3,587 results match your criteria Nature methods[Journal]


Publisher Correction: Noninvasive monitoring of single-cell mechanics by acoustic scattering.

Nat Methods 2019 Feb 19. Epub 2019 Feb 19.

Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.

The version of this paper originally published online contained an error in the x-axis of Fig. 2c: the LatB concentrations should be 0.4 and 1 μM, but during typesetting, the 1 μM label was incorrectly changed to 0. Read More

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http://dx.doi.org/10.1038/s41592-019-0354-6DOI Listing
February 2019

Noninvasive monitoring of single-cell mechanics by acoustic scattering.

Nat Methods 2019 Feb 11. Epub 2019 Feb 11.

Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.

The monitoring of mechanics in a single cell throughout the cell cycle has been hampered by the invasiveness of mechanical measurements. Here we quantify mechanical properties via acoustic scattering of waves from a cell inside a fluid-filled vibrating cantilever with a temporal resolution of < 1 min. Through simulations, experiments with hydrogels and the use of chemically perturbed cells, we show that our readout, the size-normalized acoustic scattering (SNACS), measures stiffness. Read More

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http://dx.doi.org/10.1038/s41592-019-0326-xDOI Listing
February 2019

Fast interpolation-based t-SNE for improved visualization of single-cell RNA-seq data.

Nat Methods 2019 Feb 11. Epub 2019 Feb 11.

Applied Mathematics Program, Yale University, New Haven, CT, USA.

t-distributed stochastic neighbor embedding (t-SNE) is widely used for visualizing single-cell RNA-sequencing (scRNA-seq) data, but it scales poorly to large datasets. We dramatically accelerate t-SNE, obviating the need for data downsampling, and hence allowing visualization of rare cell populations. Furthermore, we implement a heatmap-style visualization for scRNA-seq based on one-dimensional t-SNE for simultaneously visualizing the expression patterns of thousands of genes. Read More

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http://dx.doi.org/10.1038/s41592-018-0308-4DOI Listing
February 2019

Flow-enhanced vascularization and maturation of kidney organoids in vitro.

Nat Methods 2019 Feb 11. Epub 2019 Feb 11.

Renal Division, Brigham and Women's Hospital, Boston, MA, USA.

Kidney organoids derived from human pluripotent stem cells have glomerular- and tubular-like compartments that are largely avascular and immature in static culture. Here we report an in vitro method for culturing kidney organoids under flow on millifluidic chips, which expands their endogenous pool of endothelial progenitor cells and generates vascular networks with perfusable lumens surrounded by mural cells. We found that vascularized kidney organoids cultured under flow had more mature podocyte and tubular compartments with enhanced cellular polarity and adult gene expression compared with that in static controls. Read More

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http://www.nature.com/articles/s41592-019-0325-y
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http://dx.doi.org/10.1038/s41592-019-0325-yDOI Listing
February 2019
1 Read

In vivo RNA editing of point mutations via RNA-guided adenosine deaminases.

Nat Methods 2019 Feb 8. Epub 2019 Feb 8.

Department of Bioengineering, University of California, San Diego, CA, USA.

We present in vivo sequence-specific RNA base editing via adenosine deaminases acting on RNA (ADAR) enzymes with associated ADAR guide RNAs (adRNAs). To achieve this, we systematically engineered adRNAs to harness ADARs, and comprehensively evaluated the specificity and activity of the toolsets in vitro and in vivo via two mouse models of human disease. We anticipate that this platform will enable tunable and reversible engineering of cellular RNAs for diverse applications. Read More

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http://dx.doi.org/10.1038/s41592-019-0323-0DOI Listing
February 2019

How editors edit.

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Nat Methods 2019 Feb;16(2):135

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http://dx.doi.org/10.1038/s41592-019-0324-zDOI Listing
February 2019

T cell antigen discovery via trogocytosis.

Nat Methods 2019 Feb 28;16(2):183-190. Epub 2019 Jan 28.

Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.

T cell receptor (TCR) ligand discovery is essential for understanding and manipulating immune responses to tumors. We developed a cell-based selection platform for TCR ligand discovery that exploits a membrane transfer phenomenon called trogocytosis. We discovered that T cell membrane proteins are transferred specifically to target cells that present cognate peptide-major histocompatibility complex (MHC) molecules. Read More

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http://dx.doi.org/10.1038/s41592-018-0305-7DOI Listing
February 2019
1 Read

T cell antigen discovery via signaling and antigen-presenting bifunctional receptors.

Nat Methods 2019 Feb 28;16(2):191-198. Epub 2019 Jan 28.

Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.

CD8 T cells recognize and eliminate tumors in an antigen-specific manner. Despite progress in characterizing the antitumor T cell repertoire and function, the identification of target antigens remains a challenge. Here we describe the use of chimeric receptors called signaling and antigen-presenting bifunctional receptors (SABRs) in a cell-based platform for T cell receptor (TCR) antigen discovery. Read More

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http://dx.doi.org/10.1038/s41592-018-0304-8DOI Listing
February 2019

Optogenetic tools light up phase separation.

Authors:
Lei Tang

Nat Methods 2019 Feb;16(2):139

Nature Methods, .

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http://dx.doi.org/10.1038/s41592-019-0310-5DOI Listing
February 2019

Harnessing fungal bioluminescence.

Authors:
Rita Strack

Nat Methods 2019 Feb;16(2):140

Nature Methods, .

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http://dx.doi.org/10.1038/s41592-019-0311-4DOI Listing
February 2019

Creating epigenetic memory.

Authors:
Nicole Rusk

Nat Methods 2019 Feb;16(2):141

Nature Methods, .

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http://dx.doi.org/10.1038/s41592-019-0312-3DOI Listing
February 2019

Touch-and-go sensing.

Authors:
Karin Kuehnel

Nat Methods 2019 Feb;16(2):145

Nature Methods, .

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http://dx.doi.org/10.1038/s41592-019-0314-1DOI Listing
February 2019

Unbiased, whole-brain imaging of neural circuits.

Authors:
Nina Vogt

Nat Methods 2019 Feb;16(2):142

Nature Methods, .

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http://dx.doi.org/10.1038/s41592-019-0313-2DOI Listing
February 2019

Examining global RNA-binding proteomes.

Authors:
Lei Tang

Nat Methods 2019 Feb;16(2):144

Nature Methods, .

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http://dx.doi.org/10.1038/s41592-019-0321-2DOI Listing
February 2019

Tiny intracellular lasers.

Authors:
Rita Strack

Nat Methods 2019 Feb;16(2):144

Nature Methods, .

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http://dx.doi.org/10.1038/s41592-019-0322-1DOI Listing
February 2019

Tagged reprogramming.

Authors:
Nicole Rusk

Nat Methods 2019 Feb;16(2):144

Nature Methods, .

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http://dx.doi.org/10.1038/s41592-019-0320-3DOI Listing
February 2019

Magnetic sample orientation.

Authors:
Rita Strack

Nat Methods 2019 Feb;16(2):143

Nature Methods, .

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http://dx.doi.org/10.1038/s41592-019-0318-xDOI Listing
February 2019

Organoids that model the fetal placenta.

Authors:
Nina Vogt

Nat Methods 2019 Feb;16(2):144

Nature Methods, .

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http://dx.doi.org/10.1038/s41592-019-0319-9DOI Listing
February 2019

Pan-African genome.

Authors:
Nicole Rusk

Nat Methods 2019 Feb;16(2):143

Nature Methods, .

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http://dx.doi.org/10.1038/s41592-019-0317-yDOI Listing
February 2019

Large-scale electrophysiology with polymer-based electrodes.

Authors:
Nina Vogt

Nat Methods 2019 Feb;16(2):143

Nature Methods, .

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http://dx.doi.org/10.1038/s41592-019-0315-0DOI Listing
February 2019

Detecting changes in methylation landscape.

Authors:
Lei Tang

Nat Methods 2019 Feb;16(2):143

Nature Methods, .

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http://dx.doi.org/10.1038/s41592-019-0316-zDOI Listing
February 2019

A genetically encoded near-infrared fluorescent calcium ion indicator.

Nat Methods 2019 Feb 21;16(2):171-174. Epub 2019 Jan 21.

Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada.

We report an intensiometric, near-infrared fluorescent, genetically encoded calcium ion (Ca) indicator (GECI) with excitation and emission maxima at 678 and 704 nm, respectively. This GECI, designated NIR-GECO1, enables imaging of Ca transients in cultured mammalian cells and brain tissue with sensitivity comparable to that of currently available visible-wavelength GECIs. We demonstrate that NIR-GECO1 opens up new vistas for multicolor Ca imaging in combination with other optogenetic indicators and actuators. Read More

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http://dx.doi.org/10.1038/s41592-018-0294-6DOI Listing
February 2019
1 Read

A rocky road for the maturation of embryo-editing methods.

Authors:
Vivien Marx

Nat Methods 2019 Feb;16(2):147-150

Technology editor for Nature Methods, .

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http://dx.doi.org/10.1038/s41592-018-0307-5DOI Listing
February 2019

An online resource for GPCR structure determination and analysis.

Nat Methods 2019 Feb 21;16(2):151-162. Epub 2019 Jan 21.

Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark.

G-protein-coupled receptors (GPCRs) transduce physiological and sensory stimuli into appropriate cellular responses and mediate the actions of one-third of drugs. GPCR structural studies have revealed the general bases of receptor activation, signaling, drug action and allosteric modulation, but so far cover only 13% of nonolfactory receptors. We broadly surveyed the receptor modifications/engineering and methods used to produce all available GPCR crystal and cryo-electron microscopy (cryo-EM) structures, and present an interactive resource integrated in GPCRdb ( http://www. Read More

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http://dx.doi.org/10.1038/s41592-018-0302-xDOI Listing
February 2019
1 Read

Inferring bacterial recombination rates from large-scale sequencing datasets.

Nat Methods 2019 Feb 21;16(2):199-204. Epub 2019 Jan 21.

Department of Biology and Center for Genomics and Systems Biology, New York University, New York, NY, USA.

We present a robust, computationally efficient method ( https://github.com/kussell-lab/mcorr ) for inferring the parameters of homologous recombination in bacteria, which can be applied in diverse datasets, from whole-genome sequencing to metagenomic shotgun sequencing data. Using correlation profiles of synonymous substitutions, we determine recombination rates and diversity levels of the shared gene pool that has contributed to a given sample. Read More

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http://dx.doi.org/10.1038/s41592-018-0293-7DOI Listing
February 2019
1 Read

A discriminative learning approach to differential expression analysis for single-cell RNA-seq.

Nat Methods 2019 Feb 21;16(2):163-166. Epub 2019 Jan 21.

Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.

Single-cell RNA-seq makes it possible to characterize the transcriptomes of cell types across different conditions and to identify their transcriptional signatures via differential analysis. Our method detects changes in transcript dynamics and in overall gene abundance in large numbers of cells to determine differential expression. When applied to transcript compatibility counts obtained via pseudoalignment, our approach provides a quantification-free analysis of 3' single-cell RNA-seq that can identify previously undetectable marker genes. Read More

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http://dx.doi.org/10.1038/s41592-018-0303-9DOI Listing
February 2019
1 Read

Author Correction: A pH-correctable, DNA-based fluorescent reporter for organellar calcium.

Nat Methods 2019 Feb;16(2):205

Department of Chemistry, The University of Chicago, Chicago, IL, USA.

The originally published paper has been updated to include the following new reference, added as ref. 18: Albrecht, T., Zhao, Y. Read More

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http://www.nature.com/articles/s41592-019-0309-y
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http://dx.doi.org/10.1038/s41592-019-0309-yDOI Listing
February 2019
10 Reads

idtracker.ai: tracking all individuals in small or large collectives of unmarked animals.

Nat Methods 2019 Feb 14;16(2):179-182. Epub 2019 Jan 14.

Champalimaud Research, Champalimaud Center for the Unknown, Lisbon, Portugal.

Understanding of animal collectives is limited by the ability to track each individual. We describe an algorithm and software that extract all trajectories from video, with high identification accuracy for collectives of up to 100 individuals. idtracker. Read More

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http://dx.doi.org/10.1038/s41592-018-0295-5DOI Listing
February 2019

Gonzalo G. de Polavieja.

Authors:
Vivien Marx

Nat Methods 2019 Feb;16(2):137

Nature Methods, .

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http://dx.doi.org/10.1038/s41592-018-0306-6DOI Listing
February 2019

Metagenomic engineering of the mammalian gut microbiome in situ.

Nat Methods 2019 Feb 14;16(2):167-170. Epub 2019 Jan 14.

Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.

Engineering of microbial communities in open environments remains challenging. Here we describe a platform used to identify and modify genetically tractable mammalian microbiota by engineering community-wide horizontal gene transfer events in situ. With this approach, we demonstrate that diverse taxa in the mouse gut microbiome can be modified directly with a desired genetic payload. Read More

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http://dx.doi.org/10.1038/s41592-018-0301-yDOI Listing
February 2019

A robust and versatile platform for image scanning microscopy enabling super-resolution FLIM.

Nat Methods 2019 Feb 14;16(2):175-178. Epub 2019 Jan 14.

Molecular Microscopy and Spectroscopy, Istituto Italiano di Tecnologia, Genoa, Italy.

Image scanning microscopy (ISM) can improve the effective spatial resolution of confocal microscopy to its theoretical limit. However, current implementations are not robust or versatile, and are incompatible with fluorescence lifetime imaging (FLIM). We describe an implementation of ISM based on a single-photon detector array that enables super-resolution FLIM and improves multicolor, live-cell and in-depth imaging, thereby paving the way for a massive transition from confocal microscopy to ISM. Read More

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http://www.nature.com/articles/s41592-018-0291-9
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http://dx.doi.org/10.1038/s41592-018-0291-9DOI Listing
February 2019
2 Reads

Publisher Correction: Stability, affinity, and chromatic variants of the glutamate sensor iGluSnFR.

Nat Methods 2019 Feb;16(2):206

Howard Hughes Medical Institute (HHMI), Janelia Farm Research Campus, Ashburn, VA, USA.

In the version of this paper originally published, important figure labels in Fig. 3d were not visible. An image layer present in the authors' original figure that included two small dashed outlines and text labels indicating ROI 1 and ROI 2, as well as a scale bar and the name of the cell label, was erroneously altered during image processing. Read More

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http://dx.doi.org/10.1038/s41592-018-0300-zDOI Listing
February 2019

Author Correction: Genome-wide SWAp-Tag yeast libraries for proteome exploration.

Nat Methods 2019 Feb;16(2):205

Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.

The version of Supplementary Table 1 originally published online with this article contained incorrect localization annotations for one plate. This error has been corrected in the online Supplementary Information. Read More

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http://dx.doi.org/10.1038/s41592-018-0297-3DOI Listing
February 2019

Author Correction: Faster, sharper, and deeper: structured illumination microscopy for biological imaging.

Nat Methods 2019 Feb;16(2):205

Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA.

In the version of this Perspective originally published, Fig. 4g included an incorrect inset adapted from a different figure than the main image in the panel. This error has been corrected in the PDF and HTML versions of the paper. Read More

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http://dx.doi.org/10.1038/s41592-018-0296-4DOI Listing
February 2019

Author Correction: Comparing phenotypic variation between inbred and outbred mice.

Nat Methods 2019 Feb;16(2):206

Alan Edwards Centre for Research on Pain, McGill University, Montreal, Quebec, Canada.

In the version of this Comment originally published, the authors omitted a funding source. Grant 5 P50 DA039841 (to E.J. Read More

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http://dx.doi.org/10.1038/s41592-018-0298-2DOI Listing
February 2019

Publisher Correction: Sequence meets space.

Authors:
Tal Nawy

Nat Methods 2019 Feb;16(2):206

Nature Methods, .

The originally published version of this Research Highlight incorrectly stated that Guo-Cheng Yuan is at the University of California at Los Angeles; the correct affiliation is Dana-Farber Cancer Institute. The text has been corrected in the HTML and PDF versions of the paper. Read More

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http://dx.doi.org/10.1038/s41592-018-0299-1DOI Listing
February 2019

Controls let genomics experimenters drive with a dashboard.

Authors:
Vivien Marx

Nat Methods 2019 Jan;16(1):29-32

Nature Methods, .

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http://dx.doi.org/10.1038/s41592-018-0265-yDOI Listing
January 2019

Reliability of human cortical organoid generation.

Nat Methods 2019 Jan 20;16(1):75-78. Epub 2018 Dec 20.

Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, USA.

The differentiation of pluripotent stem cells in three-dimensional cultures can recapitulate key aspects of brain development, but protocols are prone to variable results. Here we differentiated multiple human pluripotent stem cell lines for over 100 d using our previously developed approach to generate brain-region-specific organoids called cortical spheroids and, using several assays, found that spheroid generation was highly reliable and consistent. We anticipate the use of this approach for large-scale differentiation experiments and disease modeling. Read More

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http://www.nature.com/articles/s41592-018-0255-0
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http://dx.doi.org/10.1038/s41592-018-0255-0DOI Listing
January 2019
3 Reads

On their best behavior.

Nat Methods 2019 Jan;16(1):5-8

Nature Methods, .

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http://dx.doi.org/10.1038/s41592-018-0277-7DOI Listing
January 2019

Building up bioluminescence.

Authors:
Rita Strack

Nat Methods 2019 Jan;16(1):20

Nature Methods, .

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http://dx.doi.org/10.1038/s41592-018-0274-xDOI Listing
January 2019

Single-cell proteomics.

Authors:
Allison Doerr

Nat Methods 2019 Jan;16(1):20

Nature Methods, .

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http://dx.doi.org/10.1038/s41592-018-0273-yDOI Listing
January 2019
1 Read

Antitumor T cells.

Authors:
Nicole Rusk

Nat Methods 2019 Jan;16(1):19

Nature Methods, .

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http://dx.doi.org/10.1038/s41592-018-0271-0DOI Listing
January 2019

Microbial interactions.

Authors:
Lei Tang

Nat Methods 2019 Jan;16(1):19

Nature Methods, .

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http://dx.doi.org/10.1038/s41592-018-0272-zDOI Listing
January 2019

Bending the genome.

Authors:
Nicole Rusk

Nat Methods 2019 Jan;16(1):18

Nature Methods, .

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http://dx.doi.org/10.1038/s41592-018-0270-1DOI Listing
January 2019

Deep learning in imaging.

Authors:
Rita Strack

Nat Methods 2019 Jan;16(1):17

Nature Methods, .

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http://dx.doi.org/10.1038/s41592-018-0267-9DOI Listing
January 2019

Liquid phase separation.

Authors:
Lei Tang

Nat Methods 2019 Jan;16(1):18

Nature Methods, .

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http://dx.doi.org/10.1038/s41592-018-0269-7DOI Listing
January 2019

Sensing neurotransmitters.

Authors:
Nina Vogt

Nat Methods 2019 Jan;16(1):17

Nature Methods, .

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http://dx.doi.org/10.1038/s41592-018-0268-8DOI Listing
January 2019

Precision genome editing.

Authors:
Rita Strack

Nat Methods 2019 Jan;16(1):21

Nature Methods, .

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http://dx.doi.org/10.1038/s41592-018-0286-6DOI Listing
January 2019

AFM in a split second.

Nat Methods 2019 Jan;16(1):24

Nature Structural and Molecular Biology, .

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http://dx.doi.org/10.1038/s41592-018-0289-3DOI Listing
January 2019

Membrane protein complexes exposed.

Authors:
Karin Kuehnel

Nat Methods 2019 Jan;16(1):27

Nature Methods, .

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http://dx.doi.org/10.1038/s41592-018-0290-xDOI Listing
January 2019