Abstract：
:Single-cell RNA sequencing has enabled the decomposition of complex tissues into functionally distinct cell types. Often, investigators wish to assign cells to cell types through unsupervised clustering followed by manual annotation or via 'mapping' to existing data. However, manual interpretation scales poorly to large datasets, mapping approaches require purified or pre-annotated data and both are prone to batch effects. To overcome these issues, we present CellAssign, a probabilistic model that leverages prior knowledge of cell-type marker genes to annotate single-cell RNA sequencing data into predefined or de novo cell types. CellAssign automates the process of assigning cells in a highly scalable manner across large datasets while controlling for batch and sample effects. We demonstrate the advantages of CellAssign through extensive simulations and analysis of tumor microenvironment composition in high-grade serous ovarian cancer and follicular lymphoma.
journal_name
Nat Methodsjournal_title
Nature methodsauthors
Zhang AW,O'Flanagan C,Chavez EA,Lim JLP,Ceglia N,McPherson A,Wiens M,Walters P,Chan T,Hewitson B,Lai D,Mottok A,Sarkozy C,Chong L,Aoki T,Wang X,Weng AP,McAlpine JN,Aparicio S,Steidl C,Campbell KR,Shah SPdoi
10.1038/s41592-019-0529-1subject
Has Abstractpub_date
2019-10-01 00:00:00pages
1007-1015issue
10eissn
1548-7091issn
1548-7105pii
10.1038/s41592-019-0529-1journal_volume
16pub_type
杂志文章相关文献
NATURE METHODS文献大全abstract：:The ability to selectively interfere with post-translationally modified proteins would have many biological and therapeutic applications. However, post-translational modifications cannot be selectively targeted by nucleic-acid-based interference approaches. Here we describe post-translational intracellular silencing a...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.4144
更新日期：2017-03-01 00:00:00
abstract：:Zinc-finger nucleases (ZFNs) have enabled highly efficient gene targeting in multiple cell types and organisms. Here we describe methods for using simple ssDNA oligonucleotides in tandem with ZFNs to efficiently produce human cell lines with three distinct genetic outcomes: (i) targeted point mutation, (ii) targeted g...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.1653
更新日期：2011-07-17 00:00:00
abstract：:Thus far, optical recording of neuronal activity in freely behaving animals has been limited to a thin axial range. We present a head-mounted miniaturized light-field microscope (MiniLFM) capable of capturing neuronal network activity within a volume of 700 × 600 × 360 µm3 at 16 Hz in the hippocampus of freely moving ...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/s41592-018-0008-0
更新日期：2018-06-01 00:00:00
abstract：:Numerous drugs and endogenous ligands bind to cell surface receptors leading to modulation of downstream signaling cascades and frequently to adaptation of the plasma membrane proteome. In-depth analysis of dynamic processes at the cell surface is challenging due to biochemical properties and low abundances of plasma ...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/s41592-020-01022-1
更新日期：2021-01-01 00:00:00
abstract：:The commonly used, monomeric EYFP enabled imaging of intracellular protein structures beyond the optical resolution limit ('super-resolution' imaging) in living cells. By combining photoinduced activation of single EYFP fusions and time-lapse imaging, we obtained sub-40 nm resolution images of the filamentous superstr...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.1258
更新日期：2008-11-01 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：:Circular RNAs (circRNAs) produced from back-spliced exons are widely expressed, but individual circRNA functions remain poorly understood owing to the lack of adequate methods for distinguishing circRNAs from cognate messenger RNAs with overlapping exons. Here, we report that CRISPR-RfxCas13d can effectively discrimin...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/s41592-020-01011-4
更新日期：2021-01-01 00:00:00
abstract：:Cortical information processing relies on synaptic interactions between diverse classes of neurons with distinct electrophysiological and connection properties. Uncovering the operational principles of these elaborate circuits requires the probing of electrical activity from selected populations of defined neurons. He...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.1479
更新日期：2010-08-01 00:00:00
abstract：:The RNA-guided nuclease Cas9 can be reengineered as a programmable transcription factor. However, modest levels of gene activation have limited potential applications. We describe an improved transcriptional regulator obtained through the rational design of a tripartite activator, VP64-p65-Rta (VPR), fused to nuclease...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.3312
更新日期：2015-04-01 00:00:00
abstract：:Quantification of cell-cycle state at a single-cell level is essential to understand fundamental three-dimensional (3D) biological processes such as tissue development and cancer. Analysis of 3D in vivo images, however, is very challenging. Today's best practice, manual annotation of select image events, generates arb...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.3363
更新日期：2015-06-01 00:00:00
abstract：:Stable in vivo mapping and modulation of the same neurons and brain circuits over extended periods is critical to both neuroscience and medicine. Current electrical implants offer single-neuron spatiotemporal resolution but are limited by such factors as relative shear motion and chronic immune responses during long-t...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.3969
更新日期：2016-10-01 00:00:00
abstract：: ...
journal_title：Nature methods
pub_type： 评论,杂志文章
doi：10.1038/s41592-019-0315-0
更新日期：2019-02-01 00:00:00
abstract：:We present general means to greatly increase the sensitivity of antibody-based assays. Augmentation relies on a 'tadpole' protein-DNA chimera whose protein moiety binds most classes of mammalian antibodies but not avian immunoglobulin Y (IgY). We used this tadpole in affinity capture assays followed by real-time PCR t...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth1127
更新日期：2007-12-01 00:00:00
abstract：:Phenotype-based small-molecule screening is a powerful method to identify molecules that regulate cellular functions. However, such screens are generally performed in vitro under conditions that do not necessarily model complex physiological conditions or disease states. Here, we use molecular cell barcoding to enable...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.3992
更新日期：2016-10-01 00:00:00
abstract：:We describe an engineered family of highly antigenic molecules based on GFP-like fluorescent proteins. These molecules contain numerous copies of peptide epitopes and simultaneously bind IgG antibodies at each location. These 'spaghetti monster' fluorescent proteins (smFPs) distributed well in neurons, notably into sm...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.3365
更新日期：2015-06-01 00:00:00
abstract：:Circuit mapping requires knowledge of both structural and functional connectivity between cells. Although optical tools have been made to assess either the morphology and projections of neurons or their activity and functional connections, few probes integrate this information. We have generated a family of photoactiv...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.3480
更新日期：2015-09-01 00:00:00
abstract：:Using a directed evolution approach, researchers demonstrate a way of creating 'designer' receptors that are specifically activated by a ligand with no other biological activity in the cell. ...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth0507-382b
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：:We present functional ultrasound (fUS), a method for imaging transient changes in blood volume in the whole brain at better spatiotemporal resolution than with other functional brain imaging modalities. fUS uses plane-wave illumination at high frame rate and can measure blood volumes in smaller vessels than previous u...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.1641
更新日期：2011-07-03 00:00:00
abstract：:The ability to apply precise inputs to signaling species in live cells would be transformative for interrogating and understanding complex cell-signaling systems. Here we report an 'optogenetic' method for applying custom signaling inputs using feedback control of a light-gated protein-protein interaction. We applied ...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.1700
更新日期：2011-09-11 00:00:00
abstract：:Rational protein engineering requires a holistic understanding of protein function. Here, we apply deep learning to unlabeled amino-acid sequences to distill the fundamental features of a protein into a statistical representation that is semantically rich and structurally, evolutionarily and biophysically grounded. We...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/s41592-019-0598-1
更新日期：2019-12-01 00:00:00
abstract：:The Q system is a repressible binary expression system for transgenic manipulations in living organisms. Through protein engineering and in vivo functional tests, we report here variants of the Q-system transcriptional activator, including QF2, for driving strong and ubiquitous expression in all Drosophila tissues. Ou...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.3250
更新日期：2015-03-01 00:00:00
abstract：:We describe Trans-ABySS, a de novo short-read transcriptome assembly and analysis pipeline that addresses variation in local read densities by assembling read substrings with varying stringencies and then merging the resulting contigs before analysis. Analyzing 7.4 gigabases of 50-base-pair paired-end Illumina reads f...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.1517
更新日期：2010-11-01 00:00:00
abstract：:Glial cells have been identified as key signaling components in the brain; however, methods to investigate their structure and function in vivo have been lacking. Here, we describe a new, highly selective approach for labeling astrocytes in intact rodent neocortex that allows in vivo imaging using two-photon microscop...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth706
更新日期：2004-10-01 00:00:00
abstract：:Tumors from individuals with cancer are frequently genetically profiled for information about the driving forces behind the disease. We present the CancerMine resource, a text-mined and routinely updated database of drivers, oncogenes and tumor suppressors in different types of cancer. All data are available online ( ...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/s41592-019-0422-y
更新日期：2019-06-01 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：:The need for automated and efficient systems for tracking full animal pose has increased with the complexity of behavioral data and analyses. Here we introduce LEAP (LEAP estimates animal pose), a deep-learning-based method for predicting the positions of animal body parts. This framework consists of a graphical inter...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/s41592-018-0234-5
更新日期：2019-01-01 00:00:00
abstract：:Recent work has demonstrated that environmental factors experienced by parents can affect their offspring across multiple generations, and that such transgenerational transmission can depend on the germline. Causal evidence for the involvement of germ cells is rare, however, and the underlying molecular mechanisms rem...
journal_title：Nature methods
pub_type： 杂志文章,评审
doi：10.1038/nmeth.4181
更新日期：2017-02-28 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：:We established a conditional site-specific recombination system based on dimerizable Cre recombinase-mediated recombination in the apicomplexan parasite Toxoplasma gondii. Using a new single-vector strategy that allows ligand-dependent, efficient removal of a gene of interest, we generated three knockouts of apicomple...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.2301
更新日期：2013-02-01 00:00:00
