Experience

Take a look at what I have studied, where I have worked, my awards, and my publications.

Education

Doctorate in Computer science
Department of Computer science, ETH Zürich
2011 - 2014

I obtained a PhD in bioinformatics under the mentorship of Prof. Dr. sc. Gaston Gonnet and Prof. Dr. sc. Christophe Dessimoz. My graduation thesis is entitled "Computational prediction of gene function under the Open World Assumption."
Diploma in Bioprocess Engineering
Faculty of Food Technology and Biotechnology, University of Zagreb
2001 - 2005

My graduation thesis is entitled "Analysis of polyketide synthase genes in the Dictyostelium discoideum genome." I graduated with the top grade point average in the graduation year.

Career

Product trainer

Appway
2016 - present

  • Designing, creating and maintaining Appway Academy teaching materials.

  • Delivering training across various channels: in the classroom, via webinars, in private coaching sessions, and as e-learning.

Postdoctoral Fellow

Department of Computer science, ETH Zürich
2014 - 2016

  • Co-editing book on the Gene Ontology: editing a book with 21 book chapters; communicating with 27 authors; soliciting, tracking, and reviewing contributions for the chapters.

  • Teaching experience: taught lectures and practical sessions for three MSc. courses, each with about 50 students; organized oral and written student evaluations.

Research Assistant

Department of Computer science, ETH Zürich
2011 - 2014

  • Improving computational function prediction: applied and benchmarked machine learning algorithms on high-performance clusters (Bash, Darwin, and R); my results were evaluated favorably in a community assessment.Setting up a pipeline to annotate genes in an orthology database Selected trust-worthy data to include in the analysis; implemented the analysis pipeline (Darwin and Python); parsed and connected multiple databases in text format (Python); visualized results (R); case analysis.

  • Evaluating the reliability of large-scale computational predictions: developed and implemented the analysis of dozens of releases of bioinformatics databases (Darwin and R); innovative use of data visualization (R and gVis).

  • Summarizing multiple primary research articles on the topic of detecting Horizontal Gene Transfer Summarized knowledge; illustrated the text (Adobe Illustrator); the article is available for the general public on Wikipedia.

  • Statistical analysis and visualization: Provided insight into the protein function of the ferret genome (R).

  • Project management, collaboration, and tasks: collaborated on or led 10 projects, all of which were successfully completed and published in the scientific literature; presented at conferences and in scientific journals; taught lectures and practical sessions for four MSc. courses; organized student evaluations; organized two conferences; refereed for three scientific journals; provided feedback on colleagues' work.

  • Extracurricular projects: wrote articles, created visualizations, and lectored for the ETH student magazine Visionen.

Research Assistant

Ruđer Bošković Institute, Zagreb
2007 - 2011

  • Applying machine learning algorithms to assign function to bacterial proteins: applied Random Forest and k-Nearest Neighbours classifiers in binary and multi-label classification (Java, Darwin); built computational evaluation frameworks that were verified with independent \textit{in vitro} experiments.

  • Analysis of prokaryotic genomes: created an in-house mySQL database that was used in three other scientific publications (SQL and Java).

  • Project management and tasks: wrote a successful grant proposal; presented at scientific conferences and workshops.

Research Assistant

Faculty of Food Technology and Biotechnology, University of Zagreb
March - August 2007

  • Identification and annotation of polyketide synthase genes: used Hidden Markov Models; performed phylogenetic analysis; analyzed and visualized results (Perl and bioinformatics tools).

  • Collaboration and tasks: held practical sessions for MSc. students.


Honors and awards

Travel fellowship
Biocuration Conference
2014

Awarded to 6 applicants. This fellowship allowed me to hold a talk at the Biocuration Conference 2014 in Toronto (Canada) and was awarded by The International Society for Biocuration.
Best poster award
ISMB Conference Automatic Function Prediction SIG
2013

The award acknowledged my work on assessing protein function predictions in light of the Open World Assumption, as highlighted in the proceedings of the conference.
Travel fellowship
Biocuration Conference
2012

Awarded to 10 participants. This fellowship allowed me to hold a talk at the Biocuration Conference 2012 in Washington DC (USA) and was awarded by The International Society for Biocuration.
Best poster award
Biocuration conference
2012

Highlighting my work among the 159 presented, this award acknowledged my work on the quality of non-experimental curated and electronic Gene Ontology annotations, as mentioned in the Meeting Report from the fifth International Biocuration Conference.
Fellowship of the Croatian Science Foundation
May 2010 to February 2011

I wrote the project proposal to collaborate with the CBRG group at ETH Zürich. My successfully finished project scored 93 points out of 100 possible in the final evaluation.

Collaborations

I readily volunteer my skills to various causes. Contact me if we can work together! Here are some of the things I have done before.

2014 - 2015I lectored and contributed articles for the ETH Zürich student magazine VISIONEN.
July 2014I co-organized the OntoSIB meeting, held at ETH Zürich (Switzerland).
July 2012I co-organized the PhyloSIB meeting, held at ETH Zürich (Switzerland).
2011 - 2014I was a referee for Bioinformatics, Briefings in Bioinformatics, and PLOS One.

Invited talks and workshops

During my PhD at ETH Zürich I was invited to hold talks at numerous venues, some of which are listed below.


EBI/Sanger Institute, Hinxton (UK)

September 2014

The open world of protein function prediction
Metagenomics workshop, TGAC, Norwich (UK)

September 2014

Pairwise evolutionary relations; Computational function inference; A primer on the Gene Ontology; The open world of computational function annotation
OntoSIB meeting, Geneva (Switzerland)

May 2014

Phylogenetic profiling: how much input data is enough?
Biocuration 2014, Toronto (Canada)

April 2014

The importance of more data for phylogenetic profiling
Alphy/PhyloSIB 2014, Geneva (Switzerland)

February 2014

The importance of newly sequenced genomes and functional annotations for phylogenetic profiling
RA Fisher Centre Meeting, London (UK)


November 2013

Including paralogs in phylogenetic profiles improves protein function prediction
OntoSIB meeting, Geneva (Switzerland)

August 2013

Quality of Computationally Inferred Gene Ontology Annotations: new developments
Automated Function Prediction SIG 2013, Berlin (Germany)

July 2013

Assessing protein function predictions in light of the Open World Assumption
Quest for orthologs meeting, Lausanne University (Switzerland)

July 2013

Quality of Computationally Inferred Gene Ontology Annotations: new developments
Biocuration 2012, Washington DC (USA)

April 2012

Quality of Computationally Inferred Gene Ontology Annotations

Publications

You can find the list of my scientific publications on Google Scholar.