Current position: PhD student

About me

I am a PhD student, focusing on methodological development in comparative pangenomic to understand the adaptive potential of bacteria and the evolutionary dynamics behind the metabolic diversity of microorganisms. I am supervised by Dr Alexandra Calteau and Dr David Vallenet both of them researcher at the LABGeM. My first area of training was biology, but with the years I had a growing interest in mathematical and statistical aspects of data analysis, which lead me to began IT development. In the same time, I developed more interest for microbiology and ecosystem study as human gut microbiome for example. Today I am developing methods and software to analyze prokaryotic pangenomes and using those methods to analyze multiple species and ecosystems.

Current projects

• Thesis: Methods for comparative analysis of prokaryotic pangenomes: exploring interspecies genomic diversity for a better understanding of metabolism
• PPanGGOLiN
• PanGraph-DB : An oriented graph database for the storage and analyzes of multiple pangenomes

Experiences

• Comparative pangenomics tools development – Bioinformatician Apprentice (Master degree-second year, LABGeM, 2019-2021):
  • Development of a homologous gene family construction pipeline
  • Functional and statistical partitioning analysis
  • Integration of gene families into the Microscope platform and use for genome-wide and synteny calculations
  • Development of a defragmentation strategy
  • Use of MMSeqs2
• Metagenomics analyzes of Lactobacillus gut bacteria on the human health – Bioinformatician intern (Master degree-first year, APC Microbiome, 2019):
  • Multivariate analysis of metagenomic data with R
  • Scripting in python
  • Metabolomic analysis
  • Epidemiological study
• Metagenomic analysis to study bacterial populations with a new wastewater disinfection method (Bachelor degree-third year, CEFREM, 2018):
  • Development of a metagenomic analysis pipeline
  • Use of FROGS and Galaxy
  • Statistical analysis with R

Education

• Master of Bioinformatics and statistical modelling – Normandie Rouen University 2021
• Bachelor of Biochemistry, Molecular and Cellular Biology and Physiology – Normandie Rouen University 2018

Contributed publications

Tarini Shankar Ghosh, Jerome Arnoux & Paul W. O’Toole (2020) Metagenomic analysis reveals distinct patterns of gut lactobacillus prevalence, abundance, and geographical variation in health and disease. Gut Microbes, 12:1, 1822729, DOI:10.1080/19490976.2020.1822729