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Nature Methods Contents: August 2017 Volume 14 pp 753 - 825

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TABLE OF CONTENTS

August 2017 Volume 14, Issue 8

In This Issue
Editorial
This Month
Correspondence
Research Highlights
Technology Feature
Resource
Analysis
Brief Communications
Articles
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npj Molecular Phenomics is an online-only, open access journal that provides a forum for cutting-edge scientific advances in the emerging field of phenomics, the study of the physical and chemical characteristics of an individual in quantitative terms.

Part of the Nature Partner Journals series, npj Molecular Phenomics is published in partnership with Fudan University. The journal is now open for submissions. 

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In This Issue

Top

In This Issue   

 

Editorial

Top

Sharing images   p753
doi:10.1038/nmeth.4389
Images are among the richest data types that biologists collect, yet most biological images are not available for reanalysis or reuse. This may be changing.

 

This Month

Top

The Author File: Melike Lakadamyali   p755
Vivien Marx
doi:10.1038/nmeth.4369
DNA origami, super-resolution microscopy and creative flashes on a bike.

 

Points of Significance: Classification and regression trees   pp757 - 758
Martin Krzywinski and Naomi Altman
doi:10.1038/nmeth.4370
Decision trees are a simple but powerful prediction method.

 

Correspondence

Top

Probes & Drugs portal: an interactive, open data resource for chemical biology   pp759 - 760
Ctibor Skuta, Martin Popr, Tomas Muller, Jindrich Jindrich, Michal Kahle et al.
doi:10.1038/nmeth.4365

 

sCMOS noise-correction algorithm for microscopy images   pp760 - 761
Sheng Liu, Michael J Mlodzianoski, Zhenhua Hu, Yuan Ren, Kristi McElmurry et al.
doi:10.1038/nmeth.4379

 

Research Highlights

Top

Tailoring optogenetic illumination through tapered fibers
A tapered optical fiber delivers spatially precise and efficient optogenetic illumination to the rodent brain.

Synthetic epigenetic memory
Combining an inducible methyltransferase with a methylation-sensitive zinc finger creates an epigenetic memory circuit.

Bottoms-up!
Developments in data-independent-acquisition mass spectrometry allow efficient and accurate quantitation of peptidoforms across large sample cohorts.

A community repository for microfluidics
The Metafluidics initiative encourages researchers to upload and share open-source microfluidics designs.

Super-resolution imaging with mCherry
A chemical caging strategy allows mCherry to be used for localization microscopy.

Methods in Brief

Speckle-free OCT | This is your brain on fiber | Interference-based force microscopy | Better 2D visualization of 3D image stacks

Tools in Brief

A switch for manipulating active neurons | Separating the primed from the naïve | An all-in-one cell cycle reporter | A comprehensive map of human protein complexes

Methods
JOBS of the week
Bioinformatics Scientist
King Abdullah University of Science and Technology (KAUST)
Junior Principal Investigator (Unit Leader)
IFOM the FIRC Institute of Molecualr Oncology
Postdoctoral fellow
University of Gothenburg, Institute of Biomedicine
Research Fellow in Single Molecule Biophysics
University of Leeds
Postdoctoral Scholar
The University of Iowa
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19.04.18
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Technology Feature

Top

Genetics: new tales from ancient DNA   pp771 - 774
Vivien Marx
doi:10.1038/nmeth.4367
Coaxing ancient DNA to reveal its history delivers surprises and even improves ways of working with badly damaged present-day DNA.

 

Resource

Top

Image Data Resource: a bioimage data integration and publication platform   pp775 - 781
Eleanor Williams, Josh Moore, Simon W Li, Gabriella Rustici, Aleksandra Tarkowska et al.
doi:10.1038/nmeth.4326
This Resource describes the Image Data Resource (IDR), a prototype online system for biological image data that links experimental and analytic data across multiple data sets and promotes image data sharing and reanalysis.

 

Analysis

Top

Comparison of algorithms for the detection of cancer drivers at subgene resolution   pp782 - 788
Eduard Porta-Pardo, Atanas Kamburov, David Tamborero, Tirso Pons, Daniela Grases et al.
doi:10.1038/nmeth.4364
13 algorithms for the detection of cancer driver genes at the subgene level are assessed for their advantages and limitations.

 

Brief Communications

Top

A DNA origami platform for quantifying protein copy number in super-resolution   pp789 - 792
Francesca Cella Zanacchi, Carlo Manzo, Angel S Alvarez, Nathan D Derr, Maria F Garcia-Parajo et al.
doi:10.1038/nmeth.4342
A DNA-origami-based calibration method determines and accounts for labeling stoichiometry and fluorophore photophysics to improve protein counting in quantitative super-resolution imaging.

 

Addressing preferred specimen orientation in single-particle cryo-EM through tilting   pp793 - 796
Yong Zi Tan, Philip R Baldwin, Joseph H Davis, James R Williamson, Clinton S Potter et al.
doi:10.1038/nmeth.4347
The preferred specimen orientation problem limits accuracy and resolution in structure determination by cryo-EM. Collecting data at defined sample tilts yielded near-atomic-resolution structures for the influenza hemagglutinin trimer and ribosomal biogenesis intermediates.

 

RosettaES: a sampling strategy enabling automated interpretation of difficult cryo-EM maps   pp797 - 800
Brandon Frenz, Alexandra C Walls, Edward H Egelman, David Veesler and Frank DiMaio
doi:10.1038/nmeth.4340
RosettaES, an algorithm that uses a fragment-based sampling strategy, improves macromolecular structure modeling from cryo-EM data at 3-5-Å resolution.

 

Visualizing adenosine-to-inosine RNA editing in single mammalian cells   pp801 - 804
Ian A Mellis, Rohit Gupte, Arjun Raj and Sara H Rouhanifard
doi:10.1038/nmeth.4332
inoFISH uses fluorescence in situ hybridization to visualize and localize adenosine-to-inosine-edited transcripts.

 
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Articles

Top

High-speed fixed-target serial virus crystallography   pp805 - 810
Philip Roedig, Helen M Ginn, Tim Pakendorf, Geoff Sutton, Karl Harlos et al.
doi:10.1038/nmeth.4335
A new sample-delivery method for serial X-ray crystallography exploits the full repetition rate of the X-ray free-electron laser at the LCLS facility, thus enabling efficient, high-speed data collection to solve the three-dimensional structures of viruses.

 

Video rate volumetric Ca2+ imaging across cortex using seeded iterative demixing (SID) microscopy   pp811 - 818
Tobias Nöbauer, Oliver Skocek, Alejandro J Pernía-Andrade, Lukas Weilguny, Francisca Martínez Traub et al.
doi:10.1038/nmeth.4341
The seeded iterative demixing strategy, when used in combination with light-field microscopy, enables calcium imaging at single-neuron resolution in the mouse brain at high volumetric imaging rates and depths of up to 380 [mu]m.

 

CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping   pp819 - 825
Shelly A Trigg, Renee M Garza, Andrew MacWilliams, Joseph R Nery, Anna Bartlett et al.
doi:10.1038/nmeth.4343
CrY2H-seq, a Cre recombinase reporter-mediated yeast two-hybrid method coupled with next-generation sequencing, enables ultra-high-throughput screening of transcription factor interactions in Arabidopsis thaliana.

 
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