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Citations per year

Number of citations per year for the bioinformatics software tool CoPub
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Protocols

CoPub specifications

Information


Unique identifier OMICS_01178
Name CoPub
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 5.0
Stability No
Maintained No

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Publications for CoPub

CoPub citations

 (29)
library_books

Translational Biomedical Informatics and Pharmacometrics Approaches in the Drug Interactions Research

2018
PMCID: 5824109
PMID: 29193890
DOI: 10.1002/psp4.12267

[…] uruoka & Tsujii developed a search engine for Medline abstracts, called FACTA, which retrieves textual evidence of associations between the query terms and the concepts. Frijters et al. developed the CoPub discovery tool to assess the significance of co‐occurrence based on the mutual information measure and mine the new relationships between biomedical concepts. Finally, Yetisgen‐Yildiz & Pratt pr […]

library_books

Navigating the Functional Landscape of Transcription Factors via Non Negative Tensor Factorization Analysis of MEDLINE Abstracts

2017
Front Bioeng Biotechnol
PMCID: 5581332
PMID: 28894735
DOI: 10.3389/fbioe.2017.00048

[…] veral decades ago and is increasingly being discussed in the scientific community (Swanson, ; Blagosklonny and Pardee, ; Soldatova and Rzhetsky, ). Several co-occurrence based-LBD approaches, such as CoPub Mapper (Alako et al., ), PubGene (Jenssen et al., ), Chilibot (Chen and Sharp, ), and GeneWays (Rzhetsky et al., ), have been developed. Other approaches have focused on capturing higher order i […]

library_books

Enriching plausible new hypothesis generation in PubMed

2017
PLoS One
PMCID: 5498031
PMID: 28678852
DOI: 10.1371/journal.pone.0180539

[…] key limitations found in many of previous works. First, the discovered novel hypotheses were often unconfirmed with a clinical test [–]. Such studies stayed as they found the existing facts. Although CoPub Discovery conducted experimental validation for testing their new hypotheses [], its elicited hypotheses lacked context information and were merely based on the co-occurrence relationship like m […]

library_books

Prioritizing Environmental Chemicals for Obesity and Diabetes Outcomes Research: A Screening Approach Using ToxCast™ High Throughput Data

2016
Environ Health Perspect
PMCID: 4977057
PMID: 26978842
DOI: 10.1289/ehp.1510456

[…] relevant assays for our models. We considered selecting assay targets based on bioinformatics-based biological process/pathway databases, such as Kyoto Encyclopedia of Genes and Genomes (KEGG) () or CoPub (), but we decided to utilize expert opinion for several reasons. First, the gene coverage of biological pathways within ToxCast™ varies and is limited for pathways related to diabetes and obesi […]

library_books

Recent Advances and Emerging Applications in Text and Data Mining for Biomedical Discovery

2015
Brief Bioinform
PMCID: 4719073
PMID: 26420781
DOI: 10.1093/bib/bbv087

[…] use of a computational approach as an efficient, yet powerful, approach to drug discovery [, ]. Frijters et al. successfully found links between genes, drugs, pathways and diseases through their tool CoPub Discovery that mines the biomedical literature for the elucidation of new relationships between these concepts []. Based on their predictions, they validated two different drugs’ role in cell pr […]

library_books

The Disintegrin and Metalloprotease ADAM12 Is Associated with TGF β Induced Epithelial to Mesenchymal Transition

2015
PLoS One
PMCID: 4583281
PMID: 26407179
DOI: 10.1371/journal.pone.0139179

[…] Gene array data were extracted from the genomics data repository, Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/). Text mining analysis was performed using CoPub tool (http://services.nbic.nl/copub5). […]


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CoPub institution(s)
Computational Drug Discovery (CDD), CMBI, NCMLS, Radboud University Nijmegen Medical Centre, Netherlands Bioinformatics Centre (NBIC), HB Nijmegen, Molecular Design and Informatics, MSD, BH Oss and SARA Computing and Network Services, Amsterdam, Netherlands

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