Nature Methods Contents: July 2018, Volume 15 No 7

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TABLE OF CONTENTS July 2018 Volume 15, Issue 7 Editorial This Month Correspondence Research Highlights Technology Feature News & Views Analysis Brief Communications Articles Amendments & Corrections   Advertisement nature.com webcasts Nature Research Custom Media presents a webcast on: Combining scRNA-seq and Flow Analyses   Date: Tuesday, July 24, 2018   Join our webcast to learn how fluorescence intensity information from flow parameters can be merged into a single-cell RNA expression matrix and analysed.   This webcast has been produced on behalf of the sponsor who retains sole responsibility for content   Register for FREE    Sponsored by: SeqGeq   Advertisement Nature Index 2018 Japan Some of Japan's smallest institutions are among the most efficient in the production of high quality scientific research, though the decline in Japan's high quality scientific research output continues. This supplement examines reform efforts in light of the country's aim to become a "super-smart" society.  Read the full supplement   Editorial   US universities go East    p471 doi:10.1038/s41592-018-0060-9 This Month   John T. Ngo    p473 Vivien Marx doi:10.1038/s41592-018-0047-6 Advertisement Nature Spotlight on Hong Kong: Building science innovation  Hong Kong is maximising major scientific innovation and commercial benefits through its proximity to the research and development hubs in mainland China. Yet barriers to collaboration remain.  Access the full supplement for more   Correspondence   Bioconda: sustainable and comprehensive software distribution for the life sciences    pp475 - 476 Björn Grüning, Ryan Dale, Andreas Sjödin, Brad A. Chapman, Jillian Rowe et al. doi:10.1038/s41592-018-0046-7 Advertisement nature.com webcasts Nature Research Custom Media presents a webcast on: Optical Trapping of Ion Coulomb Crystals Date: Tuesday, July 31, 2018 Join our webcast to understand the trapping of neutral and charged atoms and how to exploit optically trapped ions to investigate quantum-phase transitions. This webcast has been produced on behalf of the sponsor who retains sole responsibility for content  Register for FREE  Sponsored by: Andor    Research Highlights   Weighing single proteins with light    p477 Rita Strack doi:10.1038/s41592-018-0055-6 Corrected in vivo imaging    p478 Zachary J. Lapin doi:10.1038/s41592-018-0056-5 Correlating behavior and neural activity at high resolution    p479 Nina Vogt doi:10.1038/s41592-018-0057-4 Transcripts from a spliceosome    p480 Tal Nawy doi:10.1038/s41592-018-0058-3 Targeting Cas9    p481 Nicole Rusk doi:10.1038/s41592-018-0061-8 Sensing cellular metabolites    p481 Rita Strack doi:10.1038/s41592-018-0062-7 Higher-order genetic interactions    p481 Nicole Rusk doi:10.1038/s41592-018-0063-6 Inferring neuronal activity from gene expression    p481 Nina Vogt doi:10.1038/s41592-018-0064-5 Speedy optogenetics in red    p482 Nina Vogt doi:10.1038/s41592-018-0065-4 DNA molecular forceps    p482 Allison Doerr doi:10.1038/s41592-018-0066-3 Metastasis in a dish    p482 Tal Nawy doi:10.1038/s41592-018-0067-2 Clocking translation in live cells    p482 Rita Strack doi:10.1038/s41592-018-0068-1 Polymer model predicts chromatin folding    p483 Lei Tang doi:10.1038/s41592-018-0059-2 Methods JOBS of the week Assistant / Associate Professor, Tenure Track New York University School of Medicine Postdoctoral Fellow - Translational Cancer Research University of Pennsylvania Faculty Position in the Center for Life Sciences Skolkovo Institute of Science and Technology Postdoctoral Researcher, Antibodies production UBFC - Universite Bourgogne Franche-Comté Postdoctoral Research Assistant Queen Mary University of London More Science jobs from Methods EVENT International Conference on Statistics, Mathematical Modelling and Analysis (SMMA 2018) 15.09.18 Chongqing, China More science events from Technology Feature   What makes birds and bats the talk of the town    pp485 - 488 Vivien Marx doi:10.1038/s41592-018-0050-y News & Views   Controlling protein function with HCV protease    pp489 - 490 Bryan C. Dickinson doi:10.1038/s41592-018-0043-x Analysis   A comparison of methods to assess cell mechanical properties    pp491 - 498 Pei-Hsun Wu, Dikla Raz-Ben Aroush, Atef Asnacios, Wei-Chiang Chen, Maxim E. Dokukin et al. doi:10.1038/s41592-018-0015-1 This Analysis compares and contrasts methods for measuring the mechanical properties of cells by applying the different approaches to the same breast cancer cell line.   A reassessment of DNA-immunoprecipitation-based genomic profiling    pp499 - 504 Antonio Lentini, Cathrine Lagerwall, Svante Vikingsson, Heidi K. Mjoseng, Karolos Douvlataniotis et al. doi:10.1038/s41592-018-0038-7 Reanalysis of DNA-immunoprecipitation-based data shows that modification-specific antibodies bind unmodified short tandem repeats, and IgG controls are needed to avoid false positives.   Comprehensive comparative analysis of 5′-end RNA-sequencing methods    pp505 - 511 Xian Adiconis, Adam L. Haber, Sean K. Simmons, Ami Levy Moonshine, Zhe Ji et al. doi:10.1038/s41592-018-0014-2 A direct comparison of 5′-end RNA-seq methods reveals strong performance by CAGE, and identifies differential transcriptional start site usage among brain-related samples.   Brief Communications   CRISPR off-target analysis in genetically engineered rats and mice    pp512 - 514 Keith R. Anderson, Maximilian Haeussler, Colin Watanabe, Vasantharajan Janakiraman, Jessica Lund et al. doi:10.1038/s41592-018-0011-5 Off-targets identified by whole-genome sequencing of CRISPR-treated mouse embryos and their genetic parents are compared to predictions from GUIDE-seq and computational methods.   Automated, parallel mass spectrometry imaging and structural identification of lipids    pp515 - 518 Shane R. Ellis, Martin R. L. Paine, Gert B. Eijkel, Josch K. Pauling, Peter Husen et al. doi:10.1038/s41592-018-0010-6 An automated method coupling tandem mass spectrometry with high-resolution mass spectrometry imaging simultaneously reveals both the molecular structure of lipids and their spatial locations in tissue.   Chemogenetic control of gene expression and cell signaling with antiviral drugs    pp519 - 522 doi:10.1038/s41592-018-0042-y Ligand-inducible connection (LInC) combines HCV protease and protease inhibitors to offer an orthogonal chemogenetic approach for controlling protein functions including protein localization, gene expression, and cell–cell communication.   StaPLs: versatile genetically encoded modules for engineering drug-inducible proteins    pp523 - 526 Conor L. Jacobs, Ryan K. Badiee & Michael Z. Lin doi:10.1038/s41592-018-0041-z Stabilizable polypeptide linkages (StaPLs) based on hepatitis C virus protease enable robust, reversible, and orthogonal chemogenetic control of protein functions, including CRISPR–Cas9 activity, transcription, and protein dimerization.   EASI-tag enables accurate multiplexed and interference-free MS2-based proteome quantification    pp527 - 530 Sebastian Virreira Winter, Florian Meier, Christoph Wichmann, Juergen Cox, Matthias Mann et al. doi:10.1038/s41592-018-0037-8 EASI-tag, a new type of isobaric labeling reagents, enables multiplexed and highly accurate proteome quantification by mass spectrometry.   DeTiN: overcoming tumor-in-normal contamination    pp531 - 534 Amaro Taylor-Weiner, Chip Stewart, Thomas Giordano, Mendy Miller, Mara Rosenberg et al. doi:10.1038/s41592-018-0036-9 DeTiN can identify and account for signal from tumor cells that contaminate normal samples, for more sensitive somatic variant detection.   Efficient and precise editing of endogenous transcripts with SNAP-tagged ADARs    pp535 - 538 Paul Vogel, Matin Moschref, Qin Li, Tobias Merkle, Karthika D. Selvasaravanan et al. doi:10.1038/s41592-018-0017-z Fusion of a guide RNA directly to an adenosine deaminase via a SNAP-tag allows for precise and efficient RNA editing.   SAVER: gene expression recovery for single-cell RNA sequencing    pp539 - 542 Mo Huang, Jingshu Wang, Eduardo Torre, Hannah Dueck, Sydney Shaffer et al. doi:10.1038/s41592-018-0033-z SAVER accurately recovers expression values in single-cell RNA-sequencing data to improve downstream analysis.   GeNets: a unified web platform for network-based genomic analyses    pp543 - 546 Taibo Li, April Kim, Joseph Rosenbluh, Heiko Horn, Liraz Greenfeld et al. doi:10.1038/s41592-018-0039-6 The GeNets web platform can identify the most informative network, as well as execute, store and share network-based analyses of RNA-seq or genomic datasets.   Articles   Mapping the physical network of cellular interactions    pp547 - 553 Jean-Charles Boisset, Judith Vivié, Dominic Grün, Mauro J. Muraro, Anna Lyubimova et al. doi:10.1038/s41592-018-0009-z The ProximID approach generates single-cell expression profiles and a network of enriched physical cellular interactions within a tissue.   Amendments & Corrections   Author Correction: Informed-Proteomics: open-source software package for top-down proteomics    p554 Jungkap Park, Paul D Piehowski, Christopher Wilkins, Mowei Zhou, Joshua Mendoza et al. doi:10.1038/s41592-018-0040-0 Advertisement Nature Briefing is an essential round-up of science news, opinion and analysis, free in your inbox every weekday. With Nature Briefing, we'll keep you updated on the latest research, so you can focus on yours. Click here to sign up.   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. 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