Volume 12 Issue 4, April 2015

Math, mass spectrometry and imaging can mix, but it takes some woodworking.

Incorporate new evidence to update prior information.

A new calcium sensor allows the permanent labeling of neurons that are active at defined periods of time.

Atomic force microscopy is applied to image the location of chemical groups inside single protein complexes.

A new method uses click chemistry to covalently modify any RNA of interest.

A new platform detains single cells in picoliter wells to generate transcriptional profiles in large numbers.

A collection of genomic tools helps researchers exploit a short-lived fish species as a model for human aging.

Synthetic small RNA transcriptional activators can regulate gene transcription in Escherichia coli.

Scientific animations have tremendous potential as instruments of insight and dissemination. However, audiences are often unable to determine the degree to which visualizations are informed by scientific evidence. By providing a more detailed account of source use, developers can increase the credibility of animations as scientific tools.

Data integration and tool interoperability can ease analyses of cancer 'omics data and yield surprises.

Nanopore sequencing gets a boost with accurate error modeling and variant-calling tools for Oxford Nanopore Technology's highly anticipated MinION platform.

Two methods for early tagging of sample RNA before RT-qPCR or full RNA-seq open the door to experiments with fewer technical batch effects.

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.

FIB-SEM sample size is limited by cumulative milling artifacts and long imaging times.Ultrathick sectioning, followed by parallel FIB-SEM imaging and volume stitching,overcomes this limit, generating data sets of high quality for large-scale connectomics.

RNAtag-seq barcodes transcripts prior to cDNA synthesis, thereby allowing pooled library generation from many input samples.

The fusion of three transcriptional activation domains to a nuclease-deficient Cas9 achieves robust induction of gene expression and can induce differentiation of hiPSCs.

A workflow for preserving disulfide links in proteins in conjunction with pLink-SS enables the analysis of disulfide bonds across the proteome.

LEAP (liability estimator as a phenotype) corrects for confounding factors in case-control GWAS with increased power.

New detector technology has improved the resolution of cryo-electron microscopy (cryo-EM), but tools for structure determination from high-resolution maps have lagged behind. Wang et al. describe a de novo approach for structure determination from high-resolution cryo-EM maps. Also in this issue, DiMaio et al. report structure determination using a homologous structure as a starting model.

CaptureSeq was used to quantitatively profile transcripts with low expression, resulting in a catalog of long noncoding RNA expression in 20 human tissues.

META RNA profiling allows the simultaneous quantification of a broad selection of mRNAs or microRNAs in many samples via early sample pooling.

The GIREMI tool allows the accurate and sensitive detection of RNA editing sites from single RNA-seq data sets, without the need for genomic data.

Improved error assessment and read alignment on the MinION nanopore sequencing platform allow for calling of single-nucleotide variants and resolving the repeat structure of an assembly gap in the human X chromosome.

HISAT (hierarchical indexing for spliced alignment of transcripts) uses global and local indices for fast, sensitive alignment with small memory requirements.

New detector technology has improved the resolution of cryo-electron microscopy (cryo-EM), but tools for structure determination from high-resolution maps have lagged behind. DiMaio et al. report structure determination from high-resolution cryo-EM maps using a homologous structure as a starting model. Also in this issue, Wang et al. describe a de novo approach for structure determination that does not require a starting model.

An approach to fuse images from imaging mass spectrometry and microscopy provides biological insights into molecular tissue distributions beyond what can be obtained from either modality individually.