Volume 19 Issue 4, April 2022

Building a sustainable open source toolbox to track social behavior and how to get in the zone.

During the COVID-19 pandemic, genomics and bioinformatics have emerged as essential public health tools. The genomic data acquired using these methods have supported the global health response, facilitated the development of testing methods and allowed the timely tracking of novel SARS-CoV-2 variants. Yet the virtually unlimited potential for rapid generation and analysis of genomic data is also coupled with unique technical, scientific and organizational challenges. Here, we discuss the application of genomic and computational methods for efficient data-driven COVID-19 response, the advantages of the democratization of viral sequencing around the world and the challenges associated with viral genome data collection and processing.

High-resolution structural information is critical for rapid development of vaccines and therapeutics against emerging human pathogens. Structural biology methods have been at the forefront of research on SARS-CoV-2 since the beginning of the COVID-19 pandemic. These technologies will continue to be powerful tools to fend off future public health threats.

Interactions between carbohydrates and the proteins that bind them (lectins) are often some of the first between a host cell and a viral invader. With its highly glycosylated spike protein, SARS-CoV-2 is no exception. Interrogating glycosylation is vital to understand viral infection, yet it has been a challenge. Improvement in methods ranging from mass spectrometry to glycan arrays and modeling simulations are yielding atomic-level information about the glycans that decorate viruses and host cells alike.

Critical technological advances have enabled the rapid investigations into the immune responses elicited by SARS-CoV-2, the pathogen responsible for the COVID-19 pandemic. We discuss the cutting-edge methods used to deconvolve the B-cell responses against this virus and the impact they have had in the ongoing public health crisis.

This Comment discusses the main animal models that have had a key role in our understanding of the immune and viral dynamics of SARS-CoV-2.

We asked scientists around the globe for their views on the basic research methods, tools and resources needed to fight future emerging pathogenic threats.

A lensless microscope captures 3D fluorescence images of complex biological tissues.

Embryogram allows stress measurements during migration of the lateral line primordium in zebrafish embryos.

Evolutionary trees link ancient and modern human genomes.

Long-read proteogenomics helps delineate isoform diversity in full-length proteins.

Single-nuclei isoform RNA sequencing enables cell-type specific isoform analysis in frozen brain samples.

Against the backdrop of its many battles with infectious disease, the Global South applies networking and creative grit to face COVID-19.

Engineered viral entry combined with single-cell sequencing technology makes it possible to identify specific ligand–receptor interactions in a high-throughput manner.

Two new toolkits that leverage deep-learning approaches can track the positions of multiple animals and estimate poses in different experimental paradigms.

By providing challenges to the metagenomics community based on complex and realistic metagenome benchmark datasets, CAMI — the community-driven initiative for the Critical Assessment of Metagenome Interpretation — has created a comprehensive assessment of the performance of metagenomics software for common analyses. As part of its second contest, CAMI II, it evaluates ~5,000 submissions from 76 software programs and their different versions.

A new single-objective light-sheet microscope has been developed that uses novel optics and imaging protocols to increase resolution without compromising imaging speed and volume.

A simple and affordable technique passively clears and images whole mammalian bodies or large tissues. This technique is compatible with the use of endogeneous fluoresent proteins, without the loss of signal associated with other existing methods for whole-animal clearing.

This Perspective discusses the use of organoid technology, its current limitations and unmet needs in the context of SARS-CoV-2 research.

This study presents the results of the second round of the Critical Assessment of Metagenome Interpretation challenges (CAMI II), which is a community-driven effort for comprehensively benchmarking tools for metagenomics data analysis.

CoLoRd achieves high compression rates for long-read sequencing data without affecting downstream analyses.

This work describes a strategy for estimating the population frequency of structural variations by searching the raw alignments of large population sequencing samples using the STIX framework.

RAPTR, a lentivirus surface display-based library-on-library screening method to decipher antigen and immunoreceptor identities

The DaXi single-objective light-sheet microscope achieves fast, high-quality imaging of large volumes. DaXi’s design allows increased scanning range without sacrificing imaging speed or quality, multiview imaging and versatile sample mounting.

SEUDO is a tool for detecting and correcting errors introduced by automated processing of calcium imaging data.

HYBRiD is a tissue-clearing approach that combines elements of solvent-based and aqueous, hydrogel-based methods, thereby achieving high transparency while maintaining fluorescence.

SLEAP is a versatile deep learning-based multi-animal pose-tracking tool designed to work on videos of diverse animals, including during social behavior.

DeepLabCut is extended to enable multi-animal pose estimation, animal identification and tracking, thereby enabling the analysis of social behaviors.