clustering

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.

Mapping Gene Expression to an Interpretable Semantic Space

The paper introduces MESIC, a method that maps gene expression data into an interpretable semantic space using gene annotations, enabling biological interpretation of clusters and outliers.

Time-Series Foundation Models for Cognitive Workload Classification using Eye-Tracking Data

This study evaluates two time-series foundation models for cognitive workload classification from eye-tracking data, showing better generalization to unseen individuals than task-specific models.

ConvexGating infers gating strategies from clusters in single cell cytometry data

ConvexGating automatically learns unbiased, interpretable gating strategies for flow cytometry data, improving consistency and reducing contamination in cell population identification.

Spatially resolved multimodal hallmarks of response to neoadjuvant immunotherapies in the melanoma ecosystem in 2D and 3D

The paper analyzes the spatial molecular architecture of melanoma tumors under different immunotherapy regimens and identifies biomarkers predicting response to treatment.

Convergent activity but divergent anxiety dimensions in male and female C57BL/6 mice across the open field and elevated plus maze

This study examines sex differences in anxiety-like behavior in male and female mice using open field and elevated plus maze tests, finding convergent activity measures but divergent anxiety dimensions.

A Hybrid Residual-Swin Transformer Design with Attention for Prostate Cancer Segmentation

The paper introduces RSAUNet, a deep learning model for prostate cancer segmentation in MRI scans, achieving high Dice and Jaccard scores.

Distinct RNA-RNA spatial interaction sub-networks of transcription factors in hepatic cells

The paper uses RIC-seq and integrates multi-omics data to classify transcription factors into two clusters based on RNA-RNA spatial interactions and their genomic and clinical features.

Goliath clades and in vivo tracking of clonal dynamics show three phases of UV-induced skin carcinogenesis

This study identifies three phases of UV-induced skin carcinogenesis using a mouse model, showing the emergence of large clades, clonal selection, and lesion formation.

Punctuated mutagenesis promotes multi-stepevolutionary adaptation in human cancers

This study shows that punctuated mutagenesis in cancer enhances adaptation by facilitating crossing of fitness valleys through clustered mutations.

BGC Atlas v2: biosynthetic gene clusters with taxonomic and environmental context at scale

BGC Atlas v2 expands the collection of predicted biosynthetic gene clusters to over 16 million, providing taxonomic and environmental context for natural product discovery.

Cross-Serogroup Analysis of Representative Top-Seven Shiga toxin-producing Escherichia coli Plasmids Reveals Lineage-Specific Patterns

The paper analyzes plasmid sequences from seven STEC serogroups to identify lineage-specific virulence and resistance patterns and mobility features.

Setting the SCENE for Interpretable Cell-Gene Embeddings in Single-Cell RNA-seq

This paper introduces SCENE, a probabilistic model for embedding cells and genes in scRNA-seq data, achieving state-of-the-art performance and interpretable visualization.

A Novel Cortico-Striatal NREM Sleep Rhythm in Mice and Non-Human Primates

The paper identifies a novel 5-10 Hz cortico-striatal NREM sleep rhythm in mice and non-human primates that supports learning and performance gains through enhanced cortico-striatal interactions.

Somatic genetic variation shapes clonal selection of memory NK cells

Whole-exome sequencing of memory NK cells from 81 CMV-seropositive donors reveals dominant somatic clones, early-life origin, and positive selection, with Kmt2d loss shifting mouse NK fitness.

Extensive nuclear introgression accompanied ancient mitochondrial capture in the common ancestor of two sister hare species

The paper quantifies and localizes nuclear introgression in two hare species by combining demographic, phylogenomic, and polarisation-based methods, revealing extensive gene flow from mountain hare.