clustering

Genomic insights into the human gut commensal Megasphaera elsdenii: Relatedness and metabolic potential compared to animal isolates

This study compares Megasphaera elsdenii genomes from human and animal gut isolates, finding they are genetically similar and share metabolic functions, with no host-specific clustering or virulence genes.

Macaque Area LIP Reflects Confidence-Dependent Changes in Decision Policy

This study shows that neural activity in macaque lateral intraparietal area (LIP) reflects confidence-dependent changes in decision policy, linking confidence to subsequent decision-making.

Integrative taxonomy using traits and genomic data for Species Delimitation with Deep learning

This paper introduces a deep learning method that integrates genomic and trait data to improve species delimitation in complex speciation scenarios.

OocystMeter, a machine-learning algorithm to count and measure Plasmodium oocysts, reveals clustering patterns in the Anopheles midgut

OocystMeter automates oocyst counting and sizing in mosquito midguts, revealing clustered spatial patterns in malaria infections.

Data-driven gait cycle decomposition based on whole-body coordination dynamics

This study decomposes gait cycles using a dynamic system framework to identify coordination patterns in human locomotion.

STRIDE: A Sequencing Depth-Insensitive Metric for Robust Comparison between Sparse Chromosome Conformation Capture Data

This paper introduces STRIDE, a sequencing depth-insensitive metric for comparing sparse single-cell Hi-C data, enabling robust analysis of 3D genome organization.

Comparative genome analysis of Corynebacterium ulcerans Japanese isolates revealed domestically and globally diverse geographical distribution of the organism of different types.

The paper analyzes over 700 genomes of Corynebacterium ulcerans and C. ramonii isolates to reveal geographic differences in sequence types and toxigenic prophage compositions, with ST337 predominating in Japan and associations between prophage types and toxin production.

Programmable acoustic single cell manipulation with model-free machine learning

This paper introduces VeLO, a model-free machine learning algorithm for programmable two-dimensional single-cell manipulation using acoustic standing waves, achieving robust control across multiple cell types.

The Compositional Encoding of Hand-Eye Coordinated Movements for Single Neurons in the Posterior Parietal Cortex

The paper shows that PPC neurons encode hand-eye movements additively, allowing modular decoding of coordinated movements.

3D Reconstruction of Nanoparticle Distribution in Tumor Spheroids with Volume Electron Microscopy

The paper presents an end-to-end pipeline for segmenting nanoparticles and cellular structures in 3D electron microscopy data of tumor spheroids, revealing preferential NP clustering near nuclei.

Isolation to Extinction: Landscape Fragmentation and Connectivity in Sloth Bears of the Indian Terai

This study uses landscape genetics to analyze sloth bear populations in the Indian Terai, finding agriculture and proximity to water as key barriers to gene flow and highlighting low genetic diversity.

Increasing Cancer Stemness Drives Prostate Cancer Progression, Plasticity, Therapy Resistance and Poor Patient Survival

This study quantifies cancer stemness in prostate cancer across progression stages, showing its association with therapy resistance, poor survival, and lineage plasticity.

FennoTraits: Dataset of plant functional traits and community composition in northern European flora

The paper introduces FennoTraits, a dataset of plant functional traits and community composition from northern European flora, highlighting trait patterns and species distribution across seven study areas.

A historical specimen of False Lingzhi (Ganoderma lucidum) resolves a 245-year-old confusion within an important medicinal mushroom group

The paper resolves a 245-year-old taxonomic confusion between Ganoderma lingzhi and G. lucidum using a historical specimen and genomic analysis, showing they diverged over 12 million years ago.

Beyond the Billion: Dose-Response Immunophenotyping and Machine Learning Classification of Live versus Heat-Inactivated Gram-Positive Probiotic Strains in Human Peripheral Blood Mononuclear Cells

This study challenges assumptions about probiotic efficacy by showing heat-treated strains can match live strains in immunological activity at higher doses, using flow cytometry and machine learning to classify probiotic strains.

CULTURE AND ISOLATION OF BACTERIA ASSOCIATED WITH MEDITERRANEAN CORALS

The paper isolates and cultures bacteria from four Mediterranean corals, identifying 84 pure isolates, including novel species, to better understand their roles in the coral holobiont.

Single-cell multiomics reveals archetypal regulatory programs shared across CD4 and CD8 T cell subsets in viral infection

Quantitative assessment of mesoscale cellular order and organization in the mouse hippocampus

The paper quantifies mesoscale cellular organization in the mouse hippocampus using a new software tool, revealing cell-type-specific nuclear shape variations and positionally ordered but orientationally disordered dense regions.

Immune-Epithelial Interactions via TGF-β Orchestrates Stem-Cell Niche Formation and Morphogenesis

This study shows immune cells influence stem-cell niche formation and organoid development through TGF-β signaling in a 3D breast organoid model.

Rapid thermoforming of polycarbonate cell culture accessories from 3D printed molds

This paper introduces a method to rapidly create customized, autoclavable cell culture accessories using polycarbonate thermoforming from 3D printed molds, demonstrating compatibility with human iPSC culture and differentiation.

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.

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.

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.

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.

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.

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.

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.

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.