Abstract：
:Computational modelling has become increasingly common in life science research. To provide a platform to support universal sharing, easy accessibility and model reproducibility, BioModels (https://www.ebi.ac.uk/biomodels/), a repository for mathematical models, was established in 2005. The current BioModels platform allows submission of models encoded in diverse modelling formats, including SBML, CellML, PharmML, COMBINE archive, MATLAB, Mathematica, R, Python or C++. The models submitted to BioModels are curated to verify the computational representation of the biological process and the reproducibility of the simulation results in the reference publication. The curation also involves encoding models in standard formats and annotation with controlled vocabularies following MIRIAM (minimal information required in the annotation of biochemical models) guidelines. BioModels now accepts large-scale submission of auto-generated computational models. With gradual growth in content over 15 years, BioModels currently hosts about 2000 models from the published literature. With about 800 curated models, BioModels has become the world's largest repository of curated models and emerged as the third most used data resource after PubMed and Google Scholar among the scientists who use modelling in their research. Thus, BioModels benefits modellers by providing access to reliable and semantically enriched curated models in standard formats that are easy to share, reproduce and reuse.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Malik-Sheriff RS,Glont M,Nguyen TVN,Tiwari K,Roberts MG,Xavier A,Vu MT,Men J,Maire M,Kananathan S,Fairbanks EL,Meyer JP,Arankalle C,Varusai TM,Knight-Schrijver V,Li L,Dueñas-Roca C,Dass G,Keating SM,Park YM,Buso Ndoi
10.1093/nar/gkz1055subject
Has Abstractpub_date
2020-01-08 00:00:00pages
D407-D415issue
D1eissn
0305-1048issn
1362-4962pii
5614569journal_volume
48pub_type
杂志文章abstract：:The effect of amino groups attached at positions 2 and 8 of the hypoxanthine moiety in the structure, reactivity and stability of DNA duplexes and triplexes is studied by means of quantum mechanical calculations, as well as extended molecular dynamics (MD) and thermodynamic integration (MD/TI) simulations. Theoretical...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.12.2522
更新日期：2001-06-15 00:00:00
abstract：:FRS1 and FRS2, the structural genes encoding the large (alpha) and small (beta) subunits of yeast phenylalanyl-tRNA synthetase (PheRS) were placed under the control of the lacZ promoter by creating an artificial operon. The FRS2 gene was fused next to the promoter, followed by a 14 base pair intergenic sequence contai...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.8.2087
更新日期：1990-04-25 00:00:00
abstract：:We studied the interaction of ethidium bromide with rye and calf thymus chromatin. Both types of chromatin have the same dye accessibility, which is about 50% of that of DNA. From this result we conclude that the molecular structure of these two chromatins is similar. For rye, the extraction of H1 produces no change i...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/3.9.2193
更新日期：1976-09-01 00:00:00
abstract：:The 'Atlas of Genetics and Cytogenetics in Oncology and Haematology' (http://www.infobiogen.fr/services/chromcancer) is an Internet database aimed at genes involved in cancer, cytogenetics and clinical entities in cancer, and cancer-prone diseases. It presents information in concise and updated reviews (cards) or long...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.1.303
更新日期：2001-01-01 00:00:00
abstract：:As an approach to gene therapy for the respiratory manifestations of cystic fibrosis (CF), in vivo plasmid-mediated direct transfer of the normal CF transmembrane conductance regulator (CFTR) gene to the airway epithelium was investigated in mice. To evaluate the feasibility of this strategy, pRSVL, a plasmid composed...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.12.3233
更新日期：1992-06-25 00:00:00
abstract：:Rapidly evolving pathogens cause a diverse array of diseases and epidemics that threaten crop yield, food security as well as human, animal and ecosystem health. To combat infection greater comparative knowledge is required on the pathogenic process in multiple species. The Pathogen-Host Interactions database (PHI-bas...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku1165
更新日期：2015-01-01 00:00:00
abstract：:The first step in DNA cleavage at V(D)J recombination signals by RAG1 and RAG2 is creation of a nick at the heptamer/coding flank border. Under proper conditions in vitro the second step, hairpin formation, requires two signals with spacers of 12 and 23 bp, a restriction referred to as the 12/23 rule. Under these cond...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.21.4370
更新日期：1997-11-01 00:00:00
abstract：:To understand the epigenetic regulation of transcriptional response of macrophages during early-stage M. tuberculosis (Mtb) infection, we performed ChIPseq analysis of H3K4 monomethylation (H3K4me1), a marker of poised or active enhancers. De novo H3K4me1 peaks in infected cells were associated with genes implicated i...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw782
更新日期：2016-12-15 00:00:00
abstract：:We had shown previously (3) that the E. coli argE gene could be turned-on by an IS3 element inserted in orientation II near the 5' end of the gene. Here we show that this effect is due to the presence of an outward promoter located on IS3. The exact site of insertion of IS3 was determined by DNA sequencing. Using the ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.19.5935
更新日期：1982-10-11 00:00:00
abstract：:We report the first isolation and characterisation of a human Ig V lambda gene. The gene was isolated from a recombinant phage library of human chromosome 22 using a mouse Ig lambda cDNA as probe. DNA sequence analysis predicts a short leader peptide interrupted by an intron of 88 nucleotides, and a mature polypeptide...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.17.6647
更新日期：1984-09-11 00:00:00
abstract：:The cause of 50S ribosomal subunit collapse reportedly triggered by hybridization of a 14-base cDNA probe to the alpha-sarcin region of 23S rRNA was investigated by physical measurement of probe-subunit complexes in varying buffer conditions. The results reported here show that this probe was unable to hybridize to it...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.22.10817
更新日期：1988-11-25 00:00:00
abstract：:Human T-cell leukemia virus type 1 (HTLV-1) is the etiological agent of adult T-cell leukemia (ATL). The HTLV-1 basic leucine zipper protein (HBZ) is expressed in all cases of ATL and is directly associated with virus pathogenicity. The two isoforms of the HBZ protein are synthesized from antisense messenger RNAs (mRN...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky802
更新日期：2018-11-16 00:00:00
abstract：:The nucleotide sequence of a 2.14 kb fragment of Bacillus subtilis DNA containing the citG gene encoding fumarase was determined using the dideoxy chain termination method. The citG coding region of 1392 base pairs (464 codons) was identified, and the deduced Mr (50425) is in good agreement with that of the protein id...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/13.1.131
更新日期：1985-01-11 00:00:00
abstract：:We present the complete nucleotide sequence of the larval beta I-globin gene of Xenopus laevis including 240 nucleotides of the 5' flanking region and 594 nucleotides beyond the polyadenylation site. The site of transcription initiation was mapped by S1 nuclease, and the site of polyadenylation was determined by compa...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.20.7705
更新日期：1984-10-25 00:00:00
abstract：:The availability of the complete sequence of the Saccharomyces cerevisiae genome has allowed a comprehensive analysis of the genes encoding cytoplasmic ribosomal proteins in this organism. On the basis of this complete inventory a new nomenclature for the yeast ribosomal proteins is presented. ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.24.4872
更新日期：1997-12-15 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
pub_type： 杂志文章
doi：10.1093/nar/14.1.5
更新日期：1986-01-10 00:00:00
abstract：:Pre-mRNA transcripts in a variety of organisms, including plants, Drosophila and Caenorhabditis elegans, contain introns which are significantly richer in adenosine and uridine residues than their flanking exons. Previous analyses using exonic and intronic replacements between two nonequivalent 5'splice sites in the 4...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.5.1071
更新日期：1997-03-01 00:00:00
abstract：:The biogenesis of ribosomes in vivo is an essential process for cellular functions. Transcription of ribosomal RNA (rRNA) genes is the rate-limiting step in ribosome biogenesis controlled by environmental conditions. Here, we investigated the role of folate antagonist on changes of DNA double-strand breaks (DSBs) land...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw1208
更新日期：2017-03-17 00:00:00
abstract：:Single nucleotide polymorphisms (SNPs) are, together with copy number variation, the primary source of variation in the human genome. SNPs are associated with altered response to drug treatment, susceptibility to disease and other phenotypic variation. Furthermore, during genetic screens for disease-associated mutatio...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm979
更新日期：2008-01-01 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
pub_type： 杂志文章
doi：10.1093/nar/gkq943
更新日期：2011-01-01 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：:DNA dodecamers have been designed with two cytosines on each end and intervening A and T stretches, such that the oligomers have fully complementary A:T base pairs when aligned in the parallel orientation. Spectroscopic (UV, CD and IR), NMR and molecular dynamics studies have shown that oligomers having the sequences ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/30.7.1500
更新日期：2002-04-01 00:00:00
abstract：:For the rapid and sensitive detection of p53 'hot spot' mutations, we combined polymerase chain reaction based single-strand conformational polymorphism (PCR-SSCP) analysis with sequence specific-clamping by peptide nucleic acids (PNAs) in a one-step reaction tube protocol. For this purpose, we designed two PNA molecu...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.5.1356
更新日期：1998-03-01 00:00:00
abstract：:Infrared spectroscopy was used to identify hydration-sensitive structural differences between single- stranded phosphorothioate (PS) and phosphodiester (PO) oligodeoxyribonucleotides. Spectra were recorded in the mid-infrared region, 500-1800 cm-1, at relative humidities between 0 and 98%; the PS and PO spectra are su...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.16.3261
更新日期：1996-08-15 00:00:00
abstract：:An algorithm is presented which compares two restriction maps, yielding a measure of distance between the maps and relating the maps by an alignment. This new algorithm finds the minimum weighted sum of genetic events required to convert one map into the other, where the genetic events are the appearance/disappearance...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.1part1.237
更新日期：1984-01-11 00:00:00
abstract：:We present version 2 of the SPINE system for structural proteomics. SPINE is available over the web at http://nesg.org. It serves as the central hub for the Northeast Structural Genomics Consortium, allowing collaborative structural proteomics to be carried out in a distributed fashion. The core of SPINE is a laborato...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg397
更新日期：2003-06-01 00:00:00
abstract：:The catalytic strategies of small self-cleaving ribozymes often involve interactions between nucleobases and the ribonucleic acid (RNA) backbone. Here we show that multiply protonated, gaseous RNA has an intrinsic preference for the formation of ionic hydrogen bonds between adenine protonated at N3 and the phosphodies...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz574
更新日期：2019-08-22 00:00:00
abstract：:The type I insulin-like growth factor receptor (IGF-IR) is an integral component in the control of cell proliferation, differentiation and apoptosis. The IGF-IR mRNA contains an extraordinarily long (1038 nt) 5'-untranslated region (5'-UTR), and we have characterized a diverse series of proteins interacting with this ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki603
更新日期：2005-05-24 00:00:00
abstract：:We present a www server for AUGUSTUS, a novel software program for ab initio gene prediction in eukaryotic genomic sequences. Our method is based on a generalized Hidden Markov Model with a new method for modeling the intron length distribution. This method allows approximation of the true intron length distribution m...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh379
更新日期：2004-07-01 00:00:00
abstract：:Yeast tRNA Lys2 codes preferentially for AAA and contains a 2-thiouridine derivative (U) at the 5'-position of the anticodon. Removal of the 2-thio group from U by treatment with CNBr did not affect the amino acid accepting activity of the modified tRNA Lys2. CNBr treated tRNA Lys2 was active in protein synthesis but ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/3.3.523
更新日期：1976-03-01 00:00:00
