matrix factorization

Evolutionary dynamics of Aegilops revealed through comparative genome assembly of all 25 species

The paper presents high-quality genome assemblies for all 25 Aegilops species, revealing evolutionary dynamics and gene content variation through comparative genomics.

Spatial transcriptomic programs relate to spectrolaminar rhythms across macaque cortex

The paper develops a spectro-omic framework to relate spatial transcriptomics and laminar LFP dynamics in macaque cortex, finding transcriptomic predictors improve spectral composition prediction.

Assessing tensor decomposition quality of immune profiling data from a dictionary learning perspective

The paper introduces metrics for assessing tensor decomposition quality in immune profiling data using a dictionary learning framework.

FEATMAP: Targeted Correction of Acquisition Signatures Harmonizes Medical Foundation Model Embeddings and Enables Robust Task Generalization

FEATMAP corrects acquisition signatures in medical foundation model embeddings to improve cross-condition similarity and task generalization without retraining.

Within-family attenuation of polygenic risk score accuracy: Investigating the effects of principal component analysis, LD score regression, and mixed model association in the UK Biobank

This study evaluates how population structure adjustment methods affect polygenic risk score performance in within-family settings using UK Biobank data.

Mouse-to-human modeling of microglia single-nuclei transcriptomics identifies immune signaling pathways and potential therapeutic candidates associated with Alzheimer's disease

The paper integrates mouse and human microglia transcriptomics to identify AD-related pathways and drugs using TransComp-R, finding FDA-approved drugs that mimic healthy human microglia in mice.

State-Dependent Transcriptomic Collapse of the Brain's Lactate and Ketone Thermodynamic Sensors in Schizophrenia

The paper identifies structural genomic variances in the HCAR2/HCAR1 locus that disrupt thermodynamic sensing in schizophrenia, linking metabolic dysfunction to clinical symptoms.

Revisiting the genome assembly of Lupinus species reveals differential diploidization after a shared whole-genome duplication

The paper corrects genome assemblies of two Lupinus species, revealing differential diploidization after a shared whole-genome duplication across six Lupinus species.

Genomic insights into bacterial kidney disease resistance in Arctic charr (Salvelinus alpinus) via a 72k SNP array

This study develops a 72k SNP array to assess BKD resistance in Arctic charr and finds genomic prediction is feasible with moderate accuracy.

ParTIpy: A Scalable Framework for Archetypal Analysis and Pareto Task Inference

ParTIpy scales archetypal analysis for biological trade-offs and integrates with single-cell workflows, enabling task inference in large datasets.

Disentangling adiposity-related and non-adiposity-related genetic pathways for type 2 diabetes

This paper identifies 29 circulating proteins associated with type 2 diabetes risk independent of BMI using GWAS-by-subtraction, proteome-wide Mendelian randomization, and colocalization analyses.

A network approach to DNA methylation clocks

This paper uses a network approach to analyze DNA methylation clocks, revealing module structures that improve clock performance and transferability across platforms.

A Multi-Context Regulome-Wide Association Atlas for Genetic Studies of Aging Brain Disorders

This paper introduces FGMB, a multi-context regulome-wide association atlas, and applies it to Alzheimer's disease to identify 327 regulatory associations and resolve 86 gene-molecular-trait pairs.

Rapid and consistent clustering of millions of genomes highlights the diversity of prokaryotic life

The paper introduces a fast clustering tool for bacterial genomes, enabling efficient analysis of millions of genomes and revealing taxonomic insights.

A systematic imputation framework for sparse, multimodal space biology datasets: application to retinal imaging and omics from the RR9 mission

The paper presents a framework for imputing sparse, multimodal space biology datasets and shows that MICE-Elastic and a hybrid strategy preserve biological signal better than other methods.

The blueprint of human functional architecture shifts from cognition to anatomy during perturbations of consciousness

This study shows that cognitive co-activation dominates fMRI synchrony in the awake brain but is replaced by anatomical and molecular constraints during consciousness perturbations.

A Unified Spatial AI Framework for Cross-Domain Tissue-State Analysis in Trauma, Oral, and Cardiovascular Pathology

This paper develops a spatial AI framework to identify conserved tissue-state organization across trauma, oral, and cardiovascular pathology using spatial transcriptomic data, finding six conserved fuzzy tissue states.

Salmonella Genomic Markers for Risk to Food Safety

The paper identifies genomic markers in Salmonella isolates that correlate with infection risk, showing lineage-specific associations and a conserved prophage marker in Salmonella Agona.

Comparative Proteomics Across Tissues and Crop Agroecosystems Reveals Agricultural Stressor Responses in the Western Honey Bee

The paper uses tissue-resolved proteomics to analyze how pesticide and pathogen stressors affect honey bee tissues across crop ecosystems, finding stable tissue-specific patterns and crop-associated changes.

Population genomics reveals divergent lineages across Europein the vulnerable mire plant Drosera rotundifolia

This study uses population genomics to show genetic differentiation and structure in Drosera rotundifolia across Europe, linked to climate and postglacial history.

Non-saturating dimensionality, contextual dependence, and the limits of unsupervised decoding in motor cortex

The paper shows that unsupervised dimensionality in motor cortex does not reflect movement complexity but instead scales with neuron count and is context-dependent, challenging assumptions about neural representation.

Diversity, host-specificity, and environmental drivers of the coral reef eukaryome

The paper characterizes the eukaryotic diversity in coral reef environments, revealing high diversity and identifying environmental drivers shaping these communities.

Multi-Omics Characterization of Human Molecular Responses to Spaceflight Across Two Independent Missions

This study analyzes multi-omics data from two spaceflight missions to identify molecular changes in immune, skeletal, and vascular systems, providing insights for mitigating health risks during space travel.

Reachability-Preserving Minimum Edge Cut Problem and Applications in Biology

The paper introduces the Reachability Preserving Minimum Edge Cut problem to model biological pathway interventions, showing when fast algorithms work and when exact methods are needed.

Competition among freshwater clades explains cave colonization in blind cavefishes

The paper uses genomic data to determine whether flatfish asymmetry evolved once or multiple times, finding strong support for a single origin.

Region-specific cortico-striatal transcriptomic remodeling following early postnatal dopaminergic disturbance

This study identifies region-specific transcriptomic changes in the prefrontal cortex and striatum of mice with early postnatal dopaminergic disturbance using bulk RNA-seq and WGCNA.

Unraveling a comparative landscape of protein-coding genes linked to neuroimmune function during adulthood consequent of prenatal alcohol exposure

This study identifies region-specific neuroimmune gene expression changes in adult mice following prenatal alcohol exposure, revealing proinflammatory pathways and transcriptional regulators linked to FASD.

A Multi-Omics Atlas of Naturally Occurring Myelomeningocele in a Large-Animal Model Reveals Heritable Architecture.

The paper presents a multi-omics atlas of myelomeningocele in sheep, identifying heritable genetic and epigenetic factors and shared biological pathways across tissues.

A Pleiotropic Map of Brain Imaging Genetics Reveals Biologically Distinct Latent Endophenotypes

The paper introduces DIMPLE-GWAS, a dimensionality reduction framework for GWAS of brain scans, identifying 25 latent phenotypes with higher heritability and discovering 104 new significant loci.

BandHiC: a memory-efficient and user-friendly Python package for organizing and analyzing Hi-C matrices down to sub-kilobase resolution

BandHiC reduces memory usage for Hi-C matrices by 99% using a banded storage strategy while enabling efficient analysis of ultra-high-resolution data.