Abstract:
:With recent advancements in techniques for cellular data acquisition, information on cellular processes has been increasing at a dramatic rate. Visualization is critical to analyzing and interpreting complex information; representing cellular processes or pathways is no exception. VISIBIOweb is a free, open-source, web-based pathway visualization and layout service for pathway models in BioPAX format. With VISIBIOweb, one can obtain well-laid-out views of pathway models using the standard notation of the Systems Biology Graphical Notation (SBGN), and can embed such views within one's web pages as desired. Pathway views may be navigated using zoom and scroll tools; pathway object properties, including any external database references available in the data, may be inspected interactively. The automatic layout component of VISIBIOweb may also be accessed programmatically from other tools using Hypertext Transfer Protocol (HTTP). The web site is free and open to all users and there is no login requirement. It is available at: http://visibioweb.patika.org.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Dilek A,Belviranli ME,Dogrusoz Udoi
10.1093/nar/gkq352subject
Has Abstractpub_date
2010-07-01 00:00:00pages
W150-4issue
Web Server issueeissn
0305-1048issn
1362-4962pii
gkq352journal_volume
38pub_type
杂志文章abstract::Atomistic molecular dynamics (MD) simulations generate a wealth of information related to the dynamics of proteins. If properly analyzed, this information can lead to new insights regarding protein function and assist wet-lab experiments. Aiming to identify interactions between individual amino acid residues and the r...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky381
更新日期:2018-07-02 00:00:00
abstract::We have investigated the attachment of the DNA to the nuclear matrix during the division cycle of the plasmodial slime mold Physarum polycephalum. The DNA of plasmodia was pulse labelled at different times during the S phase and the label distribution was studied by graded DNase digestion of the matrix-DNA complexes p...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.4.1181
更新日期:1983-02-25 00:00:00
abstract::p53 is thought to function in the maintenance of genomic stability by modulating transcription and interacting with cellular proteins to influence the cell cycle, DNA repair and apoptosis. p53 mutations occur in >50% of human cancers, and cells which lack wild type p53 accumulate karyotypic abnormalities such as ampli...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.19.3868
更新日期:1997-10-01 00:00:00
abstract::Human thymine-DNA glycosylase (TDG) is well known to excise thymine and uracil from G.T and G.U mismatches, respectively, and was therefore proposed to play a central role in the cellular defense against genetic mutation through spontaneous deamination of 5-methylcytosine and cytosine. In this study, we characterized ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg344
更新日期:2003-05-01 00:00:00
abstract::ApiDB (http://ApiDB.org) represents a unified entry point for the NIH-funded Apicomplexan Bioinformatics Resource Center (BRC) that integrates numerous database resources and multiple data types. The phylum Apicomplexa comprises numerous veterinary and medically important parasitic protozoa including human pathogenic ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl880
更新日期:2007-01-01 00:00:00
abstract::Adaptive Laboratory Evolution (ALE) has emerged as an experimental approach to discover causal mutations that confer desired phenotypic functions. ALE not only represents a controllable experimental approach to systematically discover genotype-phenotype relationships, but also allows for the revelation of the series o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky983
更新日期:2019-01-08 00:00:00
abstract::Despite the extensive use of Saccharomyces cerevisiae as a platform for synthetic biology, strain engineering remains slow and laborious. Here, we employ CRISPR/Cas9 technology to build a cloning-free toolkit that addresses commonly encountered obstacles in metabolic engineering, including chromosomal integration locu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1023
更新日期:2017-01-09 00:00:00
abstract::Fully modified 4'-thioDNA, an oligonucleotide only comprising 2'-deoxy-4'-thionucleosides, exhibited resistance to an endonuclease, in addition to preferable hybridization with RNA. Therefore, 4'-thioDNA is promising for application as a functional oligonucleotide. Fully modified 4'-thioDNA was found to behave like an...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn011
更新日期:2008-04-01 00:00:00
abstract::Primase synthesizes decaribonucleotides for priming of lagging and possibly leading strand synthesis at a replication fork. The sites of initiation by purified mouse primase were shown to be highly specific within the SV40 origin of replication. This study further examines the role of the 27-bp inverted repeat in the ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.5.1953
更新日期:1989-03-11 00:00:00
abstract::Oligoamines (spermidine, dipropylenetriamine and propylenediamine) were covalently attached to acridine via a hexamethylene linker. These oligoamine-acridine conjugates were efficiently bound to gap sites in substrate DNA, and promoted the DNA hydrolysis by a homogeneous Ce(IV)/ethylenediamine-N,N,N',N'-tetraacetate (...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg634
更新日期:2003-08-01 00:00:00
abstract::Bacteriophage Mu has one of the best studied, most efficient and largest transposition machineries of the prokaryotic world. To harness this attractive integration machinery for use in mammalian cells, we cloned the coding sequences of the phage factors MuA and MuB in a eukaryotic expression cassette and fused them to...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.23.e104
更新日期:2000-12-01 00:00:00
abstract::Only the deproteinized DNA preparations of the simian adenovirus of the type 7 (SA 7) exhibited transforming and tumorigenic activity. The complex of the SA7 DNA with terminal protein (TP) did not exhibit either transforming or tumorigenic activity in cell cultures. In contrast to the transforming potential the infect...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/6.9.3119
更新日期:1979-07-11 00:00:00
abstract::Developmental stage-specific expression of the β-type globin genes is regulated by many cis- and trans-acting components. The adult β-globin gene contains an E-box located 60 bp downstream of the transcription start site that has been shown to bind transcription factor upstream stimulatory factor (USF) and to contribu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku107
更新日期:2014-04-01 00:00:00
abstract::Eukaryotic transcription factor B (TFB) proteins are homologous to KsgA/Dim1 ribosomal RNA (rRNA) methyltransferases. The mammalian TFB1, mitochondrial (TFB1M) factor is an essential protein necessary for mitochondrial gene expression. TFB1M mediates an rRNA modification in the small ribosomal subunit and thus plays a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt547
更新日期:2013-09-01 00:00:00
abstract::The investigation of RNA structure, dynamics and biological function often requires the site-specific incorporation of non-natural moieties. Here we describe the functionalization of RNA transcripts by aldehyde-hydrazine chemistry using a simple initiator nucleotide that carries an acetal-protected aldehyde function. ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl1110
更新日期:2007-01-01 00:00:00
abstract::Residual dipolar coupling (RDC) represents one of the most exciting emerging NMR techniques for protein structure studies. However, solving a protein structure using RDC data alone is still a highly challenging problem. We report here a computer program, RDC-PROSPECT, for protein structure prediction based on a struct...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh204
更新日期:2004-01-26 00:00:00
abstract::The far upstream region of herpes simplex virus (HSV) immediate early (IE) gene 3 has previously been shown to increase gene expression in an enhancer-like manner, and to contain sequences which respond to stimulation of transcription by a virion polypeptide, Vmw65. To analyse the specific DNA sequences which mediate ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.2.929
更新日期:1986-01-24 00:00:00
abstract::The primary rRNA transcript contains a large external transcribed spacer (ETS) approximately 4,000 nucleotides in length. We have used subcloned DNA probes derived from the 5' end of the ETS in conjunction with Northern blot analysis of murine nuclear RNA to examine processing of this region. In agreement with the res...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.18.7187
更新日期:1984-09-25 00:00:00
abstract::Transcriptionally non-co-linear (NCL) transcripts can originate from trans-splicing (trans-spliced RNA; 'tsRNA') or cis-backsplicing (circular RNA; 'circRNA'). While numerous circRNAs have been detected in various species, tsRNAs remain largely uninvestigated. Here, we utilize integrative transcriptome sequencing of p...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky032
更新日期:2018-04-20 00:00:00
abstract::Puromycin, an analog of the 3' end of aminoacyl-tRNA, causes premature termination of translation by being linked non-specifically to growing polypeptide chains. Here we report the interesting phenomenon that puromycin acting as a non-inhibitor at very low concentration (e.g. 0.04 microM) can bond only to full-length ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.5.1176
更新日期:2000-03-01 00:00:00
abstract::ADAR enzymes, adenosine deaminases that act on RNA, form a family of RNA editing enzymes that convert adenosine to inosine within RNA that is completely or largely double-stranded. Site-selective A-->I editing has been detected at specific sites within a few structured pre-mRNAs of metazoans. We have analyzed the edit...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg681
更新日期:2003-08-15 00:00:00
abstract::The essential elements of the sea urchin L. variegatus U1 snRNA promoter were mapped by microinjection of a U1 maxigene into sea urchin zygotes. Two elements are required for expression: a distal sequence element (DSE) located between -318 and -300 and a proximal sequence element (PSE) centered at -55. Removal or alte...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.14.3743
更新日期:1992-07-25 00:00:00
abstract::During protein synthesis, the nascent peptide chain traverses the peptide exit tunnel of the ribosome. We monitor the co-translational movement of the nascent peptide using a fluorescent probe attached to the N-terminus of the nascent chain. Due to fluorophore quenching, the time-dependent fluorescence signal emitted ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky740
更新日期:2018-12-14 00:00:00
abstract::Chicken erythrocyte inner histones (H2A, H2B, H3 and H4) were associated with the two complementary homopolymeric polydeoxyribonucleotides and the two alternating copolymeric polydeoxyribonucleotides. No evidence for formation of chromatin-like structures was obtained for the complexes with poly(dG) . poly(dC) or poly...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/6.4.1387
更新日期:1979-04-01 00:00:00
abstract::Nucleotide sequences of three cloned restriction fragments of Tetrahymena mtDNA which showed hybridization with mitochondrial tRNA have been determined. EcoRI fragment 5 (4.1 kbp) contains the tRNAphe gene sequence with anticodon GAA; Hind III fragment 6 (2.0 kbp) the tRNAhis with anticodon GTG; and EcoRI fragment 7 (...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.9.3273
更新日期:1985-05-10 00:00:00
abstract::The rDNA cluster in Saccharomyces cerevisiae is located 450 kb from the left end and 610 kb from the right end of chromosome XII and consists of approximately 150 tandemly repeated copies of a 9.1 kb rDNA unit. To explore the biological significance of this specific chromosomal context, chromosome XII was split at bot...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl293
更新日期:2006-05-31 00:00:00
abstract::In the past year, DDBJ (http://www.ddbj.nig.ac.jp) collected and released 1,956,826 entries or 1,741,313,111 bases. The released data include approximately 90,000 ESTs and cDNAs of Macaca fascicularis, and 280 million bases of mouse GSS. In addition to the data collection, we have indexed the submitted data to the Int...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkj111
更新日期:2006-01-01 00:00:00
abstract::Transcription of ribosomal RNA genes is generally accepted to correlate with cell growth. Using primary cultures of adult bovine aortic endothelial (ABAE) cells, we have shown that transcription of rDNA in confluent cells falls to 5% of the transcription level in growing cells. Protein kinase NII appears to be a limit...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.16.6625
更新日期:1989-08-25 00:00:00
abstract::GC content bias describes the dependence between fragment count (read coverage) and GC content found in Illumina sequencing data. This bias can dominate the signal of interest for analyses that focus on measuring fragment abundance within a genome, such as copy number estimation (DNA-seq). The bias is not consistent b...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks001
更新日期:2012-05-01 00:00:00
abstract::Bovine mitochondrial (mt) phenylalanine tRNA (tRNA(Phe)), which lacks the 'conserved' GG and T psi YCG sequences, was efficiently purified by the selective hybridization method using a solid phase DNA probe. The entire nucleotide sequence of the tRNA, including modified nucleotides, was determined and its higher-order...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.3.347
更新日期:1994-02-11 00:00:00