clustering

A self-limiting mechanotransduction feedback loop ensures robust organ formation

The paper shows Yap mechanotransduction creates a self-limiting feedback loop for zebrafish semicircular canal formation, integrating mechanical forces and transcriptional responses to ensure robust development.

Water Kefir as a Model for Aggregative Development of Microbial Multicellularity within a Multispecies Biofilm

This study investigates water kefir grains as a model for microbial multicellularity, revealing an emergent growth function in multispecies biofilms.

Functional tradeoffs promote morphological disparity in the bat nasal cavity

The paper examines how functional tradeoffs in bat nasal cavity morphology, specifically turbinal structures, are influenced by echolocation mode and diet, revealing patterns of morphological diversity.

Southern South American Maize Landraces: A Source of Phenotypic Diversity

This study evaluates phenotypic diversity in Argentine maize landraces, finding substantial variation and associations between traits and altitude.

scProfiterole: Clustering of Single-Cell Proteomic DataUsing Graph Contrastive Learning via Spectral Filters

The paper introduces scProfiterole, a framework for clustering single-cell proteomic data using graph contrastive learning with spectral filters, showing improved cell type identification.

Systematic evaluation of integration methods and parameters on single-cell RNA-sequencing biological insights: a case study on cattle embryos.

The paper evaluates integration methods and parameters on cattle embryos to assess their impact on biological insights, finding that parameter choices affect cell type classification and functional interpretation.

A synthetic xeno-free extracellular matrix surrogate supports robust human induced pluripotent stem cell maintenance and multilineage differentiation

This study demonstrates that BIOINSTRUCT, a synthetic extracellular matrix surrogate, supports robust human iPSC maintenance and multilineage differentiation comparable to Matrigel.

Spatiotemporal Mapping of Glomerular Endothelial Regeneration Identifies Apold1 as an Intrinsic Regulator of Repair

This study identifies Apold1 as a key regulator of glomerular endothelial regeneration using single-cell RNA sequencing and spatial transcriptomics in a mouse model.

Learning Interpretable Switching Dynamics in Shared Neural-Behavioral Latent Space

This paper introduces SSLD, a framework that learns shared neural-behavioral latent dynamics and private modality-specific variables, showing it accurately reconstructs signals and isolates behaviorally relevant information across multiple datasets.

Fluorescence-based sorting of extracellular vesicles enables detection and omics

This paper develops a NanoFACS workflow for isolating and characterizing extracellular vesicles with high purity and RNA yield for downstream analysis.

VesiScope: A stand-alone tool for the automatic detection, quantification and size analysis of GUVs from phase contrast microscopy images

VesiScope detects and analyzes GUVs from phase contrast images using a YOLOv11 model, enabling accurate and efficient label-free quantification.

Perceptual decision-making: extending a standardized rodent task to humans

The paper compares perceptual decision-making strategies between humans and mice using a standardized task, finding that instructed humans perform better than uninstructed humans.

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.

Evolutionarily informed gene sets reveal conserved and lineage-modified transcriptional programs during vertebrate forebrain evolution

This study uses a multispecies comparative framework to analyze forebrain cell types across vertebrates, revealing conserved transcriptional programs and lineage-specific modifications.

Programmable antigen-presenting scaffolds expand rare tumor-antigen-specific T cells from peripheral blood

This paper introduces APC-ms, a platform that expands rare tumor-antigen-specific T cells from peripheral blood, achieving higher enrichment and functional properties compared to conventional methods.

SpatialOmicsLab: an integrated research environment for AI co-scientists in spatial transcriptomics

SpatialOmicsLab provides an integrated environment with AI tools for spatial transcriptomics analysis, outperforming expert workflows in multiple tasks.

Genotype-dependent behavioral signatures of opioid withdrawal revealed by automated behavioral quantification

This study uses automated behavioral quantification to show that opioid withdrawal behaviors vary with genetic background, but severity can still be assessed within strains.

Automated Segmentation and Tractography of Brainstem and Subcortical White Matter

The paper develops an automated pipeline for segmenting and parcellating brainstem and subcortical white matter pathways using diffusion MRI data.

"Spilling-in" versus "Filling-in": Disentangling bottom-up drive from predictive completion in human V1 to V3

The paper dissociates bottom-up and top-down contributions in human visual areas V1-V3 using BOLD responses to full-field and central scotoma stimuli.

Septins regulate cytokinesis and multicellular development in the closest living relatives of animals

This study shows that septins regulate cytokinesis and multicellular development in Salpingoeca rosetta, a choanoflagellate closely related to animals.

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.

Estimating the completeness of large-scale single-cell sequencing projects

This paper estimates the completeness of large-scale single-cell sequencing projects using ecological richness metrics applied to cellular diversity data.

Multi-Trajectory Pseudotime Inference via Permutation Factorizations

Factorizing multiple monotone pseudotimes into one shared donor permutation plus cluster-specific warps (HiP-BIND) yields Alzheimer's donor orderings agreeing better with Braak, ADNC and CERAD staging than single-trajectory B-BIND.

scStable: assessing scRNA-seq analysis stability under bulk-derived between-sample variation

scStable evaluates scRNA-seq analysis stability by generating synthetic samples with between-sample variation, showing better performance than existing methods in gastric cancer data.

Accurate Reconstruction of Adaptive Immune Receptor Repertoires from FACS-partitioned B and T Cell Subsets

The paper develops computational methods to accurately reconstruct adaptive immune receptor repertoires from partitioned B and T cell subsets, showing improved accuracy compared to pooling sub-repertoires.

Redundancy relocated: the distributed metaparalog pool of an Arctic Pelagibacterales population

The paper analyzes metaparalog diversity in an Arctic Pelagibacterales population, showing high diversity within a single population and highlighting the importance of pangenome studies for microbiology.

Connectomics by Sequencing Reveals Self-Organizing Principles of Neuronal Networks in Cerebral Organoids

The paper develops COSCO to map neuronal connectivity in cerebral organoids and shows self-organizing network motifs and disease-related topological changes.

Retinal cell mosaics in the valproate-induced rat model of autism spectrum disorder

The paper examines changes in retinal neuron density and spatial organization in a rat model of autism spectrum disorder induced by prenatal valproate exposure.

Information regimes in population-graph neuroimaging: cohort context and implementation-dependent evaluation sensitivity

The paper evaluates how population-graph models' performance varies with evaluation context, showing implementation-dependent differences in AUC across splits.

Developmental enrichment reorganizes the directional topography of mouse proprioceptive cortex

This study shows that environmental enrichment reorganizes the directional topography of mouse proprioceptive cortex by coordinating its sensory and motor components.