Fellowship programme

During his PhD, Luis Miguel de Oliveira Vilaca studied the mechanisms generating variation and complexity of forms during animal development. His research aimed at understanding hair morphogenesis in two specific rodents - the laboratory mouse (Mus musculus) and the spiny mouse (Acomys dimidiatus) - and snake moults. He used tools of comparative phylogeny to investigate how this diversity of morphologies has been induced.  (SIB Evolutionary Development of Complexity Group, supervised by Michel Milinkovitch, at the University of Geneva; Leenaards Foundation fellowship).

Emma Ricart is working on the combination of bioinformatics tools and MS analyses for high-throughput discovery of new bioactive peptides (SIB Proteome Informatics Group, supervised by Markus Muller and Frédérique Lisacek, at the University of Geneva; University of Geneva fellowship).

Monica Ticlla started her PhD in September 2015 on a cross-talk between infectious diseases, non-communicable diseases and the gut microbiome. (SIB Computational PathoGenOmics Group, supervised by Sebastian Gagneux and Tanja Stadler, at the Swiss TPH Institute and the University of Basel; R.Geigy Foundation fellowship).

During his PhD studies, Christos Dimitrakopoulos  focused on the integration of large-scale multi - omics data to explain the extensive inter-patient tumor heterogeneity observed between patients of the same cancer type. He also designed a pipeline for the detection of biomarkers (in specific single nucleotide polymorphisms) that identify patients at risk for fast pancreatic tumor progression (Thesis completed in September 2018 in the SIB Computational Biology Group, supervised by Niko Beerenwinkel, at the ETHZ; SystemsX.ch fellowship).

Circular RNAs (circRNAs) are a newly discovered class of presumable non-coding RNAs in the mammalian transcriptome. During her PhD, Franziska Gruhl analyzed the genomic properties of circRNAs using RNA-sequencing data from different mammalian species. She has provided first evidence that the formation of many circRNAs is tightly linked to the presence of species-specific and recently active transposable elements (TEs) suggesting an overall neutral and TE-driven model of circRNA formation and evolution (Thesis completed in July 2017 in the SIB Functional Evolutionary Genomics Group, supervisor Henrik Kaessmann, at the University of Lausanne; Leenaards Foundation fellowship).

Malgorzata Nowicka has worked on statistical method development and design of computational pipelines for differential analyses of high-throughput data, including DNA, microarrays, RNA Sequencing and HDCyto data. Two of her main sub-projects were related to DTU analysis based on RNA-seq, which resulted in the DRIMSeq package, and the differential analysis of cytometry data, which resulted in the CyTOF workflow. (Thesis completed in June 2017 in the SIB Statistical Bioinformatics Group, supervised by Mark Robinson, at the University of Zurich; University of Zurich fellowship).

Structural information is key for a detailed understanding of protein function. However, experimental structure determination is an expensive and often laborious process. Computational methods for generating 3D models of proteins are therefore an attractive alternative. In his thesis, Gabriel Studer evaluates state-of-the-art modelling methods, discusses solutions for current shortcomings and provides efficient implementations thereof. The outcome of the thesis has been made available to the scientific community through the SWISS-MODEL web server (Thesis completed in June 2017 in the SIB Computational Structural Biology Group, supervised by Torsten Schwede, at the University of Basel; Swiss Foundation for Excellence and Talent in Biomedical Research fellowship).

Despite its fundamental importance, the question of what terminates growth of organs at their appropriate size is still largely unresolved. In his PhD, Jannik Vollmer has analyzed the growth of the Drosophila eye imaginal disc combining computational modelling and quantitative measurements. He found that the growth rate declines inversely proportional to the area increase and identified the dilution of the cytokine Unpaired as a possible candidate mechanism for growth control (Thesis completed in April 2017 in the SIB Computational Biology CoBi Group, supervised by Dagmar Iber, at the ETHZ; SystemsX.ch fellowship).