Volume 16 Issue 4, April 2019

Tools for metabolomics

A computational tool facilitates molecular formula, metabolite class and structure assignment of plant metabolites from LC-MS data.

See Tsugawa et al.

Cover design: Erin Dewalt.

Editorial

Editorial | 28 March 2019

Tightening the handle on malaria

Different methods have contributed to a better understanding of the malaria parasite, but improvements are still needed to uncover basic Plasmodium biology.

This Month

This Month | 18 March 2019

Haribabu Arthanari

A spin-jock’s path to biomolecular dynamics with NMR, and why solitude matters.
- Vivien Marx
This Month | 28 March 2019

Analyzing outliers: robust methods to the rescue

Robust regression generates more reliable estimates by detecting and downweighting outliers.
- Luca Greco
- , George Luta
- & Naomi Altman

Correspondence

Correspondence | 18 March 2019

FPbase: a community-editable fluorescent protein database
- Talley J. Lambert
Correspondence | 18 March 2019

3Dscript: animating 3D/4D microscopy data using a natural-language-based syntax
- Benjamin Schmid
- , Philipp Tripal
- & Ralf Palmisano

Research Highlights

Research Highlight | 28 March 2019

Investigating heterogeneity in HeLa cells

Multi-omic study uncovers biological variation across 14 HeLa cell samples, which might help to explain the growing concerns about reproducibility issues in cell culture.
- Lei Tang
Research Highlight | 28 March 2019

Dissecting neuronal circuitry

A virus-based tracing approach in combination with recombinase-mediated labeling allows the dissection of neuronal circuit motifs with subtype specificity.
- Nina Vogt
Research Highlight | 28 March 2019

Double the fun

An eight-letter genetic alphabet can form a double helix resembling natural DNA and can be transcribed into RNA.
- Irene Jarchum
Research Highlight | 28 March 2019

Bridging the nanoscale measurement gap

Single-molecule imaging enables accurate distance measurements from two to hundreds of nanometers.
- Rita Strack
In Brief | 28 March 2019

RNA editing with endogenous ADARs
- Nicole Rusk
In Brief | 28 March 2019

Mapping the marmoset brain
- Nina Vogt
In Brief | 28 March 2019

Template-free visual proteomics
- Allison Doerr
In Brief | 28 March 2019

On algorithmic resolution
- Rita Strack
In Brief | 28 March 2019

Human gut bacterial genome reference
- Lei Tang
In Brief | 28 March 2019

Human immunity to Cas9
- Nicole Rusk
In Brief | 28 March 2019

Improved exosome detection
- Rita Strack
In Brief | 28 March 2019

Bisulfite-free epigenetic sequencing
- Lei Tang
Research Highlight | 28 March 2019

Spatially resolved isotope labeling

Electron-energy-loss spectroscopy with a scanning transmission electron microscope enables spatially resolved imaging of isotope-labeled molecules.
- Christian Schnell

Technology Feature

Technology Feature | 28 March 2019

What to do about those immunoprecipitation blues

ChIP-seq, DIP-seq and related techniques are informative genome-wide assays, but they don’t always work as planned.
- Vivien Marx
Collection:
- NatureTech

News & Views

News & Views | 18 March 2019

Peering into cells at high resolution just got easier

Light-sheet fluorescence microscopes are making it possible to follow subcellular dynamics with unprecedented detail, but they are complex to build and maintain. A new method that can generate arbitrary light sheets provides much-needed simplicity and additional versatility.
- Manu Forero-Shelton

Brief Communications

Brief Communication | 28 March 2019

A cheminformatics approach to characterize metabolomes in stable-isotope-labeled organisms

A computational approach facilitates molecular formula, metabolite class, and structure assignment for plant metabolites on the basis of LC–MS analysis of fully ¹³C-labeled and unlabeled plants.
- Hiroshi Tsugawa
- , Ryo Nakabayashi
- & Kazuki Saito
Brief Communication | 18 March 2019

SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information

SIRIUS 4 is a fast and highly accurate tool for molecular structure interpretation from mass-spectrometry-based metabolomics data.
- Kai Dührkop
- , Markus Fleischauer
- & Sebastian Böcker
Brief Communication | 11 March 2019

A multiplexable assay for screening antibiotic lethality against drug-tolerant bacteria

The solid media portable cell killing assay uses metabolism-sensitive staining to illuminate the killing of antibiotic-tolerant bacteria under resource-depleted conditions, thereby enabling multiplex, genome-scale analyses for the identification of target strains.
- Jonathan M. Stokes
- , Arnaud Gutierrez
- & James J. Collins
Brief Communication | 25 March 2019

Deep-learning augmented RNA-seq analysis of transcript splicing

DARTS first uses public domain data to train a deep neural network to predict differential alternative splicing; the predictions are then combined with observed RNA-seq data in a Bayesian framework to infer changes in alternative splicing between biological samples.
- Zijun Zhang
- , Zhicheng Pan
- & Yi Xing
Brief Communication | 18 March 2019

Scalable analysis of cell-type composition from single-cell transcriptomics using deep recurrent learning

scScope uses a recurrent network to remove batch effects and iteratively impute zero values in scRNA-seq data.
- Yue Deng
- , Feng Bao
- & Steven J. Altschuler
Brief Communication | 28 March 2019

Selene: a PyTorch-based deep learning library for sequence data

Selene is a deep learning library that enables the expansion of existing deep learning models to new data, the development of new model architectures, and the evaluation of these new models on biological sequence data.
- Kathleen M. Chen
- , Evan M. Cofer
- & Olga G. Troyanskaya
Brief Communication | 25 March 2019

SNAC-tag for sequence-specific chemical protein cleavage

SNAC-tags allow for versatile sequence-specific cleavage of soluble and membrane proteins with Ni²⁺ under biocompatible conditions, bypassing enzymatic cleavage and enabling cleavage in situations where commonly used enzymes fail.
- Bobo Dang
- , Marco Mravic
- & William F. DeGrado
Brief Communication | 28 March 2019

Single-cell chromatin immunocleavage sequencing (scChIC-seq) to profile histone modification

Covalent linking of a histone-modification-specific antibody to MNase allows for the isolation of fragments with the desired histone mark, which can be amplified and sequenced. This approach is sensitive enough to profile histone modifications in single cells.
- Wai Lim Ku
- , Kosuke Nakamura
- & Keji Zhao

Articles

Article | 18 March 2019

Cell composition analysis of bulk genomics using single-cell data

Cell Population Mapping (CPM) leverages single-cell RNA-seq data as a rich reference to predict the composition of cell types and cell states from bulk RNA-seq data.
- Amit Frishberg
- , Naama Peshes-Yaloz
- & Irit Gat-Viks
Article | 11 March 2019

Aromatic ¹⁹F-¹³C TROSY: a background-free approach to probe biomolecular structure, function, and dynamics

The development of ¹⁹F-¹³C TROSY provides a new avenue for the collection of high-sensitivity, background-free information about the structure and dynamics of challenging biomolecular systems by NMR spectroscopy.
- Andras Boeszoermenyi
- , Sandeep Chhabra
- & Haribabu Arthanari
Article | 11 March 2019

An active texture-based digital atlas enables automated mapping of structures and markers across brains

An active atlas for automatic alignment of brains to a reference atlas is presented. The method uses the fine-scale pattern of tissue. The atlas is refined by each new brain and can inform on the structural variability between different brains.
- Yuncong Chen
- , Lauren E. McElvain
- & David Kleinfeld
Collection:
- Deep learning in microscopy

Amendments & Corrections

Author Correction | 25 February 2019

Author Correction: U-Net: deep learning for cell counting, detection, and morphometry
- Thorsten Falk
- , Dominic Mai
- & Olaf Ronneberger
Author Correction | 28 February 2019

Author Correction: Stability, affinity, and chromatic variants of the glutamate sensor iGluSnFR
- Jonathan S. Marvin
- , Benjamin Scholl
- & Loren L. Looger
Author Correction | 08 March 2019

Author Correction: Methods to study RNA–protein interactions
- Muthukumar Ramanathan
- , Douglas F. Porter
- & Paul A. Khavari

Volume 16 Issue 4, April 2019

Tools for metabolomics

Editorial

This Month

Correspondence

Research Highlights

Technology Feature

News & Views

Brief Communications

Articles

Amendments & Corrections

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