I have been working in the field of RNA secondary structure prediction for almost 5 years. During this period, I deployed several machine learning, optimization and statistics techniques which resulted in several software that could be found on Github
Currently, as part of a Postdoc, I am collaborating with Prof. Christine Heitsch and Dr. Alain Laederach where we are working on the development of a new RNA structure predictive method that makes use of experimental data.
I am a former member of the AMIBIO research group where I did prepare my doctorate; I had the chance to work with Prof. Mireille Régnier , Dr. Bruno Sargueil and my father in science Dr. Yann Ponty. My research focuses on the development of new integrative approaches to experimental data in order to better predict the secondary structure of RNA. If you are curious you can find my PhD work at
"Multi-dimensional probing for RNA secondary structure(s) prediction"
In 2015, as part of my master's internship, I had the chance to go through the Soeding laboratory of the Maxplank Institute for Biochemestry and work on improving the BBcontact software developed by Jessica Andreani, who was a great supervisor.
IPANEMAP takes as input an RNA sequence with profiling data, denoted by reactivities, from various experimental conditions. IPANEMAP proceeds, first, with a stochastic sampling that results into samples of predicted secondary structure. The data-driven predicted structures are then gathered in one sample, serving as input for the clustering step. IPANEMAP proceeds, then, with an iterative clustering that ends once a stopping criterion is reached. This step allows to identify the adequate number of clusters k to be considered. The k resulting clusters are then represented by their centroid structures. Clusters figuring on the 2D-Pareto frontier are considered to be optimal and subsequently their corresponding centroids are reported as the predicted structure through IPANEMAP
My passion for photography started in 2017; the photo on the right is my "Coup de coeur", taken in Paris in 2018.
IPANEMAP is a software for predicting stable RNA secondary structures compatible with multiple chemical probing (SHAPE, DMS, Enzymatic...) reactivities profiles; Startingg from one or several input sequences, one or several reactivity profiles, IPANEMAP computes and outputs one or several secondary structures that are the bestly supported by experimental data and by thermodynamics.
NormProbing is a software for parsing QuShape outputs. It computes and outputs normalized reactivity data while giving the user the possibility of choosing the nature of the nucleotides to be taken into account for the normalization.
(Under development) R + python code for viewing raw mutation data and the corresponding relative differences. It outputs raw mutation count and Relative difference heatmaps.
Last Updated: Dec 23, 2020
Yes it is me on the background picture ;) Bled, Slovenia (2018)