clustering

Nation-scale recovery of complete environmental plasmids pushes the boundaries of plasmid diversity through long-read sequencing

The paper expands plasmid diversity by analyzing long-read metagenomes, identifying novel plasmid lineages and providing tools for plasmid discovery.

Conserved synteny reveals a saccharolytic lifestyle across Kiritimatiellia

The paper uses conserved synteny analysis to reveal a shared saccharolytic lifestyle across Kiritimatiellia genomes.

Spatially resolved transcriptomics of poplar reveals tissue organization across shoot-associated organs

This study creates a spatial transcriptome atlas of poplar shoot-associated organs, revealing tissue organization and gene expression patterns across different developmental stages and anatomical contexts.

Mastodon: the Command Center for Large-Scale Lineage-Tracing Microscopy Datasets

Mastodon is a software platform for analyzing large-scale lineage-tracing microscopy datasets, enabling manual and automated cell tracking and lineage analysis in complex 3D geometries.

How the brain distinguishes a bilingual's languages is partly shared across people and partly their own

The paper decodes language state in bilinguals using fMRI and identifies shared and individual brain organization patterns.

REZCUE: Rescuing 3D spatial omics from archived FFPE tissue

REZCUE enables 3D spatial multi-omic analysis of archived FFPE tissue by preserving nucleic acids and proteins for subsequent assays.

Sensory receptor expansion and neural accommodation in butterfly color vision

The paper investigates how butterflies expand their color vision by adding a second R7 photoreceptor and how the brain accommodates this change through developmental mechanisms.

Distinct bacterial and protist plankton diversity dynamics uncovered through DNA-based monitoring in the Baltic Sea area

The paper analyzes protist and bacterial diversity in the Baltic Sea using DNA metabarcoding, finding salinity has a stronger effect on bacterial than protist communities.

Temporal organization of shared brain states characterizes heterogeneity in major depressive disorder

This study identifies shared brain states in MDD and healthy controls using resting-state fMRI and hidden Markov modeling, revealing two distinct neurodynamic architectures associated with different symptom patterns.

3D MERFISH reveals cell-type diversity generated by mRNA partitioning in spiralian embryogenesis

The paper uses 3D MERFISH to show that mRNA partitioning during cell division generates transcriptomically distinct cell types in Crepidula atrasolea embryos.

Directionally tuned signals in mouse visual and subicular cortex during passive rotation

This study compares directional activity in mouse visual and subicular cortex during passive rotation, finding differences in how visual cues influence their directional tuning.

Conserved cellular architecture and developmental mechanisms of the zebrafish meninges

This study defines zebrafish meningeal development, identifies conserved Foxc1 and Wnt signaling roles, and reveals limited regenerative capacity and developmental defects upon meningeal loss.

Generating a Collection of Single-Gene Deletions in the eps Operon in Bacillus subtilis Strain NCIB 3610

The paper generates single-gene deletions in the epsA-O operon of Bacillus subtilis to assess gene contributions to EPS production and biofilm formation.

The RNA-binding protein TRIM71 Promotes Supporting Cell Reprogramming and Hair Cell Regeneration by Activating Sall4

This study shows TRIM71 promotes hair cell regeneration by reprogramming supporting cells and activating Sall4 in cochlear organoids and explants.

Conserved Fibroblast Subsets Drive Shared Fibrotic Mechanisms in Osteoarthritis Synovium and Systemic Sclerosis Skin

This study identifies conserved fibroblast subsets and fibrotic mechanisms in osteoarthritis and systemic sclerosis using single-cell RNA-seq and spatial transcriptomics.

Machine Learning Identification of Functional Trait Syndromes Associated with Responsiveness to Arbuscular Mycorrhizal Fungi

The paper develops a machine learning framework to predict plant responsiveness to arbuscular mycorrhizal fungi using functional traits and environmental variables, finding that specific leaf and root traits are key predictors.

Slice, Subtract, Segment: Efficient 2D and Physiologically Informed 3D Brain Tumor Segmentation

This paper evaluates two approaches for improving brain tumor segmentation: a novel 2D U-Net architecture and a multi-channel input representation using cross-modal subtraction maps, showing both contribute to performance improvements.

Large Language Models Predict Human Social Behavior via Interpretable Mechanisms

This study evaluates LLMs' ability to predict human social behavior through interpretable cognitive models in socioeconomic games.

Deep Learning-Meets-Active Surfaces: A Unified Framework for Multi-Object Segmentation and Shape Analysis in 3D Fluorescence Microscopy

This paper introduces Nagini3D, a 3D image segmentation method combining deep learning and active surfaces for improved shape analysis and consistency across 3D volumes.

Intrinsic dimensionality of deep learning representations reveals cell death-associated heterogeneity in Parkinsons disease iPSC-derived neurons

The paper uses deep learning to identify cell death-related heterogeneity in Parkinson's disease iPSC-derived neurons by analyzing intrinsic dimensionality.

Macrophages from Holstein and Normande cows respond differently to Escherichia coli and Streptococcus uberis

The paper compares immune responses of Holstein and Normande cattle macrophages to E. coli and S. uberis, finding breed-specific gene expression differences and differential bacterial survival.

BettaAI: a machine-learning object detection model for the quantification of aggressive displays in the Siamese fighting fish Betta splendens

BettaAI is a deep learning model that accurately detects and quantifies aggressive displays in Siamese fighting fish using video analysis.

Behavioral arousal organizes visual cortical population micro-states across the sleep-wake cycle

The paper shows that visual cortical population micro-states are organized by behavioral arousal rather than discrete sleep-wake states in mice.

Genomically and ecologically cohesive subspecies as biologically meaningful units in the global ocean microbiome

The paper identifies genomically discrete and ecologically cohesive subspecies in the global ocean microbiome, showing they are biologically meaningful units driven by environmental factors.

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.

Epigenetic regulators partition the genome by evolutionary and developmental constraint

The paper uses single-cell RNA sequencing to analyze mutant phenotypes of epigenetic regulators in mouse embryos, revealing how these regulators partition the genome based on developmental and evolutionary constraints.

Matched primary-metastasis single-nucleus and spatial profiling of leiomyosarcoma identifies antigen-presenting fibroblasts at the tumor-organ interface

This study uses single-nucleus RNA sequencing and spatial transcriptomics to compare primary and metastatic leiomyosarcoma, identifying antigen-presenting fibroblasts associated with metastasis.

Targeting catecholate siderophore systems enables precision depletion of gut enterobacteria during colitis

This study shows that targeting catecholate siderophore systems reduces AIEC colonization in colitis by immunization, preserving gut microbiome composition.

Explainable t-SNE for Single-Cell RNA-seq Data Analysis: A Cell-DrivenInformation Fusion Framework

The paper introduces c-UMAP, a cell-driven information fusion framework for single-cell RNA-seq data that improves clustering accuracy and interpretability over traditional methods.

Slide-level batch structure limits histology-guided supervision of transcriptomic foundation models

This paper investigates whether histology can improve transcriptomic foundation models by providing cross-modal supervision, but finds limited benefits due to slide-specific structure in gene-expression embeddings.