Volume 13 Issue 4, April 2016

Team sports and team efforts lead to a new tool that helps with immune profiling.

Some outliers influence the regression fit more than others.

Synthetic Notch receptors with chimeric extra- and intracellular domains can be tailored to tune cell-cell communication.

Researchers exploit crystal imperfections to solve protein structures at resolutions beyond the X-ray diffraction limit.

Short single-stranded DNA donors that asymmetrically span the Cas9 cut site show high efficiency in homology-directed editing.

Researchers have developed a set of fluorescent-protein-based sensors for endogenous nitric oxide.

Alternative splicing imparts distinct functions through isoform-specific protein–protein interactions.

Genetic background trumps tissue of origin as a source of variability between induced pluripotent stem cell lines, diminishing the role of somatic memory in reprogrammed cells.

Emerging ways to lower the error rate when hunting low-frequency mutations.

Lattice light-sheet-PAINT brings localization microscopy to large volumes, and SuReSim enables ground truth modeling of super-resolution experiments.

This comparison of ten computational methods for detecting transcription factor binding sites in DNase hypersensitive regions in the genome determines which methods work consistently well, how DNase-seq experimental artifacts should be corrected for and which score is best for ranking methods.

The HPN-DREAM community challenge assessed the ability of computational methods to infer causal molecular networks, focusing specifically on the task of inferring causal protein signaling networks in cancer cell lines.

SuReSim software simulates single-molecule localization microscopy data for structures with known ground truth models to facilitate proper design, interpretation and validation of super-resolution imaging experiments.

EpiGBS (epi-genotyping by sequencing) constructs de novo references using reduced representation bisulfite sequencing followed by variant calling and methylation detection.

Frame-projected independent-fiber photometry (FIP) enables the concurrent monitoring and manipulation of neural activity at multiple sites in the brains of freely behaving mice.

The TraCeR tool extracts full-length, paired T cell receptor sequences from single-cell RNA-sequencing data from T lymphocytes, enabling a combination of clonotype and functional analysis.

A high-resolution, Orbitrap-based, native mass spectrometry approach allows the direct characterization of lipid, peptide and drug binding to intact membrane proteins.

High-field fMRI with single-vessel resolution allows one to decipher the contribution of different types of vessels to hemodynamic activity evoked by sensory or optogenetic stimulation in the rat brain.

This report describes an imaging and analysis platform enabling high-throughput single-molecule fluorescence investigations of fast, transient molecular recognition events.

A saposin protein–lipid nanoparticle system stabilizes diverse, fragile membrane proteins in a lipid environment for structural and functional studies.

HomoFRET sensors based on G6PD homodimerization allow direct sensing of NADPH/NADP⁺ redox state in living cells. Spectrally tuning the Apollo-NADP⁺ sensor allows multiplex imaging for studies of oxidative stress in beta cells.

Lattice light-sheet and PAINT microscopy are combined to achieve low-background detection of dense molecular labels, yielding super-resolution localization microscopy images of intricate 3D structures within dividing cells and embryos.

This resource contains 394 human cell type– and tissue-specific transcriptional networks and finds that disease-associated genetic variants often perturb regulatory modules in tissues specific for that disease.

The SWAp-Tag method allows for easy replacement of a tag in a parental strain with an expression cassette of choice to rapidly create new yeast libraries that will enable researchers to address biological questions in Saccharomyces cerevisiae.