matrix factorization

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.

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.

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.

Reference-guided comparative genomics of seven Indonesian rice cultivars identifies conserved gene space and trait-associated sequence candidates

The paper generates consensus genomes for seven Indonesian rice cultivars, identifies conserved gene space, and prioritizes trait-associated sequence candidates for functional validation.

Genomic resources of Ascidiella aspersa and comparative analysis across tunicates reveal class-level features and evolutionary diversification

The paper constructs genomic resources for Ascidiella aspersa and 35 other tunicate species, revealing class-level genomic features and evolutionary patterns through comparative analysis.

Comparative genomic and transcriptomic analyses of Strongylus vulgaris reveal developmental and evolutionary deployment of parasitism in a migratory equine nematode

This paper presents a genomic and transcriptomic analysis of Strongylus vulgaris, revealing developmental and evolutionary aspects of its parasitic lifestyle and identifying key genes and isoforms involved in its biology.

An Integrative Single-Cell Epigenomic Atlas Annotates the Regulatory Genome of the Adult Mouse Brain

The paper constructs an integrative single-cell epigenomic atlas of the adult mouse brain, mapping chromatin states and gene regulatory programs across 100 cell subclasses.

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.

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.

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.

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.

CanVAS: A Harmonized and Imputed Canine Variant Atlas1

CanVAS harmonizes and imputes canine genotype data from multiple sources to create a unified resource for genetic studies.

A Curated Compendium of Transcriptomic Data for the Exploration of Neocortical Development

The paper compiles a large transcriptomic dataset of neocortical development and uses joint matrix decomposition to identify conserved transcriptome dynamics across mammals and developmental stages.

Shared and organ-specific gene expression programs of fibrotic diseases

This paper performs a cross-organ meta-analysis of single-cell transcriptomic data to identify shared and organ-specific gene expression programs in fibrotic diseases.

A multi-omics atlas of human hindbrain development

This paper creates a multi-omics atlas of human hindbrain development, revealing cellular diversity, regulatory programs, and disease relevance.

On ARGs, pedigrees, and genetic relatedness matrices

This paper introduces branch relatedness and efficient algorithms for computing branch GRMs using tree sequences, enabling large-scale genomic analysis.

Uncovering the Genetic Blueprint of the UAE's National Tree: Genomic Evidence to Guide Prosopis cineraria (L.) Druce Conservation

This study presents the first population genomics analysis of Prosopis cineraria in the UAE, identifying genetic clusters and diversity patterns to inform conservation strategies.

skDER & CiDDER: two scalable approaches for microbial genome dereplication

The paper introduces two tools, skDER and CiDDER, for microbial genome dereplication to select representative genomes for comparative genomic studies.

TF2TG: an online resource mining the potential gene targets of transcription factors in Drosophila

TF2TG integrates TF-DNA binding, protein-protein interactions, and transcriptomic data to identify and rank potential target genes for Drosophila transcription factors.

Uncovering Latent Biological Function Associations through Gene Set Embeddings

This study uses gene set embeddings to uncover biological function associations across species by integrating node2vec with MSigDB data.

Hypothesis Generation For Rare and Undiagnosed Diseases Through Clustering and Classifying Time-Versioned Biological Ontologies

This paper identifies potential gene-to-phenotype connections for undiagnosed diseases by clustering time-versioned biological ontologies and analyzing network data.

PARMIK: PArtial Read Matching with Inexpensive K-mers

PARMIK improves metagenomic sequence search by using inexpensive k-mers to achieve higher recall and faster alignment than BLAST.

SCIITensor: A tensor decomposition based algorithm to construct actionable TME modules with spatially resolved intercellular communications

SCIITensor constructs actionable TME modules by analyzing spatially resolved intercellular communications in ST data, identifying immunosuppressive patterns and sample-common immune-infiltration modules.

Connecting the Dots: Approaching a Standardized Nomenclature for Molecular Connectivity Combining Data and Literature

The paper introduces a standardized nomenclature for PET-based molecular connectivity and covariance to improve reproducibility and interpretation across imaging modalities and radiotracers.

Analysis of Methicillin Resistance in Staphylococcus Aureus Sepsis Using TDbasedUFE

The paper uses TDbasedUFE to analyze scATAC-seq data from S. aureus sepsis patients, identifying genes with differential responses between methicillin-resistant and sensitive strains and their functional associations.

Fulgor: A fast and compact k-mer index for large-scale matching and color queries

Fulgor is a compact k-mer index for efficient sequence matching and color queries, outperforming existing methods in space and speed.

Fast, lightweight, and accurate metagenomic functional profiling using FracMinHash sketches

This paper introduces fmh-funprofiler, a fast and lightweight metagenomic functional profiler using FracMinHash sketches, showing improved purity and speed compared to alignment-based methods.

Single-cell multi-omics map of human foetal blood in Down's Syndrome

This study integrates single-cell multi-omics data from human foetal blood to show that trisomy restructures enhancer-gene maps, leading to dysregulated erythroid differentiation and haematological abnormalities in Down's Syndrome.

Delineating mouse β-cell identity during lifetime and in diabetes with a single cell atlas

This paper integrates multiple scRNA-seq datasets to create a mouse islet atlas, revealing new insights into β-cell states and differences across diabetes models.