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The paper introduces CellHub Database, a consolidated ligand-receptor interaction resource for cell-cell communication analysis across multiple species.

BiomiX 3.0 is a multi-omics integration platform that introduces PRAMIGO, a supervised heterogeneous graph transformer, and benchmarks five methods on CLL and PTB datasets, showing that no single method captures all biologically relevant signals.

The paper introduces MorphAgent, a biologically grounded AI framework for cell profiling across microscopy modalities, improving feature design and performance in drug screening and disease analysis.

Non3nExonFinder identifies shared non-triplet coding exons across transcripts, prioritizing candidates based on CDS status and divisibility by three, with high concordance in validation.

The paper evaluates tabular foundation models on genetic data, identifies ancestry-dependent non-stationarity as a key challenge, and proposes synthetic tasks to improve performance across ancestry groups.

CSGDA predicts drug responses across biological heterogeneities by addressing distribution shifts using a cell state-guided graph domain adaptation framework.

A marker audit finds 97.9% of CEREBRI's 45,051 official 'glutamatergic neuron' cells are not glutamatergic (four-check composite 82.6%), creating false ion-channel and OXPHOS signals; true neurons show acute KCNC3 up-regulation.

This paper introduces spEnhance, a computational framework that improves spatial resolution and reliability of spot-level spatial omics data across multiple modalities.

AtlasOT improves multimodal integration of disease atlases by addressing unpaired data constraints through a novel optimal transport framework.

ProDive detects cross-family local conservation using a pHMM-based framework, identifying 318,289 high confidence segment correspondences across 25,545 Pfam families.

Luxar compresses volumetric microscopy data into compact archives for interactive web visualization without requiring specialized software.

RNabel is a software tool for annotating tandem mass spectra of modified RNAs, supporting various modifications and formats, and providing quality metrics for spectral analysis.

AF3 Inspector provides an interactive web tool to visualize and analyze all AlphaFold 3 structural models, addressing limitations in the official service.

YieldLearn estimates yield-related traits in durum wheat using physiological indicators and machine learning, showing moderate accuracy and feature importance.

DS5 is an open-source framework that standardizes HTS data storage, analysis, and drug prioritization, validated against public benchmarks and applied in clinical settings.

NexuST is a hierarchical foundation model for spatial transcriptomics that improves cell-type annotation and spatial prediction by integrating gene-level and cell-level modeling.

This study evaluates genomic foundation models for viral sequence classification, finding that NTv3-650M achieves high accuracy comparable to BLAST on standard-length sequences.

Serval is a modular framework for decoding spatial transcriptomics data that introduces Cosine, a method improving transcript recovery and correlation with expression references.

CryoMV generates and validates continuous protein conformations from cryo-EM data using structure priors and real-particle validation, achieving high resolution and robustness on benchmark datasets.

UniWave-2 improves nucleic acid sequence analysis by integrating hydrophobicity, enhancing waveform resolution with Fourier and wavelet transforms, and using a lightweight GRU model for efficient feature extraction.