Table of contents


Top

Editorial

The difficulty of a fair comparison p273

doi:10.1038/nmeth.3359

Comparing methods in a fair and informative manner is often not straightforward. Benchmark data sets, thoughtfully applied metrics and clear reporting can help.


Top

This Month

The Author File: Richard Caprioli p275

Vivien Marx

doi:10.1038/nmeth.3338

Math, mass spectrometry and imaging can mix, but it takes some woodworking.


Points of Significance: Bayes' theorem pp277 - 278

Jorge López Puga, Martin Krzywinski & Naomi Altman

doi:10.1038/nmeth.3335

Incorporate new evidence to update prior information.


Top

Correspondence

Plotting intersections p281

Giovanni Lentini & Solomon Habtemariam

doi:10.1038/nmeth.3328


Response to "Plotting intersections" by Lentini p281

Alexander Lex & Nils Gehlenborg

doi:10.1038/nmeth.3331


Top

Research Highlights

A snapshot of active neurons p283

A new calcium sensor allows the permanent labeling of neurons that are active at defined periods of time.

Peering inside protein complexes with AFM pp284 - 285

Atomic force microscopy is applied to image the location of chemical groups inside single protein complexes.

Site-specific RNA labeling in mammalian cells pp284 - 285

A new method uses click chemistry to covalently modify any RNA of interest.

Cellular diversity in a snapshot p286

A new platform detains single cells in picoliter wells to generate transcriptional profiles in large numbers.

Short-lived excitement p289

A collection of genomic tools helps researchers exploit a short-lived fish species as a model for human aging.

RNA that activates transcription p290

Synthetic small RNA transcriptional activators can regulate gene transcription in Escherichia coli.

Methods in Brief

Tools in Brief

Top

Commentary

Transparency in film: increasing credibility of scientific animation using citation pp293 - 297

Stuart G Jantzen, Jodie Jenkinson & Gaël McGill

doi:10.1038/nmeth.3334

Scientific animations have tremendous potential as instruments of insight and dissemination. However, audiences are often unable to determine the degree to which visualizations are informed by scientific evidence. By providing a more detailed account of source use, developers can increase the credibility of animations as scientific tools.


Top

Technology Feature

Cancer: smoother journeys for molecular data pp299 - 302

Vivien Marx

doi:10.1038/nmeth.3332

Data integration and tool interoperability can ease analyses of cancer 'omics data and yield surprises.


Top

News and Views

Successful test launch for nanopore sequencing pp303 - 304

Nicholas J Loman & Mick Watson

doi:10.1038/nmeth.3327

Nanopore sequencing gets a boost with accurate error modeling and variant-calling tools for Oxford Nanopore Technology's highly anticipated MinION platform.

See also: Article by Jain et al.


Better together: multiplexing samples to improve the preparation and reliability of gene expression studies pp304 - 305

Ali Mortazavi

doi:10.1038/nmeth.3333

Two methods for early tagging of sample RNA before RT-qPCR or full RNA-seq open the door to experiments with fewer technical batch effects.

See also: Brief Communication by Shishkin et al. | Brief Communication by Narayan et al.


ADVERTISEMENT



Top

Perspective

Integrative, dynamic structural biology at atomic resolution—it's about time pp307 - 318

Henry van den Bedem & James S Fraser

doi:10.1038/nmeth.3324

In this Perspective, the authors advance a view of macromolecules as collections ofinterchanging structural ensembles, and discuss how a synergistic combination of NMR,X-ray crystallography, and computational simulations can reveal the structural basis for conformational dynamics at atomic resolution.


Top

Brief Communications

Ultrastructurally smooth thick partitioning and volume stitching for large-scale connectomics pp319 - 322

Kenneth J Hayworth, C Shan Xu, Zhiyuan Lu, Graham W Knott, Richard D Fetter, Juan Carlos Tapia, Jeff W Lichtman & Harald F Hess

doi:10.1038/nmeth.3292

FIB-SEM sample size is limited by cumulative milling artifacts and long imaging times.Ultrathick sectioning, followed by parallel FIB-SEM imaging and volume stitching,overcomes this limit, generating data sets of high quality for large-scale connectomics.


Simultaneous generation of many RNA-seq libraries in a single reaction pp323 - 325

Alexander A Shishkin, Georgia Giannoukos, Alper Kucukural, Dawn Ciulla, Michele Busby, Christine Surka, Jenny Chen, Roby P Bhattacharyya, Robert F Rudy, Milesh M Patel, Nathaniel Novod, Deborah T Hung, Andreas Gnirke, Manuel Garber, Mitchell Guttman & Jonathan Livny

doi:10.1038/nmeth.3313

RNAtag-seq barcodes transcripts prior to cDNA synthesis, thereby allowing pooled library generation from many input samples.

See also: News and Views by Mortazavi


Highly efficient Cas9-mediated transcriptional programming pp326 - 328

Alejandro Chavez, Jonathan Scheiman, Suhani Vora, Benjamin W Pruitt, Marcelle Tuttle, Eswar P R Iyer, Shuailiang Lin, Samira Kiani, Christopher D Guzman, Daniel J Wiegand, Dmitry Ter-Ovanesyan, Jonathan L Braff, Noah Davidsohn, Benjamin E Housden, Norbert Perrimon, Ron Weiss, John Aach, James J Collins & George M Church

doi:10.1038/nmeth.3312

The fusion of three transcriptional activation domains to a nuclease-deficient Cas9 achieves robust induction of gene expression and can induce differentiation of hiPSCs.


Mapping native disulfide bonds at a proteome scale pp329 - 331

Shan Lu, Sheng-Bo Fan, Bing Yang, Yu-Xin Li, Jia-Ming Meng, Long Wu, Pin Li, Kun Zhang, Mei-Jun Zhang, Yan Fu, Jincai Luo, Rui-Xiang Sun, Si-Min He & Meng-Qiu Dong

doi:10.1038/nmeth.3283

A workflow for preserving disulfide links in proteins in conjunction with pLink-SS enables the analysis of disulfide bonds across the proteome.


Accurate liability estimation improves power in ascertained case-control studies pp332 - 334

Omer Weissbrod, Christoph Lippert, Dan Geiger & David Heckerman

doi:10.1038/nmeth.3285

LEAP (liability estimator as a phenotype) corrects for confounding factors in case-control GWAS with increased power.


De novo protein structure determination from near-atomic-resolution cryo-EM maps pp335 - 338

Ray Yu-Ruei Wang, Mikhail Kudryashev, Xueming Li, Edward H Egelman, Marek Basler, Yifan Cheng, David Baker & Frank DiMaio

doi:10.1038/nmeth.3287

New detector technology has improved the resolution of cryo-electron microscopy (cryo-EM), but tools for structure determination from high-resolution maps have lagged behind. Wang et al. describe a de novo approach for structure determination from high-resolution cryo-EM maps. Also in this issue, DiMaio et al. report structure determination using a homologous structure as a starting model.


Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing pp339 - 342

Michael B Clark, Tim R Mercer, Giovanni Bussotti, Tommaso Leonardi, Katelin R Haynes, Joanna Crawford, Marion E Brunck, Kim-Anh Lê Cao, Gethin P Thomas, Wendy Y Chen, Ryan J Taft, Lars K Nielsen, Anton J Enright, John S Mattick & Marcel E Dinger

doi:10.1038/nmeth.3321

CaptureSeq was used to quantitatively profile transcripts with low expression, resulting in a catalog of long noncoding RNA expression in 20 human tissues.


High-throughput RNA profiling via up-front sample parallelization pp343 - 346

Azeet Narayan, Ananth Bommakanti & Abhijit A Patel

doi:10.1038/nmeth.3311

META RNA profiling allows the simultaneous quantification of a broad selection of mRNAs or microRNAs in many samples via early sample pooling.

See also: News and Views by Mortazavi


Genome sequence–independent identification of RNA editing sites pp347 - 350

Qing Zhang & Xinshu Xiao

doi:10.1038/nmeth.3314

The GIREMI tool allows the accurate and sensitive detection of RNA editing sites from single RNA-seq data sets, without the need for genomic data.


Top

Articles

Improved data analysis for the MinION nanopore sequencer pp351 - 356

Miten Jain, Ian T Fiddes, Karen H Miga, Hugh E Olsen, Benedict Paten & Mark Akeson

doi:10.1038/nmeth.3290

Improved error assessment and read alignment on the MinION nanopore sequencing platform allow for calling of single-nucleotide variants and resolving the repeat structure of an assembly gap in the human X chromosome.

See also: News and Views by Loman & Watson


HISAT: a fast spliced aligner with low memory requirements pp357 - 360

Daehwan Kim, Ben Langmead & Steven L Salzberg

doi:10.1038/nmeth.3317

HISAT (hierarchical indexing for spliced alignment of transcripts) uses global and local indices for fast, sensitive alignment with small memory requirements.


Atomic-accuracy models from 4.5-Å cryo-electron microscopy data with density-guided iterative local refinement pp361 - 365

Frank DiMaio, Yifan Song, Xueming Li, Matthias J Brunner, Chunfu Xu, Vincent Conticello, Edward Egelman, Thomas C Marlovits, Yifan Cheng & David Baker

doi:10.1038/nmeth.3286

New detector technology has improved the resolution of cryo-electron microscopy (cryo-EM), but tools for structure determination from high-resolution maps have lagged behind. DiMaio et al. report structure determination from high-resolution cryo-EM maps using a homologous structure as a starting model. Also in this issue, Wang et al. describe a de novo approach for structure determination that does not require a starting model.


Image fusion of mass spectrometry and microscopy: a multimodality paradigm for molecular tissue mapping pp366 - 372

Raf Van de Plas, Junhai Yang, Jeffrey Spraggins & Richard M Caprioli

doi:10.1038/nmeth.3296

An approach to fuse images from imaging mass spectrometry and microscopy provides biological insights into molecular tissue distributions beyond what can be obtained from either modality individually.


ADVERTISEMENT



Top

Extra navigation

Subscribe to Nature Methods

Subscribe

natureevents

ADVERTISEMENT