Human cervical organoids mimic dynamics of cancer and sexually transmitted infections.

The iNMF algorithm efficiently integrates large-scale, continually arriving single-cell multi-omic datasets.

An approach involving barcoded viral tracing provides insights into cell–cell interactions at single-cell resolution.

Researchers work towards improving the efficiency and specificity of prime editors, as well as their delivery system in plants and animals.

Researchers, funders, database managers and journals all have a role to play in accounting for diversity and prioritizing inclusion at the basic science level.

Composite in situ imaging leverages gene expression patterns to improve the efficiency of highly multiplexed single-molecule FISH measurements by orders of magnitude.

The most commonly used omics databases are a compilation of results from primarily male-only and sex-agnostic studies. The pervasive use of these databases critically hinders progress toward fully accounting for the biology of sex differences.

Although fluorescence microscopy is ubiquitous in biomedical research, microscopy methods reporting is inconsistent and perhaps undervalued. We emphasize the importance of appropriate microscopy methods reporting and seek to educate researchers about how microscopy metadata impact data interpretation. We provide comprehensive guidelines and resources to enable accurate reporting for the most common

Single-cell profiling methods have had a profound impact on the understanding of cellular heterogeneity. While genomes and transcriptomes can be explored at the single-cell level, single-cell profiling of proteomes is not yet established. Here we describe new single-molecule protein sequencing and identification technologies alongside innovations in mass spectrometry that will eventually enable broad

Cytosine base editors (CBEs) have the potential to correct human pathogenic point mutations. However, their genome-wide specificity remains poorly understood. Here we report Detect-seq for the evaluation of CBE specificity. It enables sensitive detection of CBE-induced off-target sites at the genome-wide level. Detect-seq leverages chemical labeling and biotin pulldown to trace the editing intermediate

Recent efforts have shown that structural variations (SVs) can disrupt three-dimensional genome organization and induce enhancer hijacking, yet no computational tools exist to identify such events from chromatin interaction data. Here, we develop NeoLoopFinder, a computational framework to identify the chromatin interactions induced by SVs, including interchromosomal translocations, large deletions

L1CAM is a transmembrane protein expressed on neurons that was presumed to be found on neuron-derived extracellular vesicles (NDEVs) in human biofluids. We developed a panel of single-molecule array assays to evaluate the use of L1CAM for NDEV isolation. We demonstrate that L1CAM is not associated with extracellular vesicles in human plasma or cerebrospinal fluid and therefore recommend against its

Reaching ground truth in super-res microscopy, powered by a love of cooking and food.

Understanding cellular organization demands the best possible spatial resolution in all three dimensions. In fluorescence microscopy, this is achieved by 4Pi nanoscopy methods that combine the concepts of using two opposing objectives for optimal diffraction-limited 3D resolution with switching fluorescent molecules between bright and dark states to break the diffraction limit. However, optical aberrations

Single-molecule localization microscopy (SMLM) relies on the blinking behavior of a fluorophore, which is the stochastic switching between fluorescent and dark states. Blinking creates multiple localizations belonging to the same fluorophore, confounding quantitative analyses and interpretations. Here we present a method, termed distance distribution correction (DDC), to eliminate blinking-caused repeat

We demonstrate residual channel attention networks (RCAN) for the restoration and enhancement of volumetric time-lapse (four-dimensional) fluorescence microscopy data. First we modify RCAN to handle image volumes, showing that our network enables denoising competitive with three other state-of-the-art neural networks. We use RCAN to restore noisy four-dimensional super-resolution data, enabling image

Cell atlas projects and high-throughput perturbation screens require single-cell sequencing at a scale that is challenging with current technology. To enable cost-effective single-cell sequencing for millions of individual cells, we developed ‘single-cell combinatorial fluidic indexing’ (scifi). The scifi-RNA-seq assay combines one-step combinatorial preindexing of entire transcriptomes inside permeabilized

There’s an evolving choice of ways to track the temporal dynamic of RNA biographies.

Bioimaging data have significant potential for reuse, but unlocking this potential requires systematic archiving of data and metadata in public databases. We propose draft metadata guidelines to begin addressing the needs of diverse communities within light and electron microscopy. We hope this publication and the proposed Recommended Metadata for Biological Images (REMBI) will stimulate discussions

The community-driven initiative Quality Assessment and Reproducibility for Instruments & Images in Light Microscopy (QUAREP-LiMi) wants to improve reproducibility for light microscopy image data through quality control (QC) management of instruments and images. It aims for a common set of QC guidelines for hardware calibration and image acquisition, management and analysis.

Immunogenomics studies have been largely limited to individuals of European ancestry, restricting the ability to identify variation in human adaptive immune responses across populations. Inclusion of a greater diversity of individuals in immunogenomics studies will substantially enhance our understanding of human immunology.

We introduce the TRUST4 open-source algorithm for reconstruction of immune receptor repertoires in αβ/γδ T cells and B cells from RNA-sequencing (RNA-seq) data. Compared with competing methods, TRUST4 supports both FASTQ and BAM format and is faster and more sensitive in assembling longer—even full-length—receptor repertoires. TRUST4 can also call repertoire sequences from single-cell RNA-seq (scRNA-seq)

Accurate microbial identification and abundance estimation are crucial for metagenomics analysis. Various methods for classification of metagenomic data and estimation of taxonomic profiles, broadly referred to as metagenomic profilers, have been developed. Nevertheless, benchmarking of metagenomic profilers remains challenging because some tools are designed to report relative sequence abundance while

Ultra-high-performance liquid chromatography high-resolution mass spectrometry (UHPLC–HRMS) variants currently represent the best tools to tackle the challenges of complexity and lack of comprehensive coverage of the metabolome. UHPLC offers flexible and efficient separation coupled with high-sensitivity detection via HRMS, allowing for the detection and identification of a broad range of metabolites

The Cell-TALKING technique probes DNA modifications around a histone modification in fixed cells.

Phased genomes from diverse human populations are assembled using multiple sequencing technologies.

Photonic resonator interferometric scattering microscopy offers label-free imaging of biomolecules in vitro with improved signal-to-noise ratio.

The Protein Data Bank (PDB) is the primary data resource for structural biology. On its 50th anniversary, we celebrate the future of this ever-growing field.

Interest in cryo-ET is rapidly growing, but many technical challenges still require solutions.

Polymer physics, comparing ways to assess chromatin structure and taking in tales at the Italian seaside.

Integrative structural biology, the culmination of experimental and theoretical methods, will provide a holistic view of molecular processes.

It is time for structural biologists to embrace the challenge of quantitatively describing functional energy landscapes.

Fusions of human and chimp iPS cells help study how divergence in gene expression affects phenotypic traits.

Cryo-ET, which yields both structural and spatial information, will help unlock the molecular architecture of cells.

Whole-cell models, still in the early stages of development, are poised to open the next frontier in integrative modeling.

A study applies polymer physics to assess the advantages and limitations of three sequencing-based approaches for determining the structure of genomes and genomic domains.

Many challenges and considerations must be evaluated when expanding and supporting new cryo-electron microscopy facilities.

The future of macromolecular crystallography includes new X-ray sources, enhanced remote-accessible capabilities and time-resolved methods to capture intermediate structures along reaction pathways.

Computational protein modeling rapidly advances structural knowledge of viral proteins, but methods for modeling protein complexes still need improvement.

Two independent teams have developed the first in vitro human blastocysts.

Advances in cryo-EM technology will open a new era of RNA-only 3D structure determination.

Light-field microscopes can image three-dimensional dynamics of biological samples at unprecedented speed, but the computational reconstruction necessary for image formation is artifact-prone and time-consuming. Deep learning closes this gap between imaging and reconstruction speed.

Biocurators, the backbone of the wwPDB, manage structural biology data deposition, quality, and integrity, and provide integral support to the research community worldwide.

RNA-binding proteins (RBPs) are critical regulators of gene expression and RNA processing that are required for gene function. Yet the dynamics of RBP regulation in single cells is unknown. To address this gap in understanding, we developed STAMP (Surveying Targets by APOBEC-Mediated Profiling), which efficiently detects RBP–RNA interactions. STAMP does not rely on ultraviolet cross-linking or immunoprecipitation

Cryo-electron microscopy (cryo-EM) is rapidly becoming an attractive method in the field of structural biology. With the exploding popularity of cryo-EM, sample preparation must evolve to prevent congestion in the workflow. The dire need for improved microscopy samples has led to a diversification of methods. This Review aims to categorize and explain the principles behind various techniques in the

Hi-C, split-pool recognition of interactions by tag extension (SPRITE) and genome architecture mapping (GAM) are powerful technologies utilized to probe chromatin interactions genome wide, but how faithfully they capture three-dimensional (3D) contacts and how they perform relative to each other is unclear, as no benchmark exists. Here, we compare these methods in silico in a simplified, yet controlled

Visualizing dynamic processes over large, three-dimensional fields of view at high speed is essential for many applications in the life sciences. Light-field microscopy (LFM) has emerged as a tool for fast volumetric image acquisition, but its effective throughput and widespread use in biology has been hampered by a computationally demanding and artifact-prone image reconstruction process. Here, we

Two new technologies enable the profiling of single cells for RNA transcription as well as modifications to histone proteins. Each takes a similar strategy to capture both properties, but with different methods for cell indexing, and they are applied to two different areas: neuroscience and developmental biology, respectively.

Deciphering mechanisms in cell-fate decisions requires single-cell holistic reconstructions of multidimensional epigenomic states in transcriptional regulation. Here we develop CoTECH, a combinatorial barcoding method allowing high-throughput single-cell joint detection of chromatin occupancy and transcriptome. We used CoTECH to examine bivalent histone marks (H3K4me3 and H3K27me3) with transcription

Imaging technologies are used throughout the life and biomedical sciences to understand mechanisms in biology and diagnosis and therapy in animal and human medicine. We present criteria for globally applicable guidelines for open image data tools and resources for the rapidly developing fields of biological and biomedical imaging.

CEPT, a small-molecule cocktail, improves the viability of human pluripotent stem cells, protects cells during culture and cryopreservation, and promotes in vitro differentiation and organoid formation.

Human pluripotent stem cells (hPSCs) are capable of extensive self-renewal yet remain highly sensitive to environmental perturbations in vitro, posing challenges to their therapeutic use. There is an urgent need to advance strategies that ensure safe and robust long-term growth and functional differentiation of these cells. Here, we deployed high-throughput screening strategies to identify a small-molecule

Competitive coevolution between microbes and viruses has led to the diversification of CRISPR–Cas defense systems against infectious agents. By analyzing metagenomic terabase datasets, we identified two compact families (775 to 803 amino acids (aa)) of CRISPR–Cas ribonucleases from hypersaline samples, named Cas13X and Cas13Y. We engineered Cas13X.1 (775 aa) for RNA interference experiments in mammalian

With grit, urgency and creativity, scientists address the puzzle of long-haul COVID.

With protein structure prediction recently getting a seismic boost in accuracy, hopes are also up to better predict unstructured protein regions that can adopt diverse conformations. CAID, a community effort to revive systematic benchmarking, should help.

A new approach tracks animal movements in 3D from multiple camera views using volumetric triangulation, reconciling occlusions and ambiguities present in any one camera view.

Intrinsically disordered proteins, defying the traditional protein structure–function paradigm, are a challenge to study experimentally. Because a large part of our knowledge rests on computational predictions, it is crucial that their accuracy is high. The Critical Assessment of protein Intrinsic Disorder prediction (CAID) experiment was established as a community-based blind test to determine the

Comprehensive descriptions of animal behavior require precise three-dimensional (3D) measurements of whole-body movements. Although two-dimensional approaches can track visible landmarks in restrictive environments, performance drops in freely moving animals, due to occlusions and appearance changes. Therefore, we designed DANNCE to robustly track anatomical landmarks in 3D across species and behaviors