1998-2004: BSc/MSc in Molecular biology at the Faculty of science, Zagreb, Croatia. Diploma thesis "INCA – codon usage analysis software and its application to prokaryotic genomes " (website; supervisor: Kristian Vlahoviček).

2005-2010: PhD student at the Laboratory for Information Systems, Rudjer Boskovic Institute, Croatia. Title of thesis: "Detecting natural selection for translational efficiency in bacterial and archaeal genomes: a machine learning approach." (supervisor: Tomislav Šmuc).

During this time, I published 8 papers, of which 4 with first authorship (in Proteomics, PLoS Genetics, Genetics and Investigational New Drugs), participated in a number of conferences (ISMB, ECCB) and courses, won the Croatian National Science Award and the FameLab 2007 science communication contest. I have also contributed to the S3++ summer school for highschool students as a project leader and as the school organizer. Please refer to for a detailed CV.

2010-present: postdoc at the Comparative Genomics Group at the CRG, Barcelona, Spain, under supervision of Toni Gabaldón and Ben Lehner. Funded by a Marie Curie INTERPOD grant. Project title: "Large-scale inference of basic modes of gene regulation from microbial genomes and the implications to environmental adaptation"

Some of the software I've written:

REVIGO - a Web application that takes long lists of Gene Ontology terms and summarizes them by removing redundant GO terms. The remaining terms can be visualized in semantic similarity-based scatterplots, interactive graphs, or tag clouds.

INCA - implements many of the commonly used methods for codon usage analysis, such as the codon adaptation index (CAI), the "codon bias" and MILC distances, and PCA.

FastRandomForest - a re-implementation of the Random Forest classifier (RF) for the Weka environment that brings speed and memory use improvements over the original Weka RF.

Some keywords that describe my past research:

Fran Supek

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Joined: 2010-12-02

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