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In this Analysis, Liu et al. benchmark more than 200 pairwise statistics for functional brain connectivity in tasks such as hub mapping, distance relationships, structure–function coupling and behavior prediction, revealing varying effectiveness for specific neurophysiological applications.
This analysis provides a collection of sequencing datasets generated from long-read and short-read RNA sequencing, serving as a valuable resource for transcriptome profiling.
The results of the Fifth RNA-Puzzles contest highlights advances in RNA three-dimensional structure prediction and uncovers new insights into RNA folding and structure.
A systematic analysis of the influence of different sample preparation steps on proteoform identification by top-down proteomics serves as a useful reference for designing appropriate workflows for specific research questions.
This Analysis study compares computational methods for single-cell multi-omics prediction and integration, generating useful insights for method users and developers working with different analysis purposes and biological problems.
The dyes chosen for DNA-PAINT microscopy are pivotal for data quality. This Analysis shows a comprehensive comparison of 18 fluorescent dyes in DNA-PAINT and offers guidance for optimum dye selection in single-color and multiplexed imaging.
This analysis presents a systematic comparison of 11 sequencing-based spatial transcriptomics methods using well-characterized references, which offers insights into performance variations in spatial transcriptomic techniques.
The EMDataResource Ligand Model Challenge aimed at assessing the reliability and reproducibility of modeling ligands bound to protein and protein–nucleic acid complexes in cryo-EM maps determined at near-atomic resolution. This analysis presents the results and recommends best practices for assessing cryo-EM structures of liganded macromolecules.
The Consortium for Top-Down Proteomics conducted a study to develop and test protocols for native mass spectrometry combined with top-down fragmentation of proteins and protein complexes across eleven instruments in nine laboratories. They report the summary of the outcomes and their recommendations in this Analysis.
Cell segmentation is crucial in many image analysis pipelines. This analysis compares many tools on a multimodal cell segmentation benchmark. A Transformer-based model performed best in terms of performance and general applicability.
This analysis provides 108 noncoding CRISPR screens collated by the ENCODE4 consortium and establishes experimental guidelines for future CRISPRi screens characterizing functional cis-regulatory elements.
This analysis leverages experimentally sequenced data and in silico mixtures to simulate transcript expression differences, which enables a performance assessment of long-read tools developed for isoform detection, differential transcript expression analysis and differential transcript usage analysis.
This study describes benchmarking and validation of computational tools for detecting circRNAs, finding most to be highly precise with variations in sensitivity and total detection. The study also finds over 315,000 putative human circRNAs.
This updated analysis of the Cell Tracking Challenge explores how algorithms for cell segmentation and tracking in both 2D and 3D have advanced in recent years, pointing users to high-performing tools and developers to open challenges.
This paper compares different transformation approaches for analysis of single-cell RNA-sequencing data and provides recommendations for method selection.
