Perspectives

An interactive online resource integrated in the GPCRdb hub presents tools to design GPCR constructs and determine appropriate experimental conditions for structural studies by crystallography and cryo-EM.

Expansion microscopy allows super-resolution images of diverse samples to be acquired on conventional microscopes, thus democratizing super-resolution imaging. This Perspective reviews available methods and provides practical guidance for users.

A Perspective on super-resolution structured illumination microscopy reviews advances in these methods and focuses on matching user needs in terms of imaging speed, sample depth, and desired resolution with the appropriate instrumentation.

This Perspective highlights recent advances in the use of nanoparticles in super-resolution microscopy and single-molecule tracking. It offers guidance for users interested in these tools and discusses potential future directions.

This Perspective reviews nanoscopy via stimulated emission depletion (STED), focusing on challenges for biologists and how technical advances are helping to meet these challenges.

This Perspective examines single-cell RNA-seq data challenges and the need for normalization methods designed specifically for single-cell data in order to remove technical biases.

This Perspective introduces the development and use of adaptive optics in correcting aberrations in deep optical imaging applications.

OpenMS is a flexible, user-friendly, open-source software platform for the biological analysis of mass spectrometry proteomics and metabolomics data. The modular platform allows developers to seamlessly generate custom data-analysis workflows and directly make such ready-made workflows available to biologist end-users. Also in this issue, see the Perspective by Tyanova et al.

Perseus is a comprehensive, user-friendly software platform for the biological analysis of quantitative proteomics data. It is intended to help biologists with little bioinformatics training to interpret protein expression, post-translational modification and interaction data. Also in this issue, see the Perspective by Röst et al.

The Perspective by Sung, Baek and Hager discusses consensus, remaining issues and hurdles for genomic footprinting.

This Perspective by Vierstra and Stamatoyannopoulos discusses the prospects and challenges of genomic footprinting applied to complex genomes.

International Cancer Genome Consortium members review and recommend approaches to pathway and network analysis to uncover molecular processes that contribute to tumor biology.

In this Perspective, the authors advance a view of macromolecules as collections ofinterchanging structural ensembles, and discuss how a synergistic combination of NMR,X-ray crystallography, and computational simulations can reveal the structural basis for conformational dynamics at atomic resolution.

A Perspective on the open-source and open-development software project Bioconductor provides an overview for prospective users and developers dealing with high-throughput data in genomics and molecular biology.

This Perspective discusses methods to measure single-cell mass and their relative strengths and weaknesses for different applications.

Tumor-specific peptides missed in standard mass spectrometry–based workflows can be identified by integrating genomic information to interpret proteomic data. As discussed in this Perspective, an onco-proteogenomic approach to study tumor biology could have a substantial impact on cancer research. Also in this issue, Nesvizhskii reviews proteogenomic technology.

This Perspective discusses the power of large mutational scans for the study of protein properties, the analytical challenges posed by the resulting data sets and the potential of this approach to further our understanding of human genetic variation.

This Perspective takes the reader through the important steps in bacterial genome assembly and activation and concludes with an outlook on how customized genomes may be achieved.

Optofluidic biolasers are emerging as a highly sensitive way to measure changes in biological molecules. Biolasers, which incorporate biological material into the gain medium and contain an optical cavity in a fluidic environment, take advantage of the amplification that occurs during laser generation to quantify tiny changes in biological processes in the gain medium. This Perspective describes the principle of the optofluidic biolaser, reviews recent progress and provides outlooks on potential applications and directions for developing this enabling technology.

This Perspective describes statistical measures commonly used to quantify whether nodes in biological networks have similar interaction profiles and discusses which indices are best suited for specific tasks.