Abstract:
:Accurate identification of cell subsets in complex populations is key to discovering novelty in multidimensional single-cell experiments. We present X-shift (http://web.stanford.edu/~samusik/vortex/), an algorithm that processes data sets using fast k-nearest-neighbor estimation of cell event density and arranges populations by marker-based classification. X-shift enables automated cell-subset clustering and access to biological insights that 'prior knowledge' might prevent the researcher from discovering.
journal_name
Nat Methodsjournal_title
Nature methodsauthors
Samusik N,Good Z,Spitzer MH,Davis KL,Nolan GPdoi
10.1038/nmeth.3863subject
Has Abstractpub_date
2016-06-01 00:00:00pages
493-6issue
6eissn
1548-7091issn
1548-7105pii
nmeth.3863journal_volume
13pub_type
杂志文章相关文献
NATURE METHODS文献大全abstract::Drug-inducible systems allowing the control of gene expression in mammalian cells are invaluable tools for genetic research, and could also fulfill essential roles in gene- and cell-based therapy. Currently available systems, however, often have limited in vivo functionality because of leakiness, insufficient levels o...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth846
更新日期:2006-02-01 00:00:00
abstract::A quantitative high-throughput FRET-based method of screening fluorescent protein fusion libraries brings the promise of more detailed interactome maps. ...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth0207-112b
更新日期:2007-02-01 00:00:00
abstract::Gap junction channels assembled from connexin protein subunits mediate intercellular transfer of ions and metabolites. Impaired channel function is implicated in several hereditary human diseases. In particular, defective permeation of cAMP or inositol-1,4,5-trisphosphate (InsP(3)) through connexin channels is associa...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth1031
更新日期:2007-04-01 00:00:00
abstract::We developed a general approach that allows unnatural amino acids with diverse physicochemical and biological properties to be genetically encoded in mammalian cells. A mutant Escherichia coli aminoacyl-tRNA synthetase (aaRS) is first evolved in yeast to selectively aminoacylate its tRNA with the unnatural amino acid ...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth1016
更新日期:2007-03-01 00:00:00
abstract::The stable expansion of tissue-specific stem cells in vitro has contributed to research on several organs. Alveolar epithelial type II (AT2) cells function as tissue stem cells in the lung, but robust models for studying human AT2 cells are lacking. Here we report a method for the efficient generation and long-term ex...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.4448
更新日期:2017-11-01 00:00:00
abstract::Identifying groups of similar objects is a popular first step in biomedical data analysis, but it is error-prone and impossible to perform manually. Many computational methods have been developed to tackle this problem. Here we assessed 13 well-known methods using 24 data sets ranging from gene expression to protein d...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.3583
更新日期:2015-11-01 00:00:00
abstract::We discuss the advantages and challenges of the open-source strategy in biological image analysis and argue that its full impact will not be realized without better support and recognition of software engineers' contributions to the biological sciences and more support of this development model from funders and instit...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.2082
更新日期:2012-06-28 00:00:00
abstract::By combining activity-based proteomics and metabolomics, researchers have developed a new systems biology strategy for characterizing enzymes in the context of metabolic networks. ...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth0107-8b
更新日期:2007-01-01 00:00:00
abstract::Researchers designed an enzyme to carry out the Diels-Alder reaction, an activity not found in nature. ...
journal_title:Nature methods
pub_type: 评论,杂志文章
doi:10.1038/nmeth0910-671
更新日期:2010-09-01 00:00:00
abstract::To enable the detection of expression signatures specific to individual cells, we developed PLAYR (proximity ligation assay for RNA), a method for highly multiplexed transcript quantification by flow and mass cytometry that is compatible with standard antibody staining. When used with mass cytometry, PLAYR allowed for...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.3742
更新日期:2016-03-01 00:00:00
abstract::We developed genetically encoded RNA probes for characterizing localization and dynamics of mitochondrial RNA (mtRNA) in single living cells. The probes consist of two RNA-binding domains of PUMILIO1, each connected with split fragments of a fluorescent protein capable of reconstituting upon binding to a target RNA. W...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth1030
更新日期:2007-05-01 00:00:00
abstract::Targeted quantification of DNA methylation allows for interrogation of the most informative loci across many samples quickly and cost-effectively. Here we report improved bisulfite padlock probes (BSPPs) with a design algorithm to generate efficient padlock probes, a library-free protocol that dramatically reduces sam...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.1871
更新日期:2012-02-05 00:00:00
abstract::Cryogenic electron microscopy (cryo-EM) is widely used to study biological macromolecules that comprise regions with disorder, flexibility or partial occupancy. For example, membrane proteins are often kept in solution with detergent micelles and lipid nanodiscs that are locally disordered. Such spatial variability ne...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/s41592-020-00990-8
更新日期:2020-12-01 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::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::To enable sophisticated optogenetic manipulation of neural circuits throughout the nervous system with limited disruption of animal behavior, light-delivery systems beyond fiber optic tethering and large, head-mounted wireless receivers are desirable. We report the development of an easy-to-construct, implantable wire...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.3536
更新日期:2015-10-01 00:00:00
abstract::Counting molecules in complexes is challenging, even with super-resolution microscopy. Here, we use the programmable and specific binding of dye-labeled DNA probes to count integer numbers of targets. This method, called quantitative points accumulation in nanoscale topography (qPAINT), works independently of dye phot...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.3804
更新日期:2016-05-01 00:00:00
abstract:: ...
journal_title:Nature methods
pub_type: 社论
doi:10.1038/s41592-018-0257-y
更新日期:2018-12-01 00:00:00
abstract::We introduce CIBERSORT, a method for characterizing cell composition of complex tissues from their gene expression profiles. When applied to enumeration of hematopoietic subsets in RNA mixtures from fresh, frozen and fixed tissues, including solid tumors, CIBERSORT outperformed other methods with respect to noise, unk...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.3337
更新日期:2015-05-01 00:00:00
abstract::RNA-guided Cas9 nucleases derived from clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems have dramatically transformed our ability to edit the genomes of diverse organisms. We believe tools and techniques based on Cas9, a single unifying factor capable of colocalizing RNA, DNA and protein,...
journal_title:Nature methods
pub_type: 杂志文章,评审
doi:10.1038/nmeth.2649
更新日期:2013-10-01 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::To trace cell lineages in a developing vertebrate and to observe, in vivo, how behaviors of individual cells are affected by the genes they express, we created a zebrafish line containing a transgene called mosaic analysis in zebrafish (MAZe), built around a self-excising hsp70:Cre cassette. Heat shock triggers Cre re...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.1423
更新日期:2010-03-01 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::Despite its biological importance, tRNA has not been adequately sequenced by standard methods because of its abundant post-transcriptional modifications and stable structure, which interfere with cDNA synthesis. We achieved efficient and quantitative tRNA sequencing in HEK293T cells by using engineered demethylases to...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.3478
更新日期:2015-09-01 00:00:00
abstract::In mass-spectrometry-based proteomics, the identification and quantification of peptides and proteins heavily rely on sequence database searching or spectral library matching. The lack of accurate predictive models for fragment ion intensities impairs the realization of the full potential of these approaches. Here, we...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/s41592-019-0426-7
更新日期:2019-06-01 00:00:00
abstract::Spontaneous and sensory-evoked activity propagates across varying spatial scales in the mammalian cortex, but technical challenges have limited conceptual links between the function of local neuronal circuits and brain-wide network dynamics. We present a method for simultaneous cellular-resolution two-photon calcium i...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/s41592-019-0625-2
更新日期:2020-01-01 00:00:00
abstract::Physical modeling is increasingly important for generating insights into intracellular processes. We describe situations in which combined spatial and stochastic aspects of chemical reactions are needed to capture the relevant dynamics of biochemical systems. ...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.2253
更新日期:2012-12-01 00:00:00
abstract::Monomeric (m)Eos2 is an engineered photoactivatable fluorescent protein widely used for super-resolution microscopy. We show that mEos2 forms oligomers at high concentrations and forms aggregates when labeling membrane proteins, limiting its application as a fusion partner. We solved the crystal structure of tetrameri...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.2021
更新日期:2012-05-13 00:00:00
abstract::The quality of genetically encoded calcium indicators (GECIs) has improved dramatically in recent years, but high-performing ratiometric indicators are still rare. Here we describe a series of fluorescence resonance energy transfer (FRET)-based calcium biosensors with a reduced number of calcium binding sites per sens...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.2773
更新日期:2014-02-01 00:00:00
abstract::The occurrence of multiple strains of prions may reflect conformational variability of PrP(Sc), a disease-associated, aggregated variant of the cellular prion protein, PrP(C). Here we used luminescent conjugated polymers (LCPs), which emit conformation-dependent fluorescence spectra, for characterizing prion strains. ...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth1131
更新日期:2007-12-01 00:00:00