Abstract:
UNLABELLED:The PubMed® database of biomedical citations allows the retrieval of scientific articles studying the function of chemicals in biology and medicine. Mining millions of available citations to search reported associations between chemicals and topics of interest would require substantial human time. We have implemented the Alkemio text mining web tool and SOAP web service to help in this task. The tool uses biomedical articles discussing chemicals (including drugs), predicts their relatedness to the query topic with a naïve Bayesian classifier and ranks all chemicals by P-values computed from random simulations. Benchmarks on seven human pathways showed good retrieval performance (areas under the receiver operating characteristic curves ranged from 73.6 to 94.5%). Comparison with existing tools to retrieve chemicals associated to eight diseases showed the higher precision and recall of Alkemio when considering the top 10 candidate chemicals. Alkemio is a high performing web tool ranking chemicals for any biomedical topics and it is free to non-commercial users. AVAILABILITY:http://cbdm.mdc-berlin.de/∼medlineranker/cms/alkemio.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Gijón-Correas JA,Andrade-Navarro MA,Fontaine JFdoi
10.1093/nar/gku432subject
Has Abstractpub_date
2014-07-01 00:00:00pages
W422-9issue
Web Server issueeissn
0305-1048issn
1362-4962pii
nar/gku432journal_volume
42pub_type
杂志文章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
pub_type: 杂志文章
doi:10.1093/nar/gki480
更新日期:2005-07-01 00:00:00
abstract::While proteins are highly biochemically competent, DNA offers the ability to program, both reactions and the assembly of nanostructures, with a control that is unprecedented by any other molecule. Their joining: DNA-protein conjugates - offer the ability to combine the programmability of DNA with the competence of pro...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx707
更新日期:2017-10-13 00:00:00
abstract::We have constructed simple test-plasmids to study transcriptional enhancers in yeast. In this paper the reporter-gene is a plasmid borne deletion-substitution derivative (his-del4) of the Saccharomyces cerevisiae HIS3 gene in which the native promoter has been replaced by a dormant, susceptible pseudopromoter. We inve...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.18.8847
更新日期:1988-09-26 00:00:00
abstract::Metnase is a human protein with methylase (SET) and nuclease domains that is widely expressed, especially in proliferating tissues. Metnase promotes non-homologous end-joining (NHEJ), and knockdown causes mild hypersensitivity to ionizing radiation. Metnase also promotes plasmid and viral DNA integration, and topoisom...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq339
更新日期:2010-09-01 00:00:00
abstract::Herein, we describe a case study into the population dynamics of in vitro selection, using RNA-cleaving DNAzymes as a model system. We sought to understand how the composition of the population can change over time in response to different levels of selection pressure, and how well these changes are correlated with se...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp222
更新日期:2009-06-01 00:00:00
abstract::RNA sequencing has become an important method to perform hypothesis-free characterization of global gene expression. One of the limitations of RNA sequencing is that most sequence reads represent highly expressed transcripts, whereas low level transcripts are challenging to detect. To combine the benefits of tradition...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks816
更新日期:2013-01-07 00:00:00
abstract::In continuation with work regarding the evaluation of the energy of association of various RNA bases with various base pairs, the results of the computations of the electrostatic interaction energy of A-U base pair with four RNA bases viz. Adenine, Uracil, Guanine and Cytosine have been reported. Non bonded induced po...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.17.3983
更新日期:1980-09-11 00:00:00
abstract::Most microbes have not been cultured, and many of those that are cultivatable are difficult, dangerous or expensive to propagate or are genetically intractable. Routine cloning of large genome fractions or whole genomes from these organisms would significantly enhance their discovery and genetic and functional charact...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq119
更新日期:2010-05-01 00:00:00
abstract::Genes in the germline (micronuclear) genome of hypotrichous ciliates are interrupted by multiple, short, non-coding, AT-rich sequences called internal eliminated segments, or IESs. During conversion of a micronucleus to a somatic nucleus (macronucleus) after cell mating, all IESs are excised from the germline genes an...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/27.5.1243
更新日期:1999-03-01 00:00:00
abstract::The base excision repair DNA glycosylase MutY homolog (MYH) is responsible for removing adenines misincorporated into DNA opposite guanine or 7,8-dihydro-8-oxo-guanine (8-oxoG), thereby preventing G:C to T:A mutations. Biallelic germline mutations in the human MYH gene predispose individuals to multiple colorectal ade...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki209
更新日期:2005-01-26 00:00:00
abstract::alpha2-Macroglobulin covalently linked to poly(L)-lysine can be used as a vehicle for receptor-mediated gene transfer. This modified alpha2-macroglobulin maintains its ability to bind to the alpha2-macroglobulin receptor, and was shown to introduce a luciferase reporter gene plasmid into HepG2 human hepatoma cells in ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.19.3873
更新日期:1996-10-01 00:00:00
abstract::Here we compare several methods for predicting oligonucleotide frequencies in 691 kb of Drosophila melanogaster DNA. As in previous work on Escherichia coli and Saccharomyces cerevisiae, a relatively simple equation based on tetranucleotide frequencies can be used in predicting frequencies of higher order oligonucleot...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.14.3651
更新日期:1992-07-25 00:00:00
abstract::Zinc finger protein with KRAB and SCAN domains 3 (ZKSCAN3) has long been known as a master transcriptional repressor of autophagy. Here, we identify a novel role for ZKSCAN3 in alleviating senescence that is independent of its autophagy-related activity. Downregulation of ZKSCAN3 is observed in aged human mesenchymal ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa425
更新日期:2020-06-19 00:00:00
abstract::Active DNA demethylation (ADDM) in mammals occurs via hydroxylation of 5-methylcytosine (5mC) by TET and/or deamination by AID/APOBEC family enzymes. The resulting 5mC derivatives are removed through the base excision repair (BER) pathway. At present, it is unclear how the cell manages to eliminate closely spaced 5mC ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw059
更新日期:2016-05-05 00:00:00
abstract::The beta protein encoded by the Streptococcus pyogenes plasmid pSM19035 is a site-specific recombinase involved in both resolution of plasmid multimers into monomers and DNA inversion. It has been proposed that the DNA region to which the beta recombinase binds to mediate recombination includes a promoter from which o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.10.1855
更新日期:1994-05-25 00:00:00
abstract::We investigated how Escherichia coli ClpXP targets the helicase-nuclease (HsdR) subunit of the bacterial Type I restriction-modification enzyme EcoKI during restriction alleviation (RA). RA is a temporary reduction in endonuclease activity that occurs when Type I enzymes bind unmodified recognition sites on the host g...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku851
更新日期:2014-10-29 00:00:00
abstract::The structure of eukaryotic chromatin has been investigated by isolating and analyzing the "accessible" DNA fraction of rat liver chromatin. This DNA fraction has been isolated by titrating the chromatin with the protese-resistant D isomer of polylysine to bind the "accessible" DNA sites. After removal of chromosomal ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/2.5.667
更新日期:1975-05-01 00:00:00
abstract::Real-time PCR is being used increasingly as the method of choice for mRNA quantification, allowing rapid analysis of gene expression from low quantities of starting template. Despite a wide range of approaches, the same principles underlie all data analysis, with standard approaches broadly classified as either absolu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gng073
更新日期:2003-07-15 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
pub_type: 杂志文章
doi:10.1093/nar/gkg914
更新日期:2003-12-15 00:00:00
abstract::The chloroplast ribosomal protein CS1 is an essential component of the plastids translational machinery involved in translation initiation. Southern analysis suggests that the corresponding nuclear gene is present in one copy in the spinach genome. We have isolated and sequenced the gene (rps1) to study its expression...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.16.4153
更新日期:1992-08-25 00:00:00
abstract::The sarcomeric myosin gene, Myh7b, encodes an intronic microRNA, miR-499, which regulates cardiac and skeletal muscle biology, yet little is known about its transcriptional regulation. To identify the transcription factors involved in regulating Myh7b/miR-499 gene expression, we have mapped the transcriptional start s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks466
更新日期:2012-08-01 00:00:00
abstract::Plasmids containing a dihydrofolate reductase (DHFR) expression unit were transfected into DHFR-deficient Chinese hamster ovary (CHO) cells. Methotrexate exposure was used to select cells with amplified DHFR sequences. Three cell lines were isolated containing amplified copies of transfected DNA that had integrated in...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.4.1697
更新日期:1989-02-25 00:00:00
abstract::We analysed the basic mechanisms of signal transmission in DNA and the origins of the allostery exhibited by systems such as the ternary complex BAMHI-DNA-GRDBD. We found that perturbation information generated by a primary protein binding event travels as a wave to distant regions of DNA following a hopping mechanism...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky549
更新日期:2018-09-06 00:00:00
abstract::Bulk replicative DNA synthesis in eukaryotes is highly accurate and efficient, primarily because of two DNA polymerases (Pols): Pols δ and ε. The high fidelity of these enzymes is due to their intrinsic base selectivity and proofreading exonuclease activity which, when coupled with post-replication mismatch repair, he...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1034
更新日期:2011-03-01 00:00:00
abstract::We have compiled the DNA sequence data for E. coli available from the GENBANK and EMBL data libraries and over a period of several years independently from the literature. This is the fifth listing replacing and increasing the former listings substantially. However, in order to save space this printed version contains...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.13.2973
更新日期:1993-07-01 00:00:00
abstract::Many genetic manipulations are limited by difficulty in obtaining adequate levels of protein expression. Bioinformatic and experimental studies have identified nucleotide sequence features that may increase expression, however it is difficult to assess the relative influence of these features. Zebrafish embryos are ra...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv035
更新日期:2015-04-20 00:00:00
abstract::Comparative analysis of mutants using transfection is complicated by clones exhibiting variable levels of gene expression due to copy number differences and genomic position effects. Recombinase-mediated cassette exchange (RMCE) can overcome these problems by introducing the target gene into pre-determined chromosomal...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gni145
更新日期:2005-10-04 00:00:00
abstract::T-region transfer from wild-type Agrobacterium strains is thought to be an orientated process, starting at the right border repeat and terminating at the left border repeat of the T-region. Here we demonstrate that a right border repeat in the inverted orientation relative to the onc-genes can also mediate transfer of...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.21.10225
更新日期:1988-11-11 00:00:00
abstract::A sixty base pair DNA duplex containing the nucleotide sequence of the bacteriophage T5 early (T5P25) promoter has been constructed using a combination of chemical synthesis and enzymatic methods. Subsequent to cloning into pBR322, the promoter has been demonstrated to be biologically active being capable of directing...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.17.5921
更新日期:1983-09-10 00:00:00
abstract::The Chemical Effects in Biological Systems database (CEBS) is a comprehensive and unique toxicology resource that compiles individual and summary animal data from the National Toxicology Program (NTP) testing program and other depositors into a single electronic repository. CEBS has undergone significant updates in re...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1077
更新日期:2017-01-04 00:00:00