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vrijdag 8 juni 2018

Nature Methods Contents: June 2018, Volume 15 No 6

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Nature Methods

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TABLE OF CONTENTS

June 2018 Volume 15, Issue 6

Editorial
This Month
Correspondence
Research Highlights
Technology Feature
Perspectives
Brief Communications
Articles
Amendments & Corrections
 
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Editorial

 

Better research through metrology    p395
doi:10.1038/s41592-018-0035-x

This Month

 

Laurent Cognet    p397
Vivien Marx
doi:10.1038/s41592-018-0013-3

The curse(s) of dimensionality    pp399 - 400
Naomi Altman & Martin Krzywinski
doi:10.1038/s41592-018-0019-x

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Correspondence

 

MaxQuant goes Linux    p401
Pavel Sinitcyn, Shivani Tiwary, Jan Rudolph, Petra Gutenbrunner, Christoph Wichmann et al.
doi:10.1038/s41592-018-0018-y

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Research Highlights

 

Deep learning advances super-resolution imaging    p403
Rita Strack
doi:10.1038/s41592-018-0028-9

A home for brain organoids    p404
Tal Nawy
doi:10.1038/s41592-018-0029-8

RNAs that shape the genome    p405
Nicole Rusk
doi:10.1038/s41592-018-0030-2

Simulating the imaging process in scattering tissue    p406
Nina Vogt
doi:10.1038/s41592-018-0031-1

A pan-cancer atlas    p407
Tal Nawy
doi:10.1038/s41592-018-0020-4

Analyzing Drosophila activity    p407
Nina Vogt
doi:10.1038/s41592-018-0021-3

What hPSCs need    p407
Nicole Rusk
doi:10.1038/s41592-018-0022-2

Hessian structured illumination microscopy    p407
Rita Strack
doi:10.1038/s41592-018-0023-1

Cross-linking with SuFEx chemistry    p408
Allison Doerr
doi:10.1038/s41592-018-0024-0

RBP census    p408
Nicole Rusk
doi:10.1038/s41592-018-0025-z

Super-long single-molecule tracking    p408
Rita Strack
doi:10.1038/s41592-018-0026-y

Tissue-specific oncogene screens    p408
Tal Nawy
doi:10.1038/s41592-018-0027-x

A home for integrative structural models    p409
Allison Doerr
doi:10.1038/s41592-018-0032-0

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Technology Feature

 

Stem cells: lineage tracing lets single cells talk about their past    pp411 - 414
Vivien Marx
doi:10.1038/s41592-018-0016-0

Perspectives

 

Nanoparticles for super-resolution microscopy and single-molecule tracking    pp415 - 423
Dayong Jin, Peng Xi, Baoming Wang, Le Zhang, Jörg Enderlein et al.
doi:10.1038/s41592-018-0012-4

This Perspective highlights recent advances in the use of nanoparticles in super-resolution microscopy and single-molecule tracking. It offers guidance for users interested in these tools and discusses potential future directions.

 

Brief Communications

 

Single-shot super-resolution total internal reflection fluorescence microscopy    pp425 - 428
Min Guo, Panagiotis Chandris, John Paul Giannini, Adam J. Trexler, Robert Fischer et al.
doi:10.1038/s41592-018-0004-4

Instant structured illumination and total internal reflection fluorescence microscopy are combined to carry out time-lapse super-resolution TIRF imaging at frame rates up to 100 Hz, enabling observation of fast biological processes.

 

High-speed volumetric imaging of neuronal activity in freely moving rodents    pp429 - 432
Oliver Skocek, Tobias Nöbauer, Lukas Weilguny, Francisca Martínez Traub, Chuying Naomi Xia et al.
doi:10.1038/s41592-018-0008-0

A miniature light-field microscope in combination with a signal-extraction approach enables high-speed volumetric calcium imaging in freely moving mice.

 

C-BERST: defining subnuclear proteomic landscapes at genomic elements with dCas9–APEX2    pp433 - 436
Xin D. Gao, Li-Chun Tu, Aamir Mir, Tomás Rodriguez, Yuehe Ding et al.
doi:10.1038/s41592-018-0006-2

dCas9 fused to ascorbate peroxidase (APEX2) biotinylates proteins around targeted loci so they can be enriched and characterized.

 

Discovery of proteins associated with a predefined genomic locus via dCas9–APEX-mediated proximity labeling    pp437 - 439
Samuel A. Myers, Jason Wright, Ryan Peckner, Brian T. Kalish, Feng Zhang et al.
doi:10.1038/s41592-018-0007-1

After CRISPR-mediated targeting of the peroxidase APEX2 to a genomic locus of interest, the proteins at that locus are labeled, enriched and identified via quantitative proteomics.

 

Articles

 

BoxCar acquisition method enables single-shot proteomics at a depth of 10,000 proteins in 100 minutes    pp440 - 448

doi:10.1038/s41592-018-0003-5

BoxCar, a mass spectrometry data acquisition method, greatly increases sensitivity and the detection of low-abundance peptides with a minimal amount of instrument time.

 

Self-interference 3D super-resolution microscopy for deep tissue investigations    pp449 - 454
Pierre Bon, Jeanne Linarès-Loyez, Maxime Feyeux, Kevin Alessandri, Brahim Lounis et al.
doi:10.1038/s41592-018-0005-3

Several methods make it possible to obtain depth information in 3D super-resolution microscopy. Here the authors exploit a self-interference phenomenon to allow deep imaging within tissue samples, as well as isotropic imaging.

 

Picky comprehensively detects high-resolution structural variants in nanopore long reads    pp455 - 460
Liang Gong, Chee-Hong Wong, Wei-Chung Cheng, Harianto Tjong, Francesca Menghi et al.
doi:10.1038/s41592-018-0002-6

The computational pipeline Picky detects the full spectrum of structural variants and their breakpoints in long nanopore sequence reads.

 

Accurate detection of complex structural variations using single-molecule sequencing    pp461 - 468
Fritz J. Sedlazeck, Philipp Rescheneder, Moritz Smolka, Han Fang, Maria Nattestad et al.
doi:10.1038/s41592-018-0001-7

NGMLR and Sniffles perform highly accurate alignment and structural variation detection from long-read sequencing data.

 

Amendments & Corrections

 

Author Correction: High-speed volumetric imaging of neuronal activity in freely moving rodents    p469
Oliver Skocek, Tobias Nöbauer, Lukas Weilguny, Francisca Martínez Traub, Chuying Naomi Xia et al.
doi:10.1038/s41592-018-0034-y

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