Volume 16 Issue 5, May 2019

His enhancer-discovery tool cisTopic is both wet-lab and dry-lab. John Coltrane matters, too.

Combining photoactivation and spontaneous blinking enables long time-lapse localization microscopy.

Metabolic labeling enables researchers to spatiotemporally assess nascent protein deposition in 3D hydrogels and then study how nascent proteins influence cell behaviors.

Comparisons of genome organization in many individual cells with high-throughput FISH show extensive variation.

A newly identified bacterial biosynthetic pathway enables the production of nonstandard amino acids.

An optimized chemogenetic tool enables highly specific and potent neuronal manipulations.

The materials–biology interface is challenging to characterize, but new assays are on the way.

This paper reviews the cryo-EM technique of microcrystal electron diffraction (MicroED), providing a broad overview of the technique, the unique structures determined, and the opportunities for future development.

Among 17 measures of association tested, measures of proportionality consistently performed well for inference of gene and cellular networks, cell clusters and links to disease from scRNA-seq data. In contrast, several widely used measures of association performed well on only a subset of tasks.

This study reports results from the second community-wide single-molecule localization microscopy software challenge, which tested over 30 software packages on realistic simulated data for multiple popular 3D image acquisition modes, as well as 2D localization microscopy.

As an unsupervised Bayesian framework, cisTopic classifies regions in scATAC-seq data into regulatory topics, which are used for clustering.

To address the issue of intra-tissue heterogeneity in cancer genomics, we developed Texomer, which enables joint analysis of bulk DNA and RNA sequencing data for allele-specific deconvolution and quantification of tumor heterogeneity.

Massively parallel Cpf1 array profiling (MCAP) targets genes and gene pairs that are candidate drivers of metastasis in cancer. In vivo profiling of single and double gene knockouts enables quantitative mapping of the genes’ contribution to metastatic phenotypes.

ECCITE-seq combines the single-cell analysis of multiple modalities, for example transcriptome, immune cell receptors, cell surface proteins and single-guide RNAs.

High-throughput screening of fragment libraries of yeast genes yields dominant negative polypeptides on the basis of their decreased frequencies in cells after a growth selection.

A mass-spectrometry-compatible surfactant called Azo effectively solubilizes proteins, is rapidly degraded by ultraviolet irradiation and enables top-down proteomic analysis of membrane proteins.

A method for protein binder selection and identification, NestLink, uses barcoding peptides detectable by mass spectrometry to select and biophysically characterize thousands of binders without requiring the handling of individual clones.

Replication initiation is stochastic and obscured in population sequencing; D-NAscent reports the use of long nanopore reads to detect base analogs and thus to assess replication initiation at the individual molecule level.

Ribonucleotidyl transferases tethered to an RNA reporter add untemplated RNA tails. TRAID-seq identifies the activities of 22 enzymes, including the addition of poly(UG).