matrix factorization

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

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.

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.

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

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

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.

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.

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

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

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.

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

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

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.

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.

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

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

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

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

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.

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.

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

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.

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

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

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

This study characterizes human cerebral cortex metabolic connectivity using PET-FDG data, finding a superior-inferior gradient driven by low-frequency signals.