Fran Supek

Fran Supek

+385 1 456 1080

1270

Krilo 1/108

Centre for Genomic Regulation
C/ Doctor Aiguader, 88
08003 Barcelona, Spain
Phone: +34 933 160 282

Complete bibliography

Education

  • 1998 - 2004: BSc/MSc in Molecular biology at the Faculty of science, University of Zagreb, Croatia
  • Diploma thesis “INCA – codon usage analysis software and its application to prokaryotic genomes” (supervisor: Kristian Vlahoviček, Faculty of Science, University of Zagreb) >>> PDF (Croatian text, abstract in English)
  • 2005 - 2010: employed at the RBI and completed PhD program at the Faculty of science, University of Zagreb. Title of thesis: “Detecting natural selection for translational efficiency in bacterial and archaeal genomes: a machine learning approach” (supervisor: Tomislav Šmuc)
  • 2010 - : postdoc at the Centre for Genomic Regulation (CRG), Barcelona, Spain. Supported by the Marie Curie INTERPOD program. Supervisors: Toni Gabaldón, Ben Lehner.

Research Areas

Bioinformatics, Biochemistry and Molecular Biology, Genetics, Evolution and Phylogenetics, Interdisciplinary Technical Sciences, Microbiology

Projects

  • US patent application "An analyser and method for determining the relative importance of fractions of biological mixtures" (inventor)
  • minority shareholder in RBI's spin-off company BioZyne
  • project head: informational technology implentation project (iProject, 2008) "REViGO: Redundancy Elimination and Visualization of Gene Ontology Term Lists" http://revigo.irb.hr/

Awards and Achievements

  • 1997-1998: Scholarship of the City of Zagreb
  • 1998-2003: Scholarship of the Ministry of science, education and sports of Croatia
  • 2003: Award from the Dean of Faculty of science (University of Zagreb) for exceptional success in undergraduate studies
  • 2008: National Science Award – Annual Award for Junior Researchers >>> link

Classes

  • teaching:
     
    • 2004: Practical course „Introduction to bioinformatics“, Zagreb, Croatia. Assistant. >>> link
    • 2004, 2005 - Computer lab for students of molecular biology at the Faculty of Science, Zagreb, Croatia
    • co-mentor of a student scientific project „Horizontal Gene Transfer Analysis Using Codon Usage Patterns” by Jelena Repar – awarded the Rector’s Award at the University of Zagreb, Croatia, 2006.
  • science communication:
     

Featured Publications

Genomics:

  • Supek F, Vlahoviček K. INCA: synonymous codon usage analysis and clustering by means of self-organizing map. Bioinformatics 2004 (IF = 4.9) >>> view at publisher
  • Supek F and Šmuc T. On relevance of codon usage to expression of synthetic and natural genes in Escherichia coli. Genetics 2010 (IF = 4.1) >>> view at publisher
  • Supek F, Škunca N, Repar J, Vlahoviček K, Šmuc T. Translational selection is ubiquitous in prokaryotes. PLoS Genetics 2010 (IF = 9.5) >>> view at publisher

Drug discovery:

  • Gredičak M, Supek F et al. Computational structure-activity study directs synthesis of novel antitumor enkephalin analogs. Amino Acids 2009 (IF = 4.1) >>> view at publisher
  • Ester K, Supek F et al. Putative mechanisms of antitumor activity of cyano-substituted heteroaryles in HeLa cells. Investigational New Drugs 2010 (IF = 3.0) >>> view at publisher
  • Supek F, Šumanovac Ramljak T et al. Could LogP be a principal determinant of biological activity in 18-crown-6 ethers? Synthesis of novel active adamantane-substituted diaza-crowns. Eur J Med Chem 2011 (IF = 3.2) >>> view at publisher

Others:

  • Supek F, Bošnjak M, Škunca N, Šmuc T. REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms. PLoS One 2011 (IF = 4.4) >>> view at publisher
  • Supek F, Peharec P, Krsnik-Rasol M, Šmuc T. Enhanced analytical power of SDS-PAGE using machine learning algorithms. Proteomics 2008 (IF = 4.8) >>> view at publisher

Miscellaneous

Software I've written:

  • INCA - Interactive Codon Usage Analysis software
  • FastRandomForest – an efficient, multithreaded implemenatation of the Random Forest classifier for Java. Integrates into Weka.
  • I2SOM – for computing and visualizing self-organizing maps (Kohonen maps)

My web servers and data repositories:

  • www.adaptome.org - A repository of genome and lifestyle data for Archaea and Bacteria.
  • anticancer.irb.hr - A repository of structures, experimental data and QSAR models for molecules with antitumor activity.
  • revigo.irb.hr - REViGO: Redundancy Elimination and Visualization of Gene Ontology Term Lists
  • I collaborated on gorbi.irb.hr - Predictions of gene function in prokaryotes using phyletic profiling