clustering

msaGUI: Multispectral Analysis Graphical User Interface for Ratiometric Analysis and Background Correction

msaGUI is a no-code tool for analyzing and visualizing multispectral images through customizable workflows and exportable outputs.

Can the heartbeat-evoked potential (HEP) be separated from Cardiac Artefact (CA) using beamforming?

This paper validates EEG beamforming for separating heartbeat-evoked potentials (HEP) from cardiac artefact (CA) using simulated and empirical data, showing reliable recovery and group differences in interoceptive regions.

Microgels enable iPSCs to assemble, expand, and differentiate into organoids -- from sizable to high throughput

This paper introduces a method using PEG microgels to enable reproducible, scalable iPSC organoid production and differentiation into specific tissues.

Mouse lymph node colonization models predict human tumor metastasis in melanoma

The paper integrates mouse lymph node tumor data with human melanoma tumors to identify transcriptional programs and ecotypes associated with metastasis.

Semi-Automated CellProfiler Pipelines for Robust Quantification of Microglial Density, Distribution and Morphology

This paper introduces a semi-automated CellProfiler framework for quantifying microglial density, distribution, and morphology, improving accuracy over fully automated or manual methods.

Dentate gyrus amplifies rate-based coding while sparing global remapping across the CA3 transverse axis

This study shows that the dentate gyrus enhances rate-based coding of subtle contextual differences while preserving global remapping in CA3, supporting a dual role in contextual discrimination.

AutoWrinkleID: a machine learning pipeline for biofilm wrinkle identification and quantitative analysis

AutoWrinkleID is a machine learning pipeline for automated biofilm wrinkle detection and quantification, showing that motility-based annotations outperform manual and constitutive fluorescence annotations.

Genome-wide characterization of host factors involved in single-stranded RNA and DNA phage infection pathways

This study identifies host factors critical for ssRNA and ssDNA phage infection in E. coli, revealing conserved dependencies and lineage-specific requirements.

ViTAMIn-O: Democratizing computer vision-based machine learning for stem cell research

ViTAMIn-O is an open DL model for organoid differentiation prediction, outperforming existing models and adaptable to various datasets and imaging modalities.

Conditional Spatial Classification of Expert-Confirmed Interictal Epileptiform Discharge Epochs: An EEG-ECG Ablation and SHAP Analysis

This paper classifies expert-confirmed interictal epileptiform discharge epochs using EEG and ECG data, finding that ECG features improve categorization accuracy.

An Integrated Atlas of the Human Kidney Spanning Health and Diseases

The paper integrates multiple single-cell and single-nucleus RNA-sequencing datasets to create a comprehensive Human Kidney Cell Atlas, identifying cell types, states, and disease-associated populations.

Repeated cocaine reorganizes striatal ensembles along the ventral-dorsal axis

This study shows that repeated cocaine exposure reorganizes striatal neural activity patterns along the ventral-dorsal axis in mice, leading to distinct changes in neuronal responses.

Space partitioning by self-organized epithelial networks

This study shows epithelial cells self-organize into reticulate networks, revealing a conserved mechanism for space partitioning through mechanical and topological dynamics.

Evolutionary expression patterns in developing biofilms of uropathogenic Escherichia coli reveal embryo-like features

This study shows that uropathogenic E. coli biofilms exhibit evolutionary stratification, with gene expression becoming younger and more divergent as biofilms develop.

Female-Biased IL-17/STAT3 Signaling Marks Dementia-Associated Microglial Inflammation in Alzheimer's Disease

The paper identifies a female-biased IL-17/STAT3 signaling program in microglia associated with dementia in Alzheimer's disease using single-cell transcriptomics.

RheoScale 2.0: Revealing the Hidden Roles of Protein Positions via Substitution Patterns

RheoScale 2.0 identifies protein positions with varied substitution outcomes, revealing roles beyond neutral or deleterious, improving interpretation of high-throughput mutagenesis data.

Machine learning on subcortical brain features: A study of sample size efficiency for neurodegenerative disease classification

This study evaluates how sample size affects machine learning performance in classifying dementia stages using subcortical brain features from 2,511 ADNI samples.

Code-Multiplexed Multi-Frequency Impedance Cytometry with a Unified Deep-Unfolding Network

This paper develops a deep-unfolding network for code-multiplexed, multi-frequency impedance cytometry to resolve signal overlaps and enable label-free single-cell analysis.

Complete genome sequence of Comamonas testosteroni TA441 and comparative analysis of steroid degradation gene clusters across Proteobacteria and Actinomycetota

CD55-CD319-CX3CR1 flow cytometry gating strategy recapitulates scRNA-seq-defined memory CD8 T cell subpopulations

This paper develops a flow cytometry gating strategy using CD55, CD319, and CX3CR1 to identify transcriptionally defined CD8 T cell subpopulations, improving resolution over conventional methods.

Genome reshuffling as a route to specialization? Chromosome-level insights from the bark beetle symbiont genus Geosmithia.

This study investigates genome architecture evolution in the fungal genus Geosmithia, revealing extensive chromosome restructuring and gene family contractions associated with ecological specialization.

Hippocampal representations differentiate reactive and anticipatory responses during foraging under threat

The paper examines hippocampal activity in rats during foraging under threat, finding distinct neural representations for reactive escape and anticipatory decision-making.

Low-rank tensor decompositions reveal coupled spatiotemporal patterns of CSF tracer transport in the human brain

The paper uses low-rank tensor decompositions to analyze glymphatic MRI data and identifies spatiotemporal patterns of CSF tracer transport in the human brain, revealing differences between iNPH and reference cohorts.

Poly Pipeline: A Polyvalent Spatial Transcriptomics Workflow Validated Across Polyploid and Diploid Organisms

Poly Pipeline is a spatial transcriptomics workflow validated across polyploid and diploid organisms, demonstrating effectiveness in clustering and co-expression network analysis.

Temperature-driven dynamics of Chlorella sorokiniana and its microbiome

This study examines how temperature affects Chlorella sorokiniana and its microbiome, finding that microbial shifts and reduced microalgal biomass occur at higher temperatures, with potential implications for microalgal production systems.

Segment Any Plant (SAP): Foundation-Model Segmentation for Plant Time-Series Phenotyping

SAP provides a transferable, training-free framework for automated segmentation of plant time-series imagery across species and conditions.

SMORE: joint dimension reduction and cell population discovery on single-cell methylome data

SMORE performs joint dimensionality reduction and cell population discovery on single-cell methylome data, accurately recovering population structures in human datasets.

Transcriptomic profiling identifies cellular and molecular transitions during Merkel cell regeneration

This study uses single-cell RNA sequencing to analyze Merkel cell regeneration in zebrafish, identifying molecular transitions and conserved features across species.

QBayMic: Quantum-coupled variational Bayes for clustering and feature selection in low-signal microbiome data

QBayMic improves clustering and feature selection in low-signal microbiome data by using quantum-coupled variational Bayes, outperforming classical methods in stability and accuracy.

ssJSD: A fusion of sparsity and spatial information for HiC single-cell clustering

ssJSD improves scHiC clustering by integrating spatial interaction patterns and sparsity patterns to better distinguish cell types.