Browse Articles | Nature Methods

Live imaging of neuronal dynamics in transparent mouse brains

Making live mammalian tissues transparent for imaging experiments without compromising their normal cellular functions has been a long-standing challenge. An isotonic and minimally invasive optical clearing medium for live mammalian cells and tissues (named SeeDB-Live) paves the way for deep-tissue live imaging of cellular functions ex vivo and in vivo.

Learning genes deeply

Annevo uses deep learning to achieve unprecedented accuracy in eukaryotic gene annotation, approaching the performance of evidence-based methods.

• Michael Hiller

Highly accurate ab initio gene annotation with ANNEVO

ANNEVO advances accurate and scalable ab initio gene annotation of evolutionarily diverse genomes using deep learning approach modeling sequence evolution and long-range dependencies and mixture of experts (MoE) architecture.

• Pengyu Zhang
• Tun Xu
• Kai Ye

stVCR: spatiotemporal dynamics of single cells

stVCR models and reconstructs single-cell dynamics of cell differentiation, proliferation and migration using time-series spatial transcriptome data.

• Qiangwei Peng
• Peijie Zhou
• Tiejun Li

AF2BIND: predicting small-molecule binding sites using the pair representation of AlphaFold2

AF2BIND is a logistic regression model trained on AlphaFold2 pair features to predict small-molecule binding-site residues in proteins, without multiple sequence alignments, homology models or knowledge of the true ligand. AF2BIND was used to predict binding sites across the AF2-predicted human proteome, finding thousands of potentially new ligandable sites.

• Artem Gazizov
• Anna Lian
• Nicholas F. Polizzi

Oligomeric symmetrical scaffolds for resolving RNA structures by cryoEM

We have engineered symmetric RNA scaffolds that allow structure solution of small RNAs via single-particle cryogenic-sample electron microscopy (cryoEM). This method enabled small-molecule ligand placement in experimental maps and revealed the molecular basis for specificity of natural and synthetic RNA aptamers, thus suggesting routes for structure-guided RNA engineering.

Toward a unified framework for determining conformational ensembles of disordered proteins

This Perspective establishes a comprehensive and practical framework to guide intrinsically disordered protein (IDP) ensemble determination, benchmarking and interpretation, as well as proposes a roadmap for IDP ensemble determination, uncertainty quantification and actionable benchmarking strategies.

• Hamidreza Ghafouri
• Pavel Kadeřávek
• Alexander Miguel Monzon

High-throughput phenomics of global ant biodiversity

Antscan is a publicly accessible database of synchrotron X-ray CT images of ants. The database covers almost 800 species from more than 200 genera and is coordinated with genome sequencing projects that will enable integrative analyses.

• Julian Katzke
• Francisco Hita Garcia
• Thomas van de Kamp

It’s a colorful pangenome world

A pangenome can reveal the spectrum of genome variation within a species. The toolbox for working with pangenomes is filling up.

• Vivien Marx

A unified framework for multiomics deconvolution

The new algorithm DECODE transcends the limitations of omics-specific methods, and provides a unified framework for the deconvolution of transcriptomic, proteomic and metabolomic datasets.

• Xiaoyu Wang
• Fuyi Li
• Jiangning Song