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Nature Methods Contents: January 2016 Volume 14 pp 1 - 96

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TABLE OF CONTENTS

January 2017 Volume 14, Issue 1

In This Issue
Special Feature
Editorial
This Month
Correspondence
Research Highlights
News Feature
Commentary
Review
Methods to Watch
Technology Feature
Brief Communications
Articles
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In This Issue

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In This Issue   

Special Feature

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Method of the Year 2016
Epitranscriptome analysis is our choice for Method of the Year 2016. A News Feature looks at the history of the field, from the first discoveries of RNA modifications in the 1960s to recent transcriptome-wide methods. A Review describes the strengths and weaknesses of these methods, and a Commentary discusses the functional importance of a particular modification in stem cells. Our choice of eight methods to watch highlights areas we think will be influential in 2017 and beyond.

Editorial

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Special Feature: Method of the Year 2016
Method of the Year 2016: Epitranscriptome analysis   p1
doi:10.1038/nmeth.4142

This Month

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Points of significance: P values and the search for significance   pp3 - 4
Naomi Altman and Martin Krzywinski
doi:10.1038/nmeth.4120

Correspondence

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Quantitative predictions of protein interactions with long noncoding RNAs   pp5 - 6
Davide Cirillo, Mario Blanco, Alexandros Armaos, Andreas Buness, Philip Avner et al.
doi:10.1038/nmeth.4100

Research Highlights

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Manipulating neurons in an activity-dependent manner
Neurons that are activated in response to a particular stimulus or behavior can be labeled or manipulated with a new method.

Colorful electron microscopy
A multicolor approach specifically labels multiple targets in electron microscopy images.

Blend-and-shoot crystallography
A rapid mix-and-inject serial femtosecond crystallography approach enables structure determination of ligand-binding intermediates.

Move over, Matrigel
A synthetic hydrogel matrix gives researchers greater control over intestinal organoid culture.

Thermal therapeutics
The development of temperature-inducible molecular bioswitches allows on-demand activation of synthetic genetic circuits in microbes.

Methods in Brief

Light-sheet microscopy on AutoPilot | High-speed imaging of neural activity in behaving animals | Small RNAs from small samples | Optoacoustic imaging at multiple spatiotemporal scales

Tools in Brief

Technologies converge on the human gut | Faster to a structure with RELION-2 | A database for CRISPR screens | Reverse-polarity activity-based protein profiling

Methods
JOBS of the week
Postdoctoral Fellow
University of Utah Department of Biochemistry
Head of Data Analysis
King's College London
Exciting PhD Positions in Molecular Medicine
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
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Wellcome Trust Sanger Institute
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News Feature

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Special Feature: Method of the Year 2016
Epitranscriptomics: mixed messages   pp15 - 17
Michael Eisenstein
doi:10.1038/nmeth.4125

Commentary

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Special Feature: Method of the Year 2016
Reversible RNA modifications in meiosis and pluripotency   pp18 - 22
Arne Klungland, John Arne Dahl, Gareth Greggains, Peter Fedorcsak and Adam Filipczyk
doi:10.1038/nmeth.4111

Review

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Special Feature: Method of the Year 2016
Epitranscriptome sequencing technologies: decoding RNA modifications   pp23 - 31
Xiaoyu Li, Xushen Xiong and Chengqi Yi
doi:10.1038/nmeth.4110
This Review describes the latest methods for profiling common epitranscriptomic marks, their scale, resolution and ability to quantify. It also discusses remaining challenges.

Methods to Watch

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Special Feature: Method of the Year 2016
Global metabolomics   p32
Allison Doerr
doi:10.1038/nmeth.4112
The ability to measure the metabolome on a global scale lags behind other omics techniques.

Special Feature: Method of the Year 2016
Expansion microscopy   p32
Rita Strack
doi:10.1038/nmeth.4113
The changing face of super-resolution imaging

Special Feature: Method of the Year 2016
CRISPR targets RNA   p33
Nicole Rusk
doi:10.1038/nmeth.4114
Having revolutionized DNA editing, CRISPR turns to RNA.

Special Feature: Method of the Year 2016
How single cells do it   p33
Tal Nawy
doi:10.1038/nmeth.4119
Single-cell sequencing is poised to elucidate how cells contribute to tissue function.

Special Feature: Method of the Year 2016
Cryo-electron tomography   p34
Allison Doerr
doi:10.1038/nmeth.4115
Cryo-electron tomography may facilitate in situ structural biology on a proteomic scale.

Special Feature: Method of the Year 2016
Faster brain imaging   p34
Nina Vogt
doi:10.1038/nmeth.4118
Higher volumetric imaging rates shed light on the dynamics in neuronal networks.

Special Feature: Method of the Year 2016
Capturing microbial interactions   p35
Tal Nawy
doi:10.1038/nmeth.4117
New approaches will expose microbial dependencies and environmental interactions.

Special Feature: Method of the Year 2016
Organoid culture   p35
Natalie de Souza
doi:10.1038/nmeth.4122
Ex vivo organoid culture could revolutionize biology, but variability must be understood.

Technology Feature

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Microbiology: the return of culture   pp37 - 40
Vivien Marx
doi:10.1038/nmeth.4107
Sequencing technology drives microbiology and gives researchers new reasons to draw on classic techniques.

Brief Communications

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Photometry unlocks 3D information from 2D localization microscopy data   pp41 - 44
Christian Franke, Markus Sauer and Sebastian van de Linde
doi:10.1038/nmeth.4073
Three-dimensional localization microscopy can yield important biological insights. A photometric approach is described that allows users to gain 3D information from existing 2D images and to improve axial resolution obtained with existing biplane setups.

A statistical test for conserved RNA structure shows lack of evidence for structure in lncRNAs   pp45 - 48
Elena Rivas, Jody Clements and Sean R Eddy
doi:10.1038/nmeth.4066
A new method, R-scape, tests whether observed sequence covariation supports a conserved secondary structure in RNA. The program finds no evidence for previously proposed conserved secondary structures in several lncRNAs.

Covalently circularized nanodiscs for studying membrane proteins and viral entry   pp49 - 52
Mahmoud L Nasr, Diego Baptista, Mike Strauss, Zhen-Yu J Sun, Simina Grigoriu et al.
doi:10.1038/nmeth.4079
Membrane proteins can be stabilized in a native-like setting using lipid-bilayer-based nanodiscs encircled by a membrane scaffold protein. Covalently circularized nanodiscs now offer enhanced stability and control over nanodisc diameter size, improving the quality of structural data.

mScarlet: a bright monomeric red fluorescent protein for cellular imaging   pp53 - 56
Daphne S Bindels, Lindsay Haarbosch, Laura van Weeren, Marten Postma, Katrin E Wiese et al.
doi:10.1038/nmeth.4074
An extremely bright, truly monomeric RFP, mScarlet, is described that outperforms existing RFPs in diverse labeling applications, especially in FRET with ratiometric imaging.

FDR-controlled metabolite annotation for high-resolution imaging mass spectrometry   pp57 - 60
Andrew Palmer, Prasad Phapale, Ilya Chernyavsky, Regis Lavigne, Dominik Fay et al.
doi:10.1038/nmeth.4072
The authors present a computational framework for false-discovery-rate-controlled metabolite annotation from high-resolution imaging mass spectrometry data.

A scored human protein-protein interaction network to catalyze genomic interpretation   pp61 - 64
Taibo Li, Rasmus Wernersson, Rasmus B Hansen, Heiko Horn, Johnathan Mercer et al.
doi:10.1038/nmeth.4083
InWeb_InBioMap (InWeb_IM for short) is a scored, integrated human protein-protein interaction network resource aggregated from public, experimentally determined protein-protein interactions. The resource enables functional interpretation of large-scale genomics data.

novoBreak: local assembly for breakpoint detection in cancer genomes   pp65 - 67
Zechen Chong, Jue Ruan, Min Gao, Wanding Zhou, Tenghui Chen et al.
doi:10.1038/nmeth.4084
The novoBreak software provides sensitive, accurate, and comprehensive detection of structural variation in somatic next-generation sequencing data.

TACO produces robust multisample transcriptome assemblies from RNA-seq   pp68 - 70
Yashar S Niknafs, Balaji Pandian, Hariharan K Iyer, Arul M Chinnaiyan and Matthew K Iyer
doi:10.1038/nmeth.4078
TACO generates a consensus transcriptome with improved accuracy from multisample RNA-seq data.

CHARMM36m: an improved force field for folded and intrinsically disordered proteins   pp71 - 73
Jing Huang, Sarah Rauscher, Grzegorz Nawrocki, Ting Ran, Michael Feig et al.
doi:10.1038/nmeth.4067
An all-atom protein force field, CHARMM36m, offers improved accuracy for simulating intrinsically disordered peptides and proteins.

Articles

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DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo   pp75 - 82
Meghan Zubradt, Paromita Gupta, Sitara Persad, Alan M Lambowitz, Jonathan S Weissman et al.
doi:10.1038/nmeth.4057
DMS-MaPseq enables genome-wide and target-specific RNA secondary structure probing of even rare or heterogeneously structured RNAs in vivo and was used to study structure involved in translation regulation as well as nascent transcripts.

Robust statistical modeling improves sensitivity of high-throughput RNA structure probing experiments   pp83 - 89
Alina Selega, Christel Sirocchi, Ira Iosub, Sander Granneman and Guido Sanguinetti
doi:10.1038/nmeth.4068
BUM-HMM is a statistically robust modeling pipeline for interpreting high-throughput RNA structure probing data, including that from transcriptome-wide experiments.

Atmospheric pressure MALDI mass spectrometry imaging of tissues and cells at 1.4-μm lateral resolution   pp90 - 96
Mario Kompauer, Sven Heiles and Bernhard Spengler
doi:10.1038/nmeth.4071
An instrumental setup for atmospheric pressure MALDI-based mass spectrometry imaging with improved lateral resolution enables subcellular-level details to be resolved.

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