Perspectives

This Perspective discusses available software tools for lipidomics data analysis and provides a web-based Lipidomics Tools Guide to help guide the choice of these tools, organized by the major tasks for lipidomics research.

This Perspective describes common pitfalls that can occur when using light sheet microscopy and offers guidance for improved quantitative imaging with these instruments.

In this Perspective, technologies and challenges in the cardiac tissue engineering field are discussed and strategies to overcome these challenges are proposed.

This Perspective focuses on experimental techniques developed for circRNA studies, and provides practical guidelines for performing circRNA research.

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

This Perspective offers an overview of organic dyes commonly used as fluorescent labels and gives a chemist’s insight into their benefits and peculiarities.

This Perspective offers guidance for robust and reproducible antibody-based highly multiplexed tissue imaging.

This Perspective discusses how neuroscience can benefit from harnessing nanoscience-based tools for manipulating and recording neuronal activity.

This Perspective describes advances in computer science that enable the integration of deep learning with traditional knowledge-based modeling in biological sciences, and discusses how such integration might overcome the challenges of modeling sparse, incomplete and noisy experimental data.

This Perspective highlights workflow managers, which are useful for developing and managing complex bioinformatics pipelines.

This Perspective, from a large group of metabolomics experts, provides best practices and simplified reporting guidelines for practitioners of liquid chromatography– and gas chromatography–mass spectrometry-based metabolomics.

Comprehensive guidelines and resources to enable accurate reporting for the most common fluorescence light microscopy modalities are reported with the goal of improving microscopy reporting, rigor and reproducibility.

This Perspective describes new single-molecule protein sequencing and identification technologies alongside innovations in mass spectrometry that will eventually enable broad sequence coverage in single-cell proteomics.

This Perspective describes advances that have enabled robust directed evolution in mammalian cells. These approaches are poised to improve the development of new generations of tools to probe or modulate mammalian biology.

This Perspective describes technological advances for imaging-based screening of diverse cellular phenotypes.

The Perspective reviews the computational methods for subclonal reconstruction and recommends best practices for analyses and quality assessments.

This Perspective highlights recently developed computational models for studying chromosome organization, with a focus on how mechanistic modeling helps biologists to interpret the biological function behind the genome structures.

This Perspective reviews tools developed over the past five years in the macromolecular modeling, docking and design software Rosetta.

This Perspective discusses the challenges, progress and future of proteome profiling at specific chromatin loci for elucidating genome biology.

This Perspective highlights how high-resolution imaging has informed our view and helped overturn the textbook understanding of 4D genome organization.