INTERSPIA: a web application for exploring the dynamics of protein-protein interactions among multiple species.

abstract：:Ribosomal protein (rp)S5 belongs to the family of the highly conserved rp's that contains rpS7 from prokaryotes and rpS5 from eukaryotes. Alignment of rpS5/rpS7 from metazoans (Homo sapiens), fungi (Saccharomyces cerevisiae) and bacteria (Escherichia coli) shows that the proteins contain a conserved central/C-terminal...

journal_title：Nucleic acids research

authors： Lumsden T,Bentley AA,Beutler W,Ghosh A,Galkin O,Komar AA

更新日期：2010-03-01 00:00:00

abstract：:We updated the plant transcription factor (TF) database to version 2.0 (PlantTFDB 2.0, http://planttfdb.cbi.pku.edu.cn) which contains 53,319 putative TFs predicted from 49 species. We made detailed annotation including general information, domain feature, gene ontology, expression pattern and ortholog groups, as well...

journal_title：Nucleic acids research

authors： Zhang H,Jin J,Tang L,Zhao Y,Gu X,Gao G,Luo J

更新日期：2011-01-01 00:00:00

abstract：:The first step in gene expression, transcription, is modulated by the interaction of transcription factors with their corresponding binding sites on the DNA sequence. Pscan is a software tool that scans a set of sequences (e.g. promoters) from co-regulated or co-expressed genes with motifs describing the binding speci...

journal_title：Nucleic acids research

authors： Zambelli F,Pesole G,Pavesi G

更新日期：2009-07-01 00:00:00

abstract：:Post-translational modifications (PTMs) regulate many aspects of protein function and are indispensable for the spatio-temporal regulation of cellular processes. The proteome-wide identification of PTM targets has made significant progress in recent years, as has the characterization of their writers, readers, modifie...

journal_title：Nucleic acids research

authors： Teloni F,Altmeyer M

更新日期：2016-02-18 00:00:00

abstract：:This review presents detailed information about the structure of triplet repeat RNA and addresses the simple sequence repeats of normal and expanded lengths in the context of the physiological and pathogenic roles played in human cells. First, we discuss the occurrence and frequency of various trinucleotide repeats in...

journal_title：Nucleic acids research

authors： Krzyzosiak WJ,Sobczak K,Wojciechowska M,Fiszer A,Mykowska A,Kozlowski P

更新日期：2012-01-01 00:00:00

abstract：:DNA polymerases of the A and B families, and reverse transcriptases, share a common mechanism for preventing incorporation of ribonucleotides: a highly conserved active site residue obstructing the position that would be occupied by a 2' hydroxyl group on the incoming nucleotide. In the family Y (lesion bypass) polyme...

journal_title：Nucleic acids research

authors： DeLucia AM,Grindley ND,Joyce CM

更新日期：2003-07-15 00:00:00

abstract：:In this paper we report the characterization of a newly sequenced 5' upstream region of the human HLA-DRA gene. We performed (i) search for transcription factor motifs, (ii) analysis of CpG display and observed/expected frequency ratios, (iii) search for regions homologous to the 5' upstream sequences of the murine EA...

journal_title：Nucleic acids research

authors： Feriotto G,Mischiati C,Bianchi N,Rutigliano C,Giacomini P,Gambari R

更新日期：1995-05-25 00:00:00

abstract：:The hydroxyl radical is a powerful oxidant that generates DNA lesions including the stereoisomeric R and S 5',8-cyclo-2'-deoxyadenosine (cdA) and 5',8-cyclo-2'-deoxyguanosine (cdG) pairs that have been detected in cellular DNA. Unlike some other oxidatively generated DNA lesions, cdG and cdA are repaired by the human ...

journal_title：Nucleic acids research

authors： Kropachev K,Ding S,Terzidis MA,Masi A,Liu Z,Cai Y,Kolbanovskiy M,Chatgilialoglu C,Broyde S,Geacintov NE,Shafirovich V

更新日期：2014-04-01 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：:The opening of DNA double strands is extremely relevant to several biological functions, such as replication and transcription or binding of specific proteins. Such opening phenomenon is particularly sensitive to the aqueous solvent conditions in which the DNA molecule is dispersed, as it can be observed by considerin...

journal_title：Nucleic acids research

authors： Tempestini A,Cassina V,Brogioli D,Ziano R,Erba S,Giovannoni R,Cerrito MG,Salerno D,Mantegazza F

更新日期：2013-02-01 00:00:00

abstract：:Thermophilic viruses represent a novel source of genetic material and enzymes with great potential for use in biotechnology. We have isolated a number of thermophilic viruses from geothermal areas in Iceland, and by combining high throughput genome sequencing and state of the art bioinformatics we have identified a nu...

journal_title：Nucleic acids research

authors： Blondal T,Hjorleifsdottir SH,Fridjonsson OF,Aevarsson A,Skirnisdottir S,Hermannsdottir AG,Hreggvidsson GO,Smith AV,Kristjansson JK

更新日期：2003-12-15 00:00:00

abstract：:The EMBL Data Library was the first internationally supported central resource for nucleic acid sequence data. Working in close collaboration with its American counterpart, GenBank (1), the library prepares and makes available to the scientific community a comprehensive collection of the published nucleic acid sequenc...

journal_title：Nucleic acids research

authors： Hamm GH,Cameron GN

更新日期：1986-01-10 00:00:00

abstract：:Oligoribonucleotides with 2'-5' linkages have been synthesized on solid support. UV melting and CD experiments indicate complementary strands associate to give complexes with melting temperatures 30 to 40 degrees C lower than for duplexes formed by 3'-5' oligoribonucleotides with the same sequence. UV melting and imin...

journal_title：Nucleic acids research

authors： Kierzek R,He L,Turner DH

更新日期：1992-04-11 00:00:00

abstract：:The DINAMelt web server simulates the melting of one or two single-stranded nucleic acids in solution. The goal is to predict not just a melting temperature for a hybridized pair of nucleic acids, but entire equilibrium melting profiles as a function of temperature. The two molecules are not required to be complementa...

journal_title：Nucleic acids research

authors： Markham NR,Zuker M

更新日期：2005-07-01 00:00:00

abstract：:An improved method was developed for microdissection and cloning of metaphase as well as pachytene chromosomes. The protocol incorporates efficient ligation of chromosomal DNA with linker adaptors, abolishment of microcloning steps and the reduction of micromanipulation. The threshold for amplifying genomic DNA templa...

journal_title：Nucleic acids research

authors： Ponelies N,Stein N,Weber G

更新日期：1997-09-01 00:00:00

abstract：:The oncogene BMI1 encodes a polycomb group transcription factor that is required for embryonic development and self-renewal of stem cells. Despite these important functions little is known about the regulation of BMI1 expression. A cDNA microarray based search for target genes of E2F-1 in neuroblastoma cells expressin...

journal_title：Nucleic acids research

authors： Nowak K,Kerl K,Fehr D,Kramps C,Gessner C,Killmer K,Samans B,Berwanger B,Christiansen H,Lutz W

更新日期：2006-03-31 00:00:00

abstract：:We present NetCore, a novel network propagation approach based on node coreness, for phenotype-genotype associations and module identification. NetCore addresses the node degree bias in PPI networks by using node coreness in the random walk with restart procedure, and achieves improved re-ranking of genes after propag...

journal_title：Nucleic acids research

authors： Barel G,Herwig R

更新日期：2020-09-25 00:00:00

abstract：:Cellular membranes feature dynamic submicrometer-scale lateral domains termed lipid rafts, membrane rafts or glycosphingolipid-enriched microdomains (GEM). Numerous proteomics studies have been conducted on the lipid raft proteome, however, interpretation of individual studies is limited by potential undefined contami...

journal_title：Nucleic acids research

authors： Mohamed A,Shah AD,Chen D,Hill MM

更新日期：2019-01-08 00:00:00

abstract：:We have previously investigated the role of the N-terminal region of ribosomal protein S4 to participate in 30S ribosome assembly and function (1-3). In this report we extend these studies to the two fragments produced by the chemical cleavage of protein S4 at the tryptophan residue 167. We find that the carboxyl term...

journal_title：Nucleic acids research

authors： Changchien LM,Craven GR

更新日期：1985-09-11 00:00:00

abstract：:For the isolation of single stranded plasmid DNA, various E. coli and E. coli-Streptomyces shuttle plasmids were equipped with the phage f1 replication origin. The transformation of some representative Streptomyces species with plasmid vectors occurred irrespective of whether single or double stranded DNA was used. In...

journal_title：Nucleic acids research

authors： Hillemann D,Pühler A,Wohlleben W

更新日期：1991-02-25 00:00:00

abstract：:Tetramers of the arginine-rich histones H3 and H4 associate with supercoiled SV40 DNA either singly, giving tetrameric nucleoprotein complexes or in pairs giving octameric complexes, both of which are visualized as beads in the electron microscope. The relative amounts of the two complexes may be revealed by complete ...

journal_title：Nucleic acids research

authors： Thomas JO,Oudet P

更新日期：1979-10-10 00:00:00

abstract：:In phytohemagglutinin stimulated human lymphocytes the time relationship was determined between induction of the parameters mentioned. The results indicate that the induction occurred in a specific sequence. Thus, a simultaneous increase in the activity of DNA polymerase and thymidinekinase occurred after 15 h of incu...

journal_title：Nucleic acids research

authors： Tyrsted G,Munch-Petersen B

更新日期：1977-08-01 00:00:00

abstract：:Poly 2'-azido-2'-deoxyadenylic acid (Poly Az) was synthesized from 2'-azido-2'-deoxyadenosine diphosphate by polynucleotide phosphorylase. Poly (Az) has U.V. absorption properties similar to poly (A) and hypochromicity of 40% at 0.1 M Na+ and neutrality. CD curve also resembled to that of poly (A), but has smaller ell...

journal_title：Nucleic acids research

authors： Ikehara M,Fukui T,Kakiuchi N

更新日期：1976-08-01 00:00:00

abstract：:A mathematical model and a computer simulation were used to study PCR specificity. The model describes the occurrences of non-targeted PCR products formed through random primer-template interactions. The PCR simulation scans DNA sequence databases with primers pairs. According to the model prediction, PCR with complex...

journal_title：Nucleic acids research

authors： Rubin E,Levy AA

更新日期：1996-09-15 00:00:00

abstract：:Short oligo(deoxynucleoside phosphorothioate)s were analyzed as a pool of individual diastereomeric species. The composition of such mixtures, determined by means of HPLC, indicates that consecutive couplings in commonly used phosphoramidite chemistry lead to increasing contents of the Rp isomer. Methods of analysis a...

journal_title：Nucleic acids research

authors： Wilk A,Stec WJ

更新日期：1995-02-11 00:00:00

abstract：:The translational regulation of ferritin expression currently represents the only well characterized example for eukaryotic translational control by high affinity interactions between a specific cytoplasmic protein, iron regulatory factor [IRF], and an mRNA-binding site, the iron-responsive element [IRE], located in t...

journal_title：Nucleic acids research

authors： Stripecke R,Hentze MW

更新日期：1992-11-11 00:00:00

abstract：:ArrayExpress is a public repository for microarray data that supports the MIAME (Minimum Information About a Microarray Experiment) requirements and stores well-annotated raw and normalized data. As of November 2004, ArrayExpress contains data from approximately 12,000 hybridizations covering 35 species. Data can be s...

journal_title：Nucleic acids research

authors： Parkinson H,Sarkans U,Shojatalab M,Abeygunawardena N,Contrino S,Coulson R,Farne A,Lara GG,Holloway E,Kapushesky M,Lilja P,Mukherjee G,Oezcimen A,Rayner T,Rocca-Serra P,Sharma A,Sansone S,Brazma A

更新日期：2005-01-01 00:00:00

abstract：:This year's Database Issue of Nucleic Acids Research contains 152 papers that include descriptions of 54 new databases and update papers on 98 databases, of which 16 have not been previously featured in NAR As always, these databases cover a broad range of molecular biology subjects, including genome structure, gene e...

journal_title：Nucleic acids research

authors： Galperin MY,Fernández-Suárez XM,Rigden DJ

更新日期：2017-01-04 00:00:00

abstract：:A cDNA library was constructed from the mRNA of the ZR-75 oestrogen responsive human breast cancer cell line and screened for oestrogen regulated mRNA sequences. Of the recombinants isolated, 30 contained cDNA that corresponded to a single mRNA species of 2.1 kb that was induced between 10 and 15 fold by oestradiol tr...

journal_title：Nucleic acids research

authors： Westley BR,May FE

更新日期：1987-05-11 00:00:00

abstract：:The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. The Entrez system provides search and re...

journal_title：Nucleic acids research

authors： NCBI Resource Coordinators.

更新日期：2018-01-04 00:00:00