Nature Methods Contents: February 2018, Volume 15 No 2 pp 91 - 149

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Advertisement Can you trust your Antibody? Implications for disease research. A recent publication in Scientific Reports rigorously tested nine commercially available antibodies for specificity and sensitivity and found that only one, from Cell Signaling Technology, met all validation criteria. Read this open-access article to explore the potentially serious implications of non-specific antibodies and disease research. Read more now.   TABLE OF CONTENTS February 2018 Volume 15, Issue 2 Editorial This Month Research Highlights Technology Feature Resource Brief Communications Articles Application Note   Advertisement   NSK Manipulation System  Simplify and automate your micromanipulator workflow. Easy-to-use, PC-based system enables inexperienced operators to perform high-skill tasks, and automation reduces repetition and increases efficiency. Proprietary piezo-actuator enables highly accurate cell perforation with minimal damage. Ideal for ICSI, DNA injection, and research applications.   Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement All of your valuable samples deserve the best treatment.  With continuous quality assurance throughout the entire production process, you are guaranteed the highest quality consumables for ultimate reliability and reproducibility of your precious experiments. Eppendorf consumables — quality beyond measure.   Advertisement Nature Collection: 2017 Nobel Prize in Chemistry  Nature Research present this Collection of articles celebrating the 2017 Nobel Prize in Chemistry to Jacques Dubochet, Joachim Frank and Richard Henderson, recognised "for developing cryo-electron microscopy for the high-resolution structure determination of biomolecules in solution".  Access here >> Produced with support from  Thermo Fisher Scientific    Editorial Top The good referee   p91 doi:10.1038/nmeth.4603 Referees provide an invaluable service in advancing science. We offer some food for thought about how to effectively peer review methods papers.   This Month Top The Author File: Jennifer Phillips-Cremins   p93 Vivien Marx doi:10.1038/nmeth.4584 To better explore how genomes fold takes disparate fields and a love of math.   Research Highlights Top Putting a stamp on single cells Virus stamping can target single cells in complex tissues, both in culture and in vivo. Off-the-shelf super-resolution microscopy in whole cells The combination of DNA-PAINT and spinning-disk confocal microscopy makes super-resolution microscopy in whole cells affordable and easy to implement. Humanized yeast—erasing 1.3 billion years of evolution Cellular engineering that allows budding yeast to survive with the four core human histones opens the door to exploring the function of histone variants and their modifications. Epigenetic profiles to classify bacterial sequences Methylation patterns can help determine the origin of metagenomic sequences. Automated brain mapping A computational framework enables automated annotation, analysis, and sharing of mouse brain data at single-cell resolution. Methods in Brief Top Single-organelle sequencing | Myelin quantification at nanoscale | Assessing protein activity in single cells | Single-molecule imaging and force spectroscopy at extended depth Tools in Brief Top Big Papi uncovers genetic interactions | A colorful series of bioorthogonal probes | Biobanking breast cancers | Cell-type-specific proteomics in the in vivo mouse brain Methods JOBS of the week Postdoctoral Fellow University of Pennsylvania - Perelman School of Medicine Postdoctoral Fellow University Health Network (Toronto) Bioinformatician / Computational Biologist (PhD) University of Helsinki Postdoctoral Fellowship The University of Texas MD Anderson Cancer Center More Science jobs from Methods EVENT Materials, Methods & Technologies 2018, 20th International Conference 26.06.18 Elenite, Bulgaria More science events from Technology Feature Top Meet some code-breakers of noncoding RNAs   pp103 - 106 Vivien Marx doi:10.1038/nmeth.4594 The regulome—the part of the genome that regulates function—includes noncoding RNAs with varied functions yet to be deciphered.   Resource Top Interactome INSIDER: a structural interactome browser for genomic studies   pp107 - 114 Michael J Meyer, Juan Felipe Beltrán, Siqi Liang, Robert Fragoza, Aaron Rumack et al. doi:10.1038/nmeth.4540 Based on machine learning-predicted interaction interfaces, this resource enables interpretation of genomic variants and disease mutations in light of the protein-protein interactome.   Brief Communications Top Mapping the 3D orientation of piconewton integrin traction forces   pp115 - 118 Joshua M Brockman, Aaron T Blanchard, Victor Pui-Yan Ma, Wallace D Derricotte, Yun Zhang et al. doi:10.1038/nmeth.4536 Molecular force microscopy employs a combination of fluorescence polarization microscopy and molecular tension sensors to determine the orientation of cellular forces. The technology is demonstrated for integrin-mediated forces in platelets and fibroblasts.   Detecting hierarchical genome folding with network modularity   pp119 - 122 Heidi K Norton, Daniel J Emerson, Harvey Huang, Jesi Kim, Katelyn R Titus et al. doi:10.1038/nmeth.4560 3DNetMod identifies nested topologically associating domains (TADs) and subTADs from Hi-C data.   GIGGLE: a search engine for large-scale integrated genome analysis   pp123 - 126 Ryan M Layer, Brent S Pedersen, Tonya DiSera, Gabor T Marth, Jason Gertz et al. doi:10.1038/nmeth.4556 GIGGLE is a genome interval search engine that enables extremely fast queries of genome features from thousands of genome annotation sets.   Articles Top Biotinylation by antibody recognition—a method for proximity labeling   pp127 - 133 Daniel Z Bar, Kathleen Atkatsh, Urraca Tavarez, Michael R Erdos, Yosef Gruenbaum et al. doi:10.1038/nmeth.4533 Proximity-based labeling represents a useful approach for mapping protein environment, but current methods for this are limited to application to cell lines. This approach is now extended to primary human tissues with a method that uses antibodies to guide proximity labeling.   BRCA-deficient mouse mammary tumor organoids to study cancer-drug resistance   pp134 - 140 Alexandra A Duarte, Ewa Gogola, Norman Sachs, Marco Barazas, Stefano Annunziato et al. doi:10.1038/nmeth.4535 Mouse tumor organoids are characterized as a model to study tumor biology and drug resistance.   Resolving systematic errors in widely used enhancer activity assays in human cells   pp141 - 149 Felix Muerdter, Łukasz M Boryń, Ashley R Woodfin, Christoph Neumayr, Martina Rath et al. doi:10.1038/nmeth.4534 Using the ORI of plasmids used in enhancer assays as the sole core promoter and inhibiting the interferon I response triggered by plasmid transfection greatly reduces false positive and negative results in single-candidate and massively parallel enhancer assays and enables genome-wide enhancer screens.   Advertisement Animation on CRISPR: Gene editing and beyond  The CRISPR-Cas9 system has revolutionised gene editing, but cutting DNA isn't all it can do. This Animation, from Nature Methods, explores where CRISPR might be headed next.  Watch the Animation >>  Produced with support from:  Dharmacon    Application Note Top Making difficult things easier and simpler with a manipulation system      Top Advertisement Nature Mentoring Collection  Offering advice and support to scientist mentors and their mentees  Access the Collection    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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