903 lines
34 KiB
TeX
903 lines
34 KiB
TeX
\newcommand{\cvsecrule}{\vspace{-3mm}{\color{Prune}\hrule}\medskip}
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\chapter[CV]{Sergiu Ivanov \enspace — \enspace CV}
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\vspace{-7mm}
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\newcommand{\summaryvspace}{\vspace{1mm}}
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\hspace{\parindent}%
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\textbf{Maître de conférences --- Associate Professor}
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\summaryvspace
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IBISC Laboratory / Department of Computer Science
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Université d'Évry Paris-Saclay
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\summaryvspace
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IBGBI, 23 boulevard de France, 91034 Évry-Courcouronnes, France
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\summaryvspace
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\url{sergiu.ivanov@universite-paris-saclay.fr}
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\summaryvspace
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\url{https://www.ibisc.univ-evry.fr/~sivanov/}
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\vspace{-3mm}
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\section{Career overview}
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\label{sec:career}
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\cvsecrule
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\newcommand{\timeskip}{2mm}
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\noindent
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\begin{tabularx}{\textwidth}{>{\leavevmode\color{Prune}}p{22mm} X}
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2017-- & \textbf{Maître de conférences --- Associate Professor} (tenured) \\
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& \textit{50\% research, 50\% teaching} \\
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& IBISC Laboratory --- Department of Computer Science \\
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& Université d'Évry Paris-Saclay \\[\timeskip]
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2016--2017 & \textbf{Post-doctoral researcher} \\
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& \textit{Biomechanical modelling of blood platelet cytoskeleton during platelet activation} \\
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& Supervisor: Nicolas \textsc{Glade} \\
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& TIMC Laboratory CNRS UMR 5525, Université Grenoble-Alpes \\[\timeskip]
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2015--2016 & \textbf{Attaché Temporaire d'Enseignement et de Recherche ---} \\
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& Temporary Teaching Assistant \\
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& LACL Laboratory, Université Paris-Est Créteil \\[\timeskip]
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2012--2015 & \textbf{PhD student} \\
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& \textit{On the Power and Universality of Biologically-inspired Models of Computation} \\
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& Director: Sergey \textsc{Verlan}, defended on 2015-06-23 \\
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& $192\text{h} = 3 \times 64\text{h}$ of teaching at the Departement of Computer Science \\
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& LACL Laboratory, Université Paris-Est Créteil \\[\timeskip]
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2011--2012 & \textbf{M1 student} \\
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& MSc programme \textit{Mathematics and Computer Science} \\
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& Google Summer of Code 2012 participant \\
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& University of the Academy of Sciences of Moldova \\[\timeskip]
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2009--2012 & \textbf{Research engineer} (part time) \\
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& Supervisor: Yurii \textsc{Rogozhin} \\
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& Institute of Mathematics and Computer Science of Moldova \\[\timeskip]
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2007--2011 & \textbf{Bachelor in Computer Engineering} \\
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& Average grade over the 4 years: 10 out of 10 \\
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& Google Summer of Code 2008 participant \\
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& Technical University of Moldova
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\end{tabularx}
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\pagebreak
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\section{PhD thesis}
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\label{sec:phd-thesis}
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\cvsecrule
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\newcommand{\phdskip}{0mm}
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\begin{tabularx}{\textwidth}{>{\leavevmode\color{Prune}}lX}
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Title: & \textit{On the Power and Universality of Biologically-inspired Models of Computation} \\[\phdskip]
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Director: & \textbf{Sergey \textsc{Verlan}} \\[\phdskip]
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Defense: & June 23, 2015 (2015-06-23) \\[\phdskip]
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Institution: & LACL Laboratory, Université Paris-Est Créteil \\
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& doctoral contract attached to Université Paris-Est \\
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\end{tabularx}
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\vspace{-2mm}
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\subsection*{PhD thesis jury}
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\label{sec:phd-thesis-jury}
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\vspace{-2mm}
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\newcommand{\phdjuryskip}{0mm}
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\begin{tabularx}{\textwidth}{Xr}
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\textbf{Jean-Louis \textsc{Giavitto}} & President \\
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CNRS Senior scientist (DR CNRS) at IRCAM \\[\phdjuryskip]
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\textbf{Jérôme \textsc{Durand-Lose}} & Reviewer \\
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Full Professor at Université d'Orléans \\[\phdjuryskip]
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\textbf{Gheorghe \textsc{Păun}} & Reviewer \\
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Titular member of the Romanian Academy \\[\phdjuryskip]
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\textbf{Philippe \textsc{Schnoebelen}} & Reviewer \\
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CNRS Senior scientist (DR CNRS) at LSV lab (now LMF) \\[\phdjuryskip]
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\textbf{Enrico \textsc{Formenti}} & Examiner \\
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Full Professor at Université Côte d'Azur \\[\phdjuryskip]
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\textbf{Elisabeth \textsc{Pelz}} & Examiner \\
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Full Professor at Université Paris-Est Créteil
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\end{tabularx}
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\section{Teaching}
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\label{sec:teaching}
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\cvsecrule
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\newcommand{\chargeshared}{$\star$}
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\newcommand{\chargefull}{$\dagger$}
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My teaching spans most university years, starting from L1 (freshman
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year) through to M2 (second year of the Master's program). I mostly
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teach computer science and engineering at the \emph{licence} level
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(approximately, bachelor), and mostly theoretical biology, network
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biology, and bioinformatics at the Master's level. I have
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a CRCT (approximately, sabbatical) for the school
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year 2023--2024.
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The following tables briefly list the courses I teach, am in charge of
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(marked with the sign \chargefull), or share the responsibility of (marked
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with the sign \chargeshared), together with the typical teaching hours.
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I only describe the time period after I obtained the current tenured
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Maître de conférences --- Associate Professor position.
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\vspace{-2mm}
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\subsection{Master's level courses}
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\label{sec:teaching-msc}
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\cvsecrule
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\newcommand{\teachingskip}{1mm}
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\begin{tabularx}{\textwidth}{>{\leavevmode\color{Prune}}ll X}
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2022--2023 & M2 GENIOMHE & \textbf{Computational DNA nanotechnology}\chargeshared \\
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&& SI:\footnote{SI = hours taught by Sergiu \textsc{Ivanov}.} 7.5h CM+TD, Damien \textsc{Regnault}: 7.5h CM+TD \\[\teachingskip]
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2017--2023 & M2 GENIOMHE & \textbf{Computational Systems Biology \& Network Medicine}\chargeshared \\
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&& SI: 12h CM+TD, Franck \textsc{Delaplace}: 12CM+TD \\[\teachingskip]
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2017--2023 & M2 SSB & \textbf{Network Systems: Modelling and Analysis}\chargeshared \\
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&& SI: 12h CM+TD, Franck \textsc{Delaplace}: 9CM+TD \\[\teachingskip]
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2017--2023 & M2 CNS & \textbf{Systèmes multi-agents}\chargeshared \\
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&& SI: 9h CM+TD, Guillaume \textsc{Hutzler}: 9h CM+TD \\[\teachingskip]
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\end{tabularx}
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\vspace{-2mm}
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\subsection{Bachelor level courses}
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\label{sec:teaching-licence}
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\cvsecrule
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\begin{tabularx}{\textwidth}{>{\leavevmode\color{Prune}}ll X}
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2017--2023 & L3 informatique & \textbf{Projet Professionnel d'Études et d'Insertion}\chargefull \\
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&& SI: 9h TD \\[\teachingskip]
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2017--2023 & L3 informatique & \textbf{Systèmes d'exploitation}\chargefull \\
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&& SI: 18h CM + 18h TD \\[\teachingskip]
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2020--2023 & L2 informatique & \textbf{Programmation système} \\
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&& SI: 18h TD \\[\teachingskip]
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\end{tabularx}
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\pagebreak
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\noindent
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\begin{tabularx}{\textwidth}{>{\leavevmode\color{Prune}}ll X}
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2017--2023 & L1 informatique & \textbf{Algorithmique et programmation} \\
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&& SI: 36h TD \\[\teachingskip]
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2017--2023 & L1 informatique & \textbf{Programmation impérative} \\
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&& SI: 36h TD \\[\teachingskip]
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2020--2023 & L1 informatique & \textbf{Méthodologie} \\
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&& SI: 12h TD \\[\teachingskip]
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2019--2021 & L1 informatique & \textbf{Architecture} \\
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&& SI: 18h TD \\[\teachingskip]
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2018--2021 & L1 informatique & \textbf{Émulateur pédagogique} \\
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&& Supplementary course for Parcoursup candidates with the decision OUI-SI. \\
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&& SI: 10h TD \\[\teachingskip]
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\end{tabularx}
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\vspace{-2mm}
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\subsection{Other courses}
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\label{sec:teaching-other}
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\cvsecrule
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\begin{tabularx}{\textwidth}{>{\leavevmode\color{Prune}}ll X}
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2020 & Open online class & \textbf{Introduction to Membrane Computing}\chargeshared \\
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&& SI: 4h CM online + 4h TD online,\\
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&& David \textsc{Orellana-Martín}: 6h CM online + 4h TD online \\[\teachingskip]
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2017--2024 & Popular science & \textbf{Fête de la Science --- Science Days}\chargeshared \\
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&& SI: 2 full days on the stand + organization
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\end{tabularx}
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\subsection{Teaching and research}
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\label{sec:teaching-research}
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\cvsecrule
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All Master's level courses I teach are directly connected to my
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research. In the course \textbf{Computational DNA nanotechnology}, we
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introduce the students to DNA self-assembly and its potential
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applications, including applications in biology and medicine.
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We directly overview the state of the project I share with Damien
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\textsc{Regnault} to build a functioning pipeline for self-assembly of
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DNA nanostructures, spanning the entire spectrum from theoretical
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design to actual wet-lab production.
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Both the courses \textbf{Computational Systems Biology \& Network
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Medicine} and \textbf{Network Systems: Modelling and Analysis} focus
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on another major pillar of my research: approaching the complexity of
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biological systems using the tools of network science and discrete
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dynamical systems. More concretely, in these classes we introduce the
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students to the basics of graph theory, and then extensively discuss
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two formal models of discrete dynamical networks---Boolean networks
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and Petri nets---as well as show concrete applications for therapy
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inference or setting up formal frameworks for thinking about the
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origins of Life.
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Finally, I use the course \textbf{Systèmes multi-agents}
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(\textit{Multi-agent systems}) as an opportunity to introduce the
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students to emergent complexity of the living systems, made up of
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simple entities interacting in complex ways. In this course, we
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discuss different tools which can formalize multi-agent systems---in
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particular membrane (P) systems---and propose several practical
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assignments to help the students better understand the connection
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between abstract objects and concrete systems.
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Outside my normal teaching activity, I particularly appreciate
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\textbf{Science Days} (\textit{Fêtes de la Science}), which are always
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an excellent opportunity to illustrate the hallmarks of my research to
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school students and the general public. I have taken part in Science
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Days every year, including during the pandemic when we held online
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stands, and I have consistently invested a considerable effort in
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organizing the stands.
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Finally, even though my bachelor level courses are not in direct
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connection to my research, I always necessarily bring in discussions
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of complexity and even theoretical biology, to illustrate some
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abstract concepts on the one hand, and to challenge the students and
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push them out of their comfort zone on the other hand.
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\section{Organization of scientific events}
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\label{sec:management}
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\cvsecrule
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\newcommand{\eventskip}{1mm}
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\noindent
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\begin{tabularx}{\textwidth}{>{\leavevmode\color{Prune}}p{22mm} X}
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2022 & \textbf{IBISC Laboratory Day} \\
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& coorganization with Guillaume \textsc{Postic} \\[\eventskip]
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\end{tabularx}
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\pagebreak
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\noindent
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\begin{tabularx}{\textwidth}{>{\leavevmode\color{Prune}}p{22mm} X}
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2022 & Seminar \textbf{Workshop on the Atavistic Theory of Cancer --- ATAC2022} \\
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& coorganization with Nicolas \textsc{Glade} and Angélique \textsc{Stéphanou} \\[\eventskip]
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2020 & Online \textbf{Conference on Membrane Computing --- CMC 2020} \\
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& coorganization with Rudolf \textsc{Freund} \\[\eventskip]
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2018 & Seminar of the \textbf{French-speaking Society for Theoretical Biology (SFBT)} \\
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& coorganization with Nicolas \textsc{Glade} and Angélique \textsc{Stéphanou} \\[\eventskip]
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2018 & Joint conferences \textbf{Unconventional Computation, Natural Computation --- UCNC2018} and \textbf{Machines, Computations, and Universality --- MCU 2018} \\
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& main organizer: Sergey \textsc{Verlan} \\[\eventskip]
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2018 & \textbf{Workshop on Membrane Computing} \\
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& conference \textit{Unconventional Computation, Natural Computation --- UCNC 2018} \\
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& coorganization with Rudolf \textsc{Freund} \\[\eventskip]
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2017 & \textbf{IBISC Laboratory Day} \\
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& coorganization with Najett \textsc{Neji} \\[\eventskip]
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\end{tabularx}
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\vspace{-2mm}
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\section{Scientific roles}
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\label{sec:roles}
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\cvsecrule
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\newcommand{\roleskip}{1mm}
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\begin{tabularx}{\textwidth}{>{\leavevmode\color{Prune}}p{22mm} X}
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2022--2026 & Elected member of the \textbf{Research Commission} of Université d'Évry Paris-Saclay \\[\roleskip]
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2021--2023 & Elected member of the \textbf{IBISC Laboratory Council} \\[\roleskip]
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2019--2021 & Appointed member of the \textbf{IBISC Laboratory Council} \\[\roleskip]
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2020-- & Manager of the \textbf{work group on personalized medicine} of IBISC \\
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& coorganization with Farida \textsc{Zehraoui} \\[\roleskip]
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2017-- & IBISC representative to the group \textbf{Méthodes
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Formelles pour les Systèmes Logiciels et Matériels --- MeFoSyLoMa}
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(\textit{Formal Methods for Software and Hardware systems}) \\[\roleskip]
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\end{tabularx}
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\vspace{-2mm}
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\section{Projects and grants}
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\label{sec:projects}
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\cvsecrule
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\newcommand{\projectskip}{1mm}
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\begin{tabularx}{\textwidth}{>{\leavevmode\color{Prune}}l p{15mm} X}
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2022 & FRR\footnote{FRR = ``Fonds pour le Rayonnement de la Recherche''---project-based competitive local funding of Université d'Évry Paris-Saclay.} & \textit{Setting up experimental projects in DNA self-assembly} \\
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& \textbf{3 k€} & Role: \textbf{Principal Investigator} \\
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&& Other Principal investigator: Damien \textsc{Regnault} \\[\projectskip]
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2021 & IXXI\footnote{IXXI = ``Institut Rhônalpin des Systèmes Complexes''---Institute of Complex Systems of the Auvergne-Rhône-Alpes region.} \textbf{4~k€} &
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\textit{Exploration of evolutivity and robustness of biological
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networks — Characterisation of structural and dynamic connected
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components of sign Boolean networks, as well as of viability
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constraints} \\
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&& Role: \textbf{Investigator} \\
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&& Principal investigator: Nicolas \textsc{Glade} \\[\projectskip]
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2018--2019 & DIM RFSI & \textit{Computer Science Models for Cellular Reprogramming} \\
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& \textbf{11 k€} & Role: \textbf{Principal investigator} \\
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&& Other investigators: Franck \textsc{Delaplace}, Loïc \textsc{Paulevé} \\
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\end{tabularx}
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\vspace{-2mm}
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\section{Distinctions}
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\label{sec:distinctions}
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\cvsecrule
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\begin{tabularx}{\textwidth}{>{\leavevmode\color{Prune}}p{22mm} X}
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2023--2025 & \textbf{RIPEC C3 for scientific activity} \\
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& 3-year monthly ministerial premium for outstanding research work \\[1mm]
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2023--2024 & \textbf{Congé de Recherche ou de Conversion Thématique --- CRCT} \\
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& Leave for research or thematic conversion \\
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\end{tabularx}
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\section{Reviews and editorial activity}
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\label{sec:reviews}
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\cvsecrule
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\subsection{Program and scientific committees}
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\label{sec:program-committees}
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\vspace{-2mm}
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\newcommand{\pcskip}{0mm}
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\noindent
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\begin{tabularx}{\textwidth}{>{\leavevmode\color{Prune}}p{22mm} X}
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2023 & \textbf{Non-Classical Models of Automata and Applications} (NCMA) \\
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& Member of the Program Committee \\[\pcskip]
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2022--2023 & \textbf{Conference on Membrane Computing} (CMC) \\
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& Member of the Program Committee \\[\pcskip]
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2022-- & \textbf{Computer Science Journal of Moldova} \\
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& Member of the Editorial Board \\[\pcskip]
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2020 & \textbf{International Conference on Membrane Computing} (ICMC) \\
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& Co-chair of the Program Committee \\[\pcskip]
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2018 & \textbf{Unconventional Computation and Natural Computation} (UCNC) \\
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& Member of the Program Committee \\[\pcskip]
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2018--2019 & \textbf{Acta Biotheoretica} \\
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& Guest editor after the seminar of the \textit{Société Francophone de la Biology Théorique} \\[\pcskip]
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\end{tabularx}
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\vspace{-2mm}
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\subsection{Journal reviews}
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\label{sec:journal-reviews}
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\vspace{-2mm}
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I have reviewed and regularly review papers for the
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following journals.
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\vspace{1mm}
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{\renewcommand{\arraystretch}{.9}
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\noindent
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\begin{tabularx}{\textwidth}{XcX}
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\textbf{Theoretical Computer Science} (Elsevier) & \hspace{5mm} & \textbf{Fundamenta Informaticae} (IOS Press)\\[0pt]
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\textbf{Lecture Notes for Computer Science} (Springer) & & \textbf{Journal of Cellular Automata} (Old City Publishing)\\[0pt]
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\textbf{Swarm and Evolutionary Computation} (Elsevier) & & \textbf{Socio-Ecological Practice Research} (Springer)\\[0pt]
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\textbf{Journal of Symbolic Computation} (Elsevier) & & \textbf{Journal of Membrane Computing} (Springer)\\[0pt]
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\textbf{International Journal of Foundations of Computer Science} (World Scientific) & & \textbf{Indian Journal of Pure and Applied Mathematics} (Springer)\\[0pt]
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\textbf{Computer Science Journal of Moldova} (Institute of Mathematics and Computer Science ``Vladimir Andrunachievici'') & & \textbf{Journal of Automata, Languages, and Combinatorics} (Institut für Informatik, Justus-Liebig-Universität Giessen)\\[0pt]
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\textbf{Concurrency and Computation: Practice and Experience} (Wiley) & & \textbf{Natural Computing} (Springer)\\[0pt]
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\end{tabularx}
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}
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\noindent
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Since 2021, I am a recommender for \textbf{Peer Community In
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Mathematical and Computational Biology}.
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\vspace{-2mm}
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\subsection{Conference reviews}
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\label{sec:conference-reviews}
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I reviewed papers for the following conferences multiple times,
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without being on the Program Committee: \textbf{Conference on Membrane
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Computing} (CMC), \textbf{Machines, Computations, and Universality}
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(MCU), \textbf{Developments in Language Theory} (DLT),
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\textbf{Unconventional Computation and Natural Computation} (UCNC).
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\section{Jurys}
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\label{sec:jurys}
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\cvsecrule
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\subsection{PhD defences}
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\label{sec:phd-defences}
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\subsubsection{Sara \textsc{Riva}}
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\label{sec:sara-riva}
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\begin{tabularx}{\textwidth}{>{\leavevmode\color{Prune}}lX}
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Title: & \textbf{Factorization of Discrete Dynamic Systems} \\
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Director: & Enrico \textsc{Formenti}, Université Côte d'Azur \\
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Co-director: & Alberto \textsc{Dennunzio}, Università degli Studi di Milano-Bicocca \\
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Duration: & 2019--2022 \\
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||
Defense: & November 22, 2022 (2022-11-22) \\
|
||
Institution: & Université Côte d'Azur \\
|
||
SI's role: & \textbf{Examiner} \\
|
||
\end{tabularx}
|
||
|
||
\pagebreak
|
||
|
||
\subsection{Individual PhD monitoring committees (CSI)}
|
||
\label{sec:csi}
|
||
|
||
\newcommand{\csivspace}{\vspace{-2mm}}
|
||
|
||
\subsubsection{Hala \textsc{Djeghim}}
|
||
\label{sec:hala-djeghim}
|
||
|
||
\csivspace
|
||
|
||
\begin{tabularx}{\textwidth}{>{\leavevmode\color{Prune}}lX}
|
||
Title: & \textbf{In-details scene understanding for realistic data generation} \\
|
||
Directors: & Dro Désiré \textsc{Sidibé}, Université Évry Paris-Saclay \\
|
||
& Nathan \textsc{Piasco}, Huawei \\
|
||
Durée: & 2023-- \\
|
||
Institution: & Université Paris-Saclay \\
|
||
SI's role: & \textbf{President} \\
|
||
\end{tabularx}
|
||
|
||
\vspace{-2mm}
|
||
|
||
\subsubsection{Sofía \textsc{Vargas Ibarra}}
|
||
\label{sec:sofia-vargas}
|
||
|
||
\csivspace
|
||
|
||
\begin{tabularx}{\textwidth}{>{\leavevmode\color{Prune}}lX}
|
||
Title: & \textbf{Thrombus imaging with AI for patients stratification} \\
|
||
Directors: & Vincent \textsc{Vigneron}, Université Évry Paris-Saclay \\
|
||
& Sonia \textsc{Garcia-Salicetti}, Télécom SudParis \\
|
||
Durée: & 2022-- \\
|
||
Institution: & Université Paris-Saclay \\
|
||
SI's role: & \textbf{President} \\
|
||
\end{tabularx}
|
||
|
||
\vspace{-2mm}
|
||
|
||
\subsubsection{Rémi \textsc{Segretain}}
|
||
\label{sec:remi-segretain}
|
||
|
||
\csivspace
|
||
|
||
\begin{tabularx}{\textwidth}{>{\leavevmode\color{Prune}}lX}
|
||
Title: & \textbf{Complexity and evolution: a study of sign Boolean networks} \\
|
||
Director: & Nicolas \textsc{Glade}, Université Grenoble-Alpes \\
|
||
Duration: & 2019-- \\
|
||
Institution: & Université Grenoble-Alpes \\
|
||
SI's role: & \textbf{Member} \\
|
||
\end{tabularx}
|
||
|
||
\vspace{-2mm}
|
||
|
||
\subsection{Committees for \textit{Maître de conférences} positions (CoS)}
|
||
\label{sec:mcf}
|
||
|
||
{\renewcommand{\arraystretch}{1}
|
||
\begin{tabularx}{\textwidth}{>{\leavevmode\color{Prune}}p{17mm} X}
|
||
2022, 2024 & MCF CNU 27 at Université d'Évry Paris-Saclay (IBISC) \\
|
||
2022 & MCF CNU 27 at Université Paris-Est Créteil (EPISEN / LACL) \\
|
||
\end{tabularx}
|
||
}
|
||
|
||
\vspace{-2mm}
|
||
|
||
\section{Doctoral students}
|
||
\label{sec:phds}
|
||
|
||
\cvsecrule
|
||
|
||
\subsection*{Jérémie \textsc{Pardo}}
|
||
\label{sec:jeremie-pardo}
|
||
|
||
\begin{tabularx}{\textwidth}{>{\leavevmode\color{Prune}}lX}
|
||
Title: & \textbf{Computational methods for the inference of therapeutic targets and sequences of treatment} \\
|
||
Director: & Franck \textsc{Delaplace} 50\%, Université Paris-Saclay \\
|
||
Co-supervisor: & \textbf{Sergiu \textsc{Ivanov} 50\%} \\
|
||
Duration: & 2019--2022 \\
|
||
Defense: & February 3, 2022 (2022-02-03) \\
|
||
Institution: & Université Paris-Saclay
|
||
\end{tabularx}
|
||
|
||
\vspace{1mm}
|
||
|
||
\noindent
|
||
Dr.~Jérémie \textsc{Pardo} is currently working as a contractor for
|
||
the digital services of Thales Group.
|
||
|
||
\vspace{-3mm}
|
||
|
||
\subsubsection*{Publications}
|
||
\begin{refsection}[bib/sivanov-dblp-mod.bib]
|
||
\nocite{DBLP:conf/cmsb/PardoID19,DBLP:journals/tcs/PardoID21}
|
||
\newrefcontext[sorting=ydnt]
|
||
\printbibliography[heading=none]
|
||
\end{refsection}
|
||
|
||
\subsection*{Lousion \textsc{Crépin}}
|
||
\label{sec:lousion-crepin}
|
||
|
||
\vspace{-2mm}
|
||
|
||
\begin{tabularx}{\textwidth}{>{\leavevmode\color{Prune}}lX}
|
||
Title: & \textbf{Modelling Mechanisms of Secondary Resistance} \\
|
||
Director: & Franck \textsc{Delaplace} 50\%, Université Paris-Saclay \\
|
||
Co-supervisor: & \textbf{Sergiu \textsc{Ivanov} 50\%} \\
|
||
Duration: & 2023-- \\
|
||
Institution: & Université Paris-Saclay
|
||
\end{tabularx}
|
||
|
||
\vspace{-1mm}
|
||
|
||
\section{Research internships}
|
||
\label{sec:interns}
|
||
|
||
\cvsecrule
|
||
|
||
\newcommand{\internskip}{1mm}
|
||
|
||
\begin{refsection}[bib/sivanov-dblp-mod.bib]
|
||
|
||
\begin{tabularx}{\textwidth}{>{\leavevmode\color{Prune}}p{24mm} X}
|
||
May--Jun 2023 & \textbf{Noémie \textsc{Harmand}} --- \textit{Self-assembly of 3-dimensional shapes by DNA origami} \\
|
||
& UEVE\footnote{UEVE = Université d'Évry Paris-Saclay} 3rd year intern (L3) \\
|
||
& \textbf{SI: 75\%}, Damien \textsc{Regnault} 25\% \\[\internskip]
|
||
|
||
Sep 2022 -- \phantom{x} Jan 2023 & \textbf{Ai-Ling \textsc{Nguyen Bonnet}} --- \textit{Efficient exploration strategies in the evolutionary mille-feuille} \\
|
||
& CentraleSupélec 4th year intern \\
|
||
& \textbf{SI: 50\%}, Nicolas \textsc{Glade} 50\%\\[\internskip]
|
||
|
||
Jun-Jul 2022 & \textbf{Vincent \textsc{Ferrari-Dominguez}} --- \textit{Controllability of complex systems} \\
|
||
& ENS Paris 3rd year intern \\
|
||
& \textbf{SI: 50\%}, Nicolas \textsc{Glade} 50\%\\
|
||
& \textbf{Publications}: \cite{DBLP:journals/tcs/AlhazovFFGI23} and another draft in progress\\[\internskip]
|
||
|
||
Apr--Jun 2022 & \textbf{Saïd \textsc{Ider}} --- \textit{Phase transitions in complex systems} \\
|
||
& UEVE 3rd year intern (L3) \\
|
||
& \textbf{SI: 100\%} \\[\internskip]
|
||
|
||
Apr--Jun 2022 & \textbf{Idriss \textsc{Ben Saïd}} --- \textit{Software simulation of DNA self-assembly models} \\
|
||
& UEVE 3rd year intern (L3) \\
|
||
& \textbf{SI: 100\%} \\[\internskip]
|
||
|
||
Apr--Jun 2022 & \textbf{Mustapha \textsc{Si Kaddour}} --- \textit{DNA self-assembly and array grammars} \\
|
||
& UEVE 3rd year intern (L3) \\
|
||
& \textbf{SI: 100\%} \\[\internskip]
|
||
|
||
Jun--Aug 2021 & \textbf{Rémy \textsc{Défossez}} --- \textit{Evolutionary mille-feuille: a new formalization of evolution} \\
|
||
& ENS Paris 3rd year intern \\
|
||
& \textbf{SI: 50\%}, Nicolas \textsc{Glade} 50\%\\[\internskip]
|
||
|
||
Feb--Apr 2021 & \textbf{Aurélien \textsc{Larchères}, Maxime \textsc{Wang}} --- \textit{Artificial evolution of sign Boolean networks} \\
|
||
& UEVE 4th year research project (M1 TER) \\
|
||
& \textbf{SI: 75\%}, Nicolas \textsc{Glade} 25\%\\[\internskip]
|
||
|
||
Feb--Apr 2020 & \textbf{Yacine \textsc{Hadjar}, Imad \textsc{Bouzgou}} --- \textit{Multi-agent modelling of rheumatoid arthritis} \\
|
||
& UEVE 4th year research project (M1 TER) \\
|
||
& \textbf{SI: 75\%}, Anna \textsc{Niarakis} 25\%\\[\internskip]
|
||
|
||
Apr--June 2017 & \textbf{Clément \textsc{Hege}} --- \textit{Numerical experimental study of the diversity and survival of artificial life forms in an environment stratified under the influence of differential sedimentation} \\
|
||
& ENSIMAG 4th year research project (M1) \\
|
||
& \textbf{SI: 25\%}, Nicolas \textsc{Glade} 75\% \\[\internskip]
|
||
\end{tabularx}
|
||
|
||
\vspace{-3mm}
|
||
|
||
\subsubsection*{Internship publications}
|
||
\newrefcontext[sorting=ydnt]
|
||
\printbibliography[heading=none]
|
||
|
||
\end{refsection}
|
||
|
||
\begin{refsection}[bib/sivanov-dblp-mod.bib,bib/sivanov-extra.bib]
|
||
|
||
\section{Research overview}
|
||
\label{sec:research}
|
||
|
||
The structuring objective of my research is \emph{striking a Deal with
|
||
Life}: establishing a theoretical framework and sketching out
|
||
practical approaches for \emph{mutually beneficial interactions} with
|
||
living systems. Practically, my work falls into the following 2 broad
|
||
categories:
|
||
\begin{enumerate}
|
||
\item deepening the knowledge about complex biological systems and
|
||
suggesting improvements for health-related applications,
|
||
\item setting up formal frameworks for thinking about and better
|
||
understanding the grand processes of Life.
|
||
\end{enumerate}
|
||
|
||
The following sections provide the keywords situating the domains and
|
||
approaches I apply in my work, together with the
|
||
corresponding publications.
|
||
|
||
\subsection{Bioinformatics}
|
||
\label{sec:bioinformatics}
|
||
|
||
\begin{itemize}
|
||
\item network controllability, theoretical cell fate reprogramming,
|
||
therapy inference
|
||
\cite{doi:https://doi.org/10.1002/9781119716600.ch10,
|
||
DBLP:journals/tcs/AlhazovFFGI23,
|
||
DBLP:journals/corr/abs-2208-14723,
|
||
DBLP:journals/tcs/PardoID21,
|
||
DBLP:conf/cmsb/PardoID19%
|
||
},
|
||
Jérémie \textsc{Pardo} and Louison \textsc{Crépin}'s PhD theses,
|
||
Vincent \textsc{Ferrari-Dominguez}'s internship
|
||
\item biological modelling
|
||
\cite{DBLP:journals/tcs/AzimiG0MPP16,
|
||
DBLP:journals/tcs/AzimiGIP15,
|
||
DBLP:journals/jmemcom/IvanovP20,
|
||
DBLP:conf/birthday/0001RAP18%
|
||
}
|
||
\item a promising collaboration on multi-agent modelling of rheumatoid
|
||
arthritis with Anna \textsc{Niarakis} which fell victim to the
|
||
Covid19 pandemic (Yacine \textsc{Hadjar} and Imad \textsc{Bouzgou}'s
|
||
internship in 2020)
|
||
\end{itemize}
|
||
|
||
\subsection{Theoretical biology}
|
||
\label{sec:theoretical-biology}
|
||
|
||
\begin{itemize}
|
||
\item complexity increase during evolution
|
||
\cite{C:AB20,
|
||
DBLP:conf/complexnetworks/Segretain0TG20,
|
||
DBLP:conf/complexnetworks/VuongCIGT17%
|
||
}
|
||
\item robustness, evolvability, and viability
|
||
\cite{DBLP:conf/bibe/SegretainTG021}: Rémy \textsc{Défossez} and
|
||
Ai-Ling \textsc{Nguyen-Bonnet}'s internships
|
||
\item origins of life: Aurélien \textsc{Larchères}, Maxime
|
||
\textsc{Wang}, Saïd \textsc{Ider}, and Clément \textsc{Hege}'s
|
||
internships, ongoing collaboration with Nicolas \textsc{Glade}
|
||
\item atavistic theory of cancer: Workshop on the Atavistic Theory of
|
||
Cancer ATAC2022, ongoing collaboration with Nicolas \textsc{Glade}
|
||
and Angélique \textsc{Stéphanou}
|
||
\end{itemize}
|
||
|
||
\subsection{Natural computing}
|
||
\label{sec:tcs}
|
||
|
||
\begin{itemize}
|
||
\item membrane (P) systems, multiset rewriting, register machines
|
||
\cite{DBLP:journals/tcs/AlhazovFIV23,
|
||
DBLP:journals/tcs/AlhazovFIO22,
|
||
DBLP:journals/ijfcs/AlhazovFIV22,
|
||
DBLP:journals/jmemcom/AlhazovF021,
|
||
DBLP:journals/jmemcom/AlhazovFI21,
|
||
DBLP:journals/jmemcom/AlhazovFIV21,
|
||
DBLP:journals/tcs/AlhazovFI20,
|
||
DBLP:journals/tcs/AlhazovFIPS20,
|
||
DBLP:journals/jmemcom/VerlanFAIP20,
|
||
DBLP:journals/nc/AlhazovFI19,
|
||
DBLP:journals/nc/AlhazovFIOV18,
|
||
AlhazovFIO2015,
|
||
DBLP:journals/fuin/AlhazovF014,
|
||
DBLP:journals/ijcm/Ivanov13,
|
||
DBLP:journals/csjm/Ivanov12,
|
||
DBLP:journals/ijncr/IvanovARG11,
|
||
DBLP:journals/csjm/AlhazovCIR10,
|
||
DBLP:conf/ncma/AlhazovF019,
|
||
DBLP:conf/uc/AlhazovF018,
|
||
DBLP:conf/birthday/AlhazovF0OV18,
|
||
DBLP:conf/membrane/AlhazovFIV18,
|
||
DBLP:conf/membrane/AlhazovF017,
|
||
DBLP:journals/corr/abs-1708-06458,
|
||
DBLP:conf/membrane/AlhazovAF016,
|
||
DBLP:conf/membrane/AlhazovBF0PZ16,
|
||
DBLP:conf/uc/Freund0S15,
|
||
DBLP:conf/membrane/Freund0V15,
|
||
DBLP:conf/membrane/Ivanov14,
|
||
DBLP:conf/membrane/Ivanov11,
|
||
DBLP:conf/membrane/AlhazovCIR10,
|
||
DBLP:conf/membrane/AlhazovIR10%
|
||
}
|
||
\item string rewriting, regulated string rewriting
|
||
\cite{DBLP:journals/jalc/AlhazovF0V22,
|
||
DBLP:journals/fuin/AlhazovFIO21,
|
||
DBLP:journals/nc/IvanovV21,
|
||
DBLP:journals/fuin/IvanovV17,
|
||
DBLP:journals/ijuc/FreundIS16,
|
||
IvanovMarcus2015,
|
||
DBLP:journals/fuin/0001V15,
|
||
DBLP:conf/mcu/AlhazovFIV22,
|
||
DBLP:conf/mcu/AlhazovF018,
|
||
DBLP:conf/mcu/0001V15,
|
||
DBLP:conf/membrane/IvanovV13%
|
||
}
|
||
\item discrete dynamical networks
|
||
\cite{DBLP:journals/biosystems/DelaplaceI20,
|
||
DBLP:journals/jalc/Alhazov0PV16,
|
||
DBLP:journals/jalc/0001RV14,
|
||
DBLP:conf/dcfs/0001PV14%
|
||
}
|
||
\item array grammars
|
||
\cite{DBLP:journals/tcs/AlhazovFFISS17,
|
||
DBLP:conf/uc/FernauFISS13,
|
||
DBLP:journals/corr/FreundIOS13%
|
||
}
|
||
\end{itemize}
|
||
|
||
\subsection{DNA computing}
|
||
\label{sec:dna}
|
||
|
||
\begin{itemize}
|
||
\item DNA origami: ongoing collaboration across 3 other laboratories
|
||
in Évry: Marco Antonio \textsc{Mendoza Parra} (SysFate, ISSB), Loïc
|
||
\textsc{Hamon} (SABNP), and Guillaume \textsc{Lamour} (LAMBE)
|
||
\item new Master's level course \textit{Computational DNA
|
||
nanotechnology}
|
||
\item theory of tile-based self-assembly: Noémie \textsc{Harmand},
|
||
Idriss \textsc{Ben Saïd}, and Mustapha \textsc{Si Kaddour}'s
|
||
internships, ongoing collaboration with Damien \textsc{Regnault}
|
||
\end{itemize}
|
||
|
||
\newpage
|
||
|
||
\section{Publications}
|
||
\label{sec:publications}
|
||
|
||
\cvsecrule
|
||
|
||
\input{cv-pubs-bib}
|
||
|
||
\end{refsection}
|
||
|
||
\subsection*{Posters}
|
||
\label{sec:posters}
|
||
|
||
\begin{enumerate}
|
||
\item Poster \textbf{Small Universal Petri Nets with Inhibitor Arcs}
|
||
at the AÉRES evaluation of the LACL laboratory, Université Paris Est
|
||
Créteil (Dec 2013).
|
||
\end{enumerate}
|
||
|
||
\subsection*{Invited talks and seminars}
|
||
\label{sec:talks}
|
||
|
||
\begin{enumerate}[itemsep=-1mm]
|
||
\item Invited talk \textbf{P Systems with Reactive Membranes} at the
|
||
Workshop on Intelligent Information Systems WIIS 2023, at the
|
||
Institute of Mathematics and Computer Science ``Vladimir
|
||
Andrunachievici'' (Oct 19--21, 2023).
|
||
\item Seminar \textbf{Queens of the Hill} at the LACL laboratory,
|
||
Université Paris Est Créteil (Oct 9, 2023).
|
||
\item SIANA\footnote{SIANA is an association defining itself as an
|
||
``Artistic laboratory, and a pool of digital and hybrid resources
|
||
of the Essonne department, and the south of Île-de-France.'' ---
|
||
https://www.siana.eu/} public round table \textbf{Stakes of
|
||
digital innovations for the society} \textit{(Enjeux sociétaux des
|
||
innovations numériques)} at the Corbeil-Essonnes theater (Feb 2,
|
||
2023).
|
||
\item Invited talk \textbf{The Many Shapes of Polymorphism} at the
|
||
Conference on Membrane Computing (Trieste, Italy) and the Asian
|
||
Conference on Membrane Computing (online) (Sep 5--9, 2022).
|
||
\item Seminar \textbf{P vs. B: P Systems as a Formal Framework for
|
||
Controllability of Boolean Networks} at the TIMC laboratory,
|
||
Université Grenoble-Alpes (Jun 7, 2022).
|
||
\item Invited talk \textbf{Sequential Reprogramming of Biological
|
||
Network Fate} at the special session ``Complex systems'' of the
|
||
Finnish Mathematical Days 2022 (Jan 5, 2022).
|
||
\item Seminar \textbf{Sequential Reprogramming of Biological Network
|
||
Fate} at the University of Turku, Finland (May 28, 2019).
|
||
\item Seminar \textbf{Universality and Computational Completeness of
|
||
Controlled Leftist Insertion-deletion Systems} at the LIFO
|
||
laboratory, Université d'Orléans (Feb 6, 2017).
|
||
\item Seminar \textbf{Semilinear Sets, Register Machines, and Integer
|
||
Vector Addition (P) Systems} at the LACL laboratory, Université
|
||
Paris Est Créteil (Jan 16, 2017).
|
||
\item Online invited talk \textbf{Semilinear Sets, Register Machines,
|
||
and Integer Vector Addition (P) Systems} at the Yurii
|
||
\textsc{Rogozhin} seminar series, Institute of Mathematics and
|
||
Computer Science ``Vladimir Andrunachievici'' (Nov 11, 2016).
|
||
\item Seminar \textbf{Theory of Computer Science: Why All That Formal
|
||
Stuff?}'' at the Tekwill Center of Excellence, Chișinău, Moldova
|
||
(Dec 15, 2016).
|
||
\item Seminar \textbf{Formal Instruments for Adverse Computations} at
|
||
the LORIA laboratory, Université de Lorraine (Mar 25, 2016).
|
||
\item Seminar \textbf{Complexity of Model Checking for Reaction
|
||
Systems} at the i3S laboratory, Université Côte d'Azur (Mar 24,
|
||
2016).
|
||
\item Seminar \textbf{On the Power and Universality of
|
||
Biologically-inspired Models of Computation} at the LIF
|
||
laboratory, Aix-Marseille Université (Mar 7, 2016).
|
||
\item Seminar \textbf{Small Universal Petri Nets: Biochemical
|
||
Universality} at the LIFO laboratory, Université d'Orléans (Feb
|
||
22, 2016).
|
||
\item Seminar \textbf{Some Results on Leftist Insertion-deletion
|
||
Systems} at the LSV laboratory (now LMF), ENS Cachan (Nov 25,
|
||
2015).
|
||
\item Online invited talk \textbf{Some Results on Leftist
|
||
Insertion-deletion Systems} at the Yurii \textsc{Rogozhin} seminar
|
||
series, Institute of Mathematics and Computer Science ``Vladimir
|
||
Andrunachievici'' (Nov 13, 2015).
|
||
\item Seminar \textbf{Variants of P Systems with Toxic Objects} at
|
||
Vienna University of Technology (TU Wien) (Nov 23, 2015).
|
||
\item Seminar \textbf{Complexity of Model Checking for Reaction
|
||
Systems} at the Combio laboratory, Åbo Akademi, Turku, Finland
|
||
(Oct 2, 2014).
|
||
\item Seminar \textbf{Model Checking of Reaction Systems: Work in
|
||
Progress} at the Combio laboratory, Åbo Akademi, Turku, Finland
|
||
(May 25, 2014).
|
||
\item Seminar \textbf{Bridging Programming, Natural Computing, Formal
|
||
Languages, and Petri Nets} at the Combio laboratory, Åbo Akademi,
|
||
Turku, Finland (Apr 14, 2014).
|
||
\item Seminar \textbf{Small Universal Petri Nets} at the LACL
|
||
laboratory, Université Paris Est Créteil (Jan 27, 2014).
|
||
\end{enumerate}
|
||
|
||
\section{Research visits}
|
||
\label{sec:visits}
|
||
|
||
\cvsecrule
|
||
|
||
{\renewcommand{\arraystretch}{1.1}
|
||
\noindent
|
||
\begin{tabularx}{\textwidth}{>{\color{Prune}}r >{\bf}l X}
|
||
Apr--Aug 2024 & Damien \textsc{Woods} & \textsc{Tapdance}, Maynooth University, Ireland \\
|
||
Aug 2023 & Rudolf \textsc{Freund} & Vienna University of Technology (TU Wien), Austria \\
|
||
Jun 2022 & Nicolas \textsc{Glade} & Université Grenoble-Alpes, France \\
|
||
Jun 2022 & Nicolas \textsc{Schabanel} & ENS Lyon, France \\
|
||
Aug 2021 & Rudolf \textsc{Freund} & Vienna University of Technology (TU Wien), Austria \\
|
||
Jun 2021 & Nicolas \textsc{Glade} & Université Grenoble-Alpes, France \\
|
||
\end{tabularx}
|
||
|
||
\noindent
|
||
\begin{tabularx}{\textwidth}{>{\color{Prune}}r >{\bf}l X}
|
||
Feb 2020 & Nicolas \textsc{Glade} & Université Grenoble-Alpes, France \\
|
||
May 2019 & Nicolas \textsc{Glade} & Université Grenoble-Alpes, France \\
|
||
May 2019 & Ion \textsc{Petre} & University of Turku, Finland \\
|
||
Aug 2017 & Rudolf \textsc{Freund} & Vienna University of Technology (TU Wien), Austria \\
|
||
Aug 2016 & Rudolf \textsc{Freund} & Vienna University of Technology (TU Wien), Austria \\
|
||
Jan 2016 & Ion \textsc{Petre} & Combio, Åbo Akademi, Turku, Finlande \\
|
||
Aug 2015 & Rudolf \textsc{Freund} & Vienna University of Technology (TU Wien), Austria \\
|
||
Oct 2014 & Ion \textsc{Petre} & Combio, Åbo Akademi, Turku, Finlande \\
|
||
Apr--May 2014 & Ion \textsc{Petre} & Combio, Åbo Akademi, Turku, Finlande \\
|
||
Aug 2011 & Sergey \textsc{Verlan} & LACL, Université Paris-Est Créteil \\
|
||
\end{tabularx}
|
||
}
|
||
|
||
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||
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||
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||
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