Nature Methods Contents: September 2018, Volume 15 No 9

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Advertisement Nikon's new high-speed N-SIM S super-resolution microscope system achieves acquisition speeds up to 15 frames per second, enabling the acquisition of fast biological processes at twice the spatial resolution of conventional light microscopes.  Learn more TABLE OF CONTENTS September 2018 Volume 15, Issue 9 Editorial This Month Correspondence Research Highlights Technology Feature News & Views Review Articles Analysis Brief Communications Articles Amendments & Corrections   Advertisement   Hamamatsu's W-View Gemini-2C: Multi-wavelength, multi-camera imaging that's built for super-resolution and ready for anything. Now available with our new Extended Focus Device increasing depth of focus up to 5x by using a simple optical filter.   Editorial   Easing the burden of code review    p641 doi:10.1038/s41592-018-0137-5 This Month   Min Zhuang    p643 Vivien Marx doi:10.1038/s41592-018-0116-x 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   Correspondence   An open-source platform for analyzing and sharing worm-behavior data    pp645 - 646 Avelino Javer, Michael Currie, Chee Wai Lee, Jim Hokanson, Kezhi Li et al. doi:10.1038/s41592-018-0112-1 Research Highlights   Toward a 3D genome in high resolution    p647 Nicole Rusk doi:10.1038/s41592-018-0130-z Detecting acetylcholine    p648 Nina Vogt doi:10.1038/s41592-018-0131-y Taking inventory with shotgun EM    p649 Allison Doerr doi:10.1038/s41592-018-0132-x A path to predict RNA tertiary structures    p650 Lei Tang doi:10.1038/s41592-018-0133-9 Comprehensive mapping of ubiquitination    p651 Allison Doerr doi:10.1038/s41592-018-0122-z CRISPR and immunity    p651 Nicole Rusk doi:10.1038/s41592-018-0123-y Expansion of the transgenic toolkit in mouse    p651 Nina Vogt doi:10.1038/s41592-018-0124-x The whole fly brain in detail    p651 Nina Vogt doi:10.1038/s41592-018-0125-9 Absorption-based multicolor imaging    p652 Rita Strack doi:10.1038/s41592-018-0126-8 Improved photoacoustic imaging probes    p652 Rita Strack doi:10.1038/s41592-018-0127-7 Three tissues to gastrulation    p652 Tal Nawy doi:10.1038/s41592-018-0128-6 Organoid hosts for parasitic infection    p652 Tal Nawy doi:10.1038/s41592-018-0129-5 Enhancing photostability with FRET    p653 Rita Strack doi:10.1038/s41592-018-0134-8 Methods JOBS of the week Postdoctoral Fellow Positions in Metabolic Disorders Temple University School of Medicine Scientist – Bioinformatics Genentech, Inc. Bioinformatics Postdoctoral Positions in Algorithms, Cancer Genomics and CRISPR Children's National Medical Center Open Faculty Positions in Chemistry Okinawa Institute of Science and Technology (OIST) Faculty position in Chemistry University of California - Irvine More Science jobs from Methods EVENT Computational Methods in Systems Biology (CMSB 2018) 12.9.18 Brno, Czech Republic More science events from Technology Feature   Profiling the dress codes of RNA-binding proteins    pp655 - 658 Vivien Marx doi:10.1038/s41592-018-0117-9 News & Views   Improving probes for super-resolution    pp659 - 660 Regan P. Moore & Wesley R. Legant doi:10.1038/s41592-018-0120-1   Review Articles   Single-cell genomics to guide human stem cell and tissue engineering    pp661 - 667 J. Gray Camp, Damian Wollny & Barbara Treutlein doi:10.1038/s41592-018-0113-0 A review of how single-cell sequencing methods can be used to improve human stem cell and tissue engineering.   Analysis   Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study    pp669 - 676 Björn Hellenkamp, Sonja Schmid, Olga Doroshenko, Oleg Opanasyuk, Ralf Kühnemuth et al. doi:10.1038/s41592-018-0085-0 A multi-laboratory study finds that single-molecule FRET is a reproducible and reliable approach for determining accurate distances in dye-labeled DNA duplexes.   Brief Communications   CDeep3M—Plug-and-Play cloud-based deep learning for image segmentation    pp677 - 680 Matthias G. Haberl, Christopher Churas, Lucas Tindall, Daniela Boassa, Sébastien Phan et al. doi:10.1038/s41592-018-0106-z CDeep3M provides a user-friendly tool for deep-learning-based image segmentation via a cloud-based deep convolutional neural network. Demonstrations include challenging light, X-ray, and electron microscopy segmentation tasks.   XCMS-MRM and METLIN-MRM: a cloud library and public resource for targeted analysis of small molecules    pp681 - 684 Xavier Domingo-Almenara, J. Rafael Montenegro-Burke, Julijana Ivanisevic, Aurelien Thomas, Jonathan Sidibé et al. doi:10.1038/s41592-018-0110-3 A resource of multiple reaction monitoring–mass spectrometry transitions for quantitative analysis of biological small molecules is provided in METLIN-MRM, along with automated tools for analyzing such data in XCMS-MRM.   Modified aptamers enable quantitative sub-10-nm cellular DNA-PAINT imaging    pp685 - 688 Sebastian Strauss, Philipp C. Nickels, Maximilian T. Strauss, Vilma Jimenez Sabinina, Jan Ellenberg et al. doi:10.1038/s41592-018-0105-0 Slow off-rate modified aptamer (SOMAmer) reagents are small and versatile probes for DNA-PAINT super-resolution microscopy that enable multiplexed, quantitative, and high-resolution imaging in fixed and live cells.   Artifact-free high-density localization microscopy analysis    pp689 - 692 Richard J. Marsh, Karin Pfisterer, Pauline Bennett, Liisa M. Hirvonen, Mathias Gautel et al. doi:10.1038/s41592-018-0072-5 Preprocessing of localization microscopy datasets using Haar wavelet kernel (HAWK) analysis enables artifact-free analysis of high-density data for improved fixed and live-cell super-resolution microscopy.   Rapid and efficient induction of functional astrocytes from human pluripotent stem cells    pp693 - 696 Isaac Canals, Aurélie Ginisty, Ella Quist, Raissa Timmerman, Jonas Fritze et al. doi:10.1038/s41592-018-0103-2 A simple transcription-factor-based protocol generates functional astrocytes rapidly and efficiently from human pluripotent stem cells.   Single-DNA electron spin resonance spectroscopy in aqueous solutions    pp697 - 699 Fazhan Shi, Fei Kong, Pengju Zhao, Xiaojun Zhang, Ming Chen et al. doi:10.1038/s41592-018-0084-1 Single DNA molecules can be detected in aqueous solutions at ambient temperatures by electron spin resonance spectroscopy with diamond sensors.   Articles   Induction of myelinating oligodendrocytes in human cortical spheroids    pp700 - 706 Mayur Madhavan, Zachary S. Nevin, H. Elizabeth Shick, Eric Garrison, Cheryl Clarkson-Paredes et al. doi:10.1038/s41592-018-0081-4 A method for generating cortical spheroids from human pluripotent stem cells produces maturing oligodendrocytes that can myelinate axons and model myelin disease and drug effects.   Detecting repeated cancer evolution from multi-region tumor sequencing data    pp707 - 714 Giulio Caravagna, Ylenia Giarratano, Daniele Ramazzotti, Ian Tomlinson, Trevor A. Graham et al. doi:10.1038/s41592-018-0108-x REVOLVER uses transfer learning on multi-region tumor sequencing data to jointly infer tumor evolution models in multiple individuals and to detect repeated evolutionary trajectories. Repeated evolution can be used to stratify the cohort.   A proximity-tagging system to identify membrane protein–protein interactions    pp715 - 722 Qiang Liu, Jun Zheng, Weiping Sun, Yinbo Huo, Liye Zhang et al. doi:10.1038/s41592-018-0100-5 A proximity-based labeling system, PUP-IT, identifies membrane protein interactions.   Generation and post-injury integration of human spinal cord neural stem cells    pp723 - 731 Hiromi Kumamaru, Ken Kadoya, Andrew F. Adler, Yoshio Takashima, Lori Graham et al. doi:10.1038/s41592-018-0074-3 Spinal cord neural stem cells are generated from human pluripotent stem cells via a chemically defined, xeno-free method, and exhibit efficient and functional engraftment in rat spinal cord lesions.   Reduced MEK inhibition preserves genomic stability in naive human embryonic stem cells    pp732 - 740 Bruno Di Stefano, Mai Ueda, Shan Sabri, Justin Brumbaugh, Aaron J. Huebner et al. doi:10.1038/s41592-018-0104-1 This paper describes modifications to standard culture conditions that permit the growth of naive human pluripotent stem cells with reduced genomic instability.   Trac-looping measures genome structure and chromatin accessibility    pp741 - 747 Binbin Lai, Qingsong Tang, Wenfei Jin, Gangqing Hu, Darawalee Wangsa et al. doi:10.1038/s41592-018-0107-y Insertion of a bivalent linker between two regions of interest allows chromatin contacts to be probed without proximity ligation.   Amendments & Corrections   Author Correction: Genetically engineered cerebral organoids model brain tumor formation    p748 Shan Bian, Marko Repic, Zhenming Guo, Anoop Kavirayani, Thomas Burkard et al. doi:10.1038/s41592-018-0118-8 Publisher Correction: Single-DNA electron spin resonance spectroscopy in aqueous solutions    p749 Fazhan Shi, Fei Kong, Pengju Zhao, Xiaojun Zhang, Ming Chen et al. doi:10.1038/s41592-018-0119-7 Addendum: Biotinylation by antibody recognition—a method for proximity labeling    p749 Daniel Z Bar, Kathleen Atkatsh, Urraca Tavarez, Michael R Erdos, Yosef Gruenbaum et al. doi:10.1038/s41592-018-0073-4 Advertisement Nature Briefing is an essential round-up of science news, opinion and analysis, free in your inbox every weekday. 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