Gene integrated set profile analysis: a context-based approach for inferring biological endpoints.

abstract：:The structural simplicity and ability to capture serial correlations make Markov models a popular modeling choice in several genomic analyses, such as identification of motifs, genes and regulatory elements. A critical, yet relatively unexplored, issue is the determination of the order of the Markov model. Most biolog...

journal_title：Nucleic acids research

authors： Narlikar L,Mehta N,Galande S,Arjunwadkar M

更新日期：2013-02-01 00:00:00

abstract：:Budding yeast telomerase is mainly activated by Tel1/Mec1 (yeast ATM/ATR) on Cdc13 from late S to G2 phase of the cell cycle. Here, we demonstrated that the telomerase-recruitment domain of Cdc13 is also phosphorylated by Cdk1 at the same cell cycle stage as the Tel1/Mec1-dependent regulation. Phosphor-specific gel an...

journal_title：Nucleic acids research

authors： Tseng SF,Shen ZJ,Tsai HJ,Lin YH,Teng SC

更新日期：2009-06-01 00:00:00

abstract：:The Dnd (DNA degradation) phenotype, reflecting a novel DNA modification by sulfur in Streptomyces lividans 1326, was strongly aggravated when one (dndB) of the five genes (dndABCDE) controlling it was mutated. Electrophoretic banding patterns of a plasmid (pHZ209), reflecting DNA degradation, displayed a clear change...

journal_title：Nucleic acids research

authors： Liang J,Wang Z,He X,Li J,Zhou X,Deng Z

更新日期：2007-01-01 00:00:00

abstract：:In Saccharomyces cerevisiae the majority of the genes for 5S rRNA lie within a 9kb rDNA sequence that is present as 100-200 tandemly-repeated copies on Chromosome XII. Following our observations that about 10% of yeast 5S rRNA exists as minor variant sequences, we screened a collection of yeast DNA fragments cloned in...

journal_title：Nucleic acids research

authors： Piper PW,Lockheart A,Patel N

更新日期：1984-05-25 00:00:00

abstract：:Recombinant plasmids which contain EcoRI fragments of tobacco chloroplast DNA carrying tRNA genes were constructed. Plasmids pTC211 and pTC293 contain the base sequences for tRNAAsn in their 1.4 and 1.1 Md EcoRI fragments, respectively. These two tRNA sequences are identical and are; 5'-TCCTCAGTAGCTCAGTGGTAGAGCGGTCGGC...

journal_title：Nucleic acids research

authors： Kato A,Shimada H,Kusuda M,Sugiura M

更新日期：1981-11-11 00:00:00

abstract：:MicroRNAs (miRNAs) are small non-coding RNAs of approximately 22 nucleotides, which negatively regulate the gene expression at the post-transcriptional level. This study describes an update of the miRTarBase (http://miRTarBase.mbc.nctu.edu.tw/) that provides information about experimentally validated miRNA-target inte...

journal_title：Nucleic acids research

authors： Chou CH,Chang NW,Shrestha S,Hsu SD,Lin YL,Lee WH,Yang CD,Hong HC,Wei TY,Tu SJ,Tsai TR,Ho SY,Jian TY,Wu HY,Chen PR,Lin NC,Huang HT,Yang TL,Pai CY,Tai CS,Chen WL,Huang CY,Liu CC,Weng SL,Liao KW,Hsu WL,Hu

更新日期：2016-01-04 00:00:00

abstract：:The miRNA Registry provides a service for the assignment of miRNA gene names prior to publication. A comprehensive and searchable database of published miRNA sequences is accessible via a web interface (http://www.sanger.ac.uk/Software/Rfam/mirna/), and all sequence and annotation data are freely available for downloa...

journal_title：Nucleic acids research

authors： Griffiths-Jones S

更新日期：2004-01-01 00:00:00

abstract：:Adenosine deaminases that act on RNA (ADARs) convert adenosine to inosine within double-stranded regions of RNA, resulting in increased transcriptomic diversity, as well as protection of cellular double-stranded RNA (dsRNA) from silencing and improper immune activation. The presence of dsRNA-binding domains (dsRBDs) i...

journal_title：Nucleic acids research

authors： Rajendren S,Manning AC,Al-Awadi H,Yamada K,Takagi Y,Hundley HA

更新日期：2018-10-12 00:00:00

abstract：:dITP may be generated from dATP by a slow, nonenzymatic hydrolysis. While [3H]dITP was degraded rapidly to [3H]deoxyinosine by HeLa cell nuclear extracts, no net degradation of [3H]dITP was observed in the presence of physiological concentrations of ATP, apparently because the extract contained deoxynucleoside diphosp...

journal_title：Nucleic acids research

authors： Myrnes B,Guddal PH,Krokan H

更新日期：1982-06-25 00:00:00

abstract：:The targeted adduction of aflatoxin B1- exo -8,9-epoxide (AFB1- exo -8,9-epoxide) to a specific guanine within an oligodeoxyribonucleotide containing multiple guanines was achieved using a DNA triplex to control sequence selectivity. The oligodeoxyribonucleotide d(AGAGAAGATTTTCTTCTCTTTTTTTTCTCTT), designated '3G', spo...

journal_title：Nucleic acids research

authors： Jones WR,Stone MP

更新日期：1998-02-15 00:00:00

abstract：:About 40% of the genes in the nematode Caenorhabditis elegans have homologs in humans. Based on the history of this model system, it is clear that the application of genetic methods to the study of this set of genes would provide important clues to their function in humans. To facilitate such genetic studies, we are e...

journal_title：Nucleic acids research

authors： Edgley M,D'Souza A,Moulder G,McKay S,Shen B,Gilchrist E,Moerman D,Barstead R

更新日期：2002-06-15 00:00:00

abstract：:The MyHits web site (http://myhits.isb-sib.ch) is an integrated service dedicated to the analysis of protein sequences. Since its first description in 2004, both the user interface and the back end of the server were improved. A number of tools (e.g. MAFFT, Jacop, Dotlet, Jalview, ESTScan) were added or updated to imp...

journal_title：Nucleic acids research

authors： Pagni M,Ioannidis V,Cerutti L,Zahn-Zabal M,Jongeneel CV,Hau J,Martin O,Kuznetsov D,Falquet L

更新日期：2007-07-01 00:00:00

abstract：:SIRT6 is critical for activating transcription of Nuclear factor (erythroid-derived 2)-like 2 (NRF2) responsive genes during oxidative stress. However, while the mechanism of SIRT6-mediated silencing is well understood, the mechanism of SIRT6-mediated transcriptional activation is unknown. Here, we employed SIRT6 sepa...

journal_title：Nucleic acids research

authors： Rezazadeh S,Yang D,Tombline G,Simon M,Regan SP,Seluanov A,Gorbunova V

更新日期：2019-09-05 00:00:00

abstract：:The combination of RNA interference (RNAi) with the tetracycline-controlled transcription activation (tet) system promises to become a powerful method for conditional gene inactivation in cultured cells and in whole organisms. Here, we tested critical sequence elements that originated from miRNA mR-30 for optimal effi...

journal_title：Nucleic acids research

authors： Berger SM,Pesold B,Reber S,Schönig K,Berger AJ,Weidenfeld I,Miao J,Berger MR,Gruss OJ,Bartsch D

更新日期：2010-09-01 00:00:00

abstract：:A fluoride-cleavable phosphoramidite for biotinylation was designed, synthesized and coupled efficiently to the 5'-end of DNA on an automatic synthesizer. The diisopropylsilyl acetal functionality was used to link the biotin moiety through a tertiary hydroxide group to the 5'-end of DNA. This linkage proved to be comp...

journal_title：Nucleic acids research

authors： Fang S,Bergstrom DE

更新日期：2003-01-15 00:00:00

abstract：:Mung bean nuclease hydrolyzes synthetic esters of 3'-nucleotides to nucleosides and phosphate esters; esters of 2'-nucleotides, and 2'--> 5' internucleotide linkages, are resistant. Esters of ribonucleotides are cleaved at 100-fold the rate for deoxyribonucleotides, the increased rate being due to presence of the 2'-h...

journal_title：Nucleic acids research

authors： Kole R,Sierakowska H,Szemplińska H,Shugar D

更新日期：1974-05-01 00:00:00

abstract：:A challenge for large-scale siRNA loss-of-function studies is the biological pleiotropy resulting from multiple modes of action of siRNA reagents. A major confounding feature of these reagents is the microRNA-like translational quelling resulting from short regions of oligonucleotide complementarity to many different ...

journal_title：Nucleic acids research

authors： Zhong R,Kim J,Kim HS,Kim M,Lum L,Levine B,Xiao G,White MA,Xie Y

更新日期：2014-07-01 00:00:00

abstract：:The macronuclear genome of Euplotes crassus contains two different genes, EFA1 and EFA2, encoding EF-1alpha proteins. They are derived from micronuclear precursors in the course of a sexual process termed conjugation. We have found that two apparent micronuclear precursors exist for EFA1. They differ in their potentia...

journal_title：Nucleic acids research

authors： Florian V,Klein A

更新日期：1996-08-15 00:00:00

abstract：:To enhance our knowledge regarding biological pathway regulation, we took an integrated approach, using the biomedical literature, ontologies, network analyses and experimental investigation to infer novel genes that could modulate biological pathways. We first constructed a novel gene network via a pairwise compariso...

journal_title：Nucleic acids research

authors： Qin T,Matmati N,Tsoi LC,Mohanty BK,Gao N,Tang J,Lawson AB,Hannun YA,Zheng WJ

更新日期：2014-10-01 00:00:00

abstract：:Escherichia coli MutY is an adenine and a weak guanine DNA glycosylase involved in reducing mutagenic effects of 7,8-dihydro-8-oxo-guanine (8-oxoG). The C-terminal domain of MutY is required for 8-oxoG recognition and is critical for mutation avoidance of oxidative damage. To determine which residues of this domain ar...

journal_title：Nucleic acids research

authors： Li L,Lu AL

更新日期：2003-06-15 00:00:00

abstract：:Protein-protein interactions regulate many essential enzymatic processes in the cell. Somatic mutations outside of an enzyme active site can therefore impact cellular function by disruption of critical protein-protein interactions. In our investigation of the cellular impact of the T304I cancer mutation of DNA Polymer...

journal_title：Nucleic acids research

authors： Fang Q,Andrews J,Sharma N,Wilk A,Clark J,Slyskova J,Koczor CA,Lans H,Prakash A,Sobol RW

更新日期：2019-07-09 00:00:00

abstract：:The hypoxia-inducible factor-1 (HIF-1) was first described as a DNA binding activity that specifically recognizes an 8 bp motif known to be essential for hypoxia-inducible erythropoietin gene transcription. Subsequently HIF-1 activity has also been found in cell lines which do not express erythropoietin, suggesting th...

journal_title：Nucleic acids research

authors： Kvietikova I,Wenger RH,Marti HH,Gassmann M

更新日期：1995-11-25 00:00:00

abstract：:Bacteriophage T4 Dda helicase has recently been shown to be active as a monomer for unwinding of short duplex oligonucleotides and for displacing streptavidin from 3'-biotinylated oligonucleotides. However, its activity for streptavidin displacement and DNA unwinding has been shown to increase as the number of Dda mol...

journal_title：Nucleic acids research

authors： Byrd AK,Raney KD

更新日期：2006-05-31 00:00:00

abstract：:Four pseudorevertants of a -10 region lacP mutation were isolated. Three of these mutations were found to activate nascent promoters. These mutations were: a -2 G/C----A/T change (-2A) promoting transcription at position +11, a +1 A/T----T/A change (+1T) promoting transcription initiation at position +13, and a +10 C/...

journal_title：Nucleic acids research

authors： Karls R,Schulz V,Jovanovich SB,Flynn S,Pak A,Reznikoff WS

更新日期：1989-05-25 00:00:00

abstract：:DNA mismatches are highly polymorphic and dynamic in nature, albeit poorly characterized structurally. We utilized the antitumour antibiotic CoII(Chro)2 (Chro = chromomycin A3) to stabilize the palindromic duplex d(TTGGCGAA) DNA with two G:G mismatches, allowing X-ray crystallography-based monitoring of mismatch polym...

journal_title：Nucleic acids research

authors： Satange R,Chuang CY,Neidle S,Hou MH

更新日期：2019-09-19 00:00:00

abstract：:Signaling pathways constitute a valuable source of information that allows interpreting the way in which alterations in gene activities affect to particular cell functionalities. There are web tools available that allow viewing and editing pathways, as well as representing experimental data on them. However, few metho...

journal_title：Nucleic acids research

authors： Sebastián-León P,Carbonell J,Salavert F,Sanchez R,Medina I,Dopazo J

更新日期：2013-07-01 00:00:00

abstract：:Self-cleaving ribozymes associated with the glmS genes of many Gram-positive bacteria are activated by binding to glucosamine-6-phosphate (GlcN6P). Representatives of the glmS ribozyme class function as metabolite-sensing riboswitches whose self-cleavage activities down-regulate the expression of GlmS enzymes that syn...

journal_title：Nucleic acids research

authors： Link KH,Guo L,Breaker RR

更新日期：2006-01-01 00:00:00

abstract：:Biological and chemical DNA fragmentation generates DNA molecules with a variety of termini, including blunt ends and single-stranded overhangs. We have developed a Next Generation Sequencing (NGS) assay, XACTLY, to interrogate the termini of fragmented DNA, information traditionally lost in standard NGS library prepa...

journal_title：Nucleic acids research

authors： Harkins KM,Schaefer NK,Troll CJ,Rao V,Kapp J,Naughton C,Shapiro B,Green RE

更新日期：2020-05-07 00:00:00

abstract：:Aside from classical loops among G-quadruplexes, the unique leaped V-shape scaffold spans over three G-tetrads, without any intervening residues. This scaffold enables a sharp reversal of two adjacent strand directions and simultaneously participates in forming the G-tetrad core. These features make this scaffold itse...

journal_title：Nucleic acids research

authors： Wan C,Fu W,Jing H,Zhang N

更新日期：2019-02-20 00:00:00

abstract：:We have adapted a method for making libraries of mutations in any specific gene for use in the fission yeast Schizosaccharomyces pombe . This elegant and simple method consists of PCR amplification of the gene of interest, followed by co-transformation of fission yeast with the PCR fragment and a linearized plasmid ve...

journal_title：Nucleic acids research

authors： Kostrub CF,Lei EP,Enoch T

更新日期：1998-10-15 00:00:00