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Editorial

Communication matters p93

doi:10.1038/nmeth.3282

Is social media a new 4mat 4 science in UR community? It may be time to sign up.


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This Month

The Author File: Wesley P. Wong p95

Vivien Marx

doi:10.1038/nmeth.3260

Brainstorming leads to an invention that makes a lab workhorse gallop.


Points of view: Temporal data p97

Marc Streit & Nils Gehlenborg

doi:10.1038/nmeth.3262

Use inherent properties of time to create effective visualizations.


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Correspondence

Aquaria: simplifying discovery and insight from protein structures pp98 - 99

Seán I O'Donoghue, Kenneth S Sabir, Maria Kalemanov, Christian Stolte, Benjamin Wellmann, Vivian Ho, Manfred Roos, Nelson Perdigão, Fabian A Buske, Julian Heinrich, Burkhard Rost & Andrea Schafferhans

doi:10.1038/nmeth.3258


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Research Highlights

All-optical electrophysiology in behaving animals p101

Three different optical strategies enable the manipulation and imaging of neural activity in awake mice.

Cryo-EM strikes gold pp102 - 103

Gold supports nearly eliminate unwanted specimen motion in cryo-electron microscopy, enabling high-resolution structure determination of challenging proteins.

CRISPR gain-of-function screens pp102 - 103

An engineered dCas9–guide RNA complex containing three different transcriptional activation domains achieves consistently high expression of endogenous genes in a genome-wide screen.

Community organizers p104

Electrochemical sensors monitor communication between bacterial aggregates.

An expanded human interactome p107

An expanded catalog of binary biophysical interactions between human proteins.

XFELs probe protein dynamics p109

A new study shows that time-resolved serial femtosecond crystallography can reveal high-resolution intermediates of photoactive yellow protein.

Methods in Brief

Tools in Brief

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Perspective

Orchestrating high-throughput genomic analysis with Bioconductor pp115 - 121

Wolfgang Huber, Vincent J Carey, Robert Gentleman, Simon Anders, Marc Carlson, Benilton S Carvalho, Hector Corrada Bravo, Sean Davis, Laurent Gatto, Thomas Girke, Raphael Gottardo, Florian Hahne, Kasper D Hansen, Rafael A Irizarry, Michael Lawrence, Michael I Love, James MacDonald, Valerie Obenchain, Andrzej K Oleś, Hervé Pagès, Alejandro Reyes, Paul Shannon, Gordon K Smyth, Dan Tenenbaum, Levi Waldron & Martin Morgan

doi:10.1038/nmeth.3252

A Perspective on the open-source and open-development software project Bioconductor provides an overview for prospective users and developers dealing with high-throughput data in genomics and molecular biology.


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Brief Communications

DNA nanoswitches: a quantitative platform for gel-based biomolecular interaction analysis pp123 - 126

Mounir A Koussa, Ken Halvorsen, Andrew Ward & Wesley P Wong

doi:10.1038/nmeth.3209

A DNA nanoswitch platform enables inexpensive kinetic and thermodynamic analysis of a range of biomolecular interactions using a simple gel electrophoresis readout.


Macromolecular X-ray structure determination using weak, single-wavelength anomalous data pp127 - 130

Gábor Bunkóczi, Airlie J McCoy, Nathaniel Echols, Ralf W Grosse-Kunstleve, Paul D Adams, James M Holton, Randy J Read & Thomas C Terwilliger

doi:10.1038/nmeth.3212

An improved analysis approach for single-wavelength anomalous diffraction (SAD)-based macromolecular X-ray structure determination expands the applicability of this phasing method for macromolecules with weak anomalous signals.


Fast native-SAD phasing for routine macromolecular structure determination pp131 - 133

Tobias Weinert, Vincent Olieric, Sandro Waltersperger, Ezequiel Panepucci, Lirong Chen, Hua Zhang, Dayong Zhou, John Rose, Akio Ebihara, Seiki Kuramitsu, Dianfan Li, Nicole Howe, Gisela Schnapp, Alexander Pautsch, Katja Bargsten, Andrea E Prota, Parag Surana, Jithesh Kottur, Deepak T Nair, Federica Basilico, Valentina Cecatiello, Sebastiano Pasqualato, Andreas Boland, Oliver Weichenrieder, Bi-Cheng Wang, Michel O Steinmetz, Martin Caffrey & Meitian Wang

doi:10.1038/nmeth.3211

A native-SAD (single-wavelength anomalous diffraction) data collection strategy enables phasing using anomalous signal from a single native crystal, facilitating straightforward macromolecular X-ray structure determination.


Conformal nanopatterning of extracellular matrix proteins onto topographically complex surfaces pp134 - 136

Yan Sun, Quentin Jallerat, John M Szymanski & Adam W Feinberg

doi:10.1038/nmeth.3210

Patterning on topography printing allows nano- to microscale patterning of extracellular matrix proteins onto topologically complex surfaces.


Genetic targeting of chemical indicators in vivo pp137 - 139

Guoying Yang, Fernanda de Castro Reis, Mayya Sundukova, Sofia Pimpinella, Antonino Asaro, Laura Castaldi, Laura Batti, Daniel Bilbao, Luc Reymond, Kai Johnsson & Paul A Heppenstall

doi:10.1038/nmeth.3207

Snap-tag reporter mice allow flexible yet efficient targeting of chemical indicators to genetically labeled cells in vivo. With this strategy, cells can either be labeled fluorescently or ablated using the same reporter.


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Articles

Simultaneous all-optical manipulation and recording of neural circuit activity with cellular resolution in vivo pp140 - 146

Adam M Packer, Lloyd E Russell, Henry W P Dalgleish & Michael Häusser

doi:10.1038/nmeth.3217

Here, the authors present an approach for the simultaneous optogenetic manipulation and recording of neural activity at cellular resolution using two-photon microscopy and apply their strategy in the mouse barrel cortex.


Quantitative profiling of initiating ribosomes in vivo pp147 - 153

Xiangwei Gao, Ji Wan, Botao Liu, Ming Ma, Ben Shen & Shu-Bing Qian

doi:10.1038/nmeth.3208

QTI-seq (quantitative translation initiation sequencing) maps the position of the start codon and thus allows the determination of initiation efficiency in response to various stimuli, such as starvation, in cell culture and in vivo.


Selecting causal genes from genome-wide association studies via functionally coherent subnetworks pp154 - 159

Murat Taşan, Gabriel Musso, Tong Hao, Marc Vidal, Calum A MacRae & Frederick P Roth

doi:10.1038/nmeth.3215

The prix fixe strategy and software uses cofunction networks to identify causal genes among candidate genes in disease-associated loci from genome-wide association studies.


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Corrigenda

Corrigendum: From genes to protein mechanics on a chip p160

Marcus Otten, Wolfgang Ott, Markus A Jobst, Lukas F Milles, Tobias Verdorfer, Diana A Pippig, Michael A Nash & Hermann E Gaub

doi:10.1038/nmeth0215-160a


Corrigendum: Mining the O-glycoproteome using zinc-finger nuclease–glycoengineered SimpleCell lines p160

Catharina Steentoft, Sergey Y Vakhrushev, Malene B Vester-Christensen, Katrine T-B G Schjoldager, Yun Kong, Eric Paul Bennett, Ulla Mandel, Hans Wandall, Steven B Levery & Henrik Clausen

doi:10.1038/nmeth0215-160d


Corrigendum: Time-resolved crystallography using the Hadamard transform p160

Briony A Yorke, Godfrey S Beddard, Robin L Owen & Arwen R Pearson

doi:10.1038/nmeth0215-160e


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Errata

Erratum: Onco-proteogenomics: cancer proteomics joins forces with genomics p160

Javier A Alfaro, Ankit Sinha, Thomas Kislinger & Paul C Boutros

doi:10.1038/nmeth0215-160b


Erratum: Light microscopy with lattices p160

Nina Vogt

doi:10.1038/nmeth0215-160c


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