Squidiff is a diffusion-based model to predict transcriptomic changes in response to perturbations.

Since the chance discovery of nanobodies in the late 1980s, their uses and applications have kept growing. Researchers are now exploring new ways to harness nanobody versatility.

mScarlet3-S2 is a red fluorescent protein that is highly photostable and sufficiently bright. It is especially useful for applications such as stimulated emission depletion or structured illumination microscopy imaging with prolonged imaging times.

We highlight some of the Nature Methods team’s favorite papers published in 2025, reflecting on some trends and new technology developments.

Performing pandemic-scale phylogenetic analysis poses multifaceted challenges. This study develops methods for identifying and accounting for mutation rate variation and recurrent sequence errors, leading to an improved global phylogenetic tree of >2 million severe acute respiratory syndrome coronavirus 2 genomes.

An ion mobility-resolved mass cytometry method for single-cell metabolomics enables multidimensional metabolomic profiling. The approach was used to curate a metabolic single-cell atlas containing 45,603 primary liver cells from aging mice.

This Resource paper presents a global SARS-CoV-2 phylogenetic tree of 4,471,579 high-quality genomes consistently constructed by Viridian, an efficient amplicon-aware assembler.

DBiTplus represents an integrated experimental and computational workflow that unifies sequencing-based and imaging-based spatial omics, demonstrated by combining transcriptomic profiling and multiplexed protein imaging on the same tissue section.

MaAsLin 3 is a comprehensive and flexible framework for microbiome association studies with expanded toolsets of statistical models, tests and types of inference.

SpatialZ generates virtual single-cell spatial transcriptomics slices between experimentally measured sections, enabling accurate and efficient building of 3D cell atlases of different tissues.

As they train the next generation of scientists, some senior researchers share why they find mentoring fun and rewarding.

Generative AI technology is having substantial impacts across society, and scientific publishing is by no means immune. We highlight journal policies around the use of generative AI and discuss its responsible use in writing, peer reviewing and publishing scientific research.