Volume 16 Issue 5, May 2019

Detecting proteins and RNAs in single cells

Artistic rendition of a high-content single-cell CRISPR screen enabled by a multimodal phenotyping tool.

See Mimitou et al.

Image: New York Genome Center / Vincent Dittmer. Cover design: Erin Dewalt.

Editorial

Editorial | 30 April 2019

All the right moves

Dispelling stigmas and highlighting benefits of the Nature Research manuscript transfer service.

This Month

This Month | 10 April 2019

Stein Aerts

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

Research Highlights

Research Highlight | 30 April 2019

Bypassing bleaching with fluxional fluorophores

Combining photoactivation and spontaneous blinking enables long time-lapse localization microscopy.
- Rita Strack
Research Highlight | 30 April 2019

Nascent proteins impact cell fate

Metabolic labeling enables researchers to spatiotemporally assess nascent protein deposition in 3D hydrogels and then study how nascent proteins influence cell behaviors.
- Lei Tang
Research Highlight | 30 April 2019

Variability in genome structure

Comparisons of genome organization in many individual cells with high-throughput FISH show extensive variation.
- Nicole Rusk
Research Highlight | 30 April 2019

A bacterial treasure trove

A newly identified bacterial biosynthetic pathway enables the production of nonstandard amino acids.
- Karin Kuehnel
In Brief | 30 April 2019

Diet influences microbe–host interaction
- Lei Tang
In Brief | 30 April 2019

Imaging chromatin and RNA in embryos
- Rita Strack
In Brief | 30 April 2019

Optoacoustic imaging of neural activity
- Nina Vogt
In Brief | 30 April 2019

Mitochondrial barcodes
- Nicole Rusk
In Brief | 30 April 2019

Bright probes for EM
- Rita Strack
In Brief | 30 April 2019

Sensing norepinephrine
- Nina Vogt
In Brief | 30 April 2019

Polarization-varying anisotropic terahertz microscopy
- Lei Tang
In Brief | 30 April 2019

Optically mapping methylation
- Nicole Rusk
Research Highlight | 30 April 2019

Potent chemogenetics

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

Technology Feature

Technology Feature | 30 April 2019

How some labs put more bio into biomaterials

The materials–biology interface is challenging to characterize, but new assays are on the way.
- Vivien Marx
Collection:
- NatureTech

Perspectives

Perspective | 29 April 2019

The cryo-EM method microcrystal electron diffraction (MicroED)

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.
- Brent L. Nannenga
- & Tamir Gonen

Analysis

Analysis | 08 April 2019

Evaluating measures of association for single-cell transcriptomics

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.
- Michael A. Skinnider
- , Jordan W. Squair
- & Leonard J. Foster
Analysis | 08 April 2019

Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software

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.
- Daniel Sage
- , Thanh-An Pham
- & Seamus Holden

Brief Communications

Brief Communication | 08 April 2019

cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data

As an unsupervised Bayesian framework, cisTopic classifies regions in scATAC-seq data into regulatory topics, which are used for clustering.
- Carmen Bravo González-Blas
- , Liesbeth Minnoye
- & Stein Aerts
Brief Communication | 15 April 2019

Integrated transcriptomic–genomic tool Texomer profiles cancer tissues

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.
- Fang Wang
- , Shaojun Zhang
- & Ken Chen
Brief Communication | 08 April 2019

In vivo profiling of metastatic double knockouts through CRISPR–Cpf1 screens

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.
- Ryan D. Chow
- , Guangchuan Wang
- & Sidi Chen
Brief Communication | 22 April 2019

Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells

ECCITE-seq combines the single-cell analysis of multiple modalities, for example transcriptome, immune cell receptors, cell surface proteins and single-guide RNAs.
- Eleni P. Mimitou
- , Anthony Cheng
- & Peter Smibert
Brief Communication | 08 April 2019

High-throughput identification of dominant negative polypeptides in yeast

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.
- Michael W. Dorrity
- , Christine Queitsch
- & Stanley Fields
Brief Communication | 15 April 2019

A photocleavable surfactant for top-down proteomics

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.
- Kyle A. Brown
- , Bifan Chen
- & Ying Ge

Articles

Article | 22 April 2019

Engineered peptide barcodes for in-depth analyses of binding protein libraries

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.
- Pascal Egloff
- , Iwan Zimmermann
- & Markus A. Seeger
Article | 22 April 2019

Capturing the dynamics of genome replication on individual ultra-long nanopore sequence reads

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.
- Carolin A. Müller
- , Michael A. Boemo
- & Conrad A. Nieduszynski
Article | 15 April 2019

Unbiased screen of RNA tailing activities reveals a poly(UG) polymerase

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).
- Melanie A. Preston
- , Douglas F. Porter
- & Marvin Wickens

Amendments & Corrections

Author Correction | 09 April 2019

Author Correction: Two-level factorial experiments
- Byran Smucker
- , Martin Krzywinski
- & Naomi Altman
Publisher Correction | 16 April 2019

Publisher Correction: A cheminformatics approach to characterize metabolomes in stable-isotope-labeled organisms
- Hiroshi Tsugawa
- , Ryo Nakabayashi
- & Kazuki Saito

Volume 16 Issue 5, May 2019

Detecting proteins and RNAs in single cells

Editorial

This Month

Research Highlights

Technology Feature

Perspectives

Analysis

Brief Communications

Articles

Amendments & Corrections

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