Dr. Julien Prados

Bioinformatician (100%)

+41 22 379 56 63

After a bachelor in applied mathematics and a master degree in computer science (both at University Joseph Fourier, Grenoble), Julien got in 2009 a PhD in computer science from the University of Geneva in the field of machine learning.

He applied these techniques 1 year long in financial sector, and decided to change for bioinformatics. He joined Fasteris, a biotech startup pioneer in genomic sequencing with high-throughput instruments, in 2009 while the technology was only emerging. Here, he developed a solid understanding of Illumina technology and its various applications (miRNA-seq, ChIP-seq, DNA-seq, RNA-seq) on many organisms. In 2012, after almost 4 years at Fasteris, he joined the faculty of medicine as an embedded bioinformatician.

At the department of psychiatry of the faculty, he started to work on Human genotyping (whole exome sequencing) and methylation arrays. This introduced him to the complexities of reliable mutation calling and their inheritance using samtools, GATK, SnpEff and custom scripts. It was also the first time he was able to apply machine learning technics in a medical context.

After this period, his working time was split between two departments: the  department of fundamental neuroscience, and the department of microbiology. In the first one, he was involved in several single-cell transcriptomics projects where his skills in machine learning where specifically useful to handle the large datasets. In the microbiology department, he was involved in data integration projects from from multiple sources (genotyping, RNA-seq, CRAC-seq, Tn-seq) with in addition an interest to what is going on outside of the annotated genes. These works were often coupled with an identification of functional groups of genes through GO, GSEA, KEGG. And he worked frequently in collaboration with other groups.

In all posts he made extensive use of R/Bioconductor and BASH scripting, as well as cluster computing with SLURM.

DNA sequencing:
Whole Genome Sequencing
Whole Exome Sequencing
Transposon sequencing
Suppressor sequencing in pool

Variant calling and annotation:
samtools, GATK, SnpEff, DbSNP

RNA Sequencing:
RNA-Seq (bulk and single cell)
Ribosome footprinting

Functional annotation:
GSEA, GO, KEGG, Uniprot

MaxQuant (novice)

Data analysis:
Machine learning
Data visualisation
Graph-based methods

keras, igraph, ggplot2

bwa, bowtie, STAR


Model Organisms: 
Mus musculus, S. aureus, Homo sapiens


R/Bioconductor, C++, BASH


Operating Systems:
OSX, Linux, Windows


Data managment (organise, compress, archive)
Data submission (GEO, yareta)
High Performance Computing (baobab cluster)
Docker container