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Journal Cover Nature Methods
  [SJR: 21.715]   [H-I: 189]   [275 followers]  Follow
    
   Full-text available via subscription Subscription journal
   ISSN (Print) 1548-7091 - ISSN (Online) 1548-7105
   Published by NPG Homepage  [135 journals]
  • An homage to unusual creatures
    • Pages: 827 - 827
      Abstract: The life sciences are dominated by a handful of model organisms, but unusual creatures have their place in biological research as well.
      Citation: Nature Methods 14, 827 (2017)
      PubDate: 2017-08-31
      DOI: 10.1038/nmeth.4428
      Issue No: Vol. 14, No. 9 (2017)
       
  • The Author File: Marlon Stoeckius
    • Authors: Vivien Marx
      Pages: 829 - 829
      Abstract: Combining approaches from “different worlds” to learn more from a single cell.
      Citation: Nature Methods 14, 829 (2017)
      PubDate: 2017-08-31
      DOI: 10.1038/nmeth.4406
      Issue No: Vol. 14, No. 9 (2017)
       
  • GUIDES: sgRNA design for loss-of-function screens
    • Nature Methods 14, 831 (2017). doi:10.1038/nmeth.4423

      Authors: Joshua A Meier, Feng Zhang & Neville E Sanjana

      Nature Methods 14, 831 (2017)2017-08-31
      DOI: 10.1038/nmeth.4423
      Issue No: Vol. 14, No. 9 (2017)
       
  • Microscopy: Nanoscopic imaging that lasts
    • Authors: Rita Strack
      Pages: 833 - 833
      Abstract: Spontaneously blinking membrane probes enable live-cell super-resolution imaging for up to half an hour.
      Citation: Nature Methods 14, 833 (2017)
      PubDate: 2017-08-31
      DOI: 10.1038/nmeth.4417
      Issue No: Vol. 14, No. 9 (2017)
       
  • Biochemistry: Protein folding studies go global
    • Authors: Allison Doerr
      Pages: 834 - 835
      Abstract: A large-scale approach to analyze how protein sequence determines folding provides new insights into an old question.
      Citation: Nature Methods 14, 834 (2017)
      PubDate: 2017-08-31
      DOI: 10.1038/nmeth.4418
      Issue No: Vol. 14, No. 9 (2017)
       
  • Stem cells: Many paths from a XEN-like state
    • Authors: Tal Nawy
      Pages: 834 - 835
      Abstract: An intermediate cell state of chemical reprogramming can be induced to convert directly between cell types.
      Citation: Nature Methods 14, 834 (2017)
      PubDate: 2017-08-31
      DOI: 10.1038/nmeth.4419
      Issue No: Vol. 14, No. 9 (2017)
       
  • Neuroscience: On-demand rabies
    • Authors: Irene Jarchum
      Pages: 836 - 836
      Abstract: A self-inactivating rabies virus enables long-term tracing of neural networks without toxicity.
      Citation: Nature Methods 14, 836 (2017)
      PubDate: 2017-08-31
      DOI: 10.1038/nmeth.4420
      Issue No: Vol. 14, No. 9 (2017)
       
  • Genomics: CHAMP quantifies DNA-protein binding
    • Nature Methods 14, 837 (2017). doi:10.1038/nmeth.4409

      Nature Methods 14, 837 (2017)2017-08-31
      DOI: 10.1038/nmeth.4409
      Issue No: Vol. 14, No. 9 (2017)
       
  • Neuroscience: FAST imaging of whole brains
    • Nature Methods 14, 837 (2017). doi:10.1038/nmeth.4410

      Nature Methods 14, 837 (2017)2017-08-31
      DOI: 10.1038/nmeth.4410
      Issue No: Vol. 14, No. 9 (2017)
       
  • Epigenetics: Chromosome accessibility and methylation status in one
    • Nature Methods 14, 837 (2017). doi:10.1038/nmeth.4411

      Nature Methods 14, 837 (2017)2017-08-31
      DOI: 10.1038/nmeth.4411
      Issue No: Vol. 14, No. 9 (2017)
       
  • Genetics: Limits of gene drives
    • Nature Methods 14, 837 (2017). doi:10.1038/nmeth.4412

      Nature Methods 14, 837 (2017)2017-08-31
      DOI: 10.1038/nmeth.4412
      Issue No: Vol. 14, No. 9 (2017)
       
  • Imaging: Refractive index matching in living samples
    • Nature Methods 14, 838 (2017). doi:10.1038/nmeth.4413

      Nature Methods 14, 838 (2017)2017-08-31
      DOI: 10.1038/nmeth.4413
      Issue No: Vol. 14, No. 9 (2017)
       
  • Chemical biology: A chemical genetic screening system for yeast
    • Nature Methods 14, 838 (2017). doi:10.1038/nmeth.4414

      Nature Methods 14, 838 (2017)2017-08-31
      DOI: 10.1038/nmeth.4414
      Issue No: Vol. 14, No. 9 (2017)
       
  • Microscopy: Tools for mining microscopy data
    • Nature Methods 14, 838 (2017). doi:10.1038/nmeth.4415

      Nature Methods 14, 838 (2017)2017-08-31
      DOI: 10.1038/nmeth.4415
      Issue No: Vol. 14, No. 9 (2017)
       
  • Molecular engineering: Affimers as research reagents
    • Nature Methods 14, 838 (2017). doi:10.1038/nmeth.4416

      Nature Methods 14, 838 (2017)2017-08-31
      DOI: 10.1038/nmeth.4416
      Issue No: Vol. 14, No. 9 (2017)
       
  • Imaging: Gold glitters in transparent tissue
    • Authors: Zachary J Lapin
      Pages: 839 - 839
      Abstract: Through scattering, in situ metal particle growth enables biomolecule visualization within tissue.
      Citation: Nature Methods 14, 839 (2017)
      PubDate: 2017-08-31
      DOI: 10.1038/nmeth.4421
      Issue No: Vol. 14, No. 9 (2017)
       
  • Genomics: What comes first—genomic structure or function'
    • Authors: Nicole Rusk
      Pages: 841 - 841
      Abstract: CRISPR-mediated chromatin looping provides insight into the effect of genomic structure on gene expression.
      Citation: Nature Methods 14, 841 (2017)
      PubDate: 2017-08-31
      DOI: 10.1038/nmeth.4422
      Issue No: Vol. 14, No. 9 (2017)
       
  • Structural biology: doors open at the European XFEL
    • Authors: Vivien Marx
      Pages: 843 - 846
      Abstract: X-ray beams at 27,000 pulses per second promise high-resolution views of macromolecules.
      Citation: Nature Methods 14, 843 (2017)
      PubDate: 2017-08-31
      DOI: 10.1038/nmeth.4394
      Issue No: Vol. 14, No. 9 (2017)
       
  • Data-analysis strategies for image-based cell profiling
    • Authors: Juan C Caicedo, Sam Cooper, Florian Heigwer, Scott Warchal, Peng Qiu, Csaba Molnar, Aliaksei S Vasilevich, Joseph D Barry, Harmanjit Singh Bansal, Oren Kraus, Mathias Wawer, Lassi Paavolainen, Markus D Herrmann, Mohammad Rohban, Jane Hung, Holger Hennig, John Concannon, Ian Smith, Paul A Clemons, Shantanu Singh, Paul Rees, Peter Horvath, Roger G Linington, Anne E Carpenter
      Pages: 849 - 863
      Abstract: This Review covers the steps required to create high-quality image-based profiles from high-throughput microscopy images.
      Citation: Nature Methods 14, 849 (2017)
      PubDate: 2017-08-31
      DOI: 10.1038/nmeth.4397
      Issue No: Vol. 14, No. 9 (2017)
       
  • Simultaneous epitope and transcriptome measurement in single cells
    • Authors: Marlon Stoeckius, Christoph Hafemeister, William Stephenson, Brian Houck-Loomis, Pratip K Chattopadhyay, Harold Swerdlow, Rahul Satija, Peter Smibert
      Pages: 865 - 868
      Abstract: Using established high-throughput single-cell RNA-seq platforms, CITE-seq combines highly multiplexed, antibody-based protein marker quantification with unbiased transcriptome profiling for thousands of single cells.
      Citation: Nature Methods 14, 865 (2017)
      PubDate: 2017-07-31
      DOI: 10.1038/nmeth.4380
      Issue No: Vol. 14, No. 9 (2017)
       
  • Adaptive optics improves multiphoton super-resolution imaging
    • Authors: Wei Zheng, Yicong Wu, Peter Winter, Robert Fischer, Damian Dalle Nogare, Amy Hong, Chad McCormick, Ryan Christensen, William P Dempsey, Don B Arnold, Joshua Zimmerberg, Ajay Chitnis, James Sellers, Clare Waterman, Hari Shroff
      Pages: 869 - 872
      Abstract: Adaptive optics and two-photon instant structured illumination microscopy are combined to provide improved super-resolution imaging within optically aberrating biological samples.
      Citation: Nature Methods 14, 869 (2017)
      PubDate: 2017-06-19
      DOI: 10.1038/nmeth.4337
      Issue No: Vol. 14, No. 9 (2017)
       
  • histoCAT: analysis of cell phenotypes and interactions in multiplex image
           cytometry data
    • Authors: Denis Schapiro, Hartland W Jackson, Swetha Raghuraman, Jana R Fischer, Vito R T Zanotelli, Daniel Schulz, Charlotte Giesen, Raúl Catena, Zsuzsanna Varga, Bernd Bodenmiller
      Pages: 873 - 876
      Abstract: The histology topography cytometry analysis toolbox (histoCAT) enables quantitative analysis and exploration of highly multiplexed imaging data for better understanding of individual cells in the context of tissue architecture.
      Citation: Nature Methods 14, 873 (2017)
      PubDate: 2017-08-07
      DOI: 10.1038/nmeth.4391
      Issue No: Vol. 14, No. 9 (2017)
       
  • Conformational landscape of a virus by single-particle X-ray scattering
    • Authors: Ahmad Hosseinizadeh, Ghoncheh Mashayekhi, Jeremy Copperman, Peter Schwander, Ali Dashti, Reyhaneh Sepehr, Russell Fung, Marius Schmidt, Chun Hong Yoon, Brenda G Hogue, Garth J Williams, Andrew Aquila, Abbas Ourmazd
      Pages: 877 - 881
      Abstract: A 9-nm-resolution structure of PR772 virus and a movie of its continuous conformational changes are determined from single-particle X-ray scattering data.
      Citation: Nature Methods 14, 877 (2017)
      PubDate: 2017-08-14
      DOI: 10.1038/nmeth.4395
      Issue No: Vol. 14, No. 9 (2017)
       
  • Large-scale mapping of cortical synaptic projections with extracellular
           electrode arrays
    • Authors: Mark Shein-Idelson, Lorenz Pammer, Mike Hemberger, Gilles Laurent
      Pages: 882 - 890
      Abstract: Combining multielectrode arrays with an ex vivo preparation of the turtle brain allows identification of neurons as excitatory or inhibitory and mapping of their axonal projections.
      Citation: Nature Methods 14, 882 (2017)
      PubDate: 2017-08-14
      DOI: 10.1038/nmeth.4393
      Issue No: Vol. 14, No. 9 (2017)
       
  • Rapidly inducible Cas9 and DSB-ddPCR to probe editing kinetics
    • Authors: John C Rose, Jason J Stephany, William J Valente, Bridget M Trevillian, Ha V Dang, Jason H Bielas, Dustin J Maly, Douglas M Fowler
      Pages: 891 - 896
      Abstract: A rapidly inducible, autoinhibited SpCas9 and quantitative assessment of double-strand cleavage and indel formation allow insights into Cas9 kinetics in cell lines.
      Citation: Nature Methods 14, 891 (2017)
      PubDate: 2017-07-24
      DOI: 10.1038/nmeth.4368
      Issue No: Vol. 14, No. 9 (2017)
       
  • M3: an integrative framework for structure determination of molecular
           machines
    • Authors: Ezgi Karaca, João P G L M Rodrigues, Andrea Graziadei, Alexandre M J J Bonvin, Teresa Carlomagno
      Pages: 897 - 902
      Abstract: Structure determination of large molecular machines is facilitated by M3, a broadly applicable and user-friendly modeling method that takes diverse structural and biochemical data as inputs.
      Citation: Nature Methods 14, 897 (2017)
      PubDate: 2017-08-14
      DOI: 10.1038/nmeth.4392
      Issue No: Vol. 14, No. 9 (2017)
       
  • PECAN: library-free peptide detection for data-independent acquisition
           tandem mass spectrometry data
    • Authors: Ying S Ting, Jarrett D Egertson, James G Bollinger, Brian C Searle, Samuel H Payne, William Stafford Noble, Michael J MacCoss
      Pages: 903 - 908
      Abstract: A library-free, peptide-centric search tool, PECAN, robustly identifies peptides from data-independent acquisition mass-spectrometry-based proteomics data.
      Citation: Nature Methods 14, 903 (2017)
      PubDate: 2017-08-07
      DOI: 10.1038/nmeth.4390
      Issue No: Vol. 14, No. 9 (2017)
       
  • Informed-Proteomics: open-source software package for top-down proteomics
    • Authors: Jungkap Park, Paul D Piehowski, Christopher Wilkins, Mowei Zhou, Joshua Mendoza, Grant M Fujimoto, Bryson C Gibbons, Jared B Shaw, Yufeng Shen, Anil K Shukla, Ronald J Moore, Tao Liu, Vladislav A Petyuk, Nikola Tolić, Ljiljana Paša-Tolić, Richard D Smith, Samuel H Payne, Sangtae Kim
      Pages: 909 - 914
      Abstract: Informed-Proteomics, a software suite for top-down proteomics analysis, consists of a high-accuracy liquid chromatography–mass spectrometry feature-finding algorithm, an efficient database search tool, and an interactive results viewer.
      Citation: Nature Methods 14, 909 (2017)
      PubDate: 2017-08-07
      DOI: 10.1038/nmeth.4388
      Issue No: Vol. 14, No. 9 (2017)
       
  • Genome-wide reconstruction of complex structural variants using read
           clouds
    • Authors: Noah Spies, Ziming Weng, Alex Bishara, Jennifer McDaniel, David Catoe, Justin M Zook, Marc Salit, Robert B West, Serafim Batzoglou, Arend Sidow
      Pages: 915 - 920
      Abstract: GROC-SVs enables the accurate detection and reconstruction of large and complex structural variants from read clouds generated by the 10x Genomics platform and subsequent Illumina sequencing.
      Citation: Nature Methods 14, 915 (2017)
      PubDate: 2017-07-17
      DOI: 10.1038/nmeth.4366
      Issue No: Vol. 14, No. 9 (2017)
       
  • Statistical control of peptide and protein error rates in large-scale
           targeted data-independent acquisition analyses
    • Authors: George Rosenberger, Isabell Bludau, Uwe Schmitt, Moritz Heusel, Christie L Hunter, Yansheng Liu, Michael J MacCoss, Brendan X MacLean, Alexey I Nesvizhskii, Patrick G A Pedrioli, Lukas Reiter, Hannes L Röst, Stephen Tate, Ying S Ting, Ben C Collins, Ruedi Aebersold
      Pages: 921 - 927
      Abstract: The statistical concepts for false discovery rate control long applied in the field of data-dependent acquisition (DDA) mass spectrometry-based proteomics can be adapted for the emerging technique of data-independent acquisition (DIA) mass spectrometry.
      Citation: Nature Methods 14, 921 (2017)
      PubDate: 2017-08-21
      DOI: 10.1038/nmeth.4398
      Issue No: Vol. 14, No. 9 (2017)
       
  • Corrigendum: Classification and regression trees
    • Nature Methods 14, 928 (2017). doi:10.1038/nmeth0917-928a

      Author: Martin Krzywinksi & Naomi Altman

      Nature Methods 14, 928 (2017)2017-08-31
      DOI: 10.1038/nmeth0917-928a
      Issue No: Vol. 14, No. 9 (2017)
       
  • Erratum: Genetically encoded fluorescent sensors reveal dynamic regulation
           of NADPH metabolism
    • Nature Methods 14, 928 (2017). doi:10.1038/nmeth0917-928b

      Author: Rongkun Tao, Yuzheng Zhao, Huanyu Chu, Aoxue Wang, Jiahuan Zhu, Xianjun Chen, Yejun Zou, Mei Shi, Renmei Liu, Ni Su, Jiulin Du, Hai-Meng Zhou, Linyong Zhu, Xuhong Qian, Haiyan Liu, Joseph Loscalzo & Yi Yang

      Nature Methods 14, 928 (2017)2017-08-31
      DOI: 10.1038/nmeth0917-928b
      Issue No: Vol. 14, No. 9 (2017)
       
  • Multielectrodes join the connectome
    • Authors: Harvey A Swadlow, Jose-Manuel Alonso
      Pages: 847 - 848
      Abstract: High-density multielectrode arrays in turtle cortex allow parallel assessment of functional and structural connectomics.
      Citation: Nature Methods 14, 847 (2017)
      DOI: 10.1038/nmeth.4424
      Issue No: Vol. 14, No. 9
       
 
 
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