Brief Communications

In this study, long-read RNA sequencing achieves accurate single-nucleotide polymorphism calling, haplotype phasing and allele-specific expression analysis.

DIAMOND DeepClust provides an ultra-fast clustering method for organizing the protein universe of life at low sequence identity, enabling large-scale dimensionality reduction and improving downstream structure prediction with AlphaFold2.

GLYCAM-Web offers a suite of validated 3D oligosaccharide structure modeling tools via a convenient web server.

LazySlide combines scverse with foundation models to enable efficient whole-slide image analysis.

SpaceBar is a cellular barcoding strategy for simultaneous analysis of cell clonal and spatial identities.

DeepCor is a deep-learning-based denoising approach for task-based and resting-state fMRI data that can be used even for single participants.

CytoTRACE 2 is an interpretable deep learning framework that leverages single-cell RNA sequencing data to predict absolute developmental potential across datasets.

gReLU advances deep-learning-based modeling and analysis of DNA sequences with comprehensive toolsets and versatile applications.

Graphics processing unit-accelerated MMseqs2 offers tremendous speedups for homology retrieval from metagenomic databases, query-centered multiple sequence alignment generation for structure prediction, and structural searches with Foldseek.

MSnLib is a large-scale, open MSⁿ spectral library featuring >2.3 million MSⁿ and >357,000 MS² spectra for 30,008 unique small molecules.

A standardized, realistic phantom dataset consisting of ground-truth annotations for six diverse molecular species is provided as a community resource for cryo-electron-tomography algorithm benchmarking.

The analysis presented in this Brief Communication shows that, despite their complexity, current deep learning models do not outperform linear baselines in predicting gene perturbation effects, thus emphasizing the importance of further method development and thorough evaluation.

BEAST X advances Bayesian phylogenetic, phylogeographic and phylodynamic analysis by incorporating a broad range of complex models and leveraging advanced algorithms and techniques to boost statistical inference.

Vclust generates fast and accurate estimation of average nucleotide identity for viral genomes, scaling clustering to millions of genomes.

The NeuroXiv platform enables AI-powered open mining of a database of reconstructions of more than 175,000 mouse neurons, registered to the Common Coordinate Framework. The platform supports queries about connectivity, projection patterns and other morphological features.

PTM-Mamba is a post-translational modification-aware protein language model that integrates PTM tokens with bidirectional Mamba blocks and ESM-2 embeddings, enabling modeling of both wild-type and post-translationally modified sequences for diverse downstream applications.

Pycytominer is a user-friendly, open-source Python package that carries out key bioinformatics steps in image-based profiling.

DeepPrep is a preprocessing pipeline for functional and structural MRI data from humans. Deep learning-based modules and an efficient workflow allow DeepPrep to handle large datasets.

Foldseek-Multimer offers a fast strategy for complex-to-complex alignment to quickly identify compatible sets of chain-to-chain alignments by their superpositions. It can compare billions of complex pairs in 11 h.

FastOMA achieves fast and accurate orthology inference, with linear scalability.