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 probability-based identification of multiple distinct and active small interfering RNAs (siRNAs) targeting the same gene. We further extend this approach to establish that the optimal redundancy for efficacious RNAi collections is between 4-6 siRNAs per gene.
journal_name
Nat Methodsjournal_title
Nature methodsauthors
König R,Chiang CY,Tu BP,Yan SF,DeJesus PD,Romero A,Bergauer T,Orth A,Krueger U,Zhou Y,Chanda SKdoi
10.1038/nmeth1089subject
Has Abstractpub_date
2007-10-01 00:00:00pages
847-9issue
10eissn
1548-7091issn
1548-7105pii
nmeth1089journal_volume
4pub_type
杂志文章相关文献
NATURE METHODS文献大全abstract：:Recording light-microscopy images of large, nontransparent specimens, such as developing multicellular organisms, is complicated by decreased contrast resulting from light scattering. Early zebrafish development can be captured by standard light-sheet microscopy, but new imaging strategies are required to obtain high-...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.1476
更新日期：2010-08-01 00:00:00
abstract：: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...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/s41592-019-0372-4
更新日期：2019-05-01 00:00:00
abstract：:Recent efforts in neuroscience research have been aimed at obtaining detailed anatomical neuronal wiring maps as well as information on how neurons in these networks engage in dynamic activities. Although the entire connectivity map of the nervous system of Caenorhabditis elegans has been known for more than 25 years,...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.2637
更新日期：2013-10-01 00:00:00
abstract：: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...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/s41592-019-0355-5
更新日期：2019-04-01 00:00:00
abstract：:Epistasis analysis, which reports on the extent to which the function of one gene depends on the presence of a second, is a powerful tool for studying the functional organization of the cell. Systematic genome-wide studies of epistasis, however, have been limited, with the majority of data being collected in the buddi...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth1098
更新日期：2007-10-01 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：: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：:The dynamic reshaping of tissues during morphogenesis results from a combination of individual cell behaviors and collective cell rearrangements. However, a comprehensive framework to unambiguously measure and link cell behavior to tissue morphogenesis is lacking. Here we introduce such a kinematic framework, bridging...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.1327
更新日期：2009-06-01 00:00:00
abstract：:Sequencing of RNA 3' ends has uncovered numerous sites that do not correspond to the termination sites of known transcripts. Through their 3' untranslated regions, protein-coding RNAs interact with RNA-binding proteins and microRNAs, which regulate many properties, including RNA stability and subcellular localization....
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/s41592-018-0114-z
更新日期：2018-10-01 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：:Glycosylation, which represents the most complex posttranslational modification (PTM) event during protein maturation, has a vital role in biological processes. Glycan biosynthesis is orchestrated by numerous glycosyltransferases, each displaying different selectivities for multiple reaction sites. The precise specifi...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth1050
更新日期：2007-07-01 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：: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：:The shape of the genome is thought to play an important part in the coordination of transcription and other DNA-metabolic processes. Chromosome conformation capture (3C) technology allows us to analyze the folding of chromatin in the native cellular state at a resolution beyond that provided by current microscopy tech...
journal_title：Nature methods
pub_type： 杂志文章,评审
doi：10.1038/nmeth1114
更新日期：2007-11-01 00:00:00
abstract：:We introduce PyClone, a statistical model for inference of clonal population structures in cancers. PyClone is a Bayesian clustering method for grouping sets of deeply sequenced somatic mutations into putative clonal clusters while estimating their cellular prevalences and accounting for allelic imbalances introduced ...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.2883
更新日期：2014-04-01 00:00:00
abstract：:We examined cell cycle-dependent changes in the proteome of human cells by systematically measuring protein dynamics in individual living cells. We used time-lapse microscopy to measure the dynamics of a random subset of 20 nuclear proteins, each tagged with yellow fluorescent protein (YFP) at its endogenous chromosom...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth892
更新日期：2006-07-01 00:00:00
abstract：:We present an easy-to-use integrated software suite, DIA-NN, that exploits deep neural networks and new quantification and signal correction strategies for the processing of data-independent acquisition (DIA) proteomics experiments. DIA-NN improves the identification and quantification performance in conventional DIA ...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/s41592-019-0638-x
更新日期：2020-01-01 00:00:00
abstract：:The importance of locating proteins in their context within cells has been heightened recently by the accomplishments in molecular structure and systems biology. Although light microscopy (LM) has been extensively used for mapping protein localization, many studies require the additional resolution of the electron mic...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth791
更新日期：2005-10-01 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：: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：: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：:Microarrays have been widely used for the analysis of gene expression, but the issue of reproducibility across platforms has yet to be fully resolved. To address this apparent problem, we compared gene expression between two microarray platforms: the short oligonucleotide Affymetrix Mouse Genome 430 2.0 GeneChip and a...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth757
更新日期：2005-05-01 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：: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/s41592-020-0733-z
更新日期：2020-02-01 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：: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：: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/s41592-020-0763-6
更新日期：2020-02-01 00:00:00
abstract：:Traditionally, crystallographic analysis of macromolecules has depended on large, well-ordered crystals, which often require significant effort to obtain. Even sizable crystals sometimes suffer from pathologies that render them inappropriate for high-resolution structure determination. Here we show that fragmentation ...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.4178
更新日期：2017-02-13 00:00:00
abstract：:All-optical electrophysiology-spatially resolved simultaneous optical perturbation and measurement of membrane voltage-would open new vistas in neuroscience research. We evolved two archaerhodopsin-based voltage indicators, QuasAr1 and QuasAr2, which show improved brightness and voltage sensitivity, have microsecond r...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth.3000
更新日期：2014-08-01 00:00:00
abstract：:The successful in vitro evolution of a DNA enzyme based on a ribozyme could offer insights into early evolutionary events and provide guidelines for designing hardier catalytic oligonucleotides. ...
journal_title：Nature methods
pub_type： 杂志文章
doi：10.1038/nmeth0606-424b
更新日期：2006-06-01 00:00:00
