Abstract:
:BIOSMILE web search (BWS), a web-based NCBI-PubMed search application, which can analyze articles for selected biomedical verbs and give users relational information, such as subject, object, location, manner, time, etc. After receiving keyword query input, BWS retrieves matching PubMed abstracts and lists them along with snippets by order of relevancy to protein-protein interaction. Users can then select articles for further analysis, and BWS will find and mark up biomedical relations in the text. The analysis results can be viewed in the abstract text or in table form. To date, BWS has been field tested by over 30 biologists and questionnaires have shown that subjects are highly satisfied with its capabilities and usability. BWS is accessible free of charge at http://bioservices.cse.yzu.edu.tw/BWS.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Dai HJ,Huang CH,Lin RT,Tsai RT,Hsu WLdoi
10.1093/nar/gkn319subject
Has Abstractpub_date
2008-07-01 00:00:00pages
W390-8issue
Web Server issueeissn
0305-1048issn
1362-4962pii
gkn319journal_volume
36pub_type
杂志文章abstract::A successful application is reported of the multivariate curve resolution alternating least-squares method (MCR-ALS) for the analysis of nucleic acid melting and salt-induced transitions. Under conditions where several structures co-exist in a conformational equilibrium, MCR-ALS analysis of the UV and circular dichroi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gnf091
更新日期:2002-09-01 00:00:00
abstract::As shown in the accompanying paper (5), the oligonucleotide composition of the E. coli genome is highly asymmetric for sequences up to 6 bp in length when ranked from highest to lowest abundance. We show here that this largely reflects codon usage because heavily used codons were found in the highly abundant oligomers...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.6.2627
更新日期:1987-03-25 00:00:00
abstract::We present a simple and highly accurate computational method for operon prediction, based on intergenic distances and functional relationships between the protein products of contiguous genes, as defined by STRING database (Jensen,L.J., Kuhn,M., Stark,M., Chaffron,S., Creevey,C., Muller,J., Doerks,T., Julien,P., Roth,...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq254
更新日期:2010-07-01 00:00:00
abstract::Stabilization of stalled replication forks prevents excessive fork reversal or degradation, which can undermine genome integrity. The WRN protein is unique among the other human RecQ family members to possess exonuclease activity. However, the biological role of the WRN exonuclease is poorly defined. Recently, the WRN...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz431
更新日期:2019-07-26 00:00:00
abstract::Myocyte enhancer binding factor 2 (MEF2) proteins belong to the MADS box family of transcription factors and four MEF2 proteins, MEF2A, MEF2B, MEF2C and MEF2D, have been found. MEF2 proteins have been shown to play critical roles in differentiation of muscles and neuronal tissues. How transactivational activity of MEF...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.13.2836
更新日期:2001-07-01 00:00:00
abstract::The Agrobacterium tumefaciens Ti plasmid contains at least six transcriptional units (designated vir loci) which are essential for efficient crown gall tumorigenesis. Mutations in one of these loci, virE, result in a sharply attenuated virulence phenotype. In the present communication, we have analyzed the virE operon...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.2.825
更新日期:1987-01-26 00:00:00
abstract::Replacement of alpha-, beta- and gamma-phosphate groups in 2'-deoxynucleoside 5'-triphosphates (dNTP) with phosphonate groups yields a new set of dNTP mimics with potential biological and therapeutic applications. Here, we describe the synthesis of 15 new dNTPs modified at alpha-, beta- and gamma-phosphates containing...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.3.778
更新日期:1998-02-01 00:00:00
abstract::We have sequenced the 480 base pair (bp) repeating unit of the 5S RNA genes of the Dipteran fly Calliphora erythrocephala and compared this sequence to the three known 5S RNA gene sequences from the Dipteran Genus Drosophila (1,2). A striking series of five perfectly conserved homologies identically positioned within ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.21.8193
更新日期:1984-11-12 00:00:00
abstract::ZFP57 is necessary for maintaining repressive epigenetic modifications at Imprinting control regions (ICRs). In mouse embryonic stem cells (ESCs), ZFP57 binds ICRs (ICRBS) and many other loci (non-ICRBS). To address the role of ZFP57 on all its target sites, we performed high-throughput and multi-locus analyses of inb...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw505
更新日期:2016-09-30 00:00:00
abstract::We have isolated genomic clones from Xenopus borealis representing 3 different types of histone gene cluster. We show that the major type (H1, H2B, H2A, H4, H3), present at about 60-70 copies per haploid genome (1), is tandemly reiterated with a repeat length of 15 kb. In situ hybridization to mitotic chromosomes show...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.8.3471
更新日期:1988-04-25 00:00:00
abstract::The allele frequency net database (http://www.allelefrequencies.net) is an online repository that contains information on the frequencies of immune genes and their corresponding alleles in different populations. The extensive variability observed in genes and alleles related to the immune system response and its signi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1128
更新日期:2011-01-01 00:00:00
abstract::The development of genetic switches and their integrated forms (genetic circuits) with desired specifications/functions is key for success in synthetic biology. Due to the difficulty in rational design, genetic switches and circuits with desirable specifications are mostly obtained by directed evolution. Based on a vi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1070
更新日期:2011-02-01 00:00:00
abstract::We have sequenced 14 introns from the ciliate Tetrahymena thermophila and include these in an analysis of the 27 intron sequences available from seven T. thermophila protein-encoding genes. Consensus 5' and 3' splice junctions were determined and found to resemble the junctions of other nuclear pre-mRNA introns. Uniqu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.17.5133
更新日期:1990-09-11 00:00:00
abstract::MeCP2 is a methyl-CpG binding protein that can repress transcription of nearby genes. In humans, mutations in the MECP2 gene are the major cause of Rett syndrome. By searching expressed sequence tag (EST) databases we have found a novel MeCP2 splice isoform (MeCP2alpha) which encodes a distinct N-terminus. We demonstr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh349
更新日期:2004-03-19 00:00:00
abstract::Restriction endonucleases HindII and TaqI, but not SalI, were found to efficiently cleave synthetic hexadecanucleotide duplexes which contained either an A/C or a G/T mismatch within their respective restriction sites. Double-stranded M13 DNAs with identical mismatches were also cleaved under the assay conditions. The...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.5.1943
更新日期:1986-03-11 00:00:00
abstract::The complete nucleotide sequence of the Escherichia coli recB gene which encodes a subunit of the ATP-dependent DNase, Exonuclease V, has been determined. The proposed coding region for the RecB protein is 3543 nucleotides long and would encode a polypeptide of 1180 amino acids with a calculated molecular weight of 13...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.21.8573
更新日期:1986-11-11 00:00:00
abstract::Micrococcal nuclease has been shown to preferentially cleave chromatin in the region of genes actively engaged in transcription. We have used this preferential cleavage to show that the metallothionein (MT) gene in adult mouse liver, when induced to produce mRNA by injection of cadmium, becomes more susceptible to nuc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.10.3255
更新日期:1983-05-25 00:00:00
abstract::During carcinogenesis, cells are exposed to increased replication stress due to replication fork arrest at sites of DNA lesions and difficult to replicate genomic regions. Efficient fork restart and DNA repair are important for cancer cell proliferation. We previously showed that the ADP-ribosyltransferase PARP10 inte...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky658
更新日期:2018-09-28 00:00:00
abstract::A simple and rapid procedure to isolate clones carrying sequences from a specific region of the polytene chromosome of Drosophila is demonstrated. The procedure involves microdissection of the region of interest, amplification of the DNA by PCR using a primer designed to prime the synthesis nonspecifically, labeling o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.3.599
更新日期:1990-02-11 00:00:00
abstract::YY1 is ubiquitously expressed zinc finger DNA binding protein. It can act as a transcriptional repressor or activator and, when binding at the initiator element, as a component of the basal transcription complex. Binding sites for YY1 have been reported in a wide variety of promoters and they exhibit substantial diver...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.21.4457
更新日期:1995-11-11 00:00:00
abstract::Mismatch repair is a highly conserved cellular pathway responsible for repairing mismatched dsDNA. Errors are detected by the MutS enzyme, which most likely senses altered mechanical property of damaged dsDNA rather than a specific molecular pattern. While the curved shape of dsDNA in crystallographic MutS/DNA structu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa896
更新日期:2020-11-18 00:00:00
abstract::A precursor of modified nucleoside Q isolated from E. coli methyl-deficient tRNA was determined to be 7-(aminomethyl)-7-deazaguanosine. The structure was deduced by means of its chromatographic and electrophoretic mobilities, and UV and mass spectra, in addition to comparison with the synthesized authentic compound. T...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.7.2289
更新日期:1978-07-01 00:00:00
abstract::A straightforward enzymatic protocol for converting regular DNA into pseudo-complementary DNA could improve the performance of oligonucleotide microarrays by generating readily hybridizable structure-free targets. Here we screened several highly destabilizing analogs of G and C for one that could be used with 2-aminoa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn797
更新日期:2008-12-01 00:00:00
abstract::The transcription factor CHOP/GADD153 gene is induced by cellular stress and is involved in mediating apoptosis. We report the identification of a conserved region in the promoter of the CHOP gene responsible for its inducibility by endoplasmic reticulum (ER) stress. Deletion mutants of the human CHOP promoter identif...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.24.4987
更新日期:2000-12-15 00:00:00
abstract::The DNA sequence of the spacer (plus flanking) regions separating the 16S rRNA and 23S rRNA genes of two presumptive rDNA operons of the archaebacterium Methanococcus vannielii was determined. The spacers are 156 and 242 base pairs in size and they share a sequence homology of 49 base pairs following the 3' terminus o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.21.7537
更新日期:1983-11-11 00:00:00
abstract::Mitochondrial DNA (mtDNA) is entirely dependent on nuclear genes for its transcription and replication. One of these genes is TOP1MT, which encodes the mitochondrial DNA topoisomerase IB, involved in mtDNA relaxation. To elucidate TOP1MT regulation, we performed genome-wide profiling across the 60-cell line panel (the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr208
更新日期:2011-08-01 00:00:00
abstract::Phenotype analysis is commonly recognized to be of great importance for gaining insight into genetic interaction underlying inherited diseases. However, few computational contributions have been proposed for this purpose, mainly owing to lack of controlled clinical information easily accessible and structured for comp...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki454
更新日期:2005-07-01 00:00:00
abstract::Two analog uridine triphosphates tethering additional functionality, one a primary amino group and the second a mercapto group, were prepared and tested for their compatibility with in vitro RNA selection procedures. 5-(3-Aminopropyl)uridine triphosphate (UNH(2)) as a uridine substitute was a more effective substrate ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.17.3316
更新日期:2000-09-01 00:00:00
abstract::Here, we describe two freely available web servers for molecular docking. The PatchDock method performs structure prediction of protein-protein and protein-small molecule complexes. The SymmDock method predicts the structure of a homomultimer with cyclic symmetry given the structure of the monomeric unit. The inputs t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki481
更新日期:2005-07-01 00:00:00
abstract::Analyses of secondary structures proposed for ribosomal RNA's show that, of the different kinds of base pairs directly adjoining the ends of postulated double-helical regions, only A-G with A at the 5' end significantly exceeds the number expected for a random base distribution. An A(syn)-G(trans) hydrogen-bonded base...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.8.2701
更新日期:1982-04-24 00:00:00