Nature Methods Contents: March 2016 Volume 13 pp 185 - 275

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Advertisement Eppendorf's product portfolio offers flexible solutions for preparing, handling, and analyzing samples and cells. Special accessories and smart innovations, e.g. for centrifugation of spin columns or photometric quantification in the micro volume range, further lighten the daily work in the lab. See how Eppendorf products fit to your workflow: www.eppendorf.com/workflows TABLE OF CONTENTS March 2016 Volume 13, Issue 3 In This Issue Editorial This Month Correspondence Research Highlights Technology Feature News and Views Perspectives Brief Communications Articles Application Notes Advertisement New Ts2 Tissue Culture Microscope and Ts2R Basic Research Microscope now available from Nikon. Upgrade your routine imaging with innovative controls, a streamlined, compact body, new plastic-compatible Emboss Contrast technique and industry-leading optics. To learn more about Nikon Inverted microscope systems, please visit www.nikoninstruments.com/inverted Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement The Naturejobs Career Expo is coming to San Francisco! April 27, 2016 This career fair offers young, talented researchers an excellent opportunity to meet a diverse selection of national and international employers from academic institutions and scientific industries, such as pharmaceutical organisations, digital technology companies, science publishing and more. Register for FREE today!   Advertisement nature.com webcasts Join us for our upcoming webcast with live Q&A: COMBATING ANTIBIOTIC RESISTANCE Presented by BioPharma Dealmakers Date: Wednesday, March 9, 2016 Time: 8AM PST, 11AM EST, 4PM GMT, 5PM CET REGISTER FOR FREE Sponsored by: Antabio, Cempra, Helperby, Motif Bio, Polyphor     In This Issue Top In This Issue    Editorial Top The power of disagreement   p185 doi:10.1038/nmeth.3798 Scientific disagreement prompts a closer look at data and can promote unexpected insights. This Month Top The Author File: Markus Sauer   p187 Vivien Marx doi:10.1038/nmeth.3794 Skiing his way to multiplexed imaging. Points of View: Neural circuit diagrams   p189 Barbara Jeanine Hunnicutt and Martin Krzywinski doi:10.1038/nmeth.3777 Use alignment and consistency to untangle complex circuit diagrams. Correspondence Top The ORFeome Collaboration: a genome-scale human ORF-clone resource   pp191 - 192 The ORFeome Collaboration doi:10.1038/nmeth.3776 TeraFly: real-time three-dimensional visualization and annotation of terabytes of multidimensional volumetric images   pp192 - 194 Alessandro Bria, Giulio Iannello, Leonardo Onofri and Hanchuan Peng doi:10.1038/nmeth.3767 Research Highlights Top Monitoring 3D neural activity at large scale A combination of flexible imaging and computational methods opens new views into the dynamics of activity across large populations of neurons. Protected STED nanoscopy The use of photoswitchable fluorescent proteins in STED nanoscopy enables higher-contrast imaging with dramatically reduced photobleaching. Tracking expression through the generations A microfluidic device tracks the lineage and transcriptional profiles of individual cells. Lock-and-key PORE-igami A nanopore built from DNA allows the controlled and selective transport of organic molecules across a lipid membrane. Addicting bugs to nonstandard amino acids Scientists can maintain orthogonal translation systems over many bacterial generations by making an essential gene depend on a nonstandard amino acid. Predicting the impact of genomic variation An unsupervised approach with high predictive power provides a single measure of functional importance for each variant in the human genome. Methods in Brief Multiplexed single-cell protein and RNA measurements | Sensors destabilized by design | Adapting to aberrations in brain imaging | Mapping active translation of single mRNAs Tools in Brief Cas9 on target | An approach to study MARylation | Label-free image flow cytometry | A guide to cellular transdifferentiation Methods JOBS of the week Post-doc Position in Translational Leukemia Research (M / F) University Hospital Würzburg Postdoctoral Fellow – Immunotherapy / Protein Engineering California Institute for Biomedical Research Group leader on Integrative Biology of the Cell Institute for Integrative Biology of the Cell Director General European Molecular Biology Laboratory (EMBL) Faculty of Health Sciences and the Department of Pathology and Molecular Medicine Queen's University More Science jobs from Technology Feature Top Optimizing probes to image cleared tissue   pp205 - 209 Vivien Marx doi:10.1038/nmeth.3774 Probes and imaging finesse for a clearer view of tissue. News and Views Top Understanding the links between privacy and public data sharing   pp211 - 212 David W Craig doi:10.1038/nmeth.3779 Linking clinical and phenotype variables across data sets will both power precision medicine studies and introduce new privacy risks See also: Article by Harmanci & Gerstein Perspectives Top Genomic footprinting   pp213 - 221 Jeff Vierstra and John A Stamatoyannopoulos doi:10.1038/nmeth.3768 This Perspective by Vierstra and Stamatoyannopoulos discusses the prospects and challenges of genomic footprinting applied to complex genomes. Genome-wide footprinting: ready for prime time?   pp222 - 228 Myong-Hee Sung, Songjoon Baek and Gordon L Hager doi:10.1038/nmeth.3766 The Perspective by Sung, Baek and Hager discusses consensus, remaining issues and hurdles for genomic footprinting. Brief Communications Top Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity   pp229 - 232 Christof Angermueller, Stephen J Clark, Heather J Lee, Iain C Macaulay, Mabel J Teng et al. doi:10.1038/nmeth.3728 Parallel, genome-wide methylation and transcriptional profiling from a single cell (scM&T-seq) enables the discovery of associations between transcriptional and epigenetic variation. Predictable tuning of protein expression in bacteria   pp233 - 236 Mads T Bonde, Margit Pedersen, Michael S Klausen, Sheila I Jensen, Tune Wulff et al. doi:10.1038/nmeth.3727 The free EMOPEC web tool enables precise tuning of bacterial protein expression on the basis of small changes to the Shine-Dalgarno sequence; oligos can be generated to engineer expression of any Escherichia coli gene. An informatic framework for decoding protein complexes by top-down mass spectrometry   pp237 - 240 Owen S Skinner, Pierre C Havugimana, Nicole A Haverland, Luca Fornelli, Bryan P Early et al. doi:10.1038/nmeth.3731 A computational approach for precisely identifying and characterizing the molecular stoichiometry of multi-proteoform complexes using native top-down mass spectrometry data is reported. Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis   pp241 - 244 Jean Fan, Neeraj Salathia, Rui Liu, Gwendolyn E Kaeser, Yun C Yung et al. doi:10.1038/nmeth.3734 By testing potential sources of biological signal that drive population-level variation in single-cell gene expression, the PAGODA software enables cells to be characterized on the basis of multiple functionally relevant features such as cell type, signaling state and cell cycle state. Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace   pp245 - 247 Kun Qu, Sara Garamszegi, Felix Wu, Helga Thorvaldsdottir, Ted Liefeld et al. doi:10.1038/nmeth.3732 GenomeSpace is an open-source, cloud-based interoperability platform that facilitates integrative genomic analyses, allowing users to transition seamlessly between a diverse and growing set of bioinformatics tools and data resources. TruSPAdes: barcode assembly of TruSeq synthetic long reads   pp248 - 250 Anton Bankevich and Pavel A Pevzner doi:10.1038/nmeth.3737 Software able to assemble long synthetic reads from barcoded Illumina short-read technology improves the assembly of metagenomic data sets and analysis of the human genome. Articles Top Quantification of private information leakage from phenotype-genotype data: linking attacks   pp251 - 256 Arif Harmanci and Mark Gerstein doi:10.1038/nmeth.3746 Linking attacks can identify individuals on the basis of seemingly independent data, such as molecular phenotypes and genotypes, in different databases and are a threat to privacy. The authors statistically quantify the extent of this risk and propose means to reduce it. See also: News and Views by Craig Multi-target spectrally resolved fluorescence lifetime imaging microscopy   pp257 - 262 Thomas Niehörster, Anna Löschberger, Ingo Gregor, Benedikt Krämer, Hans-Jürgen Rahn et al. doi:10.1038/nmeth.3740 Spectrally resolved FLIM with three excitation wavelengths and detection on 32 channels combined with advanced pattern matching allows for simultaneous detection and discrimination of fluorophores with nearly identical emission spectra, enabling highly multiplexed imaging. A genetically targetable near-infrared photosensitizer   pp263 - 268 Jianjun He, Yi Wang, Maria A Missinato, Ezenwa Onuoha, Lydia A Perkins et al. doi:10.1038/nmeth.3735 A near-infrared light-activated genetically encoded photosensitizer composed of a fluorogen-activating protein and a heavy-atom-substituted fluorogen allows protein inactivation and cellular photoablation with high spatiotemporal precision and low collateral damage. Highly multiplexed simultaneous detection of RNAs and proteins in single cells   pp269 - 275 Andreas P Frei, Felice-Alessio Bava, Eli R Zunder, Elena W Y Hsieh, Shih-Yu Chen et al. doi:10.1038/nmeth.3742 PLAYR (proximity ligation assay for RNA) enables highly multiplexed transcript quantification in combination with protein marker detection in single cells using flow or mass cytometry. Application Notes Top HyVolution—the smart path to confocal super-resolution    Rolf Theodor Borlinghaus and Constantin Kappel QPrEST™—isotope-labeled multipeptide standards for quantitative mass spectrometry-based proteomics    Tove Bostrom Top 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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