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Nature Methods
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Papers 4933
1 page of 494 pages (4,933 results)
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T cells race to the scene in cancer and infection. To tease out what is special in cancer, scientists widen their scope and tool sets.
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#1Limin Xiang (University of California, Berkeley)H-Index: 9
#2Kun Chen (University of California, Berkeley)H-Index: 18
Last. Ke Xu (University of California, Berkeley)H-Index: 24
view all 5 authors...
Intracellular diffusion underlies vital cellular processes. However, it remains difficult to elucidate how an unbound protein diffuses inside the cell with good spatial resolution and sensitivity. Here we introduce single-molecule displacement/diffusivity mapping (SMdM), a super-resolution strategy that enables the nanoscale mapping of intracellular diffusivity through local statistics of the instantaneous displacements of freely diffusing single molecules. We thus show that the diffusion of an ...
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#1Davis McCarthy (St. Vincent's Institute of Medical Research)H-Index: 1
#2Raghd Rostom (EMBL-EBI: European Bioinformatics Institute)H-Index: 5
Last. Daniel J. GaffneyH-Index: 30
view all 13 authors...
Bulk and single-cell DNA sequencing has enabled reconstructing clonal substructures of somatic tissues from frequency and cooccurrence patterns of somatic variants. However, approaches to characterize phenotypic variations between clones are not established. Here we present cardelino (https://github.com/single-cell-genetics/cardelino), a computational method for inferring the clonal tree configuration and the clone of origin of individual cells assayed using single-cell RNA-seq (scRNA-seq). Card...
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#1Liangqi Xie (University of California, Berkeley)H-Index: 3
#2Peng Dong (HHMI: Howard Hughes Medical Institute)H-Index: 6
Last. Kyong-Rim Kieffer-KwonH-Index: 14
view all 20 authors...
To image the accessible genome at nanometer scale in situ, we developed three-dimensional assay for transposase-accessible chromatin-photoactivated localization microscopy (3D ATAC-PALM) that integrates an assay for transposase-accessible chromatin with visualization, PALM super-resolution imaging and lattice light-sheet microscopy. Multiplexed with oligopaint DNA–fluorescence in situ hybridization (FISH), RNA–FISH and protein fluorescence, 3D ATAC-PALM connected microscopy and genomic data, rev...
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#1Nicole D. Marino (UCSF: University of California, San Francisco)H-Index: 1
#2Rafael Pinilla-Redondo (UCPH: University of Copenhagen)
Last. Joseph Bondy-Denomy (UCSF: University of California, San Francisco)H-Index: 20
view all 4 authors...
Clustered, regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) genes, a diverse family of prokaryotic adaptive immune systems, have emerged as a biotechnological tool and therapeutic. The discovery of protein inhibitors of CRISPR-Cas systems, called anti-CRISPR (Acr) proteins, enables the development of more controllable and precise CRISPR-Cas tools. Here we discuss applications of Acr proteins for post-translational control of CRISPR-Cas systems in prokaryotic a...
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#1Jiaming Li (Harvard University)
#2Jonathan G. Van Vranken (Harvard University)
Last. Andrew H. ThompsonH-Index: 1
view all 16 authors...
Isobaric labeling empowers proteome-wide expression measurements simultaneously across multiple samples. Here an expanded set of 16 isobaric reagents based on an isobutyl-proline immonium ion reporter structure (TMTpro) is presented. These reagents have similar characteristics to existing tandem mass tag reagents but with increased fragmentation efficiency and signal. In a proteome-scale example dataset, we compared eight common cell lines with and without Torin1 treatment with three replicates,...
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#1Mihail Ivilinov Todorov (LMU: Ludwig Maximilian University of Munich)H-Index: 2
#2Johannes C. Paetzold (TUM: Technische Universität München)H-Index: 1
Last. Marie Piraud (TUM: Technische Universität München)H-Index: 5
view all 12 authors...
Tissue clearing methods enable the imaging of biological specimens without sectioning. However, reliable and scalable analysis of large imaging datasets in three dimensions remains a challenge. Here we developed a deep learning-based framework to quantify and analyze brain vasculature, named Vessel Segmentation & Analysis Pipeline (VesSAP). Our pipeline uses a convolutional neural network (CNN) with a transfer learning approach for segmentation and achieves human-level accuracy. By using VesSAP,...
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#1Tobias P. Wörner (UU: Utrecht University)H-Index: 1
#2Joost Snijder (UU: Utrecht University)H-Index: 19
Last. Albert J. R. Heck (UU: Utrecht University)H-Index: 92
view all 6 authors...
We demonstrate single-particle charge detection mass spectrometry on an Orbitrap for the analysis of megadalton biomolecular assemblies. We establish that the signal amplitudes of individual ions scale linearly with their charge, which can be used to resolve mixed ion populations, determine charge states and thus also determine the masses of individual ions. This enables the ultrasensitive analysis of heterogeneous protein assemblies including immunoglobulin oligomers, ribosomes, proteinaceous n...
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#1Mathilde Gauchier (University of Montpellier)H-Index: 1
#2Guido van Mierlo (Radboud University Nijmegen)H-Index: 5
Last. Jérôme Déjardin (University of Montpellier)H-Index: 15
view all 4 authors...
Understanding how chromatin is regulated is essential to fully grasp genome biology, and establishing the locus-specific protein composition is a major step toward this goal. Here we explain why the isolation and analysis of a specific chromatin segment are technically challenging, independently of the method. We then describe the published strategies and discuss their advantages and limitations. We conclude by discussing why significant technology developments are required to unambiguously desc...
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#1Jared O. Kafader (NU: Northwestern University)H-Index: 2
#2Rafael D. Melani (NU: Northwestern University)H-Index: 4
Last. Joshua T. Maze (Thermo Fisher Scientific)H-Index: 1
view all 16 authors...
An Orbitrap-based ion analysis procedure determines the direct charge for numerous individual protein ions to generate true mass spectra. This individual ion mass spectrometry (I2MS) method for charge detection enables the characterization of highly complicated mixtures of proteoforms and their complexes in both denatured and native modes of operation, revealing information not obtainable by typical measurements of ensembles of ions. Charge assignment for individual ions unlocks complex mixtures...
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