Nature Methods Contents: April 2016 Volume 13 pp 277 - 379

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Advertisement Go Green!    Try Non-toxic Nucleic Acid Gel Stains GreenView™ Replaces Ethidium Bromide (EtBr) More Sensitive Request a free sample>>  TABLE OF CONTENTS April 2016 Volume 13, Issue 4 In This Issue Editorial This Month Correspondence Research Highlights Technology Feature News and Views Analysis Brief Communications Articles Corrigendum Application Note Advertisement   Automated Gel Imaging The GelDoc-It®TS3 Imager is a stand-alone system for high-sensitivity imaging of gels, Coomasie Blue, SYBR Green and other dyes. Image acquisition and enhancement is automated, using an integrated, 15.6" touch screen, and UVP's TS3 Software. The imager can be upgraded, for chemiluminescence, fluorescence, multiplexing and Near IR applications. Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement nature.com webcasts Nature Publishing Group presents a custom webcast on: Accelerate discoveries with cryo-electron microscopy structure determination Tuesday April 12, 2016 8AM PDT, 11AM EDT, 4PM BST, 5PM CEST Register for the webcast and live Q&A session Sponsored by: Intel Corporation     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 All content now free to access including archives! Nature Communications is an open access journal that publishes high-quality research from all areas of the natural sciences. Papers published by the journal represent important advances of significance to specialists within each subject area including chemistry. Visit the website to explore ALL the content available within your field.    In This Issue Top In This Issue    Editorial Top Preprints in biology   p277 doi:10.1038/nmeth.3831 We remind our readers about our policies on the use of preprints: in short, we support them. A Nature Methods author can post a preprint prior to submission without fearing a penalty. This Month Top The Author File: Sarah Teichmann   p279 Vivien Marx doi:10.1038/nmeth.3808 Team sports and team efforts lead to a new tool that helps with immune profiling. Points of Significance: Analyzing outliers: influential or nuisance?   pp281 - 282 Naomi Altman and Martin Krzywinski doi:10.1038/nmeth.3812 Some outliers influence the regression fit more than others. Correspondence Top iCOBRA: open, reproducible, standardized and live method benchmarking   p283 Charlotte Soneson and Mark D Robinson doi:10.1038/nmeth.3805 Research Highlights Top Customizing cell-cell communication Synthetic Notch receptors with chimeric extra- and intracellular domains can be tailored to tune cell-cell communication. Breaking the diffraction barrier Researchers exploit crystal imperfections to solve protein structures at resolutions beyond the X-ray diffraction limit. Cas9 and the importance of asymmetry Short single-stranded DNA donors that asymmetrically span the Cas9 cut site show high efficiency in homology-directed editing. Yes to genetically encoded NO• sensors Researchers have developed a set of fluorescent-protein-based sensors for endogenous nitric oxide. Protein isoforms: more than meets the eye Alternative splicing imparts distinct functions through isoform-specific protein-protein interactions. Reprogrammed cells leave their past lives behind Genetic background trumps tissue of origin as a source of variability between induced pluripotent stem cell lines, diminishing the role of somatic memory in reprogrammed cells. Methods in Brief Expanding incorporation of nonstandard amino acids | Cellular reprogramming is not very mutagenic | Clearing the way for RNA visualization | Printing human-scale tissues in three dimensions Tools in Brief Brighter and more photostable red and green fluorescent proteins | A super-splicing split intein | A transformative tool for trans-synaptic tracing | Improved protein labeling for super-resolution microscopy Methods JOBS of the week Institute Research Scientist Target Biology The University of Texas MD Anderson Cancer Center Six Open PhD Positions in Bioinformatics Universität Bielefeld Postdoctoral Researcher - Computational Chemistry Columbia 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 Cancer: hunting rare somatic mutations   pp295 - 299 Vivien Marx doi:10.1038/nmeth.3803 Emerging ways to lower the error rate when hunting low-frequency mutations. News and Views Top Overcoming obstacles in localization microscopy   pp301 - 302 Ralf Jungmann doi:10.1038/nmeth.3813 Lattice light-sheet-PAINT brings localization microscopy to large volumes, and SuReSim enables ground truth modeling of super-resolution experiments. See also: Article by Legant et al. | Brief Communication by Venkataramani et al. Analysis Top Analysis of computational footprinting methods for DNase sequencing experiments   pp303 - 309 Eduardo G Gusmao, Manuel Allhoff, Martin Zenke and Ivan G Costa doi:10.1038/nmeth.3772 This comparison of ten computational methods for detecting transcription factor binding sites in DNase hypersensitive regions in the genome determines which methods work consistently well, how DNase-seq experimental artifacts should be corrected for and which score is best for ranking methods. Inferring causal molecular networks: empirical assessment through a community-based effort OPEN   pp310 - 318 Steven M Hill, Laura M Heiser, Thomas Cokelaer, Michael Unger, Nicole K Nesser et al. doi:10.1038/nmeth.3773 The HPN-DREAM community challenge assessed the ability of computational methods to infer causal molecular networks, focusing specifically on the task of inferring causal protein signaling networks in cancer cell lines. Brief Communications Top SuReSim: simulating localization microscopy experiments from ground truth models   pp319 - 321 Varun Venkataramani, Frank Herrmannsdörfer, Mike Heilemann and Thomas Kuner doi:10.1038/nmeth.3775 SuReSim software simulates single-molecule localization microscopy data for structures with known ground truth models to facilitate proper design, interpretation and validation of super-resolution imaging experiments. See also: News and Views by Jungmann epiGBS: reference-free reduced representation bisulfite sequencing   pp322 - 324 Thomas P van Gurp, Niels C A M Wagemaker, Björn Wouters, Philippine Vergeer, Joop N J Ouborg et al. doi:10.1038/nmeth.3763 EpiGBS (epi-genotyping by sequencing) constructs de novo references using reduced representation bisulfite sequencing followed by variant calling and methylation detection. Simultaneous fast measurement of circuit dynamics at multiple sites across the mammalian brain   pp325 - 328 Christina K Kim, Samuel J Yang, Nandini Pichamoorthy, Noah P Young, Isaac Kauvar et al. doi:10.1038/nmeth.3770 Frame-projected independent-fiber photometry (FIP) enables the concurrent monitoring and manipulation of neural activity at multiple sites in the brains of freely behaving mice. T cell fate and clonality inference from single-cell transcriptomes   pp329 - 332 Michael J T Stubbington, Tapio Lönnberg, Valentina Proserpio, Simon Clare, Anneliese O Speak et al. doi:10.1038/nmeth.3800 The TraCeR tool extracts full-length, paired T cell receptor sequences from single-cell RNA-sequencing data from T lymphocytes, enabling a combination of clonotype and functional analysis. High-resolution mass spectrometry of small molecules bound to membrane proteins   pp333 - 336 Joseph Gault, Joseph A C Donlan, Idlir Liko, Jonathan T S Hopper, Kallol Gupta et al. doi:10.1038/nmeth.3771 A high-resolution, Orbitrap-based, native mass spectrometry approach allows the direct characterization of lipid, peptide and drug binding to intact membrane proteins. Sensory and optogenetically driven single-vessel fMRI   pp337 - 340 Xin Yu, Yi He, Maosen Wang, Hellmut Merkle, Stephen J Dodd et al. doi:10.1038/nmeth.3765 High-field fMRI with single-vessel resolution allows one to decipher the contribution of different types of vessels to hemodynamic activity evoked by sensory or optogenetic stimulation in the rat brain. Single-molecule imaging of non-equilibrium molecular ensembles on the millisecond timescale   pp341 - 344 Manuel F Juette, Daniel S Terry, Michael R Wasserman, Roger B Altman, Zhou Zhou et al. doi:10.1038/nmeth.3769 This report describes an imaging and analysis platform enabling high-throughput single-molecule fluorescence investigations of fast, transient molecular recognition events. Advertisement Double-quenched qPCR probes for high-sensitivity applications  BHQnova™ probes are your solution when assay performance demands excellent quenching efficiency without sacrificing signal release across a wide dynamic range. LGC Biosearch technologies' new double-quenched BHQnova probes helps boost assay signal-to-noise (S:N) ratios resulting in robust amplification curves.   Articles Top A saposin-lipoprotein nanoparticle system for membrane proteins   pp345 - 351 Jens Frauenfeld, Robin Löving, Jean-Paul Armache, Andreas F-P Sonnen, Fatma Guettou et al. doi:10.1038/nmeth.3801 A saposin protein-lipid nanoparticle system stabilizes diverse, fragile membrane proteins in a lipid environment for structural and functional studies. Apollo-NADP+: a spectrally tunable family of genetically encoded sensors for NADP+   pp352 - 358 William D Cameron, Cindy V Bui, Ashley Hutchinson, Peter Loppnau, Susanne Gräslund et al. doi:10.1038/nmeth.3764 HomoFRET sensors based on G6PD homodimerization allow direct sensing of NADPH/NADP+ redox state in living cells. Spectrally tuning the Apollo-NADP+ sensor allows multiplex imaging for studies of oxidative stress in beta cells. High-density three-dimensional localization microscopy across large volumes   pp359 - 365 Wesley R Legant, Lin Shao, Jonathan B Grimm, Timothy A Brown, Daniel E Milkie et al. doi:10.1038/nmeth.3797 Lattice light-sheet and PAINT microscopy are combined to achieve low-background detection of dense molecular labels, yielding super-resolution localization microscopy images of intricate 3D structures within dividing cells and embryos. See also: News and Views by Jungmann Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases   pp366 - 370 Daniel Marbach, David Lamparter, Gerald Quon, Manolis Kellis, Zoltán Kutalik et al. doi:10.1038/nmeth.3799 This resource contains 394 human cell type- and tissue-specific transcriptional networks and finds that disease-associated genetic variants often perturb regulatory modules in tissues specific for that disease. One library to make them all: streamlining the creation of yeast libraries via a SWAp-Tag strategy   pp371 - 378 Ido Yofe, Uri Weill, Matthias Meurer, Silvia Chuartzman, Einat Zalckvar et al. doi:10.1038/nmeth.3795 The SWAp-Tag method allows for easy replacement of a tag in a parental strain with an expression cassette of choice to rapidly create new yeast libraries that will enable researchers to address biological questions in Saccharomyces cerevisiae. Advertisement ATTENDING AACR? MURPHY'S LAB WILL BE THERE! Everyone gets frustrated in the workplace, and we want to hear your gripes. Tell us what bothers you, and it might be featured in our next illustration. Stop by booth #2012 to pick up FREE Murphy's Lab merchandise. Date: Sunday, 17th April, 2016 Time: 1pm until supplies last Location: Nature booth #2012 LEARN MORE     Corrigendum Top Corrigendum: The field that came in from the cold   p379 Michael Eisenstein doi:10.1038/nmeth0416-379 Application Note Top Performing efficient sample preparation with hard tumor tissue: Precellys® bead-beating homogenizer solution    Sophie Dubacq Top Advertisement npj Systems Biology and Applications is a new online, open access, multi- and cross- disciplinary journal dedicated to publishing finest research on systems biology and all its approaches. Read the latest featured article:  Not just a colourful metaphor: modelling the landscape of cellular development using Hopfield networks    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. 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