matrix factorization

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.

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.

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.

Architecture of the Serotonergic Projectome in the Mouse Brain

Whole-brain axon tracing in 110 mouse brains divides raphe serotonin neurons into five projectomic groups, tied to transcriptome plus position and to dissociable behavioral effects of depletion.

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.

Principal Genes: A PCA-based approach to highly variable genes selection for scRNA-Seq analysis

This paper introduces a PCA-based method for selecting highly variable genes in scRNA-Seq data, showing it is comparable or better than dispersion-based methods and faster.

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.

Single-cell multimodal profiling of pan-cancer cell lines uncovers gene regulatory principles underlying intrinsic cell states and environmental features

This study constructs a pan-cancer single-cell multi-omic atlas to uncover gene regulatory principles in cancer cell states and environmental features across diverse cancer types.

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.

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 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.

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.

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.

Tracing cell communication programs across conditions at single cell resolution with CCC-RISE

The paper introduces CCC-RISE, a method to analyze cell-cell communication at single-cell resolution across conditions, identifying disease-relevant signaling programs and subpopulations.

Lifestyle-associated variation in type IV secretion systems between phytopathogenic and environmental Ralstonia

This study compares T4SS diversity between phytopathogenic and environmental Ralstonia species, finding more T4SS clusters in environmental strains and identifying a specialized cluster in phytopathogens.

Analysis of biological networks using Krylov subspace trajectories

The paper introduces a method using Krylov subspace trajectories for analyzing biological networks, demonstrating its application in community detection and perturbation analysis on the C. elegans neural network.

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.

SparseAEH: Scalable autoregressive expression histology discovery in spatial transcriptomics via sparse Gaussian kernels

SparseAEH accelerates spatial transcriptomics analysis by using sparse Gaussian kernels, achieving faster computation with accuracy comparable to existing methods.

Cross-species consensus atlas of the primate basal ganglia

The paper creates a cross-species consensus atlas of primate basal ganglia cell types using multiomic data from human, macaque, and marmoset, identifying 61 conserved cell types and a novel hybrid medium spiny neuron type.

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.

Integrated transcriptomic analysis reveals a metabolically quiescent state and gene expression networks related to intermediate and mature human 8-cell stage embryo resembling cells in vitro

The paper integrates scRNA-seq data to identify metabolically quiescent 8CLCs resembling human 8-cell stage embryos and characterizes their gene expression networks.

Vaccination with mRNA-encoded membrane-bound HIV Envelope trimer induces neutralizing antibodies in animal models

Membrane-bound BG505 MD39.3 Env trimer delivered as mRNA-LNP reduced base-directed antibody responses in rabbits and macaques and elicited neutralizing antibodies, with memory B cell responses documented in macaques.

Facilitate integrated analysis of single cell multiomic data by binarizing gene expression values

This paper shows that binarizing scRNA-seq data and integrating it with scATAC-seq data using TF-IDF and LSI improves clustering for multiomic analysis.

An integrated single-cell atlas of the limb skeleton from development through adulthood

The paper integrates ten scRNA-seq datasets to create a limb skeletal cell atlas covering development to adulthood, identifying 39 cell states and enabling cell-cell communication and perturbation studies.

Integrative, high-resolution analysis of single cell gene expression across experimental conditions with PARAFAC2-RISE

RISE, an adaptation of PARAFAC2, enables dimensionality reduction and analysis of single-cell RNA-seq data across experimental conditions by separating condition-specific effects from cell-to-cell variation.

Clustering individuals using INMTD: a novel versatile multi-view embedding framework integrating omics and imaging data

INMTD integrates omics and 3D imaging data to produce unconfounded individual subgroups with biologically meaningful embeddings.

Lifting the curse from high dimensional data: Automated projection pursuit clustering for the variety of biological data modalities

The paper introduces APP, a clustering method that reduces high-dimensional biological data to lower dimensions to improve clustering performance across multiple data types.

Multimodal neural correlates of childhood psychopathology

The paper identifies multimodal brain network patterns associated with dimensions of psychopathology using the Adolescent Brain Cognitive Development dataset.