Nature Methods Contents: August 2012 Volume 9 pp 765 - 846

Advertisement New! ScriptSeq™ Complete Kits Epicentre's ScriptSeq Complete Kits combine industry-leading Ribo-Zero™ technology and the rapid ScriptSeq v2 method for seamless, end-to-end preparation of directional RNA-Seq libraries in 1 day. The Low Input kits are ideal for FFPE RNA samples. Learn more: www.epicentre.com/complete TABLE OF CONTENTS August 2012 Volume 9, Issue 8 In This Issue Editorial This Month Correspondence Research Highlights Methods in Brief Tools in Brief Technology Feature News and Views Analysis Brief Communications Articles Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement Nurture your career with the new-look Naturejobs As the world's largest dedicated jobs boards for the scientific community, Naturejobs is the ideal resource to build your career. Our new and improved functionality enables you to search, save and apply for jobs quickly and easily. Search over 10,000 vacancies to find exactly the right job for you at: www.naturejobs.com.   In This Issue Top In This Issue Editorial Top In praise of referees   p765 doi:10.1038/nmeth.2136 Peer review is an essential part of scientific discourse, and referees deserve formal recognition for the service they provide. This Month Top The author file: Gustavo Stolovitzky   p767 Monya Baker doi:10.1038/nmeth.2113 Boosting accuracy by building consensus. Points of view: Mapping quantitative data to color   p769 Nils Gehlenborg and Bang Wong doi:10.1038/nmeth.2134 Data structure informs choice of color maps. Correspondence Top Reanalysis of phosphoproteomics data uncovers ADP-ribosylation sites   pp771 - 772 Ivan Matic, Ivan Ahel and Ronald T Hay doi:10.1038/nmeth.2106 jModelTest 2: more models, new heuristics and parallel computing   p772 Diego Darriba, Guillermo L Taboada, Ramón Doallo and David Posada doi:10.1038/nmeth.2109 CircadiOmics: integrating circadian genomics, transcriptomics, proteomics and metabolomics   pp772 - 773 Vishal R Patel, Kristin Eckel-Mahan, Paolo Sassone-Corsi and Pierre Baldi doi:10.1038/nmeth.2111 OpenFovea: open-source AFM data processing software   pp774 - 775 Charles Roduit, Bhaskar Saha, Livan Alonso-Sarduy, Andrea Volterra, Giovanni Dietler and Sandor Kasas doi:10.1038/nmeth.2112 Research Highlights Top Writing the histone code   p777 Recruiting chromatin modifiers to a specific locus allows the regulation of heterochromatin formation in living cells. Upgrades for the AFM   pp778 - 779 Researchers continue to improve the performance of the atomic force microscope. A blood-brain barrier in a dish   pp778 - 779 Codifferentiating human pluripotent stem cells along neural and endothelial lineages provides cues to efficiently generate blood-brain barrier endothelial cells. Ribosomes, start your engines   p780 Tracking single molecules in real time reveals the hidden dynamics of translational initiation. (Protein) timing is everything   p783 Tandem fluorescent protein timers allow measurements of both protein turnover and trafficking in the cell. Living longer, staying healthy   p784 Lifespan in nematodes is markedly extended when an unusual combination of aging components is engineered into their genome. Methods JOBS of the week PhD studentship on large-scale quantum chemistry methods applied to drug discovery University of Southampton - Chemistry Scientists Queen Mary University of London Specially Appointed Researcher (Full Time) Immunology Frontier Research Center (IFReC), Osaka University Postdoctoral positions in Computational Biology University of Michigan - Ann Arbor Scientific coordinator of a bioinformatics / biostatistics platform (M / F) IHU-A-ICM More Science jobs from Methods EVENT Sterilization Procedures Technology, Equipment & Validation 14th November - 15th Novemeber 2012 PA, US More science events from Methods in Brief Top The ins and outs of optogenetic silencers | Quantifying single transcripts | Toward deep-tissue fluorescence imaging | Neural progenitors from fibroblasts Tools in Brief Top RNA and the proteins that bind | Synaptic activity shines in red | Shutting down parts of the glycome | Long noncoding RNAs in the worm Technology Feature Top RNA imaging in situ    pp787 - 790 Monya Baker doi:10.1038/nmeth.2108 Rapidly maturing techniques reveal messengers within cells. News and Views Top High-speed microbial community profiling   pp793 - 794 Daniel H Haft and Andrey Tovchigrechko doi:10.1038/nmeth.2080 A precomputed database of lineage-restricted reference genes yields a fast and accurate tool that uses sequence similarity alone to compute clade abundances from shotgun metagenomic data sets. See also: Brief Communication by Segata et al. Connecting ecology and conservation through experiment   pp794 - 795 Nick M Haddad doi:10.1038/nmeth.2107 An experimental infrastructure consisting of environmentally controlled and spatially linked habitat patches permits studies on terrestrial animal dispersal at an unprecedented scale for an experiment with such strict control. See also: Article by Legrand et al. Analysis Top Wisdom of crowds for robust gene network inference   pp796 - 804 Daniel Marbach, James C Costello, Robert Küffner, Nicole M Vega, Robert J Prill, Diogo M Camacho, Kyle R Allison, The DREAM5 Consortium, Manolis Kellis, James J Collins and Gustavo Stolovitzky doi:10.1038/nmeth.2016 This analysis comprehensively compares methods for gene regulatory network inference submitted through the DREAM5 challenge. It demonstrates that integration of predictions from multiple methods shows the most robust performance across data sets. Brief Communications Top Targeted gene knockout by direct delivery of zinc-finger nuclease proteins   pp805 - 807 Thomas Gaj, Jing Guo, Yoshio Kato, Shannon J Sirk and Carlos F Barbas III doi:10.1038/nmeth.2030 Due to an unexpected cell-penetrating property, zinc-finger nucleases (ZFNs) can be delivered to several mammalian cell types as proteins. Dose-dependent disruption of an endogenous gene was achieved with reduced activity at known off-target sites. 2b-RAD: a simple and flexible method for genome-wide genotyping   pp808 - 810 Shi Wang, Eli Meyer, John K McKay and Mikhail V Matz doi:10.1038/nmeth.2023 Genotyping based on restriction site7ndash;associated (RAD) sequencing around type IIB enzyme recognition sites is reported. The streamlined reduced-representation approach features even and tunable genome coverage and enables large-scale genotyping studies by maximizing the amount of genotypic information that can be obtained from individuals for a given amount of sequencing. Metagenomic microbial community profiling using unique clade-specific marker genes   pp811 - 814 Nicola Segata, Levi Waldron, Annalisa Ballarini, Vagheesh Narasimhan, Olivier Jousson and Curtis Huttenhower doi:10.1038/nmeth.2066 MetaPhlAn (metagenomic phylogenetic analysis) allows the rapid and accurate identification of microbial species and higher clades from shotgun sequencing data. See also: News and Views by Haft & Tovchigrechko Multicolor two-photon tissue imaging by wavelength mixing   pp815 - 818 Pierre Mahou, Maxwell Zimmerley, Karine Loulier, Katherine S Matho, Guillaume Labroille, Xavier Morin, Willy Supatto, Jean Livet, Delphine Débarre and Emmanuel Beaurepaire doi:10.1038/nmeth.2098 This method achieves simultaneous and spatially colocalized excitation of three fluorophores with distinct spectra, doing so via two-photon microscopy using a femtosecond laser and an optical parametric oscillator and by temporally overlapping the beams. Imaging of 'Brainbow'-labeled mouse and chicken nervous tissue and of developing fly embryos is shown. forestSV: structural variant discovery through statistical learning   pp819 - 821 Jacob J Michaelson and Jonathan Sebat doi:10.1038/nmeth.2085 A machine learning-based structural-variant discovery approach that incorporates prior knowledge shows high sensitivity and specificity even on single genomes. A protease for 'middle-down' proteomics   pp822 - 824 Cong Wu, John C Tran, Leonid Zamdborg, Kenneth R Durbin, Mingxi Li, Dorothy R Ahlf, Bryan P Early, Paul M Thomas, Jonathan V Sweedler and Neil L Kelleher doi:10.1038/nmeth.2074 A rare cutting protease that creates large peptides is well suited for differentiating protein isoforms and detecting combinations of post-translational modifications by tandem mass spectrometry. Scanning angle interference microscopy reveals cell dynamics at the nanoscale   pp825 - 827 Matthew J Paszek, Christopher C DuFort, Matthew G Rubashkin, Michael W Davidson, Kurt S Thorn, Jan T Liphardt and Valerie M Weaver doi:10.1038/nmeth.2077 This paper reports a fluorescence imaging method based on interference contrast in which the incidence angle of the excitation light is actively scanned. The high axial precision and temporal resolution are used for dynamic nanoscale imaging of cytoskeleton and adhesion proteins in living cells. Advertisement PCR that Works...for Fast, High Fidelity PCR High speed, high fidelity...Excellent Results. Try PrimeSTAR GXL on standard templates, GC-rich, AT-rich, even repetitive DNA. It's the most robust high-fidelity enzyme commercially available. Put it to work for you: try a sample today.   Articles Top The Metatron: an experimental system to study dispersal and metaecosystems for terrestrial organisms   pp828 - 833 Delphine Legrand, Olivier Guillaume, Michel Baguette, Julien Cote, Audrey Trochet, Olivier Calvez, Susanne Zajitschek, Felix Zajitschek, Jane Lecomte, Quentin Bénard, Jean-François Le Galliard and Jean Clobert doi:10.1038/nmeth.2104 A flexible, environmentally controlled experimental setup for the study of terrestrial animal dispersal is reported. Its unprecedented scale should enable studies in spatial ecology and permit tests of conservation strategies in the face of environmental change. See also: News and Views by Haddad Facile backbone structure determination of human membrane proteins by NMR spectroscopy   pp834 - 839 Christian Klammt, Innokentiy Maslennikov, Monika Bayrhuber, Cédric Eichmann, Navratna Vajpai, Ellis Jeremy Chua Chiu, Katherine Y Blain, Luis Esquivies, June Hyun Jung Kwon, Bartosz Balana, Ursula Pieper, Andrej Sali, Paul A Slesinger, Witek Kwiatkowski, Roland Riek and Senyon Choe doi:10.1038/nmeth.2033 The combination of cell-free protein expression and combinatorial dual labeling-aided NMR analysis allows for the rapid backbone structure assessment of human membrane proteins. High-throughput assessment of microRNA activity and function using microRNA sensor and decoy libraries   pp840 - 846 Gavriel Mullokandov, Alessia Baccarini, Albert Ruzo, Anitha D Jayaprakash, Navpreet Tung, Benjamin Israelow, Matthew J Evans, Ravi Sachidanandam and Brian D Brown doi:10.1038/nmeth.2078 Two large-scale resources for studying microRNA function are presented: one is a library of fluorescent sensors with a corresponding assay for global profiling of microRNA activity in different cell types; the other is a decoy library for suppressing microRNA activity individually or in pooled loss-of-function screens. Advertisement The New BD FACSJaz™ Cell Sorter Perfectly tuned cell sorting is now available with the new BD FACSJazz. Built on a proven, dependable platform, it may change the way you'll think of cell sorting with ease of operation, affordability, and a benchtop fit. Exceedingly capable performance whether as a soloist or part of your core lab ensemble. bdbiosciences.com/jazz   Top Advertisement Nature Chemical Biology Focus on Metabolism in 3D In this focus issue, we feature a collection of commentary and review articles that outline some of the ideas, advances and goals that are laying the foundations for the next era of metabolism research. To access the Focus, visit: www.nature.com/nchembio/focus/metabolism3d/index.html   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

You have been sent this Table of Contents Alert because you have opted in to receive it. You can change or discontinue your e-mail alerts at any time, by modifying your preferences on your nature.com account at: www.nature.com/myaccount (You will need to log in to be recognised as a nature.com registrant) For further technical assistance, please contact our registration department For print subscription enquiries, please contact our subscription department For other enquiries, please contact our customer feedback department Nature Publishing Group | 75 Varick Street, 9th Floor | New York | NY 10013-1917 | USA Nature Publishing Group's worldwide offices: London - Paris - Munich - New Delhi - Tokyo - Melbourne San Diego - San Francisco - Washington - New York - Boston Macmillan Publishers Limited is a company incorporated in England and Wales under company number 785998 and whose registered office is located at Brunel Road, Houndmills, Basingstoke, Hampshire RG21 6XS. © 2012 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.