Volume 13 Issue 9, September 2016

Sequins can help labs see how well a sequencing experiment is going. Surfing experiments are another matter.

With four parameters I can fit an elephant and with five I can make him wiggle his trunk. —John von Neumann

Researchers plumb the depths of the cell with volumetric 4Pi nanoscopy.

By capturing and barcoding RNA in its native tissue location, researchers can visualize and quantify gene expression in situ.

Single-cell 5hmC sequencing uncovers cell-to-cell differences in the two DNA strands of a given chromosome.

SRMAtlas contains mass spectrometry assays allowing targeted analysis of nearly 100% of human proteins.

A proof-of-concept platform demonstrates the feasibility of nanopore-based sequencing of polypeptide chains.

By analogy to protein and DNA similarity searches, NBLAST provides a fast and efficient way of finding morphological similarities between neurons.

Two new platforms allow single neurons to be imaged throughout the mouse brain.

Researchers develop a new class of near-infrared fluorescent proteins from a light-harvesting phycobiliprotein.

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.

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.

Read Until allows real-time selective sequencing on a nanopore sequencer, enabling applications such as target enrichment and amplicon normalization.

LOVTRAP enables rapid optogenetic control of protein dissociation and is complementary to related optogenetic tools that mediate light-induced protein association. LOVTRAP is applied to the study of oscillatory processes at the cell membrane.

Virtual microfluidics uses hydrogel entrapment to make high-throughput single-cell and single-molecule amplification broadly accessible without the need for special equipment.

A bright and photostable far-red fluorescent protein, smURFP, was developed from a cyanobacterial phycobiliprotein. smURFP uniquely binds a highly cell-permeable biliverdin derivative to obtain fluorescence brightness comparable to that of eGFP in cells.

A network-based method and computational tool, PIUMet, reveals disease-associated molecular pathways from untargeted metabolomics data without requiring mass-spectral feature identification.

TRIC, a cross-run alignment algorithm and software tool, enables reproducible quantification of thousands of peptides across multiple targeted liquid chromatography–tandem mass spectrometry runs.

Synthetic DNA spike-ins that recapitulate genetic variation present in human genomes serve as quantitative and qualitative controls for genome sequencing and variant detection.

Synthetic spike-in standards (‘sequins’), representing spliced mRNA isoforms, provide internal controls for assessing transcript assembly and quantification within and between RNA sequencing libraries. Sequins representing fused genes can be used to determine the sensitivity limit for oncogenic fusions in cancer samples.