clustering

Identification and characterization of new P. aeruginosa phages using a surface receptor platform

The paper introduces a SURFAR platform to identify and characterize new P. aeruginosa phages by targeting specific receptors, isolating two novel phages with distinct host ranges.

DisCell: Separating Spillover from Niche Response in Spatial Transcriptomics

DisCell identifies and separates spillover from niche responses in spatial transcriptomics data, confirming a previously reported finding about esophageal cancer cells.

From Fill to Freeze: Redesigning homeRNA to Enable Robust Sampling and Scalable Downstream Processing Workflows for Remote Blood Transcriptomics

This paper validates the redesigned homeRNA platform's robustness to remote study stresses, showing it maintains RNA quality under varied conditions and storage times.

Multimodal cellular context enables molecular phenotyping from single-molecule trajectories

The paper introduces MIST, a framework that integrates single-molecule trajectory data with cellular context to improve molecular phenotyping in E. coli.

Breaking the bottleneck: semi-automated quantification of actin filament dynamics

The paper introduces SMAUG, a semi-automated tool for analyzing actin filament dynamics from TIRF microscopy images, reducing analysis time while maintaining accuracy.

Sex differences in agonistic social behavior: Effects of exercise and ovariectomy

This study examines how sex, exercise, and ovariectomy affect offensive and defensive aggression in rats, finding sex-specific behavioral differences and no effect of exercise.

Deducing splicing events from transcript sets with splicelogic

splicelogic converts transcript-set comparisons into interpretable splicing events, enabling downstream analysis of isoform changes in RNA-seq data.

Rapid, accurate, and memory-frugal sub-gene-level quantification of probe-based, multiplexed single-cell data

This paper introduces simpleaf, a tool for efficient sub-gene-level quantification of probe-based single-cell data, showing improved speed and memory use compared to existing tools.

siRNA/mRNA payload of lipid nanoparticles quantified using fluorescence microscopy and correlation spectroscopy

The paper quantifies mRNA and siRNA payload in lipid nanoparticles using fluorescence microscopy and FCS, showing size-dependent payload and coencapsulation dynamics.

Clinical relevance of diffusion tensor imaging-based parameters estimated with deep learning: the effect of model retraining

This study evaluates how retraining deep learning models affects the statistical consistency of diffusion tensor imaging parameters in bipolar disorder, showing significant variability across models.

RadMultiBench: A Reproducible Dual-Task Benchmark Exposing the Limits of Pre-Trained Vision-Language Models Across Thoracic and Breast Imaging

RadMultiBench evaluates pre-trained vision-language models on medical imaging tasks, showing performance gaps in report generation and classification across thoracic and breast imaging.

Extended Pavlovian conditioned approach training and devaluation in Long-Evans rats using time-restricted feeding

This study develops an extended Pavlovian conditioned approach paradigm in Long-Evans rats under time-restricted feeding to better identify phenotypes linked to compulsive behaviors and stress-related dysregulation.

Evaluating State-Transition Models in Short Resting-State fMRI with Continuous-Dynamics Controls

This study compares hidden Markov models (HMMs) and vector autoregressive (VAR) models in resting-state fMRI to determine if apparent state transitions reflect discrete dynamics or continuous activity, finding that VAR often outperforms HMMs in continuous cases.

A comparative transcriptomic framework across kidney organoid, assembloid, and transplantation models

The paper compares transcriptomic profiles across kidney organoid, assembloid, and transplantation models to evaluate their maturity and suitability for research.

Variation in the embryonic cell lineages of Caenorhabditis elegans natural populations

The paper quantifies developmental variation in C. elegans natural populations using embGAN, finding genotype-specific differences in cell-cycle timing that exceed within-strain variation.

Live attenuated YFV-17D vaccine induces robust B and T cell immunity in vaccine-draining lymph nodes

This study examines immune dynamics in lymph nodes after YFV-17D vaccination, identifying robust B and T cell responses and a conserved germinal center program across different vaccines.

Clonally Convergent Tph/Tfh-like CD4+ T Cells are Shared Across Recovery and Recurrence in Experimental Periodontitis

The paper identifies clonally convergent Tfh/Tph-like CD4+ T cells that persist in the mucosa after recovery from periodontitis and contribute to recurrence.

SPECHTacle: An Efficient Detection and Visualization of Cell Specific Regulation in Single Cell-Based Experiments Using a Novel Combinatorial Computational Tool

SPECHTacle efficiently identifies and visualizes cell-specific regulatory changes in single-cell experiments using optimal transport and entropy analysis.

Classifying tumors from broad category to hierarchical molecular subtype: an interpretable hierarchical framework for precision oncology

This paper introduces HHRM, a hierarchical model for tumor subtype classification, achieving high accuracy in pan-cancer and breast cancer subtyping with interpretable biomarker identification.

A Kernel-Spectral Index for Single-Neuron Input-Output Complexity

The paper introduces the Spectral Complexity Index (SCI), a white-box measure of single-neuron computational complexity that outperforms existing methods in efficiency and interpretability.

A Bias Correction Method for Substructure Estimation with Small Reference Sample Sizes

The paper evaluates how small reference sample sizes affect substructure estimation and proposes bias corrections for improved accuracy.

From smartphone to gene: Automated image-based phenotyping captures flowering diversity of common buckwheat

The paper uses smartphone imaging and automated analysis to phenotype flowering traits in buckwheat, identifying heritable traits and genomic regions associated with flowering patterns.

A new Serratia taxon found in a trombidiform mite shows genomic evidence of host adaptation but is phylogenetically distinct from Serratia symbiotica

The paper identifies a new Serratia taxon in mites with genomic signs of host adaptation but phylogenetically distinct from S. symbiotica.

Unprecedented urban freshwater microviral survey highlights shift from sewage to river water communities

The paper surveys microviruses in urban freshwater environments, finding shifts in community composition from sewage to river water, with wastewater treatment plants acting as filters.

A microstructural analysis of water intake patterns associated with light phase food and water restriction in male and female rats.

The paper examines how food and water intake patterns in rats change under light phase restrictions, finding that food access timing more strongly influences water intake than water access timing influences food intake.

brisc: a multithreaded CPU toolkit for single-cell analysis

brisc is a multithreaded CPU toolkit for single-cell analysis that is faster and more reproducible than existing tools like Scanpy and Seurat.

Single-Cell RNA Sequencing Reveals Distinct Cellular and Molecular Features of Steroid-Induced Osteonecrosis of the Femoral Head Compared to Alcohol-Induced Osteonecrosis and Hip Osteoarthritis

This study uses single-cell RNA sequencing to compare cellular and molecular features of steroid-induced and alcohol-induced osteonecrosis of the femoral head with hip osteoarthritis, identifying distinct immune and stromal cell signatures.

Uncovering cross-signal interactions in single-cell and spatial omics

CRISP identifies and localizes interactions between biological signals in single-cell and spatial transcriptomic data, revealing their effects on tissue function and gene regulation.

A large, distinct family of RNase H fold nucleases associated with numerous defense systems in prokaryotes

The paper identifies and characterizes a new family of prokaryotic defense proteins, WARDs, which are associated with various defense systems and provide phage resistance.

Sourmash accurately profiles strains from long-read metagenomes preserving gene content

This study evaluates Sourmash's ability to profile microbial strains from long-read metagenomes, showing accurate gene content recovery and abundance estimation.