Gaël Fortin

Research scientist, oncology and bioinformatics

My research interests involve applying interdisciplinary approaches to answer biological questions. I am especially interested in the use of bioinformatics for the analysis of high-throughput experiments to understand oncogenesis and drug resistance. My research is focused on the identification of mutation combinations that drive chemoresistance in acute myeloid leukemia. I develop open-source R packages and apps to make bioinformatics accessible for all.

fortin.gael@outlook.fr

(+33) 6 28 25 93 33

Experience

PhD student

De Thé team, Institut de Recherche Saint-Louis

Acute promyelocytic leukemia (APL) is a subcategory of acute myeloid leukemia characterized by a translocation that leads to the production of the PML-RARA fusion protein. It has been shown that the protein PML is essential for both treatment response and cure. However, its precise roles remain unclear. My PhD project aims at identifying how PML drives the cure in mouse models of APL, using a combination of genetic and high-throughput tools. This project is supervised by Pr Hugues de Thé.

October 2020 - Present

Creator of Smartjeunes and of the podcast 3,9

While they are essential to our success, many key topics are forgotten during our studies. How to stay organized? How to be more productive? How to make good decisions? To answer these questions (and more) and teach current and former students, I created Smartjeunes and 3,9. Smartjeunes is a website that tackles these issues and offers practical answers. I also discuss about these important topics in my podcast 3,9 in which I also interview people from which we can all learn and become better people.

August 2021 - Present

Master 2 intern

Puissant Lab, Institut de Recherche Saint-Louis

Phosphogo: a user-friendly app to predict kinases activity and relevance with phosphoproteomics.

In the last years, significant improvments in the generation and the analysis of phosphoproteomic data have allowed scientists to interrogate pathway and cell activity directly, without using other intermediates such as RNA or protein levels. However, phosphoproteomics still lack comparative and predictive tools accessible for all. Current available predictive tools that indicate kinase-substrate relationships require knowledge in bioinformatics. Phosphogo, a user-friendly app built on R and shiny, allows scientists to interrogate their phosphoproteomics datasets without prior bioinformatics skills and to predict kinase activity and relevance in the cellular context. More on

Deciphering mutationally-induced chemoresistance in acute myeloid leukemia.

Acute myeloid leukemia is the most common acute leukemia diagnosed in adults. Despite an increase in the understanding of the disease, the 5-year overall survival rate of patients remains low (around 10%) mainly due to common chemoresistant relapses after remission. Specific combinations of mutations have been identified as potential drivers of chemoresistance. This project aimed to validate these combinations and understand the underlying mechanisms leading to chemoresistance in mouse models of leukemia. This project was supervised by Dr Alexandre Puissant and Dr Nina Fenouille.

November 2019 - July 2020

Master 1 intern

Rothstein Lab, Columbia University (New York)

Deciphering the cisplatin tolerance pathways through genetic interacctions in the yeast Saccharomyces cerevisiae

Cisplatin is a drug commonly used in the treatment of many cancers. However, cancer cells often develop resistance to this compound. Understanding how cisplatin arises is thus a major challenge. I used high-throughput screens on yeast to identify genes and pathways involved in drug resistance. I developped bioinformatic approaches to analyse, visualize and interrogate genetic networks. During this internship I also supervised an intern for 2 months. This project was supervised by Dr Robert Reid.

April 2019-August 2019

Licence 3 intern

Rossoll Lab, Mayo Clinic Jacksonville (Florida)

Study of the disassembly of TDP-43 aggregates by nuclear transport factors in an amyotrophic lateral sclerosis model.

Amyotrophic lateral scleroris is a neurodegenerative and neuromuscular disease that lead to the death of motoneurons that control voluntary muscles. The presence of TDP-43 aggregates in these cells is a hallmark of ALS. During this internship, I studied how these aggregates can be disassembled by nuclear transport factors. This project was supervised by Dr Bilal Khalil.

May 2018-August 2018

President

Association Biologie et Génétique Appliquée

President of the Association BGA, the student association of the Magistère Européen de Génétique. During this one-year presidency I managed a team of 14 dedicated people in the organization of multiple festive or charity events. I learned team management and team working, communcation, working with strict and short deadlines.

March 2018-March 2019

Skills

Programming Languages & Tools

R - Every day, building packages and GUIs with shiny.

LaTeX - Building complex reports.

Deep learning - Self-learned, tabular data analysis and predictions.

Python - Acquainted.

Unix - Daily use of Linux-based distributions, standard use of bash.

Soft skills

Project management & supervision

Teamwork

Communication & popularization of science

Curiosity & willingness to learn

Organization & independence

Publications

Journal articles

Fenwarth L, Thomas X, de Botton S, Duployez N, Bourhis JH, Lesieur A, Fortin G, Meslin PA, Yakoub-Agha I, Sujobert P, Dumas PY, Récher C, Lebon D, Berthon C, Michallet M, Pigneux A, Nguyen S, Chantepie S, Vey N, Raffoux E, Celli-Lebras K, Gardin C, Lambert J, Malfuson JV, Caillot D, Maury S, Ducourneau B, Turlure P, Lemasle E, Pautas C, Chevret S, Terré C, Boissel N, Socié G, Dombret H, Preudhomme C, Itzykson R (2020) A Personalized Approach to Guide Allogeneic Stem Cell Transplantation in Younger Adults with Acute Myeloid Leukemia. Blood. DOI: 10.1182/blood.2020005524 For this study, I built a Shiny web application to help practicians to identify patients that would benefit from allogeneic stem cell transplantation based on models developped by Pr. Raphaël Itzykson. More on

Angela Su, Frank Ling, Camille Vaganay, Gaetano Sodaro, Chaïma Benaksas, Reinaldo Dal Bello, Antoine Forget, Bryann Pardieu, Kevin H Lin, Justine C Rutter, Christopher F Bassil, Gael Fortin, Justine Pasanisi, Iléana Antony-Debré, Gabriela Alexe, Jean-François Benoist, Alain Pruvost, Yana Pikman, Jun Qi, Marie-Hélène Schlageter, Jean-Baptiste Micol, Giovanni Roti, Thomas Cluzeau, Hervé Dombret, Claude Preudhomme, Nina Fenouille, Lina Benajiba, Hava M Golan, Kimberly Stegmaier, Camille Lobry, Kris C Wood, Raphael Itzykson, Alexandre Puissant (2020) The Folate Cycle Enzyme MTHFR is a Critical Regulator of Cell Response to MYC-Targeting Therapies. Cancer Discovery. DOI: 10.1158/2159-8290.cd-19-0970

Education

Practical Deep Learning for Coders

Self-training on machine learning and deep learning with the corresponding course from fast.ai. This course covers machine learning (random forest) and various deep learning domains such as image recognition, natural language processing, tabular data predictions as well as deep learning from the foundations (neural network architecture, stochastic gradient descent...).

January 2021 - Present

Mouse training

Université de Paris

A training of two weeks on animal welfare and ethics in biology. Level 'Concepteur'.

September 2020

Magistère Européen de Génétique

Université de Paris

A 3-year bachelor and master degree in genetics with specialization in oncogenesis and bioinformatics.

September 2017 - June 2020

Mouse Genetics

Institut Pasteur

A 5-week intensive training on mouse models. This course, mainly consisting of practical lessons, covers major aspects of mice use in research: genetics, behaviour, neurology, development, as well as stemness (through cell guided differenciation and iPSCs production).

January 2020 - February 2020

Licence 1 and 2 of Molecular and Cellular Sciences, international section

Université Rennes 1

1st and 2nd year of Licence in an international program.

September 2015 - June 2017

Interests

Apart from doing research, astrophysics and nature fascinate me. If making science is important, sharing it and making it accessible for all is essential for me. I love traveling to discover peoples, cultures and landscapes that challenge my way of thinking.

I like to go hiking or running and, when forced indoors, I am an aspirating chef and spend time playing games.