matrix factorization

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.

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.

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.

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.

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.

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.

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.

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.

CNSigs: An R Package for the Identification of Copy Number Mutational Signatures

CNSigs identifies copy number mutational signatures across cancers, revealing associations with survival and treatment response.

Mnemonic Demand Reconfigures the Neural Architecture of Memory Encoding

The paper shows that neural patterns reconfigure with increasing memory load, revealing a low-dimensional trajectory linked to memory performance.

A single-nucleus multiomic and spatial atlas of gene regulation in human spermatogenesis

This study creates a single-nucleus multiomic and spatial atlas of human spermatogenesis, linking gene regulatory networks to infertility-associated genetic variation and disease perturbations.

Pleiotropic genetic architecture linking schizophrenia and substance use disorders

This study identifies shared genetic architecture between schizophrenia and substance use disorders using GWAS and genomic methods, finding significant genetic correlations and bidirectional causal relationships.

Molecular Underpinnings of Retinal Traits Shared with Major Psychiatric Disorders

The paper identifies shared genetic variants between major psychiatric disorders and retinal traits, revealing molecular mechanisms linking retinal morphology to neurodevelopmental and neurotransmission processes.

KSTITCH links cellular morphology and gene expression in spatial transcriptomics

STITCH pairs size-independent tangent-PCA contour shape modes with expression factors by canonical correlation, recovering keratinocyte, fibroblast and melanoma shape-expression links in Xenium and CosMx data.

GWAS and multimodal transcriptomic profiling of human otolithic organs characterize the genetic architecture of balance in the elderly

The paper identifies genetic factors associated with balance in the elderly through GWAS and multimodal transcriptomic analysis of otolithic organs.

Dynamics-aware Evolutionary Profiling Uncouples Structural Rigidity from Functional Motion to Enable Enhanced Variant Interpretation

This paper introduces Dynamics-Aware Evolutionary Profiling to separate structural rigidity from functional motion in proteins, improving variant interpretation by identifying dynamic-conserved residues.

Long-read sequencing reveals hidden structural complexity within Alzheimers disease-associated GWAS loci

The paper uses long-read sequencing to uncover structural complexity in Alzheimer's disease GWAS loci, showing that lead SNPs often miss key regulatory variants.

Qombucha: Reconstructing unobserved progenitor methylation profiles reveals distinct developmental programs in glioblastoma

Qombucha infers unobserved progenitor methylation profiles in GBM, revealing subtype-specific developmental programs and improved subtype classification.