Abstract：
:Small-interfering RNAs (siRNAs) assemble into RISC, the RNA-induced silencing complex, which cleaves complementary mRNAs. Despite their fluctuating efficacy, siRNAs are widely used to assess gene function. Although this limitation could be ascribed, in part, to variations in the assembly and activation of RISC, downstream events in the RNA interference (RNAi) pathway, such as target site accessibility, have so far not been investigated extensively. In this study we present a comprehensive analysis of target RNA structure effects on RNAi by computing the accessibility of the target site for interaction with the siRNA. Based on our observations, we developed a novel siRNA design tool, RNAxs, by combining known siRNA functionality criteria with target site accessibility. We calibrated our method on two data sets comprising 573 siRNAs for 38 genes, and tested it on an independent set of 360 siRNAs targeting four additional genes. Overall, RNAxs proves to be a robust siRNA selection tool that substantially improves the prediction of highly efficient siRNAs.
journal_name
Nat Biotechnoljournal_title
Nature biotechnologyauthors
Tafer H,Ameres SL,Obernosterer G,Gebeshuber CA,Schroeder R,Martinez J,Hofacker ILdoi
10.1038/nbt1404subject
Has Abstractpub_date
2008-05-01 00:00:00pages
578-83issue
5eissn
1087-0156issn
1546-1696pii
nbt1404journal_volume
26pub_type
杂志文章abstract：:Elastin-like polypeptides (ELPs) undergo a reversible, inverse phase transition. Below their transition temperature (Tt), ELPs are soluble in water, but when the temperature is raised above Tt, phase transition occurs, leading to aggregation of the polypeptide. We demonstrate a method for purification of soluble fusio...
journal_title：Nature biotechnology
pub_type： 杂志文章
doi：10.1038/15100
更新日期：1999-11-01 00:00:00
abstract：:As the cost of human genome sequencing plunges and large-scale genome-phenotype studies become possible, society should do more to reward those individuals who choose to disclose their data, despite the risks. ...
journal_title：Nature biotechnology
pub_type： 评论,社论
doi：10.1038/nbt0909-777
更新日期：2009-09-01 00:00:00
abstract：:Reproducibility in research can be compromised by both biological and technical variation, but most of the focus is on removing the latter. Here we investigate the effects of biological variation in HeLa cell lines using a systems-wide approach. We determine the degree of molecular and phenotypic variability across 14...
journal_title：Nature biotechnology
pub_type： 杂志文章
doi：10.1038/s41587-019-0037-y
更新日期：2019-03-01 00:00:00
abstract：:Expansions of short tandem repeats are genetic variants that have been implicated in several neuropsychiatric and other disorders, but their assessment remains challenging with current polymerase-based methods1-4. Here we introduce a CRISPR-Cas-based enrichment strategy for nanopore sequencing combined with an algorit...
journal_title：Nature biotechnology
pub_type： 杂志文章
doi：10.1038/s41587-019-0293-x
更新日期：2019-12-01 00:00:00
abstract：:New high-dimensional, single-cell technologies offer unprecedented resolution in the analysis of heterogeneous tissues. However, because these technologies can measure dozens of parameters simultaneously in individual cells, data interpretation can be challenging. Here we present viSNE, a tool that allows one to map h...
journal_title：Nature biotechnology
pub_type： 杂志文章
doi：10.1038/nbt.2594
更新日期：2013-06-01 00:00:00
abstract：:This report describes the selection of highly efficient antibody catalysts by combining chemical selection from a synthetic library with directed in vitro protein evolution. Evolution started from a naive antibody library displayed on phage made from fully synthetic, antibody-encoding genes (the Human Combinatorial An...
journal_title：Nature biotechnology
pub_type： 杂志文章
doi：10.1038/nbt828
更新日期：2003-06-01 00:00:00
abstract：:Reagentless biosensors that can directly transduce molecular recognition to optical signals should potentiate the development of sensor arrays for a wide variety of analytes. Nucleic acid aptamers that bind ligands tightly and specifically can be readily selected, but may prove difficult to adapt to biosensor applicat...
journal_title：Nature biotechnology
pub_type： 杂志文章
doi：10.1038/82414
更新日期：2000-12-01 00:00:00
abstract：:The gold standard for clinical diagnosis of bacterial lower respiratory infections (LRIs) is culture, which has poor sensitivity and is too slow to guide early, targeted antimicrobial therapy. Metagenomic sequencing could identify LRI pathogens much faster than culture, but methods are needed to remove the large amoun...
journal_title：Nature biotechnology
pub_type： 杂志文章
doi：10.1038/s41587-019-0156-5
更新日期：2019-07-01 00:00:00
abstract：:RNA interference (RNAi) is a powerful method for specifically silencing gene expression in diverse cell types. RNAi is mediated by approximately 21-nucleotide small interfering RNAs (siRNAs), which are produced from larger double-stranded RNAs (dsRNAs) in vivo through the action of Dicer, an RNase III-family enzyme. T...
journal_title：Nature biotechnology
pub_type：
doi：10.1038/nbt792
更新日期：2003-03-01 00:00:00
abstract：:A problem in analyzing microarray-based gene expression data is the separation of genes causally involved in a disease from innocent bystander genes, whose expression levels have been secondarily altered by primary changes elsewhere. To investigate this issue systematically in the context of a class of complex human d...
journal_title：Nature biotechnology
pub_type： 杂志文章
doi：10.1038/nbt965
更新日期：2004-05-01 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 biotechnology
pub_type： 杂志文章,已发布勘误
doi：10.1038/s41587-020-0510-7
更新日期：2020-05-01 00:00:00
abstract：:Technologies that enable targeted manipulation of epigenetic marks could be used to precisely control cell phenotype or interrogate the relationship between the epigenome and transcriptional control. Here we describe a programmable, CRISPR-Cas9-based acetyltransferase consisting of the nuclease-null dCas9 protein fuse...
journal_title：Nature biotechnology
pub_type： 杂志文章
doi：10.1038/nbt.3199
更新日期：2015-05-01 00:00:00
abstract：:St. Louis wants to become a hub of agricultural biotechnology. All it needs is more start-ups and funds. ...
journal_title：Nature biotechnology
pub_type： 杂志文章
doi：10.1038/nbt0408-471
更新日期：2008-04-01 00:00:00
abstract：:Despite recent advances in optogenetics, it remains challenging to manipulate gene expression in specific populations of neurons. We present a dual-protein switch system, Cal-Light, that translates neuronal-activity-mediated calcium signaling into gene expression in a light-dependent manner. In cultured neurons and br...
journal_title：Nature biotechnology
pub_type： 杂志文章
doi：10.1038/nbt.3902
更新日期：2017-09-01 00:00:00
abstract：:Linear, medium-chain (C8-C12) hydrocarbons are important components of fuels as well as commodity and specialty chemicals. As industrial microbes do not contain pathways to produce medium-chain chemicals, approaches such as overexpression of endogenous enzymes or deletion of competing pathways are not available to the...
journal_title：Nature biotechnology
pub_type： 杂志文章,评审
doi：10.1038/nbt.4022
更新日期：2017-12-01 00:00:00
abstract：:A bacteriophage lambda surface expression system, lambda foo, was used for epitope mapping of human galectin-3. We constructed random epitope and peptide libraries and compared their efficiencies in the mapping. The galectin-3 cDNA was randomly digested by DNase 1 to make random epitope libraries. The libraries were s...
journal_title：Nature biotechnology
pub_type： 杂志文章
doi：10.1038/nbt0197-74
更新日期：1997-01-01 00:00:00
abstract：:Antifreeze proteins (AFPs) are found in cold-adapted organisms and have the unusual ability to bind to and inhibit the growth of ice crystals. However, the underlying molecular basis of their ice-binding activity is unclear because of the difficulty of studying the AFP-ice interaction directly and the lack of a common...
journal_title：Nature biotechnology
pub_type： 杂志文章
doi：10.1038/nbt1224
更新日期：2006-07-01 00:00:00
abstract：:Comparing diverse single-cell RNA sequencing (scRNA-seq) datasets generated by different technologies and in different laboratories remains a major challenge. Here we address the need for guidance in choosing algorithms leading to accurate biological interpretations of varied data types acquired with different platfor...
journal_title：Nature biotechnology
pub_type： 杂志文章
doi：10.1038/s41587-020-00748-9
更新日期：2020-12-21 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 biotechnology
pub_type： 已发布勘误
doi：10.1038/s41587-019-0253-5
更新日期：2019-09-01 00:00:00
abstract：:The Human Proteome Organization (HUPO) recently completed the first large-scale collaborative study to characterize the human serum and plasma proteomes. The study was carried out in different locations and used diverse methods and instruments to compare and integrate tandem mass spectrometry (MS/MS) data on aliquots ...
journal_title：Nature biotechnology
pub_type： 杂志文章
doi：10.1038/nbt1183
更新日期：2006-03-01 00:00:00
abstract：:A wealth of molecular interaction data is available in the literature, ranging from large-scale datasets to a single interaction confirmed by several different techniques. These data are all too often reported either as free text or in tables of variable format, and are often missing key pieces of information essentia...
journal_title：Nature biotechnology
pub_type： 杂志文章,评审
doi：10.1038/nbt1324
更新日期：2007-08-01 00:00:00
abstract：:RNA-interference (RNAi) is a potent mechanism, conserved from plants to humans for specific silencing of genes, which holds promise for functional genomics and gene-targeted therapies. Here we show that bacteria engineered to produce a short hairpin RNA (shRNA) targeting a mammalian gene induce trans-kingdom RNAi in v...
journal_title：Nature biotechnology
pub_type： 杂志文章
doi：10.1038/nbt1211
更新日期：2006-06-01 00:00:00
abstract：:Current tools for targeted RNA editing rely on the delivery of exogenous proteins or chemically modified guide RNAs, which may lead to aberrant effector activity, delivery barrier or immunogenicity. Here, we present an approach, called leveraging endogenous ADAR for programmable editing of RNA (LEAPER), that employs s...
journal_title：Nature biotechnology
pub_type： 杂志文章
doi：10.1038/s41587-019-0178-z
更新日期：2019-09-01 00:00:00
abstract：:Structural genomics has the ambitious goal of delivering three-dimensional structural information on a genome-wide scale. Yet only a small fraction of natural proteins are suitable for structure determination because of bottlenecks such as poor expression, aggregation, and misfolding of proteins, and difficulties in s...
journal_title：Nature biotechnology
pub_type： 杂志文章
doi：10.1038/nbt732
更新日期：2002-09-01 00:00:00
abstract：:Evolution of eukaryotes is mediated by sexual recombination of parental genomes. Crossovers occur in random, but homologous, positions at a frequency that depends on DNA length. As exons occupy only 1% of the human genome and introns about 24%, by far most of the crossovers occur between exons, rather than inside. The...
journal_title：Nature biotechnology
pub_type： 杂志文章,评审
doi：10.1038/88084
更新日期：2001-05-01 00:00:00
abstract：:Developments in methods for identifying antigens from infectious agents and cancers has provided exciting new opportunities in prevention and treatment through vaccination. In many of these situations, however, traditional immunization techniques do not stimulate protective immunity because they fail to fully mobilize...
journal_title：Nature biotechnology
pub_type： 杂志文章,评审
doi：10.1038/3469
更新日期：1998-11-01 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 biotechnology
pub_type： 已发布勘误
doi：10.1038/s41587-019-0292-y
更新日期：2019-11-01 00:00:00
abstract：:One-size-fits-all intravenous delivery of biologics may be giving way to alternate delivery routes that enable safer and more efficient drug administration. Michael Eisenstein reports. ...
journal_title：Nature biotechnology
pub_type： 新闻
doi：10.1038/nbt.1768
更新日期：2011-02-01 00:00:00
abstract：:Cellular function is critically regulated through degradation of substrates by the proteasome. To enable direct analysis of naturally cleaved proteasomal peptides under physiological conditions, we developed mass spectrometry analysis of proteolytic peptides (MAPP), a method for proteasomal footprinting that allows fo...
journal_title：Nature biotechnology
pub_type： 杂志文章
doi：10.1038/nbt.4279
更新日期：2018-10-22 00:00:00
abstract：:Individual genetic variation affects gene responsiveness to stimuli, often by influencing complex molecular circuits. Here we combine genomic and intermediate-scale transcriptional profiling with computational methods to identify variants that affect the responsiveness of genes to stimuli (responsiveness quantitative ...
journal_title：Nature biotechnology
pub_type： 杂志文章
doi：10.1038/nbt.2519
更新日期：2013-04-01 00:00:00
