Projects

I am passionate about making things better, and I use my strong analytical skills to drive projects forward.

During my PhD, my research interests included different aspects of computational function annotation and my work has been recognized through several awards and multiple speaking opportunities. Below you can find an overview of some of the projects I either led or was extensively involved with.

Moreover, I wrote articles, created visualizations, and lectored for the ETH student magazine Visionen during my studies. Further below are a few of the articles and visualizations I contributed.

Quality of computationally inferred gene ontology annotations

In the UniProt Gene Ontology Annotation database, the largest repository of functional annotations, over 98% of all function annotations are inferred in silico, without curator oversight. Yet these “electronic GO annotations” are generally perceived as unreliable; they are disregarded in many studies. In this article, we introduce novel methodology to systematically evaluate the quality of […]

Phylogenetic profiles with both orthologs and paralogs

While both the number and the diversity of sequenced prokaryotic genomes grow rapidly, the number of specific assignments of gene functions in the databases remains low and skewed toward the model prokaryote Escherichia coli. To aid in understanding the full set of newly sequenced genes, we created a computational model for assignment of function to […]

More data improves phylogenetic profiling

Phylogenetic profiling is a well-established approach for predicting gene function based on patterns of gene presence and absence across species. Much of the recent developments have focused on methodological improvements, but relatively little is known about the effect of input data size on the quality of predictions. In this work, we ask: how many genomes […]

Computational methods used to infer lateral gene transfer: a review

Horizontal or Lateral Gene Transfer (HGT or LGT) is the transmission of portions of genomic DNA between organisms through a process decoupled from vertical inheritance. In the presence of HGT events, different fragments of the genome are the result of different evolutionary histories. This can therefore complicate the investigations of evolutionary relatedness of lineages and species.

What would you do if you were not afraid?

Article written for Visionen 2014/4.   For me, one of the few possible answers to the question from the title would be: if I were not afraid, I would write this article.

Colours in food: should we colour-coordinate our plates?

Article written for Visionen 2015/5.   It is intuitively clear that we prefer vivid colours in our food, rather than bland brownish/beige colours. Indeed, we as a species have colour preferences that affect many aspects of our life: from buying a car (bicycle?), to selecting an outfit for a date, or choosing the colour pattern […]

A mind for numbers

Article written for Visionen 2015/3. When was the last time you felt stupid? For me, it happens practically every day. Sometimes it involves dealing with scientific papers, sometimes with a colleague who is explaining something and the concept simply cannot penetrate my thick skull, sometimes when I get a question from a student at a […]

Time management: my mix of productivity techniques

Article written for Visionen 2015/2.   Happiness is one of those concepts that is very difficult to describe, but you know it when you feel it. For me, an integral part of happiness is the feeling of being in control; unfortunately, I cannot describe how it feels to be completely in control, but I can […]

Grades visualization for Visionen

To make numbers come alive in the student magazine Visionen, I created infographics that present the overall students’ success at their courses at ETH Zürich. Some examples are shown here.

Posters for scientific conferences

During my PhD work and studies, I participated in numerous conferences, where I presented my work, both as oral presentations and poster presentations. I found poster presentations to be an especially fun and creative way to showcase my scientific contributions. Some examples of the posters I designed are shown here.