As Nature Methods celebrates a milestone anniversary, we look back on the past two decades of methods development in basic biological research.

Several researchers share tales around the development of their widely used methods.

This work presents CalicoST for inferring allele-specific copy numbers and reconstructing spatial tumor evolution by using spatial transcriptomics data.

VeloCycle is a manifold-constrained generative framework to estimate RNA velocity during the cell cycle.

This Article reports cross-linking mass spectrometry (XL-MS) standard datasets with fully controlled protein interactions that are an order of magnitude more complex than existing ones. These datasets are used to benchmark XL-MS software and establish a fast, error-controlled search tool for XL-MS with cleavable reagents.

This work presents CalicoST for inferring allele-specific copy numbers and reconstructing spatial tumor evolution by using spatial transcriptomics data.

Microscopy artifacts and tissue imperfections interfere with single-cell analysis. CyLinter software offers quality control for high-plex tissue profiling by removing artifactual cells, thereby facilitating accuracy of biological interpretation.

CryoSTAR is a deep neural network model that resolves continuous conformational heterogeneity from cryo-EM datasets using an initial atomic model as the reference to generate both density maps and reasonable coarse-grained models for different conformations.

Oligonucleotide-mediated proximity-interactome MAPping (O-MAP) enables precise multiomic characterization of biomolecular interaction networks at target RNAs. Distinct O-MAP workflows reveal RNA-adjacent proteins, transcripts and genomic loci.

When spouses are both scientists, they mix the typical research career decisions with some marriage-related ones.

For Nature Methods’ 20th anniversary, our current and past editors reminisce about their favorite papers, initiatives and projects at the journal.

For Nature Methods’ 20th anniversary, our current and past editors reminisce about their favorite papers, initiatives and projects at the journal.