Integrating pangenome and imputation framework reveals structural variants affecting stature and milk composition traits in French dairy cattle

The paper integrates long-read, short-read, and SNP data using a pangenome and imputation framework to identify structural variants associated with stature and milk traits in dairy cattle.

Estimating glioblastoma migration-to-proliferation ratio from single time-point MRI data via radial density distribution

A reaction-diffusion model fitted to shell-averaged tumor density from one pre-treatment MRI estimates glioblastoma migration/proliferation ratio (D/k); in BraTS 2017, higher D/k went with shorter overall survival.

Algorithmic Geometry Shapes the Biological Meaning of Thalamocortical Structural Covariance

The paper compares five algorithms for deriving structural covariance networks in the thalamocortical system and finds they emphasize different neurobiological aspects based on their mathematical properties.

Tandem repeat variation shapes immune cell type-specific gene expression

The paper identifies immune cell type-specific gene expression regulated by tandem repeats using multi-omics data from large cohorts.

Pulmonary Tuberculosis Is Associated with Body Site-Specific Alterations in the Respiratory and Gut Microbiome in Uganda

This study examines how pulmonary tuberculosis affects the respiratory and gut microbiomes in Ugandan adults, finding site-specific taxonomic differences but mixed results on community composition.

SORT disentangles multilevel gene programs across heterogeneous spatial transcriptomic atlases

SORT identifies multilevel gene programs and their spatial activities across diverse spatial transcriptomic datasets, revealing both shared and sample-specific patterns.

Exploiting Low-Rank Structure in Genomic Relationship Matrices for Computationally Efficient Optimum Contribution Selection

This paper introduces a method to accelerate optimum contribution selection by approximating genomic relationship matrices with low-rank structures, achieving significant speedups while maintaining accuracy.

Matrix-Mechanical Genetic Susceptibility and Reduced Inflammatory and Immediate-Early Programs in Keratoconus

This study identifies genetic susceptibility in keratoconus linked to extracellular matrix mechanisms and shows reduced inflammatory and immediate-early gene expression in corneal tissue.

Single-nucleus multi-omics reveals reversible molecular signatures in skeletal muscle of patients with heart failure with preserved ejection fraction

The paper uses single-nucleus multi-omics to study skeletal muscle changes in HFpEF patients and shows some molecular changes are reversible with lifestyle interventions.

Integrative Multi-omics Analysis of the Human Skeletal Muscle Response to Endurance or Resistance Exercise: Findings from the Molecular Transducers of Physical Activity Consortium (MoTrPAC)

In 174 sedentary adults, resistance exercise changed more muscle molecular features than endurance exercise across omes and time points; network analysis nominates MEF2A and NFIC as regulatory hubs.

Spatial mitochondrial lineage tracing uncovers a premetastatic niche and microenvironment programmed fate switching in osteosarcoma

The paper uses spatial and single-cell transcriptomics with mitochondrial lineage tracing to uncover fate switching and premetastatic niche formation in osteosarcoma.

MOSAIC: Learning Graph Node Embeddings from Spectrally Isolated Dominant Subspaces of Accumulated Diffusion Operators

MOSAIC learns graph node embeddings by analyzing dominant spectral components of diffusion operators, outperforming existing methods in biomedical graph tasks.

A widespread internal brain state for fentanyl withdrawal

A multisite LFP network (EN-Withdrawal), found with supervised dCSFA-NMF in fentanyl-withdrawing mice, classifies morphine withdrawal, tracks behavioral severity, and its rise predicts fentanyl self-administration escalation in experienced mice.

Assay coverage reshapes metabolic diagnosis and the interpretation of pathway disturbance

The paper analyzes metabolic profiles across Arabidopsis and human datasets to show how assay coverage affects diagnostic accuracy and pathway interpretation.

LGTM: Gaussian Process Modulated Neural Topic Modeling for Longitudinal Microbiome

LGTM couples a neural topic model with additive basis-function Gaussian processes, learning microbial co-abundance topics and how covariates relate to their trajectories in longitudinal gut microbiome data.

Reconstructing donor genotypes from scRNA-seq for downstream eQTL and HLA-TCR analysis

This paper introduces scTAPAS, a method to reconstruct donor genotypes from scRNA-seq data, enabling eQTL and HLA-TCR analysis without conventional genotyping.

Leveraging Shared Genetic Architecture Between Psychiatric and Other Medical Disorders Increases Power and Reveals Novel Psychiatric Risk Loci

The paper identifies shared genetic architectures between psychiatric and non-psychiatric disorders, revealing novel psychiatric risk loci through cross-trait analyses.

Why rescue-based transcript ranking can mislead: normalization displacement and shared-control coupling in perturbation transcriptomics

The paper shows how rescue-based transcript ranking can mislead in perturbation transcriptomics due to normalization issues and shared-control coupling.

Integrating CSF and EV Proteomes Enhances Biomarker Discovery by Capturing Shared Variation Across Compartments

The paper integrates CSF and EV proteomes to enhance biomarker discovery by capturing shared variation across compartments, improving biological concordance and identifying more candidates in a smaller cohort.

Cross Dataset Transcriptomic Analysis Identifies Oxidative Stress Inflammation Gene Networks Modulated by Nutrigenomic Interventions in Parkinson Disease

The paper identifies oxidative stress and inflammation gene networks in Parkinson's disease through cross-dataset transcriptomic analysis and nutrigenomic integration, revealing candidate diet-gene associations.

Pruning the Search, Not the Signal: Adaptive-Banding Needleman-Wunsch Sequence Alignment via Protein Language Model Confidence

This paper introduces AB-NW, an adaptive-banding Needleman-Wunsch alignment method that improves speed while maintaining accuracy on challenging sequence alignment tasks.

Genetic and Cellular Architecture of Breast Cancer Risk Across Ancestries

This study analyzes breast cancer GWAS across multiple ancestries, finding similar heritability and genetic correlations, and identifies shared regulatory and cellular contexts.

Caloric restriction drives age-dependent and integrated remodeling of RNA processing and lipid composition in mouse brain

This study shows that caloric restriction in mice alters RNA processing and lipid composition across adulthood, linking these changes to metabolic reprogramming and lifespan extension.

Uniformly processed transcriptome-wide alternative splicing profiles for pediatric cancer research

The paper provides a uniformly processed compendium of alternative splicing profiles from pediatric cancer and non-diseased tissues, enabling large-scale analysis of splicing aberrations in pediatric cancers.

OpenCRS: an open-source regulated human cardiorespiratory model with large-scale calibration and global sensitivity analysis at rest and during exercise

OpenCRS is a cardiorespiratory model calibrated with global sensitivity analysis to identify influential parameters and mechanisms during rest and exercise.

Cell-Autonomous and Systemic Circadian Regulation of Gene Expression in Adipocytes

The paper identifies cell-autonomous and systemic circadian gene expression programs in adipocytes using RNA sequencing and motif analysis, revealing distinct regulatory programs linked to metabolic processes.

The Contribution of Common and Rare Genetic Variation to Emotional and Behavioural Symptoms in Childhood and Adolescence

This study examines the genetic contributions to emotional and behavioural symptoms in childhood and adolescence using common and rare variants from two large cohorts.

Reproducibility of Diffusion, Shape, and Connectivity Metrics Across Scanners: Implications for Multi-Site Tractography

The paper evaluates the reproducibility of diffusion, shape, and connectivity metrics across scanners in multi-site tractography studies and finds shape metrics show the highest reproducibility.