Research

I am interested in supervising excellent students on a variety of computational biology and bioinformatics projects. These are some bioinformatics-related project topics, as well as the computational skills you will acquire along the way:
 
* separation of strains in communities of eukaryotic or prokaryotic organisms, on the basis of SNPs and SVs
 computer skills: Java, visualization libraries, statistics
 
* identification of plasmids in very large microbial (bacterial and archaeal) datasets
 computer skills: machine learning, Linux command line, Python programming
 
* reconstruction of 16S sequences in metagenomic data to identify the microbial taxonomic strains
 computer skills: Linux command line, Python programming
 
* separation of phages and CRISPR elements in mixed bacterial-phage datasets on the basis of the assembly graph
 computer skills: visualization libraries, Python
 
* modeling tools for omics datasets; integration of genomics, metabolomics, transciptomics and protein-protein interaction networks.
 computer skills: machine learning (bayesian networks), clustering (PCA, tSNE, UMAP), R or Python programming
 
* visualization tools
 computer skills: Java, visualization libraries
 
* deep learning and machine learning applications to molecular biology problems
 computer skills: Python, Keras libraries
 
* reproducibiliity of data science
 computer skills:Linux command line, Docker containers
 
I mainly work with environmental data, as well as cancer data (PCAWG and TCGA).