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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.
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.
NanoPyx optimizes bioimage analysis workflows by dynamically selecting code variations based on input data and hardware. This ensures maximum computational efficiency, enabling fast analysis of large datasets and real-time reactive microscopy.
The peptide-centric local stability assay (PELSA) can be used to determine ligand-binding targets and binding regions on a proteome-wide scale with high sensitivity.
ProHap is a Python-based tool that constructs protein sequence databases from phased genotypes of reference panels to enable researchers to account for haplotype diversity in proteomic searches.
In a technological tour de force, a whole-body 11.7-T MRI scanner has been developed. Here images of the human brain are presented while safety for the imaged human volunteers has been ascertained.
Vitessce is a robust and versatile web-based framework for interactive visualization of large-scale multiomics and spatial data at the single-cell level.
Point spread function (PSF) splitting with the ‘Circulator’, which encodes the fluorophore emission band into the PSF, improves the information content of fluorescence microscopy and enables improved super-resolution imaging and single-particle tracking.
The authors present a workflow integrating imaging mass cytometry and imaging mass spectrometry to deconvolute metabolic heterogeneity at the single-cell level.
Smart parallel automated cryo-electron tomography (SPACEtomo) uses deep learning to fully automate data collection from lamella detection to tilt series acquisition, driving the future of cryo-ET through improved throughput and statistics.
The MHz repetition rates available at second-generation X-ray free-electron lasers enable the collection of microsecond time-resolved X-ray scattering data with exceptionally low noise, providing insights into protein structural dynamics.
Scalable tools are needed for the analysis of increasingly large mass spectrometry-based proteomics datasets. quantms offers an open-source, cloud-based pipeline for massively parallel proteomics data analysis.
