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969 Newest Publications in nature methods

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Automated, parallel mass spectrometry imaging and structural identification of lipids

21-May-2018 | Shane R. Ellis; Martin R. L. Paine; Gert B. Eijkel; Josch K. Pauling; Peter Husen; Mark W. Jervelund; Martin Hermans ..., Nature Methods, 2018

Automated, parallel mass spectrometry imaging and structural identification of lipids Automated, parallel mass spectrometry imaging and structural identification of lipids, Published online: 21 May 2018; doi:10.1038/s41592-018-0010-6 An automated method coupling tandem mass spectrometry with ...

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Author Correction: High-speed volumetric imaging of neuronal activity in freely moving rodents

21-May-2018 | Oliver Skocek; Tobias Nöbauer; Lukas Weilguny; Francisca Martínez Traub; Chuying Naomi Xia; Maxim I. Molod ..., Nature Methods, 2018

In the version of this Brief Communication originally published online, ref. 21 included details for a conference paper (Pegard, N. C. et al. Paper presented at Novel Techniques in Microscopy: Optics in the Life Sciences, Vancouver, BC, Canada, 12–15 April 2015). The correct reference is the ...

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Mapping the physical network of cellular interactions

21-May-2018 | Jean-Charles Boisset; Judith Vivié; Dominic Grün; Mauro J. Muraro; Anna Lyubimova; Alexander Oudenaarden, Nature Methods, 2018

A cell’s function is influenced by the environment, or niche, in which it resides. Studies of niches usually require assumptions about the cell types present, which impedes the discovery of new cell types or interactions. Here we describe ProximID, an approach for building a cellular network ...

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CRISPR off-target analysis in genetically engineered rats and mice

21-May-2018 | Keith R. Anderson; Maximilian Haeussler; Colin Watanabe; Vasantharajan Janakiraman; Jessica Lund; Zora Modrusan; Jer ..., Nature Methods, 2018

Despite widespread use of CRISPR, comprehensive data on the frequency and impact of Cas9-mediated off-targets in modified rodents are limited. Here we present deep-sequencing data from 81 genome-editing projects on mouse and rat genomes at 1,423 predicted off-target sites, 32 of which were ...

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C-BERST: defining subnuclear proteomic landscapes at genomic elements with dCas9–APEX2

07-May-2018 | Xin D. Gao; Li-Chun Tu; Aamir Mir; Tomás Rodriguez; Yuehe Ding; John Leszyk; Job Dekker; Scott A. Shaffer; Lihu ..., Nature Methods, 2018

Mapping proteomic composition at distinct genomic loci in living cells has been a long-standing challenge. Here we report that dCas9–APEX2 biotinylation at genomic elements by restricted spatial tagging (C-BERST) allows the rapid, unbiased mapping of proteomes near defined genomic loci, as ...

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BoxCar acquisition method enables single-shot proteomics at a depth of 10,000 proteins in 100 minutes

07-May-2018 | Florian Meier; Philipp E. Geyer; Sebastian Virreira Winter; Juergen Cox; Matthias Mann, Nature Methods, 2018

Great advances have been made in sensitivity and acquisition speed on the Orbitrap mass analyzer, enabling increasingly deep proteome coverage. However, these advances have been mainly limited to the MS2 level, whereas ion beam sampling for the MS1 scans remains extremely inefficient. Here we ...

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High-speed volumetric imaging of neuronal activity in freely moving rodents

07-May-2018 | Oliver Skocek; Tobias Nöbauer; Lukas Weilguny; Francisca Martínez Traub; Chuying Naomi Xia; Maxim I. Molod ..., Nature Methods, 2018

Thus far, optical recording of neuronal activity in freely behaving animals has been limited to a thin axial range. We present a head-mounted miniaturized light-field microscope (MiniLFM) capable of capturing neuronal network activity within a volume of 700 × 600 × 360 µm3 at 16 Hz in the ...

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Single-shot super-resolution total internal reflection fluorescence microscopy

07-May-2018 | Min Guo; Panagiotis Chandris; John Paul Giannini; Adam J. Trexler; Robert Fischer; Jiji Chen; Harshad D. Vishwasrao; ..., Nature Methods, 2018

Single-shot super-resolution total internal reflection fluorescence microscopy Single-shot super-resolution total internal reflection fluorescence microscopy, Published online: 07 May 2018; doi:10.1038/s41592-018-0004-4 Instant structured illumination and total internal reflection fluorescence ...

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Discovery of proteins associated with a predefined genomic locus via dCas9–APEX-mediated proximity labeling

07-May-2018 | Samuel A. Myers; Jason Wright; Ryan Peckner; Brian T. Kalish; Feng Zhang; Steven A. Carr, Nature Methods, 2018

Discovery of proteins associated with a predefined genomic locus via dCas9–APEX-mediated proximity labeling Discovery of proteins associated with a predefined genomic locus via dCas9–APEX-mediated proximity labeling, Published online: 07 May 2018; doi:10.1038/s41592-018-0007-1 After ...

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Picky comprehensively detects high-resolution structural variants in nanopore long reads

30-Apr-2018 | Liang Gong; Chee-Hong Wong; Wei-Chung Cheng; Harianto Tjong; Francesca Menghi; Chew Yee Ngan; Edison T. Liu; Chia-Li ..., Nature Methods, 2018

Acquired genomic structural variants (SVs) are major hallmarks of cancer genomes, but they are challenging to reconstruct from short-read sequencing data. Here we exploited the long reads of the nanopore platform using our customized pipeline, Picky ( ...

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