Metastatic dynamics are revealed by integrating single-cell lineage tracing and RNA sequencing.

3D pRESOLFT enables volumetric live cell imaging with high spatial and temporal resolution.

Researchers report a method to generate two-component protein arrays on living cells, which enables controlled receptor clustering.

TopoBuilder enables de novo design of proteins bearing complex structural motifs.

At Nature Methods we are happy to engage with prospective authors and readers. Here we go through the why, what, who, when and how of talking to journal editors.

Human tonsil organoids recapitulate key features of the antigen-specific B cell response.

All that glitters is not gold. —William Shakespeare

Connecting the Ming dynasty to sharper views in brain imaging.

Single-cell technologies have made it possible to profile millions of cells, but for these resources to be useful they must be easy to query and access. To facilitate interactive and intuitive access to single-cell data we have developed scfind, a single-cell analysis tool that facilitates fast search of biologically or clinically relevant marker genes in cell atlases. Using transcriptome data from

The microscopic visualization of large-scale three-dimensional (3D) samples by optical microscopy requires overcoming challenges in imaging quality and speed and in big data acquisition and management. We report a line-illumination modulation (LiMo) technique for imaging thick tissues with high throughput and low background. Combining LiMo with thin tissue sectioning, we further develop a high-definition

The architecture of chromatin regulates eukaryotic cell states by controlling transcription factor access to sites of gene regulation. Here we describe a dual transposase–peroxidase approach, integrative DNA and protein tagging (iDAPT), which detects both DNA (iDAPT-seq) and protein (iDAPT-MS) associated with accessible regions of chromatin. In addition to direct identification of bound transcription

A genetically encoded neurotransmitter sensor, engineered from a tick lipocalin, detects serotonin in the living brain.

Illumination of fluorophores can induce a loss of the ability to fluoresce, known as photobleaching. Interestingly, some fluorophores photoconvert to a blue-shifted fluorescent molecule as an intermediate on the photobleaching pathway, which can complicate multicolor fluorescence imaging, especially under the intense laser irradiation used in super-resolution fluorescence imaging. Here, we discuss

Serotonin (5-HT) is an important signaling monoamine and neurotransmitter. We report structure-guided engineering of a green fluorescent, genetically encoded serotonin sensor (G-GESS) from a 5-HT-binding lipocalin in the soft tick Argas monolakensis. G-GESS shows fast response kinetics and high affinity, specificity, brightness and photostability. We used G-GESS to image 5-HT dynamics in cultured cells

Beyond the well-known pantheon of model organisms are others. A shift is underway to level the playing field.

RNA structure heterogeneity is a major challenge when querying RNA structures with chemical probing. We introduce DRACO, an algorithm for the deconvolution of coexisting RNA conformations from mutational profiling experiments. Analysis of the SARS-CoV-2 genome using dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) and DRACO, identifies multiple regions that fold into two mutually

Current proteomic approaches disassemble and digest nucleosome particles, blurring readouts of the ‘histone code’. To preserve nucleosome-level information, we developed Nuc-MS, which displays the landscape of histone variants and their post-translational modifications (PTMs) in a single mass spectrum. Combined with immunoprecipitation, Nuc-MS quantified nucleosome co-occupancy of histone H3.3 with

Genome-wide profiling of histone modifications can reveal not only the location and activity state of regulatory elements, but also the regulatory mechanisms involved in cell-type-specific gene expression during development and disease pathology. Conventional assays to profile histone modifications in bulk tissues lack single-cell resolution. Here we describe an ultra-high-throughput method, Paired-Tag

The paired measurement of RNA and surface proteins in single cells with cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) is a promising approach to connect transcriptional variation with cell phenotypes and functions. However, combining these paired views into a unified representation of cell state is made challenging by the unique technical characteristics of each measurement

Mapping a genetic perturbation to a change in phenotype is at the core of biological research. Advances in microscopy have transformed these studies, but they have largely been confined to examining a few strains or cell lines at a time. In parallel, there has been a revolution in creating synthetic libraries of genetically altered cells with relative ease. Here we describe methods that combine these

Light-field microscopy has emerged as a technique of choice for high-speed volumetric imaging of fast biological processes. However, artifacts, nonuniform resolution and a slow reconstruction speed have limited its full capabilities for in toto extraction of dynamic spatiotemporal patterns in samples. Here, we combined a view-channel-depth (VCD) neural network with light-field microscopy to mitigate

Global protein structure readouts help detect protein functional changes.

DeepLabCut-Live! performs pose estimation in real time and allows closed-loop feedback on behavior.

Loop-seq is a high-throughput sequencing assay that measures DNA looping and can help explain how DNA bendability contributes to nucleosome organization.

DNA-PAINT with left-handed DNA oligomers enables imaging of nuclear structures with reduced background.

In vacuum, a monolayer graphene cover enables imaging mass spectrometry of living, wet cells.

A community-wide challenge yields recommendations for improving cryo-EM structure validation.

Jumping down rabbit holes for a 3.5-Ångstrom peek at molecules.

Assembloids recapitulate organ spatial organization and interaction with high fidelity.

New year, big changes: Nature Methods now offers authors the ability to publish research papers on an open access basis, including via a Guided Open Access pilot. Here’s how it works.

Cryo-electron microscopy (cryo-EM) enables macromolecular structure determination in vitro and inside cells. In addition to aligning individual particles, accurate registration of sample motion and three-dimensional deformation during exposures are crucial for achieving high-resolution reconstructions. Here we describe M, a software tool that establishes a reference-based, multi-particle refinement

We report a means by which atomic and molecular secondary ions, including cholesterol and fatty acids, can be sputtered through single-layer graphene to enable secondary ion mass spectrometry (SIMS) imaging of untreated wet cell membranes in solution at subcellular spatial resolution. We can observe the intrinsic molecular distribution of lipids, such as cholesterol, phosphoethanolamine and various

Cryo-electron microscopy (cryo-EM) single-particle analysis has proven powerful in determining the structures of rigid macromolecules. However, many imaged protein complexes exhibit conformational and compositional heterogeneity that poses a major challenge to existing three-dimensional reconstruction methods. Here, we present cryoDRGN, an algorithm that leverages the representation power of deep neural

This paper describes outcomes of the 2019 Cryo-EM Model Challenge. The goals were to (1) assess the quality of models that can be produced from cryogenic electron microscopy (cryo-EM) maps using current modeling software, (2) evaluate reproducibility of modeling results from different software developers and users and (3) compare performance of current metrics used for model evaluation, particularly

A Correction to this paper has been published: https://doi.org/10.1038/s41592-021-01079-6.

Genome assembly projects get a boost from high-accuracy long-read sequencing.

Haplotype-resolved de novo assembly is the ultimate solution to the study of sequence variations in a genome. However, existing algorithms either collapse heterozygous alleles into one consensus copy or fail to cleanly separate the haplotypes to produce high-quality phased assemblies. Here we describe hifiasm, a de novo assembler that takes advantage of long high-fidelity sequence reads to faithfully

A Correction to this paper has been published: https://doi.org/10.1038/s41592-021-01067-w

A Correction to this paper has been published: https://doi.org/10.1038/s41592-021-01066-x

Deep neural networks have enabled astonishing transformations from low-resolution (LR) to super-resolved images. However, whether, and under what imaging conditions, such deep-learning models outperform super-resolution (SR) microscopy is poorly explored. Here, using multimodality structured illumination microscopy (SIM), we first provide an extensive dataset of LR–SR image pairs and evaluate the deep-learning

A Correction to this paper has been published: https://doi.org/10.1038/s41592-021-01065-y

A Correction to this paper has been published: https://doi.org/10.1038/s41592-021-01059-w

Many biological processes are executed and regulated through the molecular interactions of proteins and nucleic acids. Proximity labeling (PL) is a technology for tagging the endogenous interaction partners of specific protein ‘baits’, via genetic fusion to promiscuous enzymes that catalyze the generation of diffusible reactive species in living cells. Tagged molecules that interact with baits can

Exosomes have shown great potential in disease diagnostics and therapeutics. However, current isolation approaches are burdensome and suffer from low speed, yield and purity, limiting basic research and clinical applications. Here, we describe an efficient exosome detection method via the ultrafast-isolation system (EXODUS) that allows automated label-free purification of exosomes from varied biofluids

High-throughput amplicon sequencing of large genomic regions remains challenging for short-read technologies. Here, we report a high-throughput amplicon sequencing approach combining unique molecular identifiers (UMIs) with Oxford Nanopore Technologies (ONT) or Pacific Biosciences circular consensus sequencing, yielding high-accuracy single-molecule consensus sequences of large genomic regions. We

Glycoproteomics is coming of age, thanks to advances in instrumentation, experimental methodologies and computational search algorithms.

Artificial thymic organoid systems recapitulate murine thymopoiesis in vitro.

Organoids generated by spatially organizing multiple cell types, called assembloids, will enable deeper insights into tissue function.

Computational approaches help us explore complexities of the T cell receptor repertoire.

Progressive Cactus enables reference-free multiple-genome alignment for massive datasets.

Method development pushes the limit of completeness of genome sequences.

Single-objective light sheet fluorescence microscopes are driving innovation in volumetric imaging.

Phage-based natural selection helps identify highly specific covalent binders.

Prime editors enable different types of small mutations to be introduced into genomes.

Researchers are putting new spins on familiar dyes and showing their versatility for labeling living systems.

Behavioral analysis has come a long way from tedious manual annotation, and further strides in automation are expected.

The near-infrared calcium sensor iGECI shows promise for imaging neuronal activity in vivo.

Spatially resolved transcriptomics methods are changing the way we understand complex tissues.

Microfluidic channels provide a means to deliver barcodes encoding spatial information to a tissue, which allows co-profiling of gene expression and proteins of interest in a spatially resolved manner.

“We demand rigidly defined areas of doubt and uncertainty!” —D. Adams