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Research Article

Phyletic Profiling with Cliques of Orthologs Is Enhanced by Signatures of Paralogy Relationships

  • Nives Škunca mail,

    skuncan@inf.ethz.ch

    Affiliations: ETH Zurich, Computer Science, Zurich, Switzerland, Swiss Institute of Bioinformatics, Zurich, Switzerland, Ruđer Bošković Institute, Division of Electronics, Zagreb, Croatia

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  • Matko Bošnjak,

    Affiliation: Ruđer Bošković Institute, Division of Electronics, Zagreb, Croatia

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  • Anita Kriško,

    Affiliation: Mediterranean Institute for Life Sciences, Split, Croatia

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  • Panče Panov,

    Affiliation: Jozef Stefan Institute, Department of Knowledge Technologies, Ljubljana, Slovenia

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  • Sašo Džeroski,

    Affiliations: Jozef Stefan Institute, Department of Knowledge Technologies, Ljubljana, Slovenia, Jozef Stefan International Postgraduate School, Ljubljana, Slovenia, Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Ljubljana, Slovenia

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  • Tomislav Šmuc,

    Affiliation: Ruđer Bošković Institute, Division of Electronics, Zagreb, Croatia

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  • Fran Supek

    Affiliation: Ruđer Bošković Institute, Division of Electronics, Zagreb, Croatia

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  • Published: January 03, 2013
  • DOI: 10.1371/journal.pcbi.1002852

About the Authors

Nives Škunca
ETH Zurich, Computer Science, Zurich, Switzerland
Nives Škunca
Swiss Institute of Bioinformatics, Zurich, Switzerland
Nives Škunca, Matko Bošnjak, Tomislav Šmuc, Fran Supek
Ruđer Bošković Institute, Division of Electronics, Zagreb, Croatia
Anita Kriško
Mediterranean Institute for Life Sciences, Split, Croatia
Panče Panov, Sašo Džeroski
Jozef Stefan Institute, Department of Knowledge Technologies, Ljubljana, Slovenia
Sašo Džeroski
Jozef Stefan International Postgraduate School, Ljubljana, Slovenia
Sašo Džeroski
Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Ljubljana, Slovenia

Corresponding Author

Email: skuncan@inf.ethz.ch

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

Conceived and designed the experiments: NŠ SDž TS FS. Performed the experiments: NŠ PP FS. Analyzed the data: NŠ MB PP TS FS. Contributed reagents/materials/analysis tools: NŠ AK PP SDž FS. Wrote the paper: NŠ FS. Performed the experiments on Escherichia coli: AK Designed and implemented the Web site with the results: NŠ MB FS.