RNApredator: fast accessibility-based prediction of sRNA targets.

abstract：:Using a powerful computer-assisted analysis strategy, a large-scale search of small nucleolar RNA (snoRNA) genes in the recently released draft sequence of the rice genome was carried out. This analysis identified 120 different box C/D snoRNA genes with a total of 346 gene variants, which were predicted to guide 135 2...

journal_title：Nucleic acids research

authors： Chen CL,Liang D,Zhou H,Zhuo M,Chen YQ,Qu LH

更新日期：2003-05-15 00:00:00

abstract：:An important model system for studying the process leading to productive transcription is provided by the superfamily of nuclear receptors, which are for the most part ligand-controlled transcription factors. Over the past years several 'orphan' nuclear receptors have been isolated for which no ligand has yet been ide...

journal_title：Nucleic acids research

authors： Gawlas K,Stunnenberg HG

更新日期：2001-08-15 00:00:00

abstract：:The Protein Circular Dichroism Data Bank (PCDDB) has been in operation for more than 5 years as a public repository for archiving circular dichroism spectroscopic data and associated bioinformatics and experimental metadata. Since its inception, many improvements and new developments have been made in data display, se...

journal_title：Nucleic acids research

authors： Whitmore L,Miles AJ,Mavridis L,Janes RW,Wallace BA

更新日期：2017-01-04 00:00:00

abstract：:The surface accessibility of macromolecules plays a key role in modulating molecular recognition events. RNA is a complex and dynamic molecule involved in many aspects of gene expression. However, there are few experimental methods available to measure the accessible surface of RNA. Here, we investigate the accessible...

journal_title：Nucleic acids research

authors： Venditti V,Niccolai N,Butcher SE

更新日期：2008-03-01 00:00:00

abstract：:Cell surface mannose 6-phosphate/insulin-like growth factor II receptors (M6P/IGF2R) bind and target exogenous insulin-like growth factor II (IGF2) to the prelysosomes where it is degraded. Loss of heterozygosity (LOH) for M6P/IGF2R is found in cancers, with mutational inactivation of the remaining allele. We exploite...

journal_title：Nucleic acids research

authors： Huang Z,Wen Y,Shandilya R,Marks JR,Berchuck A,Murphy SK

更新日期：2006-01-23 00:00:00

abstract：:Oligodeoxyribonucleotides containing N4-methoxycytosine (mo4C), N4-methoxy-5-methylcytosine (mo4m5C) and other base-analogues were synthesised and used to compare the stabilities of duplexes containing mo4C.A and mo4C.G base pairs with those containing normal and mismatch pairs. The Tm values and other thermodynamic p...

journal_title：Nucleic acids research

authors： Anand NN,Brown DM,Salisbury SA

更新日期：1987-10-26 00:00:00

abstract：:Insertion/deletion (indel) is one of the most common methods of protein sequence variation. Recent studies showed that indels could affect their flanking regions and they are important for protein function and evolution. Here, we describe the Indel Flanking Region Database (IndelFR, http://indel.bioinfo.sdu.edu.cn), w...

journal_title：Nucleic acids research

authors： Zhang Z,Xing C,Wang L,Gong B,Liu H

更新日期：2012-01-01 00:00:00

abstract：:Aging research is a multi-disciplinary field encompassing knowledge from many areas of basic, applied and clinical research. Age-related processes occur on molecular, cellular, tissue, organ, system, organismal and even psychological levels, trigger the onset of multiple debilitating diseases and lead to a loss of fun...

journal_title：Nucleic acids research

authors： Moskalev A,Zhikrivetskaya S,Shaposhnikov M,Dobrovolskaya E,Gurinovich R,Kuryan O,Pashuk A,Jellen LC,Aliper A,Peregudov A,Zhavoronkov A

更新日期：2016-01-04 00:00:00

abstract：:We report, herein, a new class of RNAi trigger molecules based on the unconventional parallel hybridization of two oligonucleotide chains. We have prepared and studied several parallel stranded (ps) duplexes, in which the parallel orientation is achieved through incorporation of isoguanine and isocytosine to form reve...

journal_title：Nucleic acids research

authors： Habibian M,Yahyaee-Anzahaee M,Lucic M,Moroz E,Martín-Pintado N,Di Giovanni LD,Leroux JC,Hall J,González C,Damha MJ

更新日期：2018-02-28 00:00:00

abstract：:The oncogenic transformation of normal cells into malignant, rapidly proliferating cells requires major alterations in cell physiology. For example, the transformed cells remodel their metabolic processes to supply the additional demand for cellular building blocks. We have recently demonstrated essential metabolic pr...

journal_title：Nucleic acids research

authors： Shaul YD,Yuan B,Thiru P,Nutter-Upham A,McCallum S,Lanzkron C,Bell GW,Sabatini DM

更新日期：2016-01-04 00:00:00

abstract：:Two fragments cloned from purified human satellite III DNA do not cross-react with each other. One fragment, for which a partial sequence is reported, hybridises to satellite II as well as III and is shown to originate on chromosome 1. The other cloned fragment originates from the Y chromosome. This fragment has under...

journal_title：Nucleic acids research

authors： Cooke HJ,Hindley J

更新日期：1979-07-25 00:00:00

abstract：:Transgenic mice have proven to be an effective expression system for studying developmental control of the human fetal and adult beta-globin genes. In the current work we are interested in developing the transgenic mouse system for the study of the human embryonic beta-globin gene, epsilon. An epsilon-globin gene cons...

journal_title：Nucleic acids research

authors： Shih DM,Wall RJ,Shapiro SG

更新日期：1990-09-25 00:00:00

abstract：:One of the major issues in expression profiling analysis still is to outline proper thresholds to determine differential expression, while avoiding false positives. The problem being that the variance is inversely proportional to the log of signal intensities. Aiming to solve this issue, we describe a model, expressio...

journal_title：Nucleic acids research

authors： Chuchana P,Marchand D,Nugoli M,Rodriguez C,Molinari N,Garcia-Sanz JA

更新日期：2007-01-01 00:00:00

abstract：:Accurate mapping of spliced RNA-Seq reads to genomic DNA has been known as a challenging problem. Despite significant efforts invested in developing efficient algorithms, with the human genome as a primary focus, the best solution is still not known. A recently introduced tool, TrueSight, has demonstrated better perfo...

journal_title：Nucleic acids research

authors： Burns PD,Li Y,Ma J,Borodovsky M

更新日期：2014-02-01 00:00:00

abstract：:Many, if not all, mRNAs in T.brucei start with the same sequence of 35 nucleotides, separately encoded in clustered so-called mini-exon repeats. From these mini-exon repeats a 141-nt precursor RNA with the 35-nt sequence at its 5' end is transcribed. Indirect evidence suggests that this RNA is linked in a second step ...

journal_title：Nucleic acids research

authors： Kooter JM,Borst P

更新日期：1984-12-21 00:00:00

abstract：:On the tandemly linked ribosomal genes of Xenopus laevis, the RNA polymerase transcribes past the 3' end of the 40S coding region and terminates at T3 just upstream of the gene promoter. The close proximity of T3 to the gene promoter, and the functional interdependence of these two elements, has led to the suggestion ...

journal_title：Nucleic acids research

authors： Lucchini R,Reeder RH

更新日期：1989-01-11 00:00:00

abstract：:Apolipoprotein B (apoB) is a major protein component of low density and very low density lipoproteins. Because of its large size and heterogeneity, molecular studies of apoB have been difficult, and its structure and regulation remain poorly understood. We now report the identification of human apoB cDNA clones by ant...

journal_title：Nucleic acids research

authors： Mehrabian M,Schumaker VN,Fareed GC,West R,Johnson DF,Kirchgessner T,Lin HC,Wang XB,Ma YH,Mendiaz E

更新日期：1985-10-11 00:00:00

abstract：:A cDNA encoding the 60 kDa subunit of mammalian splicing factor SF3a has been isolated. The deduced protein sequence reveals a 30% identity to the PRP9 splicing protein of the yeast S.cerevisiae. The highest homology is present in a zinc finger-like region in the C-terminal domain of both proteins. The PRP9 zinc finge...

journal_title：Nucleic acids research

authors： Krämer A,Legrain P,Mulhauser F,Gröning K,Brosi R,Bilbe G

更新日期：1994-12-11 00:00:00

abstract：:The nuclear receptor vitamin D receptor (VDR) is known to associate with two vitamin D response element (VDRE) containing chromatin regions of the insulin-like growth factor binding protein 3 (IGFBP3) gene. In non-malignant MCF-10A human mammary cells, we show that the natural VDR ligand 1α,25-dihydroxyvitamin D(3) (1...

journal_title：Nucleic acids research

authors： Malinen M,Ryynänen J,Heinäniemi M,Väisänen S,Carlberg C

更新日期：2011-01-01 00:00:00

abstract：:MicroRNAs (miRNAs) are small noncoding RNAs that act as master regulators in many biological processes. miRNAs function mainly by downregulating the expression of their gene targets. Thus, accurate prediction of miRNA targets is critical for characterization of miRNA functions. To this end, we have developed an online...

journal_title：Nucleic acids research

authors： Chen Y,Wang X

更新日期：2020-01-08 00:00:00

abstract：:BmFTZ-F1 is a Bombyx mori homologue of FTZ-F1, a positive regulator of the fushi tarazu gene of Drosophila melanogaster. In order to determine the sequence recognized with this factor, we made three sets of oligonucleotide mixture which contain 4 possible nucleotides at different positions within the previously propos...

journal_title：Nucleic acids research

authors： Ueda H,Hirose S

更新日期：1991-07-11 00:00:00

abstract：:The complete DNA sequence of pO157, the large virulence plasmid of EHEC strain O157:H7 EDL 933, is presented. The 92 kb F-like plasmid is composed of segments of putative virulence genes in a framework of replication and maintenance regions, with seven insertion sequence elements, located mostly at the boundaries of t...

journal_title：Nucleic acids research

authors： Burland V,Shao Y,Perna NT,Plunkett G,Sofia HJ,Blattner FR

更新日期：1998-09-15 00:00:00

abstract：:We searched for nucleotide excision repair in human cell-free extracts using two assays: damage-specific incision of DNA (the nicking assay) and damage-stimulated DNA synthesis (the repair synthesis assay). HeLa cell-free extract prepared by the method of Manley et al. (1980) has a weak nicking activity on UV irradiat...

journal_title：Nucleic acids research

authors： Sibghatullah,Husain I,Carlton W,Sancar A

更新日期：1989-06-26 00:00:00

abstract：:The p-n-butylphenyl- and p-n-butylanilino- substituted analogs of dGTP and dATP, respectively, were tested as inhibitors of purified human placental DNA polymerases alpha and delta. It was observed that DNA polymerase alpha activity was potently inhibited by these analogs with I0.5 values as low as the nanomolar range...

journal_title：Nucleic acids research

authors： Lee MY,Toomey NL,Wright GE

更新日期：1985-12-09 00:00:00

abstract：:RNA editing in protozoan parasites is a mitochondrial RNA processing reaction in which exclusively uridylate residues are inserted into, and less frequently deleted from, pre-mRNAs. Molecules central to the process are so-called guide RNAs (gRNAs) which function as templates in the reaction. For a detailed molecular u...

journal_title：Nucleic acids research

authors： Hermann T,Schmid B,Heumann H,Göringer HU

更新日期：1997-06-15 00:00:00

abstract：:E. coli genes for tRNAasp and tRNAtrp are transcribed by eukaryotic RNA polymerase III upon injection into nuclei of Xenopus oocytes. This indicates that some bacterial tRNA genes contain RNA polymerase III promoter sequences. We discuss evolutionary aspects of this finding. ...

journal_title：Nucleic acids research

authors： Folk WR,Hofstetter H,Birnstiel ML

更新日期：1982-11-25 00:00:00

abstract：:Interferon regulatory factors IRF-3 and IRF-7 are transcription factors essential in the activation of interferon-β (IFN-β) gene in response to viral infections. Although, both proteins recognize the same consensus IRF binding site AANNGAAA, they have distinct DNA binding preferences for sites in vivo. The X-ray struc...

journal_title：Nucleic acids research

authors： De Ioannes P,Escalante CR,Aggarwal AK

更新日期：2011-09-01 00:00:00

abstract：:Chewie Nomenclature Server (chewie-NS, https://chewbbaca.online/) allows users to share genome-based gene-by-gene typing schemas and to maintain a common nomenclature, simplifying the comparison of results. The combination between local analyses and a public repository of allelic data strikes a balance between potenti...

journal_title：Nucleic acids research

authors： Mamede R,Vila-Cerqueira P,Silva M,Carriço JA,Ramirez M

更新日期：2021-01-08 00:00:00

abstract：:ATRX and MeCP2 belong to an expanding group of chromatin-associated proteins implicated in human neurodevelopmental disorders, although their gene-regulatory activities are not fully resolved. Loss of ATRX prevents full repression of an imprinted gene network in the postnatal brain and in this study we address the mec...

journal_title：Nucleic acids research

authors： Kernohan KD,Vernimmen D,Gloor GB,Bérubé NG

更新日期：2014-07-01 00:00:00

abstract：:Termination of DNA replication in Bacillus subtilis involves the polar arrest of replication forks by a specific complex formed between the replication terminator protein (RTP) and DNA terminator sites. While determination of the crystal structure of RTP has facilitated our understanding of how a single RTP dimer inte...

journal_title：Nucleic acids research

authors： Kralicek AV,Wilson PK,Ralston GB,Wake RG,King GF

更新日期：1997-02-01 00:00:00