Reviews & Analysis

A brief overview of how to derive a genome or transcriptome from a single cell.

New methods for measuring the sensitivity of chromatin to DNase digestion and Tn5 transposition help us map and interpret the genome's regulatory sequences.

RNA-seq is a recent and immensely popular technology for cataloging and comparing gene expression. Two papers from the international RGASP consortium report on large-scale competitions to identify the best algorithms for RNA-seq analysis, with surprising variability in the results.

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.

Network-based stratification (NBS) enables the subtyping of tumors on the basis of their mutational profiles, providing new avenues for cancer research and precision oncology.

Use of helper interactions to encourage weak heteromeric interactions between fluorescent protein pairs helps ensure optimal fluorescence resonance energy transfer (FRET) signals and minimizes the impact on target protein interactions.

Fourteen scientists who participated in a recent workshop to identify and address challenges of epigenome-wide association studies summarize their recommendations in this Review.

This Perspective describes current and prospective advances in genome engineering made possible with the CRISPR-Cas9 system.

An algorithm called CONTACT identifies correlated side-chain motions in proteins from X-ray crystallographic data, providing insights into dynamics and function.

With a flood of new tools for genome engineering, we can benefit from choosing the tool that best fits the job.

This Review of force-distance curve-based atomic force microscopy highlights the unique capabilities of the technique to simultaneously image the architecture of complex biological systems and map their physical, chemical and biological properties at nanometer resolution.

Massive parallelization of scanning-based super-resolution imaging allows fast imaging of large fields of view.

Methods for high-throughput and high-resolution dissection of enhancers in Drosophila are described by two independent groups.

International Cancer Genome Consortium members review and recommend computational approaches for identifying mutations that drive cancer progression from among the many sequence variants present in tumor genomes.

Two approaches to serially enrich protein post-translational modifications allow the detection of multiple modifications in a single biological sample using mass spectrometry.

More than 40 years after the invention of semiconductor pH microtransducers known as ISFETs, this transistor-based technology may revolutionize quantitative PCR.

A synthetic biology terminator toolkit enables more sophisticated circuit design and gives insight into the mechanism of transcriptional termination.

Two reports describing the use of direct-conversion electron detectors and algorithms that correct for beam-induced sample motion in single-particle electron cryomicroscopy demonstrate that this technique can solve structures of macromolecules at near-atomic resolution.

An approach for analyzing gene expression data identifies putative lineage-specifying transcription factors that may prove useful in cellular reprogramming.

With potential relevance for brain-mapping work, hydrogel-based structures can now be built from within biological tissue to allow subsequent removal of lipids without mechanical disassembly of the tissue. This process creates a tissue-hydrogel hybrid that is physically stable, that preserves fine structure, proteins and nucleic acids, and that is permeable to both visible-spectrum photons and exogenous macromolecules. Here we highlight relevant challenges and opportunities of this approach, especially with regard to integration with complementary methodologies for brain-mapping studies.