Publications

BibTex format

@inproceedings{Kaewphan:2013,
author = {Kaewphan, S and Kreula, S and Van, Landeghem S and Van, de Peer Y and Jones, PR and Ginter, F},
pages = {8--15},
title = {Integrating Large-Scale Text Mining and Co-Expression Networks: Targeting NADP (H) Metabolism in E. coli with Event Extraction},
url = {http://bioinformatics.psb.ugent.be/pdf/publications/kaewphan_et_al.pdf},
year = {2013}
}

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TY  - CPAPER
AB  - We present an application of EVEX, a literature-scale event extraction resource, in the concrete biological use case of NADP(H)metabolism regulation inEscherichia coli. We make extensive use of the EVEX event generalization based on gene family definitionsin Ensembl Genomes, to extract cross-species candidate regulators. We manually evaluate the resulting network so as to only preservecorrect events and facilitate its integration with microarray-based co-expression data. When analysing the combined network obtainedfrom text mining and co-expression, we identify 41 candidate genes involved in triangular patterns involving both subnetworks. Severalof these candidates are of particular interest, and we discuss their biological relevance further. This study is the first to present areal-world evaluation of the EVEX resource in particular and literature-scale application of the systems emerging from the BioNLPShared Task series in general. We summarize the lessons learned from this use case in order to focus future development of EVEX andsimilar literature-scale resources.
AU  - Kaewphan,S
AU  - Kreula,S
AU  - Van,Landeghem S
AU  - Van,de Peer Y
AU  - Jones,PR
AU  - Ginter,F
EP  - 15
PY  - 2013///
SP  - 8
TI  - Integrating Large-Scale Text Mining and Co-Expression Networks: Targeting NADP (H) Metabolism in E. coli with Event Extraction
UR  - http://bioinformatics.psb.ugent.be/pdf/publications/kaewphan_et_al.pdf
ER  -

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Dr. Patrik R. Jones

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RIS format (EndNote, RefMan)