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Protocols

Biomine specifications

Information


Unique identifier OMICS_06559
Name Biomine
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Plants and Fungi
    • Arabidopsis thaliana
    • Vitis vinifera
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus

Subtool


  • PlantBiomine

Maintainer


  • person_outline Vid Podpečan

Publication for Biomine

Biomine citations

 (4)
call_split

Analysis of Glioblastoma Patients' Plasma Revealed the Presence of MicroRNAs with a Prognostic Impact on Survival and Those of Viral Origin

2015
PLoS One
PMCID: 4423889
PMID: 25950799
DOI: 10.1371/journal.pone.0125791
call_split See protocol

[…] of them. The translation step is followed by the unmodified SegMine workflow which performs a search for enriched gene sets with the SEGS algorithm, clustering of SEGS rules describing gene sets, and Biomine link discovery between the biological entities (e.g. selected genes, clusters of genes, rules, clusters of rules) []. This extension also enables adding the aggregated values from voting to th […]

call_split

MFDp2

2013
PMCID: 5424793
PMID: 28516009
DOI: 10.4161/idp.24428
call_split See protocol

[…] nt with several related studies,,,, and (2) when disregarding these unannotated residues. Our benchmark data set with the 105 annotated proteins, called DP_NEW, is available on the web server page at biomine.ece.ualberta.ca/MFDp2/. […]

library_books

Protein structure based prediction of catalytic residues

2013
BMC Bioinformatics
PMCID: 3598644
PMID: 23433045
DOI: 10.1186/1471-2105-14-63

[…] 0% sequence identity. This reduced the size of the testing set to 41. For direct performance comparison with CRpred [], we downloaded the EF-fold dataset used for training of the CRpred model (http://biomine.ece.ualberta.ca/CRpred/CRpred.htm) and removed any proteins that are within 30% sequence identity to any protein in the EF-fold dataset. We were left with 29 proteins that make up our independ […]

library_books

Evolution of motif variants and positional bias of the cyclic AMP response element

2007
BMC Evol Biol
PMCID: 1796609
PMID: 17288573
DOI: 10.1186/1471-2148-7-S1-S15

[…] The authors would like to thank members of the BioMine team from the NRC, Institute of Information Technology for their efforts in the development of the software used in this study. This study was funded by the National Research Council of Canada […]

Citations

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Biomine institution(s)
Department of knowledge technologies, Institute Josef Stefan, Ljubljana, Slovenia; National Institute of biology, Ljubljana, Slovenia

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