DEQOR: a web-based tool for the design and quality control of siRNAs

scientific article

DEQOR: a web-based tool for the design and quality control of siRNAs is …
instance of (P31):
scholarly articleQ13442814

External links are
P8978DBLP publication IDjournals/nar/HenschelBH04
P356DOI10.1093/NAR/GKH408
P8608Fatcat IDrelease_bdm7wc7iwfdwdmbsr5gstzehdy
P932PMC publication ID441546
P698PubMed publication ID15215362
P5875ResearchGate publication ID8493616

P50authorFrank BuchholzQ1443007
Bianca HabermannQ30504194
P2093author name stringAndreas Henschel
P2860cites workHuman Dicer preferentially cleaves dsRNAs at their termini without a requirement for ATPQ24539076
Gapped BLAST and PSI-BLAST: a new generation of protein database search programsQ24545170
Asymmetry in the assembly of the RNAi enzyme complexQ27860763
Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cellsQ27860926
How cells respond to interferonsQ27861006
Functional siRNAs and miRNAs Exhibit Strand BiasQ27861038
siRNAs generated by recombinant human Dicer induce specific and significant but target site-independent gene silencing in human cellsQ28115192
RNA interferenceQ28131798
Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegansQ28131807
PKR; a sentinel kinase for cellular stressQ28137774
RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervalsQ29547713
Expression profiling reveals off-target gene regulation by RNAiQ29615965
Genome-wide RNAi screening in Caenorhabditis elegansQ29617900
Genome-wide RNAi analysis of Caenorhabditis elegans fat regulatory genesQ29618442
RNAi: an ever-growing puzzleQ33338316
The silence of the genesQ34026959
Post-transcriptional gene silencing across kingdomsQ34087808
Short RNA duplexes produced by hydrolysis with Escherichia coli RNase III mediate effective RNA interference in mammalian cellsQ34098170
RNA interference--2001.Q34174586
Genome-wide RNAi analysis of growth and viability in Drosophila cellsQ34295039
RNA interference: listening to the sound of silenceQ34347832
Tissue-specific RNA interference in postimplantation mouse embryos with endoribonuclease-prepared short interfering RNAQ34392950
Genome-wide analysis of nuclear mRNA export pathways in DrosophilaQ35016875
Genomewide view of gene silencing by small interfering RNAsQ35142839
Specificity of short interfering RNA determined through gene expression signaturesQ35142877
RNA interference: gene silencing in the fast laneQ35561597
Positional effects of short interfering RNAs targeting the human coagulation trigger Tissue FactorQ39597818
Identification of genes that protect the C. elegans genome against mutations by genome-wide RNAiQ39895156
Functional genomic analysis of apoptotic DNA degradation in C. elegans.Q47068768
Gene clustering based on RNAi phenotypes of ovary-enriched genes in C. elegansQ47068918
A genome-wide screen identifies 27 genes involved in transposon silencing in C. elegansQ47068988
Recombinant Dicer efficiently converts large dsRNAs into siRNAs suitable for gene silencingQ73015350
Molecular biology. RNA interferenceQ73680096
P433issueWeb Server issue
P407language of work or nameEnglishQ1860
P921main subjectquality controlQ827792
RNA designQ55213896
P304page(s)W113-20
P577publication date2004-07-01
P1433published inNucleic Acids ResearchQ135122
P1476titleDEQOR: a web-based tool for the design and quality control of siRNAs
P478volume32

Reverse relations

cites work (P2860)
Q89831441A Quantitative Genetic Interaction Map of HIV Infection
Q50997518A computational analysis of antisense off-targets in prokaryotic organisms.
Q40124517A computational protocol for the discovery of lead molecules targeting DNA unique to pathogens.
Q42323514A targeted RNAi screen identifies factors affecting diverse stages of receptor-mediated transcytosis.
Q24813042AMOD: a morpholino oligonucleotide selection tool
Q27310922APPL endosomes are not obligatory endocytic intermediates but act as stable cargo-sorting compartments
Q28299789An endoribonuclease-prepared siRNA screen in human cells identifies genes essential for cell division
Q39041304Analysis by siRNA_profile program displays novel thermodynamic characteristics of highly functional siRNA molecules
Q60912253Arrayed functional genetic screenings in pluripotency reprogramming and differentiation
Q39787083AsiDesigner: exon-based siRNA design server considering alternative splicing
Q24301077Ataxin-2 interacts with the DEAD/H-box RNA helicase DDX6 and interferes with P-bodies and stress granules
Q67407239Attachment of the blastoderm to the vitelline envelope affects gastrulation of insects.
Q46163082Bottlenecks caused by software gaps in miRNA and RNAi research
Q28567130CAPS and Munc13 utilize distinct PIP2-linked mechanisms to promote vesicle exocytosis
Q36973526Cardiomyocyte-targeted siRNA delivery by prostaglandin E(2)-Fas siRNA polyplexes formulated with reducible poly(amido amine) for preventing cardiomyocyte apoptosis
Q57083282Codon adaptation–based control of protein expression in C. elegans
Q47035962Combined RNAi and localization for functionally dissecting long noncoding RNAs.
Q33511756Comparing artificial neural networks, general linear models and support vector machines in building predictive models for small interfering RNAs
Q35829289Comparison of approaches for rational siRNA design leading to a new efficient and transparent method
Q64922761Comprehensive functional profiling of long non-coding RNAs through a novel pan-cancer integration approach and modular analysis of their protein-coding gene association networks.
Q33244915Demonstration of two novel methods for predicting functional siRNA efficiency
Q33605316Design and evaluation of genome-wide libraries for RNA interference screens
Q40469795Direct comparison of the specificity of gene silencing using antisense oligonucleotides and RNAi.
Q38373756E-RNAi: a web application for the multi-species design of RNAi reagents--2010 update
Q24813209E-RNAi: a web application to design optimized RNAi constructs
Q36450209EP400 Deposits H3.3 into Promoters and Enhancers during Gene Activation
Q43054770Effect of GSK-3 activity, enzymatic inhibition and gene silencing by RNAi on tick oviposition and egg hatching.
Q33783170Effect of small interfering RNAs on matrix metalloproteinase 1 expression
Q30820735Efficient prediction of siRNAs with siRNArules 1.0: an open-source JAVA approach to siRNA algorithms
Q33255054Enzymatically prepared RNAi libraries
Q40327702EsiRNAs inhibit Hepatitis B virus replication in mice model more efficiently than synthesized siRNAs
Q42151459Essential notes regarding the design of functional siRNAs for efficient mammalian RNAi
Q40768389Expression of human eukaryotic initiation factor 3f oscillates with cell cycle in A549 cells and is essential for cell viability.
Q46279002Expression profile of Rhipicephalus microplus vitellogenin receptor during oogenesis.
Q37869837From RNAi screens to molecular function in embryonic stem cells.
Q33315240From sequence to function: using RNAi to elucidate mechanisms of human disease.
Q35551730Functional analysis of the microtubule-interacting transcriptome
Q36293551Gene Perturbation Atlas (GPA): a single-gene perturbation repository for characterizing functional mechanisms of coding and non-coding genes
Q33277841Genome-wide resources of endoribonuclease-prepared short interfering RNAs for specific loss-of-function studies
Q39678654Global analysis reveals SRp20- and SRp75-specific mRNPs in cycling and neural cells
Q30498761Glutathione depletion and overproduction both initiate degeneration of nigral dopaminergic neurons
Q51543146Glycogen Synthase Kinase-3 is involved in glycogen metabolism control and embryogenesis of Rhodnius prolixus.
Q24293211HOT1 is a mammalian direct telomere repeat-binding protein contributing to telomerase recruitment
Q38705939Heat shock protein 90β in the Vero cell membrane binds Japanese encephalitis virus
Q34103204Improved siRNA/shRNA functionality by mismatched duplex
Q33529082In vivo RNAi rescue in Drosophila melanogaster with genomic transgenes from Drosophila pseudoobscura
Q33264731Integrated siRNA design based on surveying of features associated with high RNAi effectiveness
Q33577868MISSION esiRNA for RNAi screening in mammalian cells
Q35125807New genes that extend Caenorhabditis elegans' lifespan in response to reproductive signals
Q35668807Non-Invasive Delivery of dsRNA into De-Waxed Tick Eggs by Electroporation
Q28914776Off-target effects dominate a large-scale RNAi screen for modulators of the TGF-β pathway and reveal microRNA regulation of TGFBR2
Q37079391Oligonucleotide antiviral therapeutics: antisense and RNA interference for highly pathogenic RNA viruses
Q56937828Production of endoribonuclease-prepared short interfering RNAs for gene silencing in mammalian cells
Q39068178Production of highly potent recombinant siRNAs in Escherichia coli
Q34362288Quantitative interaction screen of telomeric repeat-containing RNA reveals novel TERRA regulators.
Q34729434RNA interference for improving the outcome of islet transplantation.
Q58493817RNA interference in postimplantation mouse embryos
Q36412870RNAi for treating hepatitis B viral infection
Q36672243RNAi in embryonic stem cells
Q34304794RNAiAtlas: a database for RNAi (siRNA) libraries and their specificity
Q38788187Recent advances in RNAi-based strategies for therapy and prevention of HIV-1/AIDS.
Q34454386SMAD signaling regulates CXCL12 expression in the bone marrow niche, affecting homing and mobilization of hematopoietic progenitors
Q45383409Silencing potential of viral derived RNAi constructs in Tomato leaf curl virus-AC4 gene suppression in tomato.
Q35614346Targeting Human Long Noncoding Transcripts by Endoribonuclease-Prepared siRNAs
Q35917049The iBeetle large-scale RNAi screen reveals gene functions for insect development and physiology
Q64937946The lincRNA MIRAT binds to IQGAP1 and modulates the MAPK pathway in NRAS mutant melanoma.
Q33638401The major yolk protein vitellogenin interferes with the anti-plasmodium response in the malaria mosquito Anopheles gambiae
Q33753640The modulation of the symbiont/host interaction between Wolbachia pipientis and Aedes fluviatilis embryos by glycogen metabolism
Q33407022Three LIF-dependent signatures and gene clusters with atypical expression profiles, identified by transcriptome studies in mouse ES cells and early derivatives
Q84713069Transgenic RNAi applications in the mouse
Q88945804UTR-specific knockdown of Distal-less and Sp8 leads to new phenotypic variants in the flour beetle Tribolium
Q37331628Vector-based siRNA delivery strategies for high-throughput screening of novel target genes
Q24530486dsCheck: highly sensitive off-target search software for double-stranded RNA-mediated RNA interference.
Q30931909siDirect 2.0: updated software for designing functional siRNA with reduced seed-dependent off-target effect
Q36021477siRNA Design Software for a Target Gene-Specific RNA Interference.
Q24797923siRNAdb: a database of siRNA sequences

Search more.