Reviews & Analysis

A new toolbox for structural biology that combines single-molecule fluorescence and molecular modeling is used to generate high-precision structures of protein complexes.

The Genome Multitool (GEM) mapper rapidly and accurately provides all alignments of a read within a user-defined number of mismatches.

Researchers adapt a popular Orbitrap-based mass spectrometer to detect and analyze large, intact protein complexes, accelerating a new frontier in structural biology.

Work from two independent groups opens the door to designing gene circuits with advanced regulatory functions.

This Perspective discusses the registered and publicly available set of Cytoscape plugins to guide potential users to suitable tools.

A new high-throughput method for monitoring G protein–coupled receptor activation is highly suited to assaying Gα_12/13-coupled receptors and is used to deorphanize a group of receptors activated by lysophosphatidylserine.

Two studies plant a signpost on the road toward a robust and detailed chromatin interaction map.

New bioinformatics tools enable the recognition of neighboring amino acids in protein complexes.

Through a collaborative effort, engineers and neuroscientists have created a method, using electrospun nanofibers as surrogate neuronal axons, to piece together the complexities of myelination.

In this perspective, the authors present the basic features of lens-free computational imaging tools and report performance comparisons with conventional microscopy methods. They also discuss the challenges that these computational on-chip microscopes face for their wide-scale biomedical application.

An experimental infrastructure consisting of environmentally controlled and spatially linked habitat patches permits studies on terrestrial animal dispersal at an unprecedented scale for an experiment with such strict control.

Two methods for estimating fluorophore positions provide useful new options to researchers performing either single-particle tracking or super-resolution imaging.

In toto imaging of living embryos has now become much faster. Light-sheet illumination and fluorescence detection with four objective lenses provide complete coverage of large samples in a snap.

Presented is an overview of the image-analysis software platform Fiji, a distribution of ImageJ that updates the underlying ImageJ architecture and adds modern software design elements to expand the capabilities of the platform and facilitate collaboration between biologists and computer scientists.

Representative members of the bioimage informatics community review the computational steps and some of the primary software tools available to biologists who are acquiring and analyzing microscopy-based digital image data, with a focus on open-source options.

Described is BioImageXD, a simple, user-friendly, open-source platform for biological image analysis. The authors outline their design criteria and how BioImageXD meets them, and demonstrate BioImageXD performance in a study of integrin clustering.

Icy is a collaborative platform for biological image analysis that extends reproducible research principles by facilitating and stimulating the contribution and sharing of algorithm-based tools and protocols between researchers.

A precomputed database of lineage-restricted reference genes yields a fast and accurate tool that uses sequence similarity alone to compute clade abundances from shotgun metagenomic data sets.

Researchers describe an approach to predict microbial-community composition across broad spatial and temporal gradients, an important step to bringing microbial ecology into the 21^st century.

Fluorescence recording of neural activity in the magnetic resonance scanner is a new strategy for examining the cellular underpinnings of blood oxygenation level–dependent (BOLD) functional magnetic resonance imaging (fMRI).