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

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Advertisement Nikon's all-new DUVB is a high-sensitivity GaAsP detector for tunable virtual channel detection and spectral applications. Available for Nikon's A1 and C2 confocal microscope systems, the DUVB delivers flexible detection of fluorescent signals with higher sensitivity. For more information visit http://www.nikoninst.com/nature/duv-b/ 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 Advertisement   Inspiration does not obey speed limits. Announcing the ORCA-Lightning from Hamamatsu. Our new 12MP sCMOS camera engineered for high speed and low noise and ready for Lightsheet microscopy.  hamamatsucameras.com Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement 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.  Find out more >>   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 More Science jobs from Methods EVENT 4th World Congress on Cancer and Prevention Methods 19.04.18 Valencia, Spain More science events from 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.   Advertisement Advanced Imaging with Proven Optics Olympus is dedicated to your work, vision, and science. Through innovation and service, we seek to aide in your discoveries, advance your research, and inspire you to explore new possibilities. Our wide range of microscopes are built with the optical excellence and proven application expertise you can depend on. Your Science Matters™. > Learn more about Olympus microscopes   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.   Advertisement When You Can’t PCR It, CATCH It Cas9-assisted targeting of chromosome segments, or CATCH, is a method for extracting large DNA targets when you don’t know enough about the sequence to use standard enrichment protocols. With the SageHLS platform for purifying HMW DNA, this approach can be an alternative for scientists who would otherwise have to waste sequencing capacity on whole-genome analysis. Learn about HLS-CATCH in this case study.   Top Advertisement HIV IMMUNITY AND ERADICATION, A HERRENHAUSEN SYMPOSIUM November 2-3, 2017 | Hanover, Germany REGISTER NOW!   Natureevents is a fully searchable, multi-disciplinary database designed to maximise exposure for events organisers. The contents of the Natureevents Directory are now live. The digital version is available here. Find the latest scientific conferences, courses, meetings and symposia on natureevents.com. For event advertising opportunities across the Nature Publishing Group portfolio please contact natureevents@nature.com More Nature Events

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