clustering

The Human Gut Cell Atlas v1.0: A Unified, Community-Built Reference of Cellular Diversity Across the Gut

The paper presents the Human Gut Cell Atlas v1.0, a unified reference of gut cell diversity, revealing how tissue structure influences cellular composition and enabling disease and organoid analysis.

How aging reshapes implicit learning: behavioral and oscillatory evidence from an EEG-adapted Fast Mapping paradigm.

This study examines age-related changes in implicit learning using EEG and behavioral measures, finding that older adults show reorganized neural mechanisms for implicit encoding.

A Multi-Omic Phenobank Reveals Axes of Glioblastoma Growth, Invasion, and Therapeutic Vulnerability

The paper establishes a multi-omic PDX resource linking GBM invasion phenotypes to molecular programs and therapeutic responses, identifying two invasion modes and a neurodevelopmental factor associated with tumor growth and survival.

AnnZarro: scalable, interactive exploration of cell-by-cell and gene-by-gene relationships in single-cell data

AnnZarro enables interactive exploration of cell-by-cell and gene-by-gene relationships in single-cell data through a browser-based viewer linked to AnnData objects.

Revisiting Hydractiniidae (Hydrozoa): Mitogenomic Insights into the Diversity, Systematics and Life-Cycle Evolution of North Atlantic and Arctic Species

This study uses mitogenomic and morphological data to reassess hydractiniid diversity, species boundaries, and life-cycle evolution in North Atlantic and Arctic species.

An integrated multi-omic atlas of the choroid plexus highlights conserved molecular programs of epithelial function

This study integrates multi-omic data from mouse and human choroid plexus to identify conserved molecular programs of epithelial function across species.

Synaptic connectome of a neurosecretory network in the Drosophila brain

The paper characterizes the synaptic connectome of neurosecretory cells in Drosophila, revealing their regulatory roles in physiology and behavior through input and output pathways.

Unsupervised decomposition of massively parallel TraDIS-Xpress fitness data from Escherichia coli identifies distinct functional and expression modules of antimicrobial resistance determinants

This paper uses ICA to analyze TraDIS-Xpress data from E. coli, identifying functional modules of antimicrobial resistance genes across multiple stress conditions.

Ethnic differences in gut microbiota composition and functional capacity persist over six years in the HELIUS multi-ethnic longitudinal cohort

The paper tracks ethnic differences in gut microbiota composition and function over six years in a multi-ethnic cohort, finding persistent disparities despite shared environment.

The social structure of a captive group of Rüppell's vultures (Gyps rueppellii)

This study examines the social structure of captive Rüppell's vultures, revealing stable dominance hierarchies and complex social bonds influenced by breeding season and pair-bond status.

Mesodermal-niche interactions direct specification and differentiation of pancreatic endocrine cells in human multilineage organoids

The paper demonstrates that mesoderm-derived cells in organoids promote endocrine commitment and β-cell differentiation in human pancreatic development.

Characterisation of Genetically-Derived Patient Clusters Highlights Genetic Heterogeneity of Inflammatory Bowel Disease

The paper uses GenePy scores and clustering to identify genetic clusters in IBD patients, finding NOD2 and NLRP1 as significant drivers with phenotypic associations.

Circadian Timekeeping in the Tropics: Rhythmic Transcriptome and Diurnal Regulatory Networks in Rubroshorea leprosula

This study characterizes the circadian transcriptome of Rubroshorea leprosula, revealing conserved but less robust circadian rhythms compared to Arabidopsis.

NeuroGraphBench: Interacting with Drosophila Connectomes at Scale for Exploring the Functional Logic of Neural Circuits

The paper introduces NeuroGraphBench, a tool for interactively exploring Drosophila connectomes to model neural circuit function.

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.

Scalable methylome-transcriptome profiling resolves clonal organization in human hematopoiesis

This paper introduces Droplet-MT, a method for joint methylome and transcriptome profiling, enabling clonal organization analysis in human hematopoiesis with high scalability and resolution.

Linear NeuroPaint: An Efficient Baseline for Cross-Session Neural Alignment and Inpainting

Linear NeuroPaint evaluates a linear model for cross-session neural alignment and inpainting, finding it less accurate than nonlinear models but computationally efficient.

Concurrent de novo inference of cell types and gene regulatory networks with NetMap

NetMap jointly infers cell-level gene regulatory networks and clusters cells based on shared regulatory programs, outperforming existing methods on synthetic data and reliably detecting regulons on real data.

Absence of the Earths magnetic field activates stress-related brain circuits in a mammal

The study identifies stress-related brain circuits activated by the absence of Earth's magnetic field in mole-rats using a novel imaging pipeline.

Unraveling phenotypic variation in multiscale behavioral dynamics

Comparing coarse-grained dynamics across resolutions, weighted by sampling uncertainty, yields phenotypic spaces linking E. coli run speed to CheB and showing paramecia experience narrows zebrafish variability.

DAP12-deficient microglia adopt a TREM2-independent antigen-presenting state with a glial-to-neuronal cascade in Nasu-Hakola disease

The paper profiles NHD microglia and shows they adopt an antigen-presenting state without TREM2 dependence, triggering glial-to-neuronal changes.

Disrupted chromatin architecture blocks B lymphopoiesis in Down syndrome

The paper develops ChromE-seq to study 3D chromatin architecture in fetal hematopoiesis, finding that T21 disrupts B-lineage development by altering chromatin connectivity and regulatory circuits.

GenDiMug: a generic inclusive multigraph framework to analyze genomic organizations and -omics data at multiple scales

GenDiMug is a multigraph framework for analyzing genomic organization and multi-omics data across scales, revealing gene expression clumping and circadian regulation in a photosynthetic alga.

Gradients of local circuit architecture shape stability and information integration across the cortical hierarchy

This study uses biologically realistic simulations to show that cortical circuit stability and information integration increase with hierarchy, linked to increased connectivity and SST cell proportion.

Cell cycle exit is required for differentiation and cell fate diversification but not neoblast specialisation in planarians

This study shows cell cycle exit is necessary for terminal differentiation but not neoblast specialization in planarians, with lineage commitment occurring in cycling neoblasts.

Comparison of intracellular and encapsidated viral RNA reveals selective constraints on reovirus recombination

The paper compares recombination rates in intracellular and encapsidated reovirus RNA, finding higher recombination in intracellular RNA and suggesting recombination occurs more frequently during plus-strand synthesis.

Genomic insights into bacterial isolates dominating honeypot ant crop microbiomes reveal metabolically distinct Fructilactobacillus sp.

The paper investigates the genomic diversity and metabolic traits of Fructilactobacillus isolates from honeypot ant crop microbiomes and identifies factors contributing to their dominance.

A surviving beta cell subpopulation enriched in patients with T1D

Regulon-based clustering of islet scRNA-seq finds an IRF1-high, cytokine-driven beta cell state with reduced identity and autoantigen genes, enriched in type 1 diabetes donors.

Winnow-tax: sensitive and precise taxonomic profiling of low-coverage organisms in shotgun metagenomes

Winnow-tax improves taxonomic profiling of low-coverage shotgun metagenomes by combining sensitive read-level classification with genome-level confirmation, achieving better precision-sensitivity balance than existing methods.

Multilayer analysis reveals extensive hidden population complexity in a dairy starter microbiome comprising few species

The paper analyzes a dairy starter microbiome with low species richness using genomic and metagenomic data to reveal hidden population complexity and phage resilience.