Abstract:
:In the originally published paper, the "before" image for the afatinib condition in Fig. 6c was incorrect. Instead of an image displaying a GBM-3 neoplastic organoid before afatinib treatment, this panel showed an image from the GBM-2 control (DMSO) group before treatment. This error has now been corrected in the HTML and PDF versions of the article; the "before, afatinib" panel in Fig. 6c now shows a representative image from the indicated experiment. The color of all error bars in Fig. 6 has also been changed to black, for consistency. All statistical analysis and all conclusions presented in the article are unaffected by this error. Nevertheless, we apologize for the mistake.
journal_name
Nat Methodsjournal_title
Nature methodsauthors
Bian S,Repic M,Guo Z,Kavirayani A,Burkard T,Bagley JA,Krauditsch C,Knoblich JAdoi
10.1038/s41592-018-0118-8subject
Has Abstractpub_date
2018-09-01 00:00:00pages
748issue
9eissn
1548-7091issn
1548-7105pii
10.1038/s41592-018-0118-8journal_volume
15pub_type
已发布勘误相关文献
NATURE METHODS文献大全abstract::We describe factored spectrally transformed linear mixed models (FaST-LMM), an algorithm for genome-wide association studies (GWAS) that scales linearly with cohort size in both run time and memory use. On Wellcome Trust data for 15,000 individuals, FaST-LMM ran an order of magnitude faster than current efficient algo...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.1681
更新日期:2011-09-04 00:00:00
abstract::Optimism about biomedicine is challenged by the increasingly complex ethical, legal and social issues it raises. Reporting of scientific methods is no longer sufficient to address the complex relationship between science and society. To promote 'ethical reproducibility', we call for transparent reporting of research e...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.2564
更新日期:2013-09-01 00:00:00
abstract::Zinc-finger nucleases (ZFNs) drive efficient genome editing by introducing a double-strand break into the targeted gene. Cleavage is induced when two custom-designed ZFNs heterodimerize upon binding DNA to form a catalytically active nuclease complex. The importance of this dimerization event for subsequent cleavage a...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.1539
更新日期:2011-01-01 00:00:00
abstract::Existing methods for human induced pluripotent stem cell (hiPSC) cardiac differentiation are efficient but require complex, undefined medium constituents that hinder further elucidation of the molecular mechanisms of cardiomyogenesis. Using hiPSCs derived under chemically defined conditions on synthetic matrices, we s...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.2999
更新日期:2014-08-01 00:00:00
abstract::Automated annotation of protein function is challenging. As the number of sequenced genomes rapidly grows, the overwhelming majority of protein products can only be annotated computationally. If computational predictions are to be relied upon, it is crucial that the accuracy of these methods be high. Here we report th...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.2340
更新日期:2013-03-01 00:00:00
abstract::We must reliably map the interactomes of cellular macromolecular complexes in order to fully explore and understand biological systems. However, there are no methods to accurately predict how to capture a given macromolecular complex with its physiological binding partners. Here, we present a screening method that com...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.3395
更新日期:2015-06-01 00:00:00
abstract::The complexity of the angiogenic cascade limits cellular approaches to studying angiogenic endothelial cells (ECs). In turn, in vivo assays do not allow the analysis of the distinct cellular behavior of ECs during angiogenesis. Here we show that ECs can be grafted as spheroids into a matrix to give rise to a complex t...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.1198
更新日期:2008-05-01 00:00:00
abstract::Fluorescent proteins have become extremely popular tools for in vivo imaging and especially for the study of localization, motility and interaction of proteins in living cells. Here we report TagRFP, a monomeric red fluorescent protein, which is characterized by high brightness, complete chromophore maturation, prolon...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth1062
更新日期:2007-07-01 00:00:00
abstract::The self-reconstructing properties of Bessel beams provide healing benefits in highly scattering media. ...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth1110-876
更新日期:2010-11-01 00:00:00
abstract::Preprocessing of functional magnetic resonance imaging (fMRI) involves numerous steps to clean and standardize the data before statistical analysis. Generally, researchers create ad hoc preprocessing workflows for each dataset, building upon a large inventory of available tools. The complexity of these workflows has s...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/s41592-018-0235-4
更新日期:2019-01-01 00:00:00
abstract::We developed a method that allows release of intact membrane protein complexes from amphipols, bicelles and nanodiscs in the gas phase for observation by mass spectrometry (MS). Current methods involve release of membrane protein complexes from detergent micelles, which reveals subunit composition and lipid binding. W...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.2691
更新日期:2013-12-01 00:00:00
abstract::We combined rapid microfluidic mixing with single-molecule fluorescence resonance energy transfer to study the folding kinetics of the intrinsically disordered human protein α-synuclein. The time-resolution of 0.2 ms revealed initial collapse of the unfolded protein induced by binding with lipid mimics and subsequent ...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.1568
更新日期:2011-03-01 00:00:00
abstract::Next-generation sequencing technology is a powerful tool for transcriptome analysis. However, under certain conditions, only a small amount of material is available, which requires more sensitive techniques that can preferably be used at the single-cell level. Here we describe a single-cell digital gene expression pro...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.1315
更新日期:2009-05-01 00:00:00
abstract::We present single-cell interpretation via multikernel learning (SIMLR), an analytic framework and software which learns a similarity measure from single-cell RNA-seq data in order to perform dimension reduction, clustering and visualization. On seven published data sets, we benchmark SIMLR against state-of-the-art met...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.4207
更新日期:2017-04-01 00:00:00
abstract::Using a line-scanning method during functional magnetic resonance imaging (fMRI), we obtained high temporal (50-ms) and spatial (50-μm) resolution information along the cortical thickness and showed that the laminar position of fMRI onset coincides with distinct neural inputs in rat somatosensory and motor cortices. T...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.2730
更新日期:2014-01-01 00:00:00
abstract::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 confirmed, and show that hig...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/s41592-018-0011-5
更新日期:2018-07-01 00:00:00
abstract::Gene expression is extensively regulated at the levels of mRNA stability, localization and translation. However, decoding functional RNA-regulatory features remains a limitation to understanding post-transcriptional regulation in vivo. Here, we developed RNA-element selection assay (RESA), a method that selects RNA el...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.4121
更新日期:2017-02-01 00:00:00
abstract::To enhance the repertoire of molecular tools for studying malaria parasite biology, we adapted a ligand-regulatable FKBP protein destabilization domain (ddFKBP) for use in P. falciparum. We destabilized the reporter yellow fluorescent protein (YFP) and the P. falciparum protease falcipain-2 in a ligand-reversible mann...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth1132
更新日期:2007-12-01 00:00:00
abstract::Focused-ion-beam scanning electron microscopy (FIB-SEM) has become an essential tool for studying neural tissue at resolutions below 10 nm × 10 nm × 10 nm, producing data sets optimized for automatic connectome tracing. We present a technical advance, ultrathick sectioning, which reliably subdivides embedded tissue sa...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.3292
更新日期:2015-04-01 00:00:00
abstract::We present DeNovoGear software for analyzing de novo mutations from familial and somatic tissue sequencing data. DeNovoGear uses likelihood-based error modeling to reduce the false positive rate of mutation discovery in exome analysis and fragment information to identify the parental origin of germ-line mutations. We ...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.2611
更新日期:2013-10-01 00:00:00
abstract::An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...
journal_title:Nature methods
pub_type: 已发布勘误
doi:10.1038/s41592-019-0588-3
更新日期:2019-10-01 00:00:00
abstract::We present Omni-ATAC, an improved ATAC-seq protocol for chromatin accessibility profiling that works across multiple applications with substantial improvement of signal-to-background ratio and information content. The Omni-ATAC protocol generates chromatin accessibility profiles from archival frozen tissue samples and...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.4396
更新日期:2017-10-01 00:00:00
abstract::Despite the widespread adoption of organoids as biomimetic tissue models, methods to comprehensively analyze cell-type-specific post-translational modification (PTM) signaling networks in organoids are absent. Here, we report multivariate single-cell analysis of such networks in organoids and organoid cocultures. Simu...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/s41592-020-0737-8
更新日期:2020-03-01 00:00:00
abstract::We show that nanoscopy based on the principle called RESOLFT (reversible saturable optical fluorescence transitions) or nonlinear structured illumination can be effectively parallelized using two incoherently superimposed orthogonal standing light waves. The intensity minima of the resulting pattern act as 'doughnuts'...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.2556
更新日期:2013-08-01 00:00:00
abstract::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 ...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/s41592-018-0308-4
更新日期:2019-03-01 00:00:00
abstract::We describe a statistical analysis methodology designed to minimize the impact of off-target activities upon large-scale RNA interference (RNAi) screens in mammalian cells. Application of this approach enhances reconfirmation rates and facilitates the experimental validation of new gene activities through the probabil...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth1089
更新日期:2007-10-01 00:00:00
abstract::We developed a caged GABA (gamma-aminobutyric acid), which, when combined with an appropriate caged glutamate, allows bimodal control of neuronal membrane potential with subcellular resolution using optically independent two-photon uncaging of each neurotransmitter. We used two-color, two-photon uncaging to fire and b...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.1413
更新日期:2010-02-01 00:00:00
abstract::Small molecules are known to stabilize membrane proteins and to modulate their function and oligomeric state, but such interactions are often hard to precisely define. Here we develop and apply a high-resolution, Orbitrap mass spectrometry-based method for analyzing intact membrane protein-ligand complexes. Using this...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.3771
更新日期:2016-04-01 00:00:00
abstract::An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...
journal_title:Nature methods
pub_type: 已发布勘误
doi:10.1038/s41592-019-0660-z
更新日期:2019-12-01 00:00:00
abstract::The self-renewal and differentiation of human pluripotent stem cells (hPSCs) have typically been studied in flat, two-dimensional (2D) environments. In this Perspective, we argue that 3D model systems may be needed in addition, as they mimic the natural 3D tissue organization more closely. We survey methods that have ...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.1671
更新日期:2011-08-30 00:00:00