Reviews & Analysis

Integrating biochemical footprinting data with molecular dynamics yields more accurate RNA three-dimensional structure predictions.

In this Review, the authors provide a guide through to the different steps involved in selected reaction monitoring as well as discuss its applications.

Using semiconductor processing to construct integrated circuits that reside close to nanopores, researchers demonstrate high-bandwidth, low-noise measurements of DNA translocation through solid-state nanopores.

A strategy that uses genetically encoded GFP-tagged antibodies allows in vivo imaging of extracellular non–genetically encoded molecules.

Current practice for the generation and maintenance of induced pluripotent stem cells (iPSCs) involves static culture in dishes. Two groups now report that mouse iPSCs can be generated efficiently in stirred suspension culture.

Single-molecule DNA sequencing takes an important step in a surprising new direction with a sequence-detection method based on magnetic tweezers.

Deletion of a genomic locus may affect the function of neighboring loci, creating genetic uncertainty. Researchers now present a computational algorithm for identifying such neighboring-gene effects and improving the quality of functional annotations.

Presented is an update on the status and current practices of the International Molecular Exchange (IMEx) consortium and on its efforts to create a single nonredundant set of protein interactions curated from the scientific literature.

Using two independent methods, researchers show that in vivo–grown crystals of soluble proteins and of membrane proteins grown in the lipidic sponge phase can be analyzed by serial femtosecond crystallography on an X-ray free electron laser.

In living systems, chemical reactions and the geometry of cells feed back on each other. Methods for computational modeling are beginning to take this complexity into account.

The Open Microscopy Environment Remote Objects (OMERO) software platform provides a server-based system for managing and analyzing microscopy images and non-image data.

Neuroimaging methods are beginning to provide promising ways of understanding the functional organization of the brain across species.

In vivo methods to capture processing events such as RNA editing in specific cell types are sparse. Researchers have now developed a method to visualize adenosine-to-inosine editing activity in individual fruit fly neurons using a reverse-engineered fluorescent reporter.

A sophisticated analysis approach based on the concept of fluorophore localization provides dynamic super-resolution data of GFP-labeled live cells using a common, arc lamp–based wide-field fluorescence microscope.

In this Perspective the authors highlight and discuss the artifacts that can arise when using immunolabeling to examine protein localization in cell culture. They call for using both alternative fixation and permeabilization protocols and live-cell imaging of fluorescent protein fusions to reliably study subcellular protein localization.

In this Review, the authors take the reader through the steps needed to analyze bisulfite-treated DNA, pointing out different considerations for data in base or color space, to ensure high-quality methylome analysis.