Expertise 

Table of Contents

 

Oxford Nanopore sequencing

nanopore

Over the last 5 years I have analysed hundreds of Oxford Nanopore datasets. I have also experience in library preparation and sequencing. My expertise includes:

  • Basic genome and transcriptome alignment
  • Comparative RNA modifications calling
  • CpG methylation calling
  • RNA expression quantification and differential expression analysis
  • Graph genome assembly and analysis

 

Functional Genomics

functional

I also have experience in a wide range of methods related to functional genomics, including the following analyses:

  • Chip-Seq for histone modifications or TF binding  
  • DNA methylation analysis by bisulfite sequencing
  • RNA differential expression/splicing analysis
  • RNA modifications detection by CLIP-Seq
  • Expression QTL analysis

 

Gene therapy and virology

virology

My PhD and first postdoc were both in viral gene therapy, in particular molecular mechanisms of viral-host interactions. I developed a method for contamination detection and quality control of viral vector genomes by sequencing which is now used for human clinical trials.  I have experience in the following areas:

  • Integration site analysis (LAM-PCR, targeted sequencing)
  • Viral preparation quality control from NGS data
  • Plasmid / Bacmid / Viral genome assembly from long read data

 

Python software development

python

I absolutely ❤️ Python. It is such an elegant and multi-faceted language.  I developed and maintain a number of tools written mainly in python, with a bit of C, javascript and HTML (See Software Development).