This Registered Report presents the results of the Long-read RNA-Seq Genome Annotation Assessment Project, which is a community effort for benchmarking long-read methods for transcriptome analyses, including transcript isoform detection, quantification and de novo transcript detection.

This Review summarizes the computational strategies for microbiome analysis using long-read sequencing data.

We provide some advice about how to best name methods and software tools.

Dimension reduction helps to visualize high-dimensional datasets. These tools should be used thoughtfully and with tuned parameters. Sometimes, these methods take a second thought.

This work presents ORFtag that enables proteome-wide functional screens by tagging and overexpression of endogenously encoded proteins via randomly integrated cassettes.

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.

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.

This work introduces CRISPRdelight, a dCas12a-based DNA-imaging tool that facilitates the imaging of non-repetitive loci and the tracking of DNA dynamics.

Gapr is an efficient platform for reconstructing neurons in large-scale light microscopy datasets. It enables various proofreading modes as well as collaboration among many annotators.

Scientific breakthroughs can change how we understand and live in the world, disrupting long-held assumptions and concepts and raising new questions for philosophy and science. To address these challenges, we describe a model for collaboration of scientists with philosophers and ethicists, and its benefits to the research process and outcomes.

Assessing forest health and resilience is an urgent, many-methods task that takes global collaboration, data collected at multiple scales and a willingness to be surprised.

Amid the brutality of war around them, some Ukrainian scientists find calm in bioinformatics.

Tissues, organs and organ systems are composed of interacting cells (the cellome). We discuss the emergence of an omics approach that we refer to as cellomics. It enables cellome-wide analysis in whole-organ or whole-body specimens, based on advanced three-dimensional imaging and image analysis technology. We think that cellomics will pave the way for the incorporation of cellular, intercellular and spatial information across millions of cells in our body.