clustering

Chaos and repetition in algal evolution: A Chrysophyceae eco-genomic framework

This study explores the eco-genomic diversity of Chrysophyceae algae, revealing their evolutionary adaptations and gene markers linked to trophic strategies and environmental responses.

High-resolution analysis of T cell subsets, clonality, and trajectories in psoriasis

This study analyzes T cell subsets, clonality, and trajectories in psoriasis using single-cell RNA and TCR sequencing, revealing tissue-specific and shared features of the T-cell repertoire.

Growing Macroscopic Functional Human Tissues on 3D Printed Peptide Hydrogels

This study demonstrates growing macroscopic functional human tissues on 3D-printed peptide hydrogels, enabling centimeter-scale neural organoids and directional axonal communication.

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.

Host genetics structure Symbiodiniaceae and prokaryotic assemblages and their co-variation in sympatric fire coral species

The paper investigates how host genetics and environment shape symbiont communities in fire corals, finding host genetics have a stronger influence than environment on microbiome composition.

Weaning imprints a hybrid cytotoxic-regulatory identity on intestinal CD4+ T lymphocytes

This study tracks intestinal CD4+ T cells from suckling to adulthood, showing they adopt a transient cytotoxic-regulatory state at weaning, influenced by microbiota and early-life commensals.

Timed binary WNT activity is sufficient to model the early human neural axis

This paper shows that timed WNT pulses can specify distinct neural domains in human pluripotent stem cells, enabling the generation of specific neuron and progenitor 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.

Movements for Grooming in Rhesus Macaques Co-opted from Feeding Movements

This study shows that grooming movements in rhesus macaques are adapted from feeding movements, with similar hand motions used for both tasks.

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.

Vascular specification from diversified mesoderm culminates in endothelial convergence

This study reconstructs mouse vasculogenesis using single-cell and spatial analyses, revealing a transient vascular-primed state and the role of VEGF in endothelial specification.

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.

A rare pre-existing progenitor-like Primed SMC compartment is the dominant inferred source of SMC-derived cellularity in vascular injury and atherosclerosis

Inferring somatic copy number aberrations from spatial transcriptomics data to study early cancer development

This study infers somatic copy number aberrations from spatial transcriptomics data to identify spatially coherent SCNA-defined populations in early cancer development.

Rapid changes in wing size and shape during the transition to laboratory conditions in a Neotropical drosophilid

This study tracks rapid wing size and shape changes in Drosophila sturtevanti across generations in lab conditions, showing genetic and environmental influences on morphology.

Genetic drivers shape TREM2-dependent myeloid responses and glioblastoma progression

This study shows TREM2's role in glioblastoma depends on genetic context and timing, with different effects in Nf1-silenced/Ras-driven and PDGFB-driven models.

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.

Cornealia: automated collective order analysis reveals density-dependent reorganization of donor corneal endothelium

Cornealia analyzes collective order in donor corneal endothelium, revealing density-dependent reorganization and mechanical responses not captured by traditional metrics.

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.

Systematic genome analysis enables long-overdue taxonomic reorganization of genus Orthoflavivirus; potential assignment of over 50 new species

The paper proposes a genetic divergence threshold for demarcating orthoflavivirus species, identifying 25 new Euflavivirus and 33 new Fusivirus species.

Climate-associated genomic variation across life stages reveals population-specific signals of local adaptation in European beech

The paper identifies climate-associated genomic variation in European beech across life stages, revealing population-specific adaptive responses to temperature and precipitation changes.

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.

Dissociating Resting-State Networks of Pedohebephilic Preference and Child Sexual Offending Using Network-Based Prediction

The paper distinguishes pedohebephilic preference from child sexual offending using resting-state functional connectivity and network-based prediction, identifying distinct neural network alterations.

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.

Cardiomyocyte Identity Crisis Without Regenerative Re-entry: A Multi-Scale Atlas of Incomplete Dedifferentiation and Intercellular Communication Rewiring in the Infarcted Human Heart

The paper constructs a multi-scale atlas of cardiomyocyte changes in infarcted hearts, showing partial identity loss without regenerative proliferation and altered intercellular communication.