Nature Methods Contents: May 2016 Volume 13 pp 381 - 458

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To learn more, please visit www.nikoninstruments.com/a1r TABLE OF CONTENTS May 2016 Volume 13, Issue 5 In This Issue Editorial This Month Correspondence Research Highlights Technology Feature Reviews Analysis Brief Communications Articles Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement Want to use CRISPR in your research?  Free CRISPR Handbook Learn about CRISPR and get useful protocols and workflows Download Now   Advertisement Premade Stable Cell Lines Each of the following cell lines is available in a number of widely-studied cancer cell lines, providing useful tools for studying cancer properties and development of effective therapies CRISPR-Cas9 Stable Cell Lines Luciferase+GFP Dual Labeled Cancer Cell Lines GFP Labeled Cancer Cell Lines Cell Structure Related Stable Cell Lines  Learn more >>   Advertisement THE GENOMICS OF COMMON DISEASES 2016  Presented by Nature Genetics in association with the Wellcome Trust September 25-28, 2016 Renaissance Baltimore Harborplace Hotel | Baltimore, MD, USA REGISTER NOW!   In This Issue Top In This Issue    Editorial Top Data sharing comes to structural biology   p381 doi:10.1038/nmeth.3862 New archives for raw X-ray crystallography and cryo-EM data will accelerate progress in structural biology. This Month Top The Author File: Judit Villen   p383 Vivien Marx doi:10.1038/nmeth.3841 Measuring phosphoproteins reproducibly and taking time to bike. Points of Significance: Regression diagnostics   pp385 - 386 Naomi Altman and Martin Krzywinski doi:10.1038/nmeth.3854 Residual plots can be used to validate assumptions about the regression model. Correspondence Top EMPIAR: a public archive for raw electron microscopy image data   pp387 - 388 Andrii Iudin, Paul K Korir, José Salavert-Torres, Gerard J Kleywegt and Ardan Patwardhan doi:10.1038/nmeth.3806 Research Highlights Top Hijacking Cas9 for live-cell RNA imaging Researchers target fluorescent protein-Cas9 fusions to specific mRNAs for tracking in live cells. Coral-on-a-chip A miniature platform for studying corals at microscale resolution sheds new light on their biology. A multi-purpose cross-linker By coupling protein cross-linking with reversible affinity purification of cross-linked fragments, a newly reported tool should enable many applications in structural and systems biology. Manipulating neurons with magnetogenetics The Magneto channel, an orthogonal tool for optogenetic actuators, provides magnetic control over neuronal activity. RNase footprints re-examined A computational tool enables the study of native nonribosomal RNA-protein complexes from ribosome profiling data. Light-responsive enzyme inhibitors A hybrid of a photo-responsive ligand and a small-molecule inhibitor enables optical control of epigenetic mechanisms. Methods in Brief Cryo-EM with the Volta phase plate | Mutational burden of neurons | Long noncoding RNA networks of suppression | Zooming in on single tumor cells Tools in Brief A minimal bacterial cell | Putting a spin on high-throughput force spectroscopy | Delivering crystals with sound | A spotlight on synaptic plasticity Methods JOBS of the week University Professor of Organic Chemistry - Synthesis and Synthetic Methods University of Innsbruck, Austria Postdoctoral Scholar in Computational Genomics University of Chicago Postdoctoral fellowships in molecular epidemiology Stanford University Postdoc scholarship in Computational Genomics Bioinformatics Lund University More Science jobs from Methods EVENT ECCO-AACR-EORTC-ESMO Methods in Clinical Cancer Research Workshop 18th June - 24th June 2016 Zeist, Netherlands More science events from Technology Feature Top Microbiology: the road to strain-level identification   pp401 - 404 Vivien Marx doi:10.1038/nmeth.3837 Tools are emerging to help labs trawl for sequences that reveal microbial strains and their functional potential in deep pools of metagenomic data. Reviews Top A practical guide to hydrogels for cell culture   pp405 - 414 Steven R Caliari and Jason A Burdick doi:10.1038/nmeth.3839 Measuring cell-generated forces: a guide to the available tools   pp415 - 423 William J Polacheck and Christopher S Chen doi:10.1038/nmeth.3834 There is a growing appreciation that mechanical forces have important roles in many aspects of biology. This review provides a survey of methods for measuring the forces exerted by cells and discusses technical barriers to their implementation. Analysis Top Standardized benchmarking in the quest for orthologs OPEN   pp425 - 430 Adrian M Altenhoff, Brigitte Boeckmann, Salvador Capella-Gutierrez, Daniel A Dalquen, Todd DeLuca et al. doi:10.1038/nmeth.3830 Brief Communications Top Plug-and-play analysis of the human phosphoproteome by targeted high-resolution mass spectrometry   pp431 - 434 Robert T Lawrence, Brian C Searle, Ariadna Llovet and Judit Villén doi:10.1038/nmeth.3811 A method (and resource) demonstrating the mining of information from large-scale phosphoproteomics data sets is presented, allowing users to build targeted parallel reaction monitoring mass spectrometry assays to study phosphosites of interest. Strain-level microbial epidemiology and population genomics from shotgun metagenomics   pp435 - 438 Matthias Scholz, Doyle V Ward, Edoardo Pasolli, Thomas Tolio, Moreno Zolfo et al. doi:10.1038/nmeth.3802 PanPhlAn detects strains and characterizes strain-specific gene content and activity within metagenomic and metatranscriptomic samples for microbial population analysis and epidemiology. Quantitative super-resolution imaging with qPAINT   pp439 - 442 Ralf Jungmann, Maier S Avendaño, Mingjie Dai, Johannes B Woehrstein, Sarit S Agasti et al. doi:10.1038/nmeth.3804 Quantitative points accumulation in nanoscale topography (qPAINT) makes use of predictable binding kinetics between DNA-PAINT imager and docking strands to achieve accurate and precise counting of molecules in spatially unresolved complexes. Sparse PCA corrects for cell type heterogeneity in epigenome-wide association studies   pp443 - 445 Elior Rahmani, Noah Zaitlen, Yael Baran, Celeste Eng, Donglei Hu et al. doi:10.1038/nmeth.3809 Principal component analysis on a subset of differentially methylated regions in a mixture of cell types is the basis of ReFACTor, a program to account for heterogeneity in epigenome-wide association studies (EWAS). Advertisement Droplet Digital™ PCR (ddPCR™) is leading the way  Droplet Digital PCR has led to more publications and discoveries than any other digital PCR platform - over 400 studies have taken advantage of ddPCR technology. Find out how   Articles Top High-efficiency cellular reprogramming with microfluidics   pp446 - 452 Camilla Luni, Stefano Giulitti, Elena Serena, Luca Ferrari, Alessandro Zambon et al. doi:10.1038/nmeth.3832 Microfluidic reprogramming of human somatic cells to induced pluripotent stem cells is rapid and highly efficient, enabling large-scale derivation from patient cells as well as seamless on-chip differentiation without cell expansion. Reprogramming eukaryotic translation with ligand-responsive synthetic RNA switches   pp453 - 458 Andrew V Anzalone, Annie J Lin, Sakellarios Zairis, Raul Rabadan and Virginia W Cornish doi:10.1038/nmeth.3807 Ligand-triggered ribosomal frameshifting allows control of the relative stoichiometry of two proteins and enables the building of logic gates from a single mRNA. 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