Constraint-based abstraction of reaction networks to Boolean networks
👋 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; - 💼 currently visiting the computer science department of the university of Iowa. I continue working on the formal analysis of Boolean networks and reaction networks;
- 🌍 currently in Iowa City (🇺🇸), previously a nancéienne (🇫🇷), lilloise (🇫🇷), 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
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
Synthesis of Boolean Networks from the Structure and Dynamics of Reaction Networks
Sélection et analyse de modèles pour les réseaux biologiques
Systems biology, reaction and Boolean networks: introduction and conversion from reaction network to Boolean networks
Differential Equations and differential invariants
ASKeD-BN: Automatic Synthesis of Boolean Networks from Knowledge and Data
From Chemical Reaction Networks to Boolean Networks, Automatically
From Quantitative SBML to Boolean Network
Modelling Biological Systems with Boolean Networks
SBML2BN: an Integrative Pipeline for the Synthesis of Boolean Networks from SBML Models
ASKeD-BN: Automatic Synthesis of Boolean Networks from Knowledge and Data
ASKeD-BN: Automatic Synthesis of Boolean Networks from Knowledge and Data
Towards an automatic conversion from SBML core to SBML qual
Quick Presentation
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)
Constrained Enumeration of Boolean Networks from Biological Data and Knowledge (prepare OLA submission)
The Search Space of the Logical Function Synthesis Problem — Application for Biological Systems
Automatic Transformation from Reaction Models to Boolean Models Using Answer-Sets Constrained by a Topology and an Abstracted Dynamic
What I've learn this summer: recap Bioregul summer school (Porquerolle) and JeBIF + JOBIM (Nantes)
Introduction to Critical Thinking (in french)
Presentation of my Thesis Project
📄 Publications
I put the pdf of my papers on HAL.This is the exhaustive list of peer-reviewed publications I co-authored. Color code: Journal Conference Thesis
- J. Niehren, C. Lhoussaine, and A. Vaginay, Core SBML and its formal semantics, in Computational methods in systems biology - 21st international conference, CMSB 2023, luxembourg city, luxembourg, september 13-15, 2023, proceedings, J. Pang and J. Niehren, Eds., in Lecture notes in computer science, vol. 14137. Springer, 2023, pp. 124–143. doi: 10.1007/978-3-031-42697-1_9.
- A. Vaginay, Synthesis of Boolean networks from the structure and dynamics of reaction networks. phd thesis, University of Lorraine, Nancy, France, 2023. https://tel.archives-ouvertes.fr/tel-04257373
- A. Vaginay, T. Boukhobza, and M. Smaïl-Tabbone, From quantitative SBML models to Boolean networks, Appl. Netw. Sci., vol. 7, no. 1, p. 73, 2022, doi: 10.1007/S41109-022-00505-8.
- Hirtz A, Lebourdais N, Rech F, Bailly Y, Vaginay A, Smaïl-Tabbone M, Dubois-Pot-Schneider H, Dumond H. GPER Agonist G-1 Disrupts Tubulin Dynamics and Potentiates Temozolomide to Impair Glioblastoma Cell Proliferation. Cells. 2021 Dec 7; 10(12):3438. doi: 10.3390/cells10123438.
- A. Vaginay, T. Boukhobza, and M. Smaïl-Tabbone, From quantitative SBML models to boolean networks, in Complex networks & their applications X - volume 2, proceedings of the tenth international conference on complex networks and their applications COMPLEX NETWORKS 2021, madrid, spain, november 30 - december 2, 2021, R. M. Benito, C. Cherifi, H. Cherifi, E. Moro, L. M. Rocha, and M. Sales-Pardo, Eds., in Studies in computational intelligence, vol. 1016. Springer, 2021, pp. 676–687. doi: 10.1007/978-3-030-93413-2_56.
- J. Niehren, A. Vaginay, and C. Versari, Abstract simulation of reaction networks via boolean networks, in Computational methods in systems biology - 20th international conference, CMSB 2022, bucharest, romania, september 14-16, 2022, proceedings, I. Petre and A. Paun, Eds., in Lecture notes in computer science, vol. 13447. Springer, 2022, pp. 21–40. doi: 10.1007/978-3-031-15034-0_2.
- A. Vaginay, T. Boukhobza, and M. Smaïl-Tabbone, Automatic synthesis of boolean networks from biological knowledge and data, in Optimization and learning - 4th international conference, OLA 2021, catania, italy, june 21-23, 2021, proceedings, B. Dorronsoro, L. Amodeo, M. Pavone, and P. Ruiz, Eds., in Communications in computer and information science, vol. 1443. Springer, 2021, pp. 156–170. doi: 10.1007/978-3-030-85672-4_12.
👩🏫 Teaching
The class links items are for the students to whom I gave the class (they require connexion on the uni website), but do not hesitate to reach out if you want to know more about it.List
- 2021-2022 (IDMC - L1 MIASH -- Anne Boyer)
Algorithmique et structure de données (semestre 1)
Arche - 2021-2022 (IDMC - L1 MIASH -- Laurent Vigneron)
Programmation C (semestre 1) - 2021-2022 (IDMC - L1 MIASH -- Armelle Brun)
Programmation C (semestre 2)
Arche - 2021-2022 (IDMC - L2 MIASH -- Maxime Amblard)
Traitement automatique des langues (semestre 2)
Arche - 2021-2022 (IDMC - M1 SC, SDL, TAL -- Mathieu d'Aquin)
Programmation Python (semestre 1)
Arche - 2021-2022 (IDMC - M2 TAL et SC)
Méthodologie, LaTeX et gestion de bibliographie
Arche - 2021-2022 (IDMC - M1 TAL et SC)
LaTeX et gestion de bibliographie
Arche - 2019-2020 (IUT Brabois - DUT GBS 1A -- Alexandre Desforges)
Bureautique et recherche documentaire -- Outils informatiques (semestre 1)
Arche - 2019-2020 (IUT Brabois - DUT GB2A 1A -- Damien Cornu)
Bureautique -- Informatique-Word-Powerpoint (semestre 1)
Arche - 2016-2017 (Univ. Paris Diderot - L1 EA)
Bureautique, vie numérique et recherche documentaire -- Outils pour la Bureautique et internet (semestre 2)
Moodle - 2014–2015 (Univ. Paris Diderot - tutorat L1)
Bureautique, vie numérique et recherche documentaire -- Outils pour la Bureautique et internet