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Knowledge-based analysis Section edited by Larry Hunter

This section incorporates all aspects of knowledge-based analysis in biology including but not limited to: methods for the processing of text, ontologies and other computational representations of biological knowledge, as well as applications of knowledge-based systems for gaining insight into biology and biological data.

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1.

Research article   Open Access

Using PPI network autocorrelation in hierarchical multi-label classification trees for gene function prediction

Daniela Stojanova, Michelangelo Ceci, Donato Malerba, Sa¿o D¿eroski BMC Bioinformatics 2013, 14:285 (26 September 2013)

Abstract | Provisional PDF | PubMed

2.

Software   Open Access

DaGO-Fun: tool for Gene Ontology-based functional analysis using term information content measures

Gaston K Mazandu, Nicola J Mulder BMC Bioinformatics 2013, 14:284 (25 September 2013)

Abstract | Full text | PDF | PubMed

3.

Software   Open Access

A modular framework for biomedical concept recognition

David Campos, Sérgio Matos, José Oliveira BMC Bioinformatics 2013, 14:281 (24 September 2013)

Abstract | Full text | PDF | PubMed

4.

Software   Open Access Highly Accessed

GOParGenPy: a high throughput method to generate Gene Ontology data matrices

Ajay Kumar, Liisa Holm, Petri Toronen BMC Bioinformatics 2013, 14:242 (8 August 2013)

Abstract | Full text | PDF | ePUB | PubMed

5.

Research article   Open Access Highly Accessed

Automatic extraction of biomolecular interactions: an empirical approach

Lifeng Zhang, Daniel Berleant, Jing Ding, Eve Wurtele BMC Bioinformatics 2013, 14:234 (24 July 2013)

Abstract | Full text | PDF | ePUB | PubMed

6.

Methodology article   Open Access

CELDA – an ontology for the comprehensive representation of cells in complex systems

Stefanie Seltmann, Harald Stachelscheid, Alexander Damaschun, Ludger Jansen, Fritz Lekschas, Jean-Fred Fontaine, Throng Nghia Nguyen-Dobinsky, Ulf Leser, Andreas Kurtz BMC Bioinformatics 2013, 14:228 (17 July 2013)

Abstract | Full text | PDF | PubMed

7.

Research article   Open Access Highly Accessed

MeSH indexing based on automatically generated summaries

Antonio J Jimeno-Yepes, Laura Plaza, James G Mork, Alan R Aronson, Alberto Díaz BMC Bioinformatics 2013, 14:208 (26 June 2013)

Abstract | Full text | PDF | ePUB | PubMed

8.

Research article   Open Access Highly Accessed

Integrative relational machine-learning for understanding drug side-effect profiles

Emmanuel Bresso, Renaud Grisoni, Gino Marchetti, Arnaud Karaboga, Souchet, Marie-Dominique Devignes, Malika Smaïl-Tabbone BMC Bioinformatics 2013, 14:207 (26 June 2013)

Abstract | Full text | PDF | ePUB | PubMed

9.

Research article   Open Access Highly Accessed

Clustering cliques for graph-based summarization of the biomedical research literature

Han Zhang, Marcelo Fiszman, Dongwook Shin, Bartlomiej Wilkowski, Thomas C Rindflesch BMC Bioinformatics 2013, 14:182 (7 June 2013)

Abstract | Full text | PDF | ePUB | PubMed | Cited on BioMed Central

10.

Research article   Open Access Highly Accessed

Large-scale extraction of accurate drug-disease treatment pairs from biomedical literature for drug repurposing

Rong Xu, QuanQiu Wang BMC Bioinformatics 2013, 14:181 (6 June 2013)

Abstract | Full text | PDF | ePUB | PubMed

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