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The paper introduces the GPCR Evolution Database, which provides evolutionary analysis of GPCRs to study their function and conservation across species.

GOlien annotates protein sequences with GO terms using a Shannon-entropy k-mer model, achieving high accuracy on Biological Process, Cellular Component, and Molecular Function.

EukaUTR is a foundation model for eukaryotic 3' UTRs that predicts function and generates new sequences with regulatory properties.

The paper introduces PlantLRR-PRR, a pipeline for annotating RLP/RLKs in tomato, revealing evolutionary patterns and TE enrichment in defense-related RLPs.

The paper introduces Atlas, a microbiome dataset, and Waypoint, a series of transformer-based models, showing improvements in downstream tasks through pretraining.

The paper identifies how hidden assumptions in nascent RNA sequencing pipelines lead to structured divergence in transcriptional profiles across datasets.

This paper introduces 3D-VirtualCM, a method to reconstruct full cardiomyocyte transcriptomes from spatial transcriptomic sections, revealing spatial and transcriptional heterogeneity in infarcted mouse hearts.

TAPAS integrates AlphaFold3 confidence and geometric features with sequence embeddings to improve TCR-pMHC binding prediction, outperforming individual metrics across benchmarks.

This study shows that k-mer-based whole-genome similarity can rapidly and accurately classify fungal taxa from genus to intraspecies variants, outperforming traditional methods in speed and efficiency.

dictyExpress 3.0 integrates bulk and single-cell transcriptomics data for Dictyostelium, offering interactive visualizations and cross-modal analysis.

This study evaluates STUNT, a meta-learning framework for microbiome-based disease classification, finding that its benefits are limited under data scarcity and diminish with more samples.

PKProbDesign optimizes thermodynamic folding probability for pseudoknotted RNA targets, achieving high pseudo-joint folding probability on most tested targets.

The paper introduces MultiStateFold, a framework that improves prediction of multiple protein conformations by integrating Parallel Tempering into a protein language model, achieving better performance than existing methods.

This paper uses quantum computing to assemble a large genome on current hardware, achieving high accuracy despite technical limitations.

CNSigs identifies copy number mutational signatures across cancers, revealing associations with survival and treatment response.

The paper uses Cell Painting to assess mammary carcinogen risk by analyzing morphological changes in chemical exposure, identifying potential risk factors with a GBA framework.

PhenoMapR maps bulk expression phenotypes to single-cell and spatial transcriptomics data to identify biologically relevant cellular populations and spatial niches.

EVd3x integrates over 22 million records from 28 public resources so one fixed molecule set can be traced from reported EV cargo through disease, pathway, cell and interaction evidence.

Foldseek-Interface clusters protein interaction interfaces from PDB data, revealing 77,167 interface clusters and novel interface types.

SCGBinner improves long-read metagenomic binning by using single-copy gene guided contrastive learning, outperforming existing methods on real-world datasets and recovering novel microbial species.