clustering

Global distribution and host specificity of plastid-bearing microeukaryotes across coral holobionts

The paper analyzes 16S rRNA gene datasets to study the diversity and distribution of plastid-bearing microeukaryotes in corals, finding widespread symbionts and host-specific patterns.

Epigenomic heterogeneity and spatial organization during human reprogramming

This study examines epigenomic and spatial changes during human reprogramming, finding distinct molecular and spatial patterns in productive versus unsuccessful trajectories.

Automated CAR-T Cell Manufacturing: from Research to Point of Care production.

This paper describes LimCORE, an automated system for CAR-T cell manufacturing that achieves comparable performance to existing methods while reducing operator time.

Reforestation without Belowground Recovery: Sediment Microbiomes and Organic Carbon in Caribbean Mangroves

This study shows that mangrove reforestation in the Caribbean does not restore sediment organic carbon or microbial communities to reference levels within a few years.

Computational identification of responding T cell clones from longitudinal repertoire sequencing

This paper introduces CloneSearch, a method to identify expanding and contracting T cell clones from longitudinal TCR sequencing without requiring antigen-specific information.

A novel clonal and axenic isolation pipeline for the human gut protist Blastocystis reveals within-subtype strain coexistence

This study develops a new cultivation method for Blastocystis, revealing that multiple strains can coexist within a single host.

CnidoSite: A Multi-Omics Database for Cnidarians

CnidoSite provides a centralized multi-omics database for cnidarians, integrating genomic, transcriptomic, proteomic, and phenotypic data to study thermal tolerance and environmental adaptation.

Social Approach Dynamics in Freely-Moving Rat Dyads are Not Impacted by Lesions to the Retrosplenial Cortex

This study shows that lesions to the retrosplenial cortex in rats do not significantly affect social approach dynamics during interactions with a social stimulus.

Establishment of Rabbit Formative-like Pluripotent Cells by Bidirectional Modulation of WNT Signaling Pathway

This paper establishes a culture system called KFiC to generate and maintain formative-like pluripotent rabbit embryonic stem cells with developmental plasticity and cross-species compatibility.

Virtual lineages: in silico lineage tracing from single-cell and spatial transcriptomes

isCORAL infers clonal relationships and cell-fate dynamics from single-cell and spatial transcriptomes, outperforming existing methods in lineage reconstruction and memory-gene identification.

Developmental trajectories organize the assembly of valence circuits in the central amygdala

The paper identifies developmental trajectories that organize valence-specific circuit assembly in the central amygdala using single-cell profiling and molecular analysis.

A community benchmark enables high-resolution, cross-lab quantification of mouse social behavior

The paper introduces a benchmark dataset and tool for cross-lab quantification of mouse social behavior, achieving high-resolution and reproducible classification.

Human brain white matter charts in international populations

The paper develops population-specific white matter charts for Chinese and Western populations, showing differences in maturation timing and improved prediction accuracy when using population-matched models.

scOmnom: scalable end-to-end single-cell RNA-seq analysis with auditable resolution selection

scOmnom provides a scalable, semi-automated workflow for single-cell RNA-seq analysis, enabling auditable clustering-resolution selection and annotation refinement across large datasets.

Hidden Markov Modeling Reveals Altered Functional Network Dynamics in Multiple Sclerosis

This study uses hidden Markov modeling to analyze dynamic functional connectivity in MS patients, finding altered state occupancy and transitions associated with disability and cognition.

The SWAN atlas: an open multimodal resource combining neuroimaging and high-resolution histology of the human brain in stereotactic space

The paper presents the SWAN atlas, a multimodal resource combining neuroimaging and high-resolution histology of the human brain in stereotactic space to improve localization accuracy for clinical applications.

Combinatorial regulation of cellular rotation by CUL-3-actomyosin-dependent oriented division, eggshell geometry, and Ras-MAPK signaling during dorsal-ventral axis establishment in Caenorhabditis elegans

The paper identifies three mechanisms regulating cellular rotation in C. elegans during dorsal-ventral axis formation and shows they act in distinct phases and roles.

Sustained antigenic engagement programs multidimensional CTL states with distinct cytotoxic capacities

This study shows that sustained antigenic engagement leads to multidimensional remodeling and functional diversification of CTLs, maintaining cytotoxic activity while creating functionally distinct states.

Ethmoid bone marrow region modulates lymphoid activation and differentiation with distinct myeloid profile in neuroinflammation

The paper investigates how neuroinflammation affects the ethmoid bone marrow region and its role in immune responses using scRNAseq and flow cytometry in a mouse model.

Order Matters: Ambient RNA correction confounds doublet detection in single-cell RNA sequencing

This study shows that ambient RNA correction can reduce doublet detection accuracy and recommends detecting doublets before correction, except when using CellBender.

NeuroMark dFNC: Transferable Dynamic-State Templates for Subject-Specific and Frequency-Resolved Chronnectomics

NeuroMark dFNC uses reference-state templates to estimate subject-specific dynamic connectivity states across datasets, enabling cross-cohort comparison while preserving individual patterns.

Inter- and intra-individual trajectories of brain sex in different neuroendocrine profiles

The paper uses machine learning to analyze brain sex classification from MRI data and links brain sex fluctuations to neuroendocrine profiles in individuals with different hormonal states.

Sequential Sampling as a Computational Principle of Episodic Memory

This paper proposes that sequential gaze sampling constructs episodic memory representations through a computational model showing how sampling history shapes memory storage and retrieval.

Heterogeneity of HCMV-Specific CD8+ T Cells is Established Early in Infection, Clonally Encoded, and Stable Over Time

The paper tracks CMV-specific CD8+ T cells over time to show that clonal diversity and phenotypes are established early and remain stable during chronic infection.

Successful coral microbiome transplant from high to low heat tolerant corals requires antibiotic pretreatment

This study shows antibiotic pretreatment improves microbiome transplant success in corals by enhancing bacterial uptake, though it does not increase core donor microbiome retention.

Enhanced stroke volume and divergence of the human left ventricle

The paper compares left ventricular phenotypes across humans, chimpanzees, and macaques to identify structural and functional traits associated with higher stroke volume in humans.

RNA exosome-mediated RNA surveillance governs developmental timing in the human cerebellum

This study shows that RNA exosome dysfunction disrupts developmental timing and lineage fidelity in human cerebellar organoids, leading to neurodevelopmental defects.

Evolutionary diversification of shared brain and nerve cord neuronal populations in Drosophila melanogaster

The paper identifies serial homology between neuronal populations in the Drosophila melanogaster brain and ventral nerve cord using lineage reporters, single-cell transcriptomics, and a connectome.

A Dataset of Human Sperm Microscopy Videos for Detection, Tracking, and Motility Parameter Analysis

The paper introduces HSMV, a dataset of human sperm microscopy videos for detection, tracking, and motility analysis, with annotated and unannotated clips for algorithm benchmarking.

scRIPT: a rapid, high-coverage single-cell lineage-tracing method applied to the hematoendothelial differentiation of embryonic stem cells

scRIPT is a single-cell lineage-tracing method that improves coverage and reliability in differentiation protocols by integrating rapid barcoding, sorting, and sequencing with quality control.