Nature Methods Contents: July 2016 Volume 13 pp 537 - 597

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To learn more, please visit: https://www.eppendorf.com/5ml/ TABLE OF CONTENTS July 2016 Volume 13, Issue 7 In This Issue Editorial This Month Research Highlights Technology Feature News and Views Analysis Brief Communications Articles Advertisement   Determine the Metabolic Phenotype of Your Cells The Agilent Seahorse XF Cell Energy Phenotype Test uses as few as 15,000 cells, and the Agilent Seahorse XFp Analyzer, to identify your cells' metabolic phenotype, as well as their metabolic potential — the relative utilization of mitochondrial respiration and glycolysis.  http://bit.ly/1Caw9Eq Subscribe   Facebook   RSS   Recommend to library   Twitter   In This Issue Top In This Issue    Editorial Top Private funding for science   p537 doi:10.1038/nmeth.3923 With federal funding for life science becoming increasingly competitive in the United States, it would be a mistake, particularly for young investigators, not to carefully consider money from private sources. This Month Top The Author File: Vladislav Verkhusha   p539 Vivien Marx doi:10.1038/nmeth.3905 A new near-infrared optogenetic system and science as a family business. Points of Significance: Logistic regression   pp541 - 542 Jake Lever, Martin Krzywinski and Naomi Altman doi:10.1038/nmeth.3904 Regression can be used on categorical responses to estimate probabilities and to classify. Research Highlights Top Watching translation of single mRNAs in cells Four studies describe methods to image the dynamics of translation at the single-transcript level in real time in living cells, with exciting results. Miniature magnetic force probes Magnetoplasmonic nanoparticles can manipulate cell surface receptors with single-molecule precision to clarify the effects of force application and receptor clustering. Topographical transcriptomes Three experimental methods generate global maps of in vivo RNA interactions. Arrival of the Argonautes An Argonaute protein enables precision genome editing in mammalian cells. Capturing transcription factors in the wild An assay that snares transcription factors with genomic DNA fragments reveals how genetic and epigenetic factors shape binding behavior. Methods in Brief Bundled reporter gene assays | A viral trap for protein interactions | In vitro model of human implantation | Counting proteins by slowing diffusion Tools in Brief A rad tool for detecting synapses and protein-protein interactions | Labeling nonprotein biomolecules for CLEM | A bright orange fluorescent protein for enhanced in vivo imaging | Painting and sorting cells of interest Technology Feature Top Plants: a tool box of cell-based assays   pp551 - 554 Vivien Marx doi:10.1038/nmeth.3900 Cell-based assays are less routine for plant biologists than for researchers who work with animal or human cells, but that is changing. News and Views Top Genotyping tumor clones from single-cell data   pp555 - 556 Nicholas E Navin and Ken Chen doi:10.1038/nmeth.3903 A new statistical approach mitigates technical errors in single-cell DNA sequencing data to advance the study of tumor evolution and diversity. See also: Brief Communication by Roth et al. Analysis Top Quantitative assessment of fluorescent proteins   pp557 - 562 Paula J Cranfill, Brittney R Sell, Michelle A Baird, John R Allen, Zeno Lavagnino et al. doi:10.1038/nmeth.3891 This Analysis provides a head-to-head comparison of >40 monomeric fluorescent proteins in terms of photophysical properties, photostability and performance in fusions to help users choose the best-performing tools. Comparison of Cas9 activators in multiple species   pp563 - 567 Alejandro Chavez, Marcelle Tuttle, Benjamin W Pruitt, Ben Ewen-Campen, Raj Chari et al. doi:10.1038/nmeth.3871 A comparison of seven dCas9-based transcriptional activators shows that VPR, SAM, and Suntag perform best in cell lines from a variety of organisms. Brief Communications Top Flyception: imaging brain activity in freely walking fruit flies   pp569 - 572 Dhruv Grover, Takeo Katsuki and Ralph J Greenspan doi:10.1038/nmeth.3866 Flyception is a tracking and imaging system that enables the monitoring of brain activity in freely walking fruit flies, making the analysis of calcium dynamics possible in studies of neural mechanisms such as those that underlie social behaviors. Clonal genotype and population structure inference from single-cell tumor sequencing   pp573 - 576 Andrew Roth, Andrew McPherson, Emma Laks, Justina Biele, Damian Yap et al. doi:10.1038/nmeth.3867 The open-source Single Cell Genotyper software addresses common artifacts in single-cell sequencing data in order to robustly infer clonal genotypes, enabling the study of tumor heterogeneity and evolution. See also: News and Views by Navin & Chen Data-driven hypothesis weighting increases detection power in genome-scale multiple testing   pp577 - 580 Nikolaos Ignatiadis, Bernd Klaus, Judith B Zaugg and Wolfgang Huber doi:10.1038/nmeth.3885 For multiple hypothesis testing in genomics and other large-scale data analyses, the independent hypothesis weighting (IHW) approach uses data-driven P-value weight assignment to improve power while controlling the false discovery rate. DADA2: High-resolution sample inference from Illumina amplicon data   pp581 - 583 Benjamin J Callahan, Paul J McMurdie, Michael J Rosen, Andrew W Han, Amy Jo A Johnson et al. doi:10.1038/nmeth.3869 DADA2 is an open-source software package that denoises and removes sequencing errors from Illumina amplicon sequence data to distinguish microbial sample sequences differing by as little as a single nucleotide. Quantitative detection of low-abundance somatic structural variants in normal cells by high-throughput sequencing   pp584 - 586 Wilber Quispe-Tintaya, Tatyana Gorbacheva, Moonsook Lee, Sergei Makhortov, Vasily N Popov et al. doi:10.1038/nmeth.3893 Structural Variant Search, a combination of a chimera-free library preparation and a non-consensus-based SV-calling algorithm, enables the quantitative detection of rare somatic variants. Advertisement Nature Index 2016 Saudi Arabia Saudi Arabia had the largest growth of its region in the production of high-quality research in 2015 tracked by the Nature Index, propelling the country into a leading position. The country has now firmly set its sights on becoming a global player in science.  Click here to see how strong and fruitful collaborations with international powerhouses have been integral to Saudi Arabia’s rapid rise. The country has now firmly set its sights on becoming a global player in science. Produced with support from: KACST    Articles Top A hybrid approach for de novo human genome sequence assembly and phasing   pp587 - 590 Yulia Mostovoy, Michal Levy-Sakin, Jessica Lam, Ernest T Lam, Alex R Hastie et al. doi:10.1038/nmeth.3865 The combination of short-read sequence data, synthetic long reads and physical genome mapping allows for a phased de novo assembly of human genomes. A bacterial phytochrome-based optogenetic system controllable with near-infrared light   pp591 - 597 Andrii A Kaberniuk, Anton A Shemetov and Vladislav V Verkhusha doi:10.1038/nmeth.3864 Optogenetic tools such as a BphP1-PpsR2 pair can be harnessed to exert spatiotemporal control over signaling pathways or transcriptional events. The BphP1-PpsR2 system is activated by near-infrared light, making it suitable for in vivo applications. 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

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