3,655 results match your criteria Nature methods[Journal]


Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells.

Nat Methods 2019 Apr 22. Epub 2019 Apr 22.

Technology Innovation Laboratory, New York Genome Center, New York, NY, USA.

Multimodal single-cell assays provide high-resolution snapshots of complex cell populations, but are mostly limited to transcriptome plus an additional modality. Here, we describe expanded CRISPR-compatible cellular indexing of transcriptomes and epitopes by sequencing (ECCITE-seq) for the high-throughput characterization of at least five modalities of information from each single cell. We demonstrate application of ECCITE-seq to multimodal CRISPR screens with robust direct single-guide RNA capture and to clonotype-aware multimodal phenotyping of cancer samples. Read More

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http://www.nature.com/articles/s41592-019-0392-0
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http://dx.doi.org/10.1038/s41592-019-0392-0DOI Listing
April 2019
1 Read

Capturing the dynamics of genome replication on individual ultra-long nanopore sequence reads.

Nat Methods 2019 Apr 22. Epub 2019 Apr 22.

Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.

Replication of eukaryotic genomes is highly stochastic, making it difficult to determine the replication dynamics of individual molecules with existing methods. We report a sequencing method for the measurement of replication fork movement on single molecules by detecting nucleotide analog signal currents on extremely long nanopore traces (D-NAscent). Using this method, we detect 5-bromodeoxyuridine (BrdU) incorporated by Saccharomyces cerevisiae to reveal, at a genomic scale and on single molecules, the DNA sequences replicated during a pulse-labeling period. Read More

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http://dx.doi.org/10.1038/s41592-019-0394-yDOI Listing

Engineered peptide barcodes for in-depth analyses of binding protein libraries.

Nat Methods 2019 Apr 22. Epub 2019 Apr 22.

Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.

Binding protein generation typically relies on laborious screening cascades that process candidate molecules individually. We have developed NestLink, a binder selection and identification technology able to biophysically characterize thousands of library members at once without the need to handle individual clones at any stage of the process. NestLink uses genetically encoded barcoding peptides termed flycodes, which were designed for maximal detectability by mass spectrometry and support accurate deep sequencing. Read More

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http://www.nature.com/articles/s41592-019-0389-8
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http://dx.doi.org/10.1038/s41592-019-0389-8DOI Listing
April 2019
1 Read

Publisher Correction: A cheminformatics approach to characterize metabolomes in stable-isotope-labeled organisms.

Nat Methods 2019 Apr 16. Epub 2019 Apr 16.

RIKEN Center for Sustainable Resource Science, Yokohama, Japan.

In the originally published Supplementary Information for this paper, the files presented as Supplementary Tables 3, 4, and 7 were duplicates of Supplementary Tables 5, 6, and 9, respectively. All Supplementary Table files are now correct online. Read More

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http://dx.doi.org/10.1038/s41592-019-0423-xDOI Listing

A photocleavable surfactant for top-down proteomics.

Nat Methods 2019 Apr 15. Epub 2019 Apr 15.

Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA.

We report the identification of a photocleavable anionic surfactant, 4-hexylphenylazosulfonate (Azo), which can be rapidly degraded by ultraviolet irradiation, for top-down proteomics. Azo can effectively solubilize proteins with performance comparable to that of sodium dodecyl sulfate (SDS) and is compatible with mass spectrometry. Azo-aided top-down proteomics enables the solubilization of membrane proteins for comprehensive characterization of post-translational modifications. Read More

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http://dx.doi.org/10.1038/s41592-019-0391-1DOI Listing

Unbiased screen of RNA tailing activities reveals a poly(UG) polymerase.

Nat Methods 2019 Apr 15. Epub 2019 Apr 15.

Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.

Ribonucleotidyl transferases (rNTases) add untemplated ribonucleotides to diverse RNAs. We have developed TRAID-seq, a screening strategy in Saccharomyces cerevisiae to identify sequences added to a reporter RNA at single-nucleotide resolution by overexpressed candidate enzymes from different organisms. The rNTase activities of 22 previously unexplored enzymes were determined. Read More

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http://www.nature.com/articles/s41592-019-0370-6
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http://dx.doi.org/10.1038/s41592-019-0370-6DOI Listing
April 2019
2 Reads

Integrated transcriptomic-genomic tool Texomer profiles cancer tissues.

Nat Methods 2019 Apr 15. Epub 2019 Apr 15.

Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

Profiling of both the genome and the transcriptome promises a comprehensive, functional readout of a tissue sample, yet analytical approaches are required to translate the increased data dimensionality, heterogeneity and complexity into patient benefits. We developed a statistical approach called Texomer ( https://github.com/KChen-lab/Texomer ) that performs allele-specific, tumor-deconvoluted transcriptome-exome integration of autologous bulk whole-exome and transcriptome sequencing data. Read More

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http://dx.doi.org/10.1038/s41592-019-0388-9DOI Listing

Stein Aerts.

Authors:
Vivien Marx

Nat Methods 2019 Apr 10. Epub 2019 Apr 10.

Nature Methods, .

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http://dx.doi.org/10.1038/s41592-019-0397-8DOI Listing

Author Correction: Two-level factorial experiments.

Nat Methods 2019 Apr 9. Epub 2019 Apr 9.

Department of Statistics, The Pennsylvania State University, University Park, PA, USA.

The initially published paper contained an error in Table 1: in the rightmost column (y), "0.09" should have been "-0.09. Read More

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http://dx.doi.org/10.1038/s41592-019-0405-zDOI Listing

Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software.

Nat Methods 2019 Apr 8. Epub 2019 Apr 8.

Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle, UK.

With the widespread uptake of two-dimensional (2D) and three-dimensional (3D) single-molecule localization microscopy (SMLM), a large set of different data analysis packages have been developed to generate super-resolution images. In a large community effort, we designed a competition to extensively characterize and rank the performance of 2D and 3D SMLM software packages. We generated realistic simulated datasets for popular imaging modalities-2D, astigmatic 3D, biplane 3D and double-helix 3D-and evaluated 36 participant packages against these data. Read More

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http://dx.doi.org/10.1038/s41592-019-0364-4DOI Listing

cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data.

Nat Methods 2019 Apr 8. Epub 2019 Apr 8.

VIB Center for Brain & Disease Research, Leuven, Belgium.

We present cisTopic, a probabilistic framework used to simultaneously discover coaccessible enhancers and stable cell states from sparse single-cell epigenomics data ( http://github.com/aertslab/cistopic ). Using a compendium of single-cell ATAC-seq datasets from differentiating hematopoietic cells, brain and transcription factor perturbations, we demonstrate that topic modeling can be exploited for robust identification of cell types, enhancers and relevant transcription factors. Read More

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http://dx.doi.org/10.1038/s41592-019-0367-1DOI Listing

In vivo profiling of metastatic double knockouts through CRISPR-Cpf1 screens.

Nat Methods 2019 Apr 8. Epub 2019 Apr 8.

Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.

Systematic investigation of the genetic interactions that influence metastatic potential has been challenging. Here we developed massively parallel CRISPR-Cpf1/Cas12a crRNA array profiling (MCAP), an approach for combinatorial interrogation of double knockouts in vivo. We designed an MCAP library of 11,934 arrays targeting 325 pairwise combinations of genes implicated in metastasis. Read More

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http://dx.doi.org/10.1038/s41592-019-0371-5DOI Listing

High-throughput identification of dominant negative polypeptides in yeast.

Nat Methods 2019 Apr 8. Epub 2019 Apr 8.

Department of Genome Sciences, University of Washington, Seattle, WA, USA.

Dominant negative polypeptides can inhibit protein function by binding to a wild-type subunit or by titrating a ligand. Here we use high-throughput sequencing of libraries composed of fragments of yeast genes to identify polypeptides that act in a dominant negative manner, in that they are depleted during cell growth. The method can uncover numerous inhibitory polypeptides for a protein and thereby define small inhibitory regions, even pinpointing individual residues with critical functional roles. Read More

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http://dx.doi.org/10.1038/s41592-019-0368-0DOI Listing

Evaluating measures of association for single-cell transcriptomics.

Nat Methods 2019 Apr 8. Epub 2019 Apr 8.

Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada.

Single-cell transcriptomics provides an opportunity to characterize cell-type-specific transcriptional networks, intercellular signaling pathways and cellular diversity with unprecedented resolution by profiling thousands of cells in a single experiment. However, owing to the unique statistical properties of scRNA-seq data, the optimal measures of association for identifying gene-gene and cell-cell relationships from single-cell transcriptomics remain unclear. Here, we conducted a large-scale evaluation of 17 measures of association for their ability to reconstruct cellular networks, cluster cells of the same type and link cell-type-specific transcriptional programs to disease. Read More

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http://dx.doi.org/10.1038/s41592-019-0372-4DOI Listing

Human immunity to Cas9.

Authors:
Nicole Rusk

Nat Methods 2019 Apr;16(4):286

Nature Methods, .

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http://dx.doi.org/10.1038/s41592-019-0385-zDOI Listing

Improved exosome detection.

Authors:
Rita Strack

Nat Methods 2019 Apr;16(4):286

Nature Methods, .

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http://dx.doi.org/10.1038/s41592-019-0386-yDOI Listing
April 2019
1 Read

Bisulfite-free epigenetic sequencing.

Authors:
Lei Tang

Nat Methods 2019 Apr;16(4):286

Nature Methods, .

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http://dx.doi.org/10.1038/s41592-019-0387-xDOI Listing
April 2019
2 Reads

Human gut bacterial genome reference.

Authors:
Lei Tang

Nat Methods 2019 Apr;16(4):286

Nature Methods, .

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http://dx.doi.org/10.1038/s41592-019-0384-0DOI Listing

On algorithmic resolution.

Authors:
Rita Strack

Nat Methods 2019 Apr;16(4):285

Nature Methods, .

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http://dx.doi.org/10.1038/s41592-019-0383-1DOI Listing
April 2019
1 Read

RNA editing with endogenous ADARs.

Authors:
Nicole Rusk

Nat Methods 2019 Apr;16(4):285

Nature Methods, .

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http://dx.doi.org/10.1038/s41592-019-0380-4DOI Listing
April 2019
1 Read

Mapping the marmoset brain.

Authors:
Nina Vogt

Nat Methods 2019 Apr;16(4):285

Nature Methods, .

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http://dx.doi.org/10.1038/s41592-019-0381-3DOI Listing

Template-free visual proteomics.

Authors:
Allison Doerr

Nat Methods 2019 Apr;16(4):285

Nature Methods, .

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http://dx.doi.org/10.1038/s41592-019-0382-2DOI Listing

Single-cell chromatin immunocleavage sequencing (scChIC-seq) to profile histone modification.

Nat Methods 2019 Apr 28;16(4):323-325. Epub 2019 Mar 28.

Laboratory of Epigenome Biology, Systems Biology Center, NHLBI, NIH, Bethesda, MD, USA.

Our method for analyzing histone modifications, scChIC-seq (single-cell chromatin immunocleavage sequencing), involves targeting of the micrococcal nuclease (MNase) to a histone mark of choice by tethering to a specific antibody. Cleaved target sites are then selectively PCR amplified. We show that scChIC-seq reliably detects H3K4me3 and H3K27me3 target sites in single human white blood cells. Read More

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http://dx.doi.org/10.1038/s41592-019-0361-7DOI Listing

What to do about those immunoprecipitation blues.

Authors:
Vivien Marx

Nat Methods 2019 Apr;16(4):289-292

Technology editor for Nature Methods, .

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http://dx.doi.org/10.1038/s41592-019-0365-3DOI Listing

Spatially resolved isotope labeling.

Nat Methods 2019 Apr;16(4):287

Nature Methods, .

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http://dx.doi.org/10.1038/s41592-019-0379-xDOI Listing

Selene: a PyTorch-based deep learning library for sequence data.

Nat Methods 2019 Apr 28;16(4):315-318. Epub 2019 Mar 28.

Flatiron Institute, Simons Foundation, New York, NY, USA.

To enable the application of deep learning in biology, we present Selene (https://selene.flatironinstitute.org/), a PyTorch-based deep learning library for fast and easy development, training, and application of deep learning model architectures for any biological sequence data. Read More

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http://dx.doi.org/10.1038/s41592-019-0360-8DOI Listing

Dissecting neuronal circuitry.

Authors:
Nina Vogt

Nat Methods 2019 Apr;16(4):282

Nature Methods, .

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http://dx.doi.org/10.1038/s41592-019-0376-0DOI Listing

A cheminformatics approach to characterize metabolomes in stable-isotope-labeled organisms.

Nat Methods 2019 Apr 28;16(4):295-298. Epub 2019 Mar 28.

RIKEN Center for Sustainable Resource Science, Yokohama, Japan.

We report a computational approach (implemented in MS-DIAL 3.0; http://prime.psc. Read More

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http://dx.doi.org/10.1038/s41592-019-0358-2DOI Listing

Bridging the nanoscale measurement gap.

Authors:
Rita Strack

Nat Methods 2019 Apr;16(4):284

Nature Methods, .

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http://dx.doi.org/10.1038/s41592-019-0378-yDOI Listing

Double the fun.

Authors:
Irene Jarchum

Nat Methods 2019 Apr;16(4):283

Nature Methods, .

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http://dx.doi.org/10.1038/s41592-019-0377-zDOI Listing

Investigating heterogeneity in HeLa cells.

Authors:
Lei Tang

Nat Methods 2019 Apr;16(4):281

Nature Methods, .

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http://dx.doi.org/10.1038/s41592-019-0375-1DOI Listing

Tightening the handle on malaria.

Authors:

Nat Methods 2019 Apr;16(4):271

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http://dx.doi.org/10.1038/s41592-019-0390-2DOI Listing

Analyzing outliers: robust methods to the rescue.

Nat Methods 2019 Apr;16(4):275-276

Professor of Statistics, The Pennsylvania State University, University Park, PA, USA.

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http://dx.doi.org/10.1038/s41592-019-0369-zDOI Listing

Deep-learning augmented RNA-seq analysis of transcript splicing.

Nat Methods 2019 Apr 25;16(4):307-310. Epub 2019 Mar 25.

Bioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, Los Angeles, CA, USA.

A major limitation of RNA sequencing (RNA-seq) analysis of alternative splicing is its reliance on high sequencing coverage. We report DARTS (https://github.com/Xinglab/DARTS), a computational framework that integrates deep-learning-based predictions with empirical RNA-seq evidence to infer differential alternative splicing between biological samples. Read More

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http://dx.doi.org/10.1038/s41592-019-0351-9DOI Listing

SNAC-tag for sequence-specific chemical protein cleavage.

Nat Methods 2019 Apr 25;16(4):319-322. Epub 2019 Mar 25.

Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA.

Site-specific protein cleavage is essential for many protein-production protocols and typically requires proteases. We report the development of a chemical protein-cleavage method that is achieved through the use of a sequence-specific nickel-assisted cleavage (SNAC)-tag. We demonstrate that the SNAC-tag can be inserted before both water-soluble and membrane proteins to achieve fusion protein cleavage under biocompatible conditions with efficiency comparable to that of enzymes, and that the method works even when enzymatic cleavages fail. Read More

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http://dx.doi.org/10.1038/s41592-019-0357-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6443254PMC

Haribabu Arthanari.

Authors:
Vivien Marx

Nat Methods 2019 Apr;16(4):273

Nature Methods, .

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http://www.nature.com/articles/s41592-019-0362-6
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http://dx.doi.org/10.1038/s41592-019-0362-6DOI Listing
April 2019
5 Reads

Peering into cells at high resolution just got easier.

Nat Methods 2019 Apr;16(4):293-294

Department of Physics, Universidad de los Andes, Bogotá, Colombia.

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http://dx.doi.org/10.1038/s41592-019-0373-3DOI Listing
April 2019
1 Read

3Dscript: animating 3D/4D microscopy data using a natural-language-based syntax.

Nat Methods 2019 Apr;16(4):278-280

Optical Imaging Centre Erlangen, University of Erlangen-Nuremberg, Erlangen, Germany.

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http://www.nature.com/articles/s41592-019-0359-1
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http://dx.doi.org/10.1038/s41592-019-0359-1DOI Listing
April 2019
4 Reads

SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information.

Nat Methods 2019 Apr 18;16(4):299-302. Epub 2019 Mar 18.

Chair for Bioinformatics, Friedrich-Schiller University, Jena, Germany.

Mass spectrometry is a predominant experimental technique in metabolomics and related fields, but metabolite structural elucidation remains highly challenging. We report SIRIUS 4 (https://bio.informatik. Read More

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http://www.nature.com/articles/s41592-019-0344-8
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http://dx.doi.org/10.1038/s41592-019-0344-8DOI Listing
April 2019
12 Reads

FPbase: a community-editable fluorescent protein database.

Authors:
Talley J Lambert

Nat Methods 2019 Apr;16(4):277-278

Department of Cell Biology, Harvard Medical School, Boston, MA, USA.

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http://dx.doi.org/10.1038/s41592-019-0352-8DOI Listing

Scalable analysis of cell-type composition from single-cell transcriptomics using deep recurrent learning.

Nat Methods 2019 Apr 18;16(4):311-314. Epub 2019 Mar 18.

Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA.

Recent advances in large-scale single-cell RNA-seq enable fine-grained characterization of phenotypically distinct cellular states in heterogeneous tissues. We present scScope, a scalable deep-learning-based approach that can accurately and rapidly identify cell-type composition from millions of noisy single-cell gene-expression profiles. Read More

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http://dx.doi.org/10.1038/s41592-019-0353-7DOI Listing

Cell composition analysis of bulk genomics using single-cell data.

Nat Methods 2019 Apr 18;16(4):327-332. Epub 2019 Mar 18.

School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.

Single-cell RNA sequencing (scRNA-seq) is a rich resource of cellular heterogeneity, opening new avenues in the study of complex tissues. We introduce Cell Population Mapping (CPM), a deconvolution algorithm in which reference scRNA-seq profiles are leveraged to infer the composition of cell types and states from bulk transcriptome data ('scBio' CRAN R-package). Analysis of individual variations in lungs of influenza-virus-infected mice reveals that the relationship between cell abundance and clinical symptoms is a cell-state-specific property that varies gradually along the continuum of cell-activation states. Read More

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http://dx.doi.org/10.1038/s41592-019-0355-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6443043PMC
April 2019
32.072 Impact Factor

An active texture-based digital atlas enables automated mapping of structures and markers across brains.

Nat Methods 2019 Apr 11;16(4):341-350. Epub 2019 Mar 11.

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

Brain atlases enable the mapping of labeled cells and projections from different brains onto a standard coordinate system. We address two issues in the construction and use of atlases. First, expert neuroanatomists ascertain the fine-scale pattern of brain tissue, the 'texture' formed by cellular organization, to define cytoarchitectural borders. Read More

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http://dx.doi.org/10.1038/s41592-019-0328-8DOI Listing

A multiplexable assay for screening antibiotic lethality against drug-tolerant bacteria.

Nat Methods 2019 Apr 11;16(4):303-306. Epub 2019 Mar 11.

Institute for Medical Engineering & Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA.

Antibiotic screens typically rely on growth inhibition to characterize compound bioactivity-an approach that cannot be used to assess the bactericidal activity of antibiotics against bacteria in drug-tolerant states. To address this limitation, we developed a multiplexed assay that uses metabolism-sensitive staining to report on the killing of antibiotic-tolerant bacteria. This method can be used with diverse bacterial species and applied to genome-scale investigations to identify therapeutic targets against tolerant pathogens. Read More

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http://dx.doi.org/10.1038/s41592-019-0333-yDOI Listing

Aromatic F-C TROSY: a background-free approach to probe biomolecular structure, function, and dynamics.

Nat Methods 2019 Apr 11;16(4):333-340. Epub 2019 Mar 11.

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.

Atomic-level information about the structure and dynamics of biomolecules is critical for an understanding of their function. Nuclear magnetic resonance (NMR) spectroscopy provides unique insights into the dynamic nature of biomolecules and their interactions, capturing transient conformers and their features. However, relaxation-induced line broadening and signal overlap make it challenging to apply NMR spectroscopy to large biological systems. Read More

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http://dx.doi.org/10.1038/s41592-019-0334-xDOI Listing
April 2019
5 Reads

Author Correction: Methods to study RNA-protein interactions.

Nat Methods 2019 Apr;16(4):351

Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA.

In the version of this paper originally published, three references were accidentally omitted: Schwartz, J. C. et al. Read More

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http://www.nature.com/articles/s41592-019-0366-2
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http://dx.doi.org/10.1038/s41592-019-0366-2DOI Listing
April 2019
7 Reads

Two-level factorial experiments.

Nat Methods 2019 Mar;16(3):211-212

Department of Statistics, The Pennsylvania State University, University Park, PA, USA.

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http://dx.doi.org/10.1038/s41592-019-0335-9DOI Listing

RNA-binding proteome redux.

Nat Methods 2019 Mar;16(3):219

Nature Methods, .

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http://dx.doi.org/10.1038/s41592-019-0349-3DOI Listing
March 2019
32.072 Impact Factor

Quantum imaging in biological samples.

Nat Methods 2019 Mar;16(3):214

Nature Methods, .

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http://dx.doi.org/10.1038/s41592-019-0346-6DOI Listing