Athénaïs Vaginay

👋 Hej! I am:

🧑‍🎓 a PhD in computational biology
I was working in CRAN/LORIA in the capsid team, supervised by Taha Boukhobza & Malika Smail-Tabbone;
💼 now looking for a post-doc in systems biology (formal modeling with Boolean networks and reaction networks);
🌍 a nancéienne (🇫🇷), ex-lilloise (🇫🇷), ex-parisienne (🇫🇷), happy to move abroad;
🐍 a Python lover (the programming language), also fond of Answer-Set Programming (ASP), but not much of R;
🐀 a rat care-taker (the cute animal);
🎸🎺 a musician (guitar and trumpet);

You may want:

📧 my e-mail address: athenais DOT vaginay AT loria DOT fr;
📰 my academic papers on HAL / Google scholar / dblp
(/!\ dblp covers publications from computer science only) ;
my LinkedIn (updated in August 2023);
my GitHub
(the code for my PhD research is stored on the private GitLab of my lab. It is accessible on request);
📭 my work address (I love letters!):
Bureau B142
Campus Scientifique, 615 Rue du Jardin-Botanique
54506 Vandœuvre-lès-Nancy

Feel free to get in touch with me (in french or english). :)

💬 Talks

The list below should be more or less exhaustive. The slides are available for most of the presentations.

List

From reaction networks to Boolean networks: why and how

14 November 2023

At CANA seminar, LIS, Marseille, France.

Slides

Abstract

One way to get new insights about complex biological systems is to convert between modelling formalisms. Here, we deal with the conversion of reaction networks interpreted with the differential semantics, into Boolean networks. The conversion is particularly challenging, as it requires a drastic change in perspective: from a process-centred description with continuous time and values to a species-centred description with discrete steps and Boolean values. The conversion I present here is based on my PhD work. It aims at preserving properties from the input reaction network, such as its structure (the direct influences between the components) and its binarised transient dynamics (the transitions between the Boolean configurations). We will see how to extract the structure and dynamics of a reaction network, and how to use answer-set programming synthesise complying Boolean networks. So far, the evaluation of the approach on toy examples and real-world reaction networks from the repository BioModels, has demonstrated it effectiveness in synthesising Boolean networks complying with the input reaction networks. It also paved the way of the formal study of the relationship between the differential semantics of reaction network and Boolean networks. The perspectives mainly concern the practical relevance of the Boolean networks we synthesise, as well as the formal exploration of the relationship with other semantics of reaction networks.

Synthesis of Boolean Networks from the Structure and Dynamics of Reaction Networks

7th July 2023

At Loria, Nancy, France (PhD defense).

Synthesis of Boolean Networks from the Structure and Dynamics of Reaction Networks

3rd July 2023

At Thematic workshop on networks and biological models inference, CIRM, Marseille, France (invited presentation).

Sélection et analyse de modèles pour les réseaux biologiques

13th December 2022

At FCH seminar, Nancy, France (invited presentation).

Slides

Systems biology, reaction and Boolean networks: introduction and conversion from reaction network to Boolean networks

27th August 2022

At Vino (summer school / reading group), Campo Tures, Italy.

Slides

Differential Equations and differential invariants

22th August 2022

At Vino (summer school / reading group), Campo Tures, Italy (book chapter presentation).

Slides

ASKeD-BN: Automatic Synthesis of Boolean Networks from Knowledge and Data

31th July 2022

At ASPOCP'22@FLoC, Haifa, Israel (paper highlight). Highlighted paper

Slides

From Chemical Reaction Networks to Boolean Networks, Automatically

3rd December 2021

At GT Bioss' virtual seminar, online (invited presentation).

Slides

From Quantitative SBML to Boolean Network

1st December 2021

At CNA'21, Madrid, Spain (paper presentation). Conference paper / journal version

Slides

Modelling Biological Systems with Boolean Networks

18th Nov 2021

At FCH' scientific day, Nancy, France (invited presentation).

Slides

SBML2BN: an Integrative Pipeline for the Synthesis of Boolean Networks from SBML Models

23rd Septembre 2021

At CMSB'21, Bordeaux, France (poster flash).

Slides Poster

ASKeD-BN: Automatic Synthesis of Boolean Networks from Knowledge and Data

7th July 2021

At JOBIM'21, online (paper highlight). Replay, abstract, highlighted paper

Slides

ASKeD-BN: Automatic Synthesis of Boolean Networks from Knowledge and Data

23th Jun. 2021

At OLA'21, online (paper presentation). Conference paper

Slides

Towards an automatic conversion from SBML core to SBML qual

30 Jul. 2019

At JeBiF'21 @ JOBIM, Nantes, France (flash poster presentation)

Slides Poster

Quick Presentation

04 Apr. 2019

Loria Departement D5' day, Nancy, France

Slides

caspid "tea-time" seminars

Those are monthly scheduled seminars of the capsid team During my PhD, the talks below have mostly been used to keep my team updated about my work, and to rehearse presentations for conferences and other seminars. This is why I keep the list separated from the other talks.

List

ASKeD-BN: Automatic Synthesis of Boolean Networks from Knowledge and Data (OLA rehearsal)

Jun. 2021