PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants.

abstract：:We have isolated the gene coding for the U2 analogue in trypanosomes. The 148 nucleotide long U2 RNA is capped and transcribed from a single copy gene. The 5' half of the molecule is highly homologous to mammalian U2 RNA, while the 3' half does not show any significant sequence homology with the mammalian counterpart....

journal_title：Nucleic acids research

authors： Tschudi C,Richards FF,Ullu E

更新日期：1986-11-25 00:00:00

abstract：:Inosine was prepared (15% yield) by treatment of 5-amino-1-beta-D-ribofuranosyl-4-imidazolecarboxamide (AICA-riboside) with chloroform in the presence of sodium methoxide. This ring closure can be reasonably explained by assuming the formation of dichlorocarbene from chloroform and alkali. Carbon tetrachloride or hexa...

journal_title：Nucleic acids research

authors： Okutsu M,Yamazaki A

更新日期：1976-01-01 00:00:00

abstract：:The mutation patterns at Cas9 targeted sites contain unique information regarding the nuclease activity and repair mechanisms in mammalian cells. However, analytical framework for extracting such information are lacking. Here, we present a novel computational platform called Rational InDel Meta-Analysis (RIMA) that en...

journal_title：Nucleic acids research

authors： Taheri-Ghahfarokhi A,Taylor BJM,Nitsch R,Lundin A,Cavallo AL,Madeyski-Bengtson K,Karlsson F,Clausen M,Hicks R,Mayr LM,Bohlooly-Y M,Maresca M

更新日期：2018-09-19 00:00:00

abstract：:DNA lengths in the structural repeat units of Chinese hamster ovary (CHO) and chicken erythrocyte chromatin were compared by analyzing the sizes of DNA fragments produced after treatment of nuclei with staphylococcal nuclease. The repeat length of CHO chromatin (173 +- 4 BP) is about 20 base pairs (BP) smaller than th...

journal_title：Nucleic acids research

authors： Rill RL,Nelson DA,Oosterhof DK,Hozier JC

更新日期：1977-04-01 00:00:00

abstract：:Carbohydrate-binding proteins play crucial roles across all organisms and viruses. The complexity of carbohydrate structures, together with inconsistencies in how their 3D structures are reported, has led to difficulties in characterizing the protein-carbohydrate interfaces. In order to better understand protein-carbo...

journal_title：Nucleic acids research

authors： Copoiu L,Torres PHM,Ascher DB,Blundell TL,Malhotra S

更新日期：2020-01-08 00:00:00

abstract：:Expressed Sequence Tag-based gene expression profiling can be used to discover functionally associated genes on a large scale. Currently available web servers and tools focus on finding differentially expressed genes in different samples or tissues rather than finding co-expressed genes. To fill this gap, we have deve...

journal_title：Nucleic acids research

authors： Wu X,Walker MG,Luo J,Wei L

更新日期：2005-07-01 00:00:00

abstract：:Improving the accuracy of prediction of gene starts is one of a few remaining open problems in computer prediction of prokaryotic genes. Its difficulty is caused by the absence of relatively strong sequence patterns identifying true translation initiation sites. In the current paper we show that the accuracy of gene s...

journal_title：Nucleic acids research

authors： Besemer J,Lomsadze A,Borodovsky M

更新日期：2001-06-15 00:00:00

abstract：:As protein-protein interactions are crucial in most biological processes, it is valuable to understand how and where protein pairs interact. We developed a web server HOMCOS (Homology Modeling of Complex Structure, http://biunit.naist.jp/homcos) to predict interacting protein pairs and interacting sites by homology mo...

journal_title：Nucleic acids research

authors： Fukuhara N,Kawabata T

更新日期：2008-07-01 00:00:00

abstract：:New transcripts generated by RNA polymerase II (RNAPII) are generally processed in order to form mature mRNAs. Two key processing steps include a precise cleavage within the 3' end of the pre-mRNA, and the subsequent polymerization of adenosines to produce the poly(A) tail. In yeast, these two functions are performed ...

journal_title：Nucleic acids research

authors： Guéguéniat J,Dupin AF,Stojko J,Beaurepaire L,Cianférani S,Mackereth CD,Minvielle-Sébastia L,Fribourg S

更新日期：2017-09-29 00:00:00

abstract：:Cationic aromatic tricyclic compounds including triphenylmethane dyes, phenazines, phenoxazines, acridines, phenothiazines, phenanthridinium compounds, anthracenes and xanthene dyes, which amplify cell killing in phleomycin-treated Escherichia coli B cells also modified phleomycin-induced breakdown of DNA to acid-solu...

journal_title：Nucleic acids research

authors： Grigg GW,Gero AM,Sasse WH,Sleigh MJ

更新日期：1984-12-11 00:00:00

abstract：:DNA non-homologous end joining, the major mechanism for the repair of DNA double-strands breaks (DSB) in mammalian cells requires the DNA-dependent protein kinase (DNA-PK), a complex composed of a large catalytic subunit of 460 kDa (DNA-PKcs) and the heterodimer Ku70-Ku80 that binds to double-stranded DNA ends. Mutati...

journal_title：Nucleic acids research

authors： Marangoni E,Foray N,O'Driscoll M,Douc-Rasy S,Bernier J,Bourhis J,Jeggo P

更新日期：2000-12-01 00:00:00

abstract：:Human somatic cells have essentially no telomerase activity. Telomerase is linked to tumor genesis and is a valuable marker for malignant growth. Extreme paucity of the enzyme neccessitated development of a PCR-based assay, 'telomeric repeat amplification protocol' (TRAP). Unfortunately, this method is not without dif...

journal_title：Nucleic acids research

authors： Krupp G,Kühne K,Tamm S,Klapper W,Heidorn K,Rott A,Parwaresch R

更新日期：1997-02-15 00:00:00

abstract：:PrankWeb is an online resource providing an interface to P2Rank, a state-of-the-art method for ligand binding site prediction. P2Rank is a template-free machine learning method based on the prediction of local chemical neighborhood ligandability centered on points placed on a solvent-accessible protein surface. Points...

journal_title：Nucleic acids research

authors： Jendele L,Krivak R,Skoda P,Novotny M,Hoksza D

更新日期：2019-07-02 00:00:00

abstract：:The sequence of 1000 nucleotides at the 3' end of tobacco mosaic virus RNA has been determined. The sequence contains the entire coat protein cistron as well as regions to its left and right. Sequence characterization was by conventional methods for use with uniformly 32P labeled RNA complemented by newer methods for ...

journal_title：Nucleic acids research

authors： Guilley H,Jonard G,Kukla B,Richards KE

更新日期：1979-04-01 00:00:00

abstract：:KUPS (The University of Kansas Proteomics Service) provides high-quality protein-protein interaction (PPI) data for researchers developing and evaluating computational models for predicting PPIs by allowing users to construct ready-to-use data sets of interacting protein pairs (IPPs), non-interacting protein pairs (NI...

journal_title：Nucleic acids research

authors： Chen XW,Jeong JC,Dermyer P

更新日期：2011-01-01 00:00:00

abstract：:Characterization of the ability of human interferons (IFNs) to rapidly induce genes led to the identification of the first two members of the STAT (signal transducers and activators of transcription) family, Stat1 and Stat2. To study the unique role of this transcription factor in IFN signaling under more physiologica...

journal_title：Nucleic acids research

authors： Park C,Lecomte MJ,Schindler C

更新日期：1999-11-01 00:00:00

abstract：:Aberration within the p53 tumor suppressor gene is the most frequently identified genetic damage in human cancer. Regulatory functions proposed for the p53 protein include modulation of the cell cycle, cellular differentiation, signal transduction, and gene expression. Additionally, the p53 gene product may guard the ...

journal_title：Nucleic acids research

authors： Hulla JE,Schneider RP

更新日期：1993-02-11 00:00:00

abstract：:A new method is described for the direct construction of randomly mutagenized genes by applying the polymerase chain reaction (PCR) to an oligonucleotide synthesized using doped nucleotide reservoirs. We have demonstrated the utility of this method by generating a library of mutant HIV-1 tat genes. Several arbitrarily...

journal_title：Nucleic acids research

authors： Siderovski DP,Matsuyama T,Frigerio E,Chui S,Min X,Erfle H,Sumner-Smith M,Barnett RW,Mak TW

更新日期：1992-10-25 00:00:00

abstract：:Type II restriction endonucleases Bam HI and Eco RI were covalently coupled to Sepharose. These insolubilized enzymes generated fragment patterns for several viral DNAs identical to those produced by the respective free enzymes. Conditions for optimal activity were similar for both bound and unbound forms of the enzym...

journal_title：Nucleic acids research

authors： Lee YH,Blakesley RW,Smith LA,Chirikjian JG

更新日期：1978-03-01 00:00:00

abstract：:Initiation of sporulation in Bacillus subtilis is controlled by several regulators which affect activation by phosphorylation of the key response regulator Spo0A or transcription of Spo0A-P-dependent genes. In vivo overexpression of one of these regulators, sinR , results in suppression of transcription from the Spo0A...

journal_title：Nucleic acids research

authors： Cervin MA,Lewis RJ,Brannigan JA,Spiegelman GB

更新日期：1998-08-15 00:00:00

abstract：:The nuclear suppressor allele NSM3 in strain FF1210-6C/170-E22 (E22), which suppresses a mutation of the yeast mitochondrial tRNA(Asp)gene in Saccharomyces cerevisiae, was cloned and identified. To isolate the NSM3 allele, a genomic DNA library using the vector YEp13 was constructed from strain E22. Nine YEp13 recombi...

journal_title：Nucleic acids research

authors： Chiang CS,Liaw GJ

更新日期：2000-04-01 00:00:00

abstract：:Due to the importance of protein phosphorylation in cellular control, many researches are undertaken to predict the kinase-specific phosphorylation sites. Referred to our previous work, KinasePhos 1.0, incorporated profile hidden Markov model (HMM) with flanking residues of the kinase-specific phosphorylation sites. H...

journal_title：Nucleic acids research

authors： Wong YH,Lee TY,Liang HK,Huang CM,Wang TY,Yang YH,Chu CH,Huang HD,Ko MT,Hwang JK

更新日期：2007-07-01 00:00:00

abstract：:A 9.2 kb segment of the maxi-circle of Trypanosoma brucei mitochondrial DNA contains the genes for cytochrome c oxidase subunits I and II (coxI and coxII) and seven Unassigned Reading Frames ("URFs"). The genes for coxI and coxII display considerable homology at the aminoacid level (38 and 25%, respectively) to the co...

journal_title：Nucleic acids research

authors： Hensgens LA,Brakenhoff J,De Vries BF,Sloof P,Tromp MC,Van Boom JH,Benne R

更新日期：1984-10-11 00:00:00

abstract：:Genomic DNA of African trypanosomes contains a hypermodified thymidine residue termed base J (beta-d-glucosyl-HOMedU). This modified base is localized primarily to repetitive DNA, namely the telomeres, and is implicated in the regulation of antigenic variation. The base is synthesized in a two-step pathway. Initially,...

journal_title：Nucleic acids research

authors： Cliffe LJ,Kieft R,Southern T,Birkeland SR,Marshall M,Sweeney K,Sabatini R

更新日期：2009-04-01 00:00:00

abstract：:The sequential arrangement of histones along DNA in nucleosome core particles was determined between 0.5 and 600 mM salt and from 0 to 8 M urea. These concentrations of salt and urea up to 6 M had no significant effect on the linear order of histones along DNA but 8 M urea caused the rearrangement of histones. Conform...

journal_title：Nucleic acids research

authors： Zayetz VW,Bavykin SG,Karpov VL,Mirzabekov AD

更新日期：1981-03-11 00:00:00

abstract：:RNA fragments from phage fr covering the complete or part of the replicase cistron initiation region have been used as templates in the formation of a ribosomal initiation complex in vitro. The results so obtained together with our earlier findings in a similar approach applied to fragments of the structurally related...

journal_title：Nucleic acids research

authors： Berzin V,Cielens I,Jansone I,Gren EJ

更新日期：1982-12-11 00:00:00

abstract：:Histone H3K4 methylation is an epigenetic mark associated with actively transcribed genes. This modification is catalyzed by the mixed lineage leukaemia (MLL) family of histone methyltransferases including MLL1, MLL2, MLL3, MLL4, SET1A and SET1B. The catalytic activity of this family is dependent on interactions with ...

journal_title：Nucleic acids research

authors： Kaustov L,Lemak A,Wu H,Faini M,Fan L,Fang X,Zeng H,Duan S,Allali-Hassani A,Li F,Wei Y,Vedadi M,Aebersold R,Wang Y,Houliston S,Arrowsmith CH

更新日期：2019-09-26 00:00:00

abstract：:Nitrated polycyclic aromatic hydrocarbons are common environmental pollutants, of which many are mutagenic and carcinogenic. 1-Nitropyrene is the most abundant nitrated polycyclic aromatic hydrocarbon, which causes DNA damage and is carcinogenic in experimental animals. Error-prone translesion synthesis of 1-nitropyre...

journal_title：Nucleic acids research

authors： Kirouac KN,Basu AK,Ling H

更新日期：2013-02-01 00:00:00

abstract：:DNA-damage response machinery is crucial to maintain the genomic integrity of cells, by enabling effective repair of even highly lethal lesions such as DNA double-strand breaks (DSBs). Defects in specific genes acquired through mutations, copy-number alterations or epigenetic changes can alter the balance of these pat...

journal_title：Nucleic acids research

authors： Liu C,Srihari S,Cao KA,Chenevix-Trench G,Simpson PT,Ragan MA,Khanna KK

更新日期：2014-06-01 00:00:00

abstract：:In a gene targeting experiment, the generation of a targeting construct often requires complex DNA manipulations. We developed a set of cassettes and plasmids useful for creating targeting vectors to modify the mammalian genome. A positive selection marker cassette (PGK/EM7p-npt), which included dual prokaryotic and e...

journal_title：Nucleic acids research

authors： Aoyama M,Agari K,Sun-Wada GH,Futai M,Wada Y

更新日期：2005-03-22 00:00:00