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AlphaFold 3 Prediction Accuracy and Reliability across RNA Structures and Protein-RNA Interfaces

This study evaluates AlphaFold 3's accuracy and reliability in predicting RNA structures and protein-RNA interfaces, finding that confidence scores do not always correlate with correct predictions.

scPCIP: cross-species annotation of plant cell types with conserved gene programs

scPCIP annotates plant cell types across species using conserved gene programs, outperforming marker-based and deep-learning methods in held-out datasets.

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.

Cross-cancer knowledge transfer for lymph node metastasis prediction: Applicability of an axillary lymph node-based deep learning model

This paper evaluates a deep learning model trained on axillary lymph nodes for predicting metastasis in lymph nodes from different anatomical regions across cancers.

Computational Analysis of Antioxidant Effects on Stress Response Mechanisms in Candida albicans

The paper uses computational methods to analyze antioxidant effects on stress response mechanisms in Candida albicans, identifying naringenin and quercetin as potential modulators of Sir2/SIRT3 pathways.

SQANTI-evidence: isoform-resolved, evidence-tiered structural annotation of unannotated genomes from long-read RNA-seq

SQANTI-evidence annotates genomes from long-read RNA-seq without a reference, achieving high precision in gene and isoform prediction across species.

Comparative Transcriptomic Analysis of Gene Expression Patterns in Neutrophils from Rheumatoid Arthritis and COVID-19

This paper compares neutrophil transcriptomic profiles in rheumatoid arthritis and COVID-19 to identify shared immune pathways and disease-specific features.

Marker-specific pixel attribution for single-cell protein quantification with PixAQ

PixAQ improves single-cell protein quantification in imaging mass cytometry by assigning pixel signals to specific markers using spatial and intensity models.

NORMA 3.0: aesthetic and group-aware visualization and analysis of annotated biological networks

NORMA 3.0 provides enhanced visualization and analysis of annotated biological networks with improved group representation and layout algorithms.

Decision benchmarking of cryo-EM re-refinement

The paper benchmarks cryo-EM re-refinement selection methods against no operation using a fixed cohort and scoring tools, finding increased disagreement with higher-resolution references.

TensorPLS: an R package for exploring molecular and temporal patterns in longitudinal omics data using PLS-DA

TensorPLS is an R package for analyzing longitudinal omics data using PLS-DA, handling missing data and providing temporal insights through VIP scores and cross-validation.

An end-to-end in silico framework for truth-based validation and regression testing of clinical genome sequencing pipelines, from simulated reads to reportable findings

This paper introduces an end-to-end in silico framework to validate and test clinical genome sequencing pipelines from simulated reads to reportable findings using a fixed truth set.

Optimiser Repairs for Living-Cell Self-Driving Laboratories: Performance and Redundancy under Experimental Constraints

This paper evaluates optimiser repairs in living-cell self-driving labs, showing when they improve performance and when constraints make them redundant.

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.

GOParsimony: parsimonious saltation across the Gene Ontology digraph for efficient functional annotation

GOParsimony filters GO terms to identify the most parsimonious functional annotations for gene/protein sets, outperforming existing methods in yeast and human data.

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.

Where single-cell foundation models help: a benchmark of annotation, perturbation and regulatory inference against simple baselines

This paper benchmarks single-cell foundation models against baselines for annotation, perturbation and regulatory inference using diverse datasets.

vafSOMA: Detecting cell-layer-fixed somatic mutations in plants

vafSOMA detects cell-layer-fixed somatic mutations in plants using tissue composition, improving mutation detection and rate estimation in bulk sequencing data.

SeCAT (Sequence Consensus Amplicon Trimming): a simulation-informed Nextflow pipeline for cross-study harmonisation of 16S rRNA metabarcoding datasets

SeCAT is a Nextflow pipeline that harmonizes 16S rRNA metabarcoding datasets by identifying a consensus sequence window and testing its impact on community structure before merging datasets.

SPaRTA: Spatial Reasoning in Text-to-SQL for Omics Analysis

SPaRTA enables non-experts to query spatial-omics data via natural language, achieving 63-77% accuracy with fine-tuning on cancer tissue datasets.