Nature Methods Contents: January 2018, Volume 15 No 1 pp 1 - 89

If you are unable to see the message below, click here to view.
m

TABLE OF CONTENTS January 2018 Volume 15, Issue 1 Special Feature Editorial This Month Correspondence Research Highlights News Feature Primer Commentaries Methods to Watch Technology Feature Resources Brief Communications Articles   Subscribe   Facebook   RSS   Recommend to library   Twitter   Special Feature Top Method of the Year 2016 Contents Editorial News feature Primer Commentaries Methods to Watch   We've chosen organoids as Method of the Year 2017, for their immense potential as tools to study human biology in health and disease. A News Feature gives a flavor of the exciting applications of these 3D constructs, and a Primer provides a short overview for newcomers to the field. Two expert Commentaries consider these tools from different angles: how cutting-edge imaging is synergizing with organoid culture to deepen our view into many biological systems, and how pluripotent stem cell-derived constructs can be used to model the human brain. As in the past, we've also chosen eight 'methods to watch' for the future. Editorial Top Special Feature: Method of the Year 2017 Method of the Year 2017: Organoids   p1 doi:10.1038/nmeth.4575 The ability to prod stem cells into three-dimensional tissue models makes for a powerful way to study human biology. But these exciting tools are still works in progress.   This Month Top The Author File: Kasper Lage   p3 Vivien Marx doi:10.1038/nmeth.4539 Scoring genes in light of their 'friends', and a naval approach to science.   Points of significance: Machine learning: supervised methods   pp5 - 6 Danilo Bzdok, Martin Krzywinski and Naomi Altman doi:10.1038/nmeth.4551 Supervised learning algorithms extract general principles from observed examples guided by a specific prediction objective.   Correspondence Top A profusion of confusion in NGS methods naming   pp7 - 8 James Hadfield and Jacques Retief doi:10.1038/nmeth.4558   motifStack for the analysis of transcription factor binding site evolution   pp8 - 9 Jianhong Ou, Scot A Wolfe, Michael H Brodsky and Lihua Julie Zhu doi:10.1038/nmeth.4555   Research Highlights Top It takes two to trans-Tango Trans-Tango allows trans-synaptic mapping of presynaptic and postsynaptic partners in Drosophila. Reflecting on light sheets Reflective coverslips can improve spatiotemporal resolution and collection efficiency in diSPIM light-sheet fluorescence microscopy. Sequencing DNA, no mistake Building redundancy into fluorogenic sequencing makes for error-free DNA sequence reads. High-resolution mapping of R loops Two novel techniques refine genome-wide mapping of R loops. Depleting endogenous proteins Using antibodies to target specific proteins for rapid degradation is a versatile approach for studying the function of endogenous proteins. Methods in Brief Top A shortcut to high-dimensional data | Nascent proteome labeling in vivo | Pooled screens expand to new phenotypes | False discovery rate estimation for metabolomics Tools in Brief Top Electrophysiology at a massive scale | Annotating full-length long noncoding RNAs | Imaging 3D enzyme dynamics in 2D | Fast curve fitting on a graphics processing unit Methods JOBS of the week Postdoctoral Researcher Leibniz Institute for Natural Product Research and Infection Biology Postdoctoral Research Scientist Columbia University Medical Center - Department of Obstetrics and Gynecology Preclinical Research Assistant Imanova Limited Staff Scientist Carnegie Institution for Science, Dept. Geophysical Laboratory Data Scientist in Biostatistics / Bioinformatics Oklahoma Medical Research Foundation (OMRF) More Science jobs from Methods EVENT SMART 2018 : Scientific Methods in Academic Research and Teaching 07.06.18 Bacau, Romania More science events from News Feature Top Special Feature: Method of the Year 2017 Organoids: the body builders   pp19 - 22 Michael Eisenstein doi:10.1038/nmeth.4538   Primer Top Special Feature: Method of the Year 2017 Organoids   p23 Natalie de Souza doi:10.1038/nmeth.4576 A brief overview of stem cell-derived organoids: how they are made and what the challenges are.   Commentaries Top Special Feature: Method of the Year 2017 Imaging organoids: a bright future ahead   pp24 - 26 Anne C Rios and Hans Clevers doi:10.1038/nmeth.4537   Special Feature: Method of the Year 2017 Organoids required! A new path to understanding human brain development and disease   pp27 - 29 Paola Arlotta doi:10.1038/nmeth.4557   Methods to Watch Top Special Feature: Method of the Year 2017 Spatial transcriptomics   p30 Tal Nawy doi:10.1038/nmeth.4542 It will soon be commonplace to localize gene expression in tissues.   Special Feature: Method of the Year 2017 Structure via super-resolution   p30 Natalie de Souza doi:10.1038/nmeth.4543 Fluorescence nanoscopy is extending its reach into structural biology.   Special Feature: Method of the Year 2017 Towards a dynamic 3D genome   p31 Nicole Rusk doi:10.1038/nmeth.4544 Sequencing and imaging bring unique aspects to genome architecture.   Special Feature: Method of the Year 2017 Transformative electrophysiology   p31 Nina Vogt doi:10.1038/nmeth.4545 Increases in throughput push electrophysiology into a new era.   Special Feature: Method of the Year 2017 Mass spectrometry imaging takes off   p32 Allison Doerr doi:10.1038/nmeth.4546 Recent advances in mass spectrometry imaging enable label-free molecular mapping in single cells and in 3D.   Special Feature: Method of the Year 2017 Tracing cellular descent   p32 Tal Nawy doi:10.1038/nmeth.4547 Sophisticated barcoding approaches are transforming cell lineaging.   Special Feature: Method of the Year 2017 The new XFELs   p33 Allison Doerr doi:10.1038/nmeth.4548 New X-ray free-electron (XFEL) facilities will broaden access to this technology, facilitate methods development, and push boundaries in structural biology.   Special Feature: Method of the Year 2017 Machine learning in neuroscience   p33 Nina Vogt doi:10.1038/nmeth.4549 In the era of big data, neuroscience can profit from deep-learning approaches.   Technology Feature Top Chemical biology: fats as research subjects   pp35 - 38 Vivien Marx doi:10.1038/nmeth.4550 Fats add structure, they signal, they interact. In the lab, lipids are tough to work with but worth the challenge.   Resources Top Multicolor quantitative confocal imaging cytometry   pp39 - 46 Daniel L Coutu, Konstantinos D Kokkaliaris, Leo Kunz and Timm Schroeder doi:10.1038/nmeth.4503 This resource paper describes the steps involved in carrying out quantitative multicolour imaging in tissue. It is applied to cleared mouse bone and plots the spatial distribution of specific cell populations within the marrow.   Systematic characterization of maturation time of fluorescent proteins in living cells   pp47 - 51 Enrique Balleza, J Mark Kim and Philippe Cluzel doi:10.1038/nmeth.4509 This work characterizes the maturation kinetics of 50 cyan to far-red fluorescent proteins and provides evidence that proteins that mature faster than their brighter but slower counterparts are more useful for quantitative evaluation of fast processes.   Brief Communications Top Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics   pp53 - 56 Zijuan Lai, Hiroshi Tsugawa, Gert Wohlgemuth, Sajjan Mehta, Matthew Mueller et al. doi:10.1038/nmeth.4512 An integrated cheminformatics workflow aids the functional and structural annotation of unknown metabolites found across multiple biological systems.   Programmable full-adder computations in communicating three-dimensional cell cultures   pp57 - 60 David Ausländer, Simon Ausländer, Xavier Pierrat, Leon Hellmann, Leila Rachid et al. doi:10.1038/nmeth.4505 Designer cells executing rationally assembled genetic programs that can process input signals with programmable logic are combined in a 3D cell culture that performs three-input, two-output full-adder computations.   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 NetSig: network-based discovery from cancer genomes   pp61 - 66 Heiko Horn, Michael S Lawrence, Candace R Chouinard, Yashaswi Shrestha, Jessica Xin Hu et al. doi:10.1038/nmeth.4514 NetSig is a network-based statistic that identifies cancer driver genes with high accuracy and can be combined with gene-based statistical tests; results are validated with a large-scale in vivo tumorigenesis assay.   PDB-wide identification of biological assemblies from conserved quaternary structure geometry   pp67 - 72 Sucharita Dey, David W Ritchie and Emmanuel D Levy doi:10.1038/nmeth.4510 Monomeric and homo-oligomeric protein quaternary structure states are predicted on a PDB-wide scale using a method that approaches the accuracy of manual annotation.   A permanent window for the murine lung enables high-resolution imaging of cancer metastasis   pp73 - 80 David Entenberg, Sonia Voiculescu, Peng Guo, Lucia Borriello, Yarong Wang et al. doi:10.1038/nmeth.4511 The window for high-resolution imaging of the lung (WHRIL) enables longitudinal imaging of the same region of murine lung tissue over a period of weeks, and this enables the visualization of spontaneous cancer metastasis from the earliest stages.   An improved MS2 system for accurate reporting of the mRNA life cycle   pp81 - 89 Evelina Tutucci, Maria Vera, Jeetayu Biswas, Jennifer Garcia, Roy Parker et al. doi:10.1038/nmeth.4502 An improved MS2-tagging system for live-cell RNA imaging allows faithful monitoring of the mRNA life cycle, overcoming degradation artifacts associated with previous versions and having implications regarding mRNA regulation in yeast.   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

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 Springer Nature | One New York Plaza, Suite 4500 | New York | NY 10004-1562 | USA Springer Nature'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 The Campus, 4 Crinan Street, London, N1 9XW. © 2018 Macmillan Publishers Limited, part of Springer Nature. All Rights Reserved.