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\newcommand{\cvsecrule}{\vspace{-3mm}{\color{Prune}\hrule}\medskip}
\ifentiredoc
\chapter[CV]{Sergiu \textsc{Ivanov} \enspace — \enspace CV}
\else
\chapter*{Sergiu \textsc{Ivanov} \enspace — \enspace CV}
\fancyhead[OL,ER]{\textcolor{Prune}{\textsl{Sergiu \textsc{Ivanov}}}}
\counterwithout{section}{chapter}
\fi
\vspace{-7mm}
\newcommand{\summaryvspace}{\vspace{1mm}}
\hspace{\parindent}%
\textbf{Maître de conférences --- Associate Professor}
\summaryvspace
\href{https://www.ibisc.univ-evry.fr/}{IBISC} Laboratory / Department of Computer Science,
\href{https://www.ibisc.univ-evry.fr/}{Université d'Évry Paris-Saclay}
\summaryvspace
IBGBI, 23 boulevard de France, 91034 Évry-Courcouronnes, France
\summaryvspace
\url{sergiu.ivanov@universite-paris-saclay.fr}
\summaryvspace
\url{https://www.ibisc.univ-evry.fr/~sivanov/}
\vspace{-3mm}
\section{Career overview}
\label{sec:career}
\cvsecrule
\newcommand{\timeskip}{2mm}
\noindent
\begin{tabularx}{\textwidth}{>{\leavevmode\color{Prune}}p{22mm} X}
2017-- & \textbf{Maître de conférences --- Associate Professor} (tenured) \\
& 50\% research, 50\% teaching \\
& IBISC Laboratory --- Department of Computer Science \\
& Université d'Évry Paris-Saclay \\[\timeskip]
2016--2017 & \textbf{Post-doctoral researcher} \\
& \textit{Biomechanical modelling of blood platelet cytoskeleton during platelet activation} \\
& Supervisor: Nicolas \textsc{Glade} \\
& \href{https://www.timc.fr/}{TIMC} Laboratory CNRS UMR 5525, Université Grenoble-Alpes \\[\timeskip]
2015--2016 & \textbf{Attaché Temporaire d'Enseignement et de Recherche ---} \\
& Temporary Teaching Assistant \\
& \href{https://www.lacl.fr/en/}{LACL} Laboratory, Université Paris-Est Créteil \\[\timeskip]
2012--2015 & \textbf{PhD student} \\
& \textit{On the Power and Universality of Biologically-inspired Models of Computation} \\
& Directed by Sergey \textsc{Verlan}, defense on 2015-06-23 \\
& $192\text{h} = 3 \times 64\text{h}$ of teaching at the Departement of Computer Science \\
& LACL Laboratory, Université Paris-Est Créteil \\[\timeskip]
2011--2012 & \textbf{M1 student} \\
& MSc programme \textit{Mathematics and Computer Science} \\
& Google Summer of Code 2012 participant \\
& University of the Academy of Sciences of Moldova \\[\timeskip]
2009--2012 & \textbf{Research engineer} (part time) \\
& Supervisor: Yurii \textsc{Rogozhin} \\
& \href{http://www.math.md/}{Institute of Mathematics and Computer Science of Moldova} \\[\timeskip]
2007--2011 & \textbf{Bachelor in Computer Engineering} \\
& Average grade over the 4 years: 10 out of 10 \\
& Google Summer of Code 2008 participant \\
& \href{https://utm.md/}{Technical University of Moldova}
\end{tabularx}
\pagebreak
\section{PhD thesis}
\label{sec:phd-thesis}
\cvsecrule
\newcommand{\phdskip}{0mm}
\begin{tabularx}{\textwidth}{>{\leavevmode\color{Prune}}lX}
Title: & \textit{On the Power and Universality of Biologically-inspired Models of Computation} \\[\phdskip]
Director: & \textbf{Sergey \textsc{Verlan}} \\[\phdskip]
Defense: & June 23, 2015 (2015-06-23) \\[\phdskip]
Institution: & LACL Laboratory, Université Paris-Est Créteil \\
& doctoral contract attached to Université Paris-Est \\
\end{tabularx}
\vspace{-4mm}
\subsection*{PhD thesis jury}
\label{sec:phd-thesis-jury}
\vspace{-2mm}
\newcommand{\phdjuryskip}{0mm}
\begin{tabularx}{\textwidth}{Xr}
\textbf{Jean-Louis \textsc{Giavitto}} & President \\
CNRS Senior scientist (DR CNRS) at IRCAM \\[\phdjuryskip]
\textbf{Jérôme \textsc{Durand-Lose}} & Reviewer \\
Full Professor at Université d'Orléans \\[\phdjuryskip]
\textbf{Gheorghe \textsc{Păun}} & Reviewer \\
Titular member of the Romanian Academy \\[\phdjuryskip]
\textbf{Philippe \textsc{Schnoebelen}} & Reviewer \\
CNRS Senior scientist (DR CNRS) at LSV lab (now LMF) \\[\phdjuryskip]
\textbf{Enrico \textsc{Formenti}} & Examiner \\
Full Professor at Université Côte d'Azur \\[\phdjuryskip]
\textbf{Elisabeth \textsc{Pelz}} & Examiner \\
Full Professor at Université Paris-Est Créteil
\end{tabularx}
\vspace{-2mm}
\section{Teaching}
\label{sec:teaching}
\cvsecrule
\newcommand{\chargeshared}{$\star$}
\newcommand{\chargefull}{$\dagger$}
My teaching spans most university years, starting from L1 (freshman
year) through to M2 (second year of the Master's program). I mostly
teach computer science and engineering at the \emph{licence} level
(approximately, bachelor), and mostly theoretical biology, network
biology, and bioinformatics at the Master's level. I have
a CRCT (approximately, sabbatical) for the school
year 2023--2024.
The following tables briefly list the courses I teach, am in charge of
(marked with the sign \chargefull), or share the responsibility of (marked
with the sign \chargeshared), together with the typical teaching hours.
I only describe the time period after I obtained the current tenured
Maître de conférences position.
\vspace{-3mm}
\subsection{Master's level courses}
\label{sec:teaching-msc}
\cvsecrule
\newcommand{\teachingskip}{0mm}
\begin{tabularx}{\textwidth}{>{\leavevmode\color{Prune}}ll X}
2022--2023 & M2 GENIOMHE & \textbf{Computational DNA nanotechnology}\chargeshared \\
&& SI:\footnote{SI = hours taught by Sergiu \textsc{Ivanov}.} 7.5h CM+TD, Damien \textsc{Regnault}: 7.5h CM+TD \\[\teachingskip]
2017--2023 & M2 GENIOMHE & \textbf{Computational Systems Biology \& Network Medicine}\chargeshared \\
&& SI: 12h CM+TD, Franck \textsc{Delaplace}: 12CM+TD \\[\teachingskip]
2017--2023 & M2 SSB & \textbf{Network Systems: Modelling and Analysis}\chargeshared \\
&& SI: 12h CM+TD, Franck \textsc{Delaplace}: 9CM+TD \\[\teachingskip]
2017--2023 & M2 CNS & \textbf{Systèmes multi-agents}\chargeshared \\
&& SI: 9h CM+TD, Guillaume \textsc{Hutzler}: 9h CM+TD \\[\teachingskip]
\end{tabularx}
\vspace{-3mm}
\subsection{Bachelor level courses}
\label{sec:teaching-licence}
\cvsecrule
\begin{tabularx}{\textwidth}{>{\leavevmode\color{Prune}}ll X}
2017--2023 & L3 informatique & \textbf{Projet Professionnel d'Études et d'Insertion}\chargefull \\
&& SI: 9h TD \\[\teachingskip]
2017--2023 & L3 informatique & \textbf{Systèmes d'exploitation}\chargefull \\
&& SI: 18h CM + 18h TD \\[\teachingskip]
2020--2023 & L2 informatique & \textbf{Programmation système} \\
&& SI: 18h TD \\[\teachingskip]
\end{tabularx}
\pagebreak
\noindent
\begin{tabularx}{\textwidth}{>{\leavevmode\color{Prune}}ll X}
2017--2023 & L1 informatique & \textbf{Algorithmique et programmation} \\
&& SI: 36h TD \\[\teachingskip]
2017--2023 & L1 informatique & \textbf{Programmation impérative} \\
&& SI: 36h TD \\[\teachingskip]
2020--2023 & L1 informatique & \textbf{Méthodologie} \\
&& SI: 12h TD \\[\teachingskip]
2019--2021 & L1 informatique & \textbf{Architecture} \\
&& SI: 18h TD \\[\teachingskip]
2018--2021 & L1 informatique & \textbf{Émulateur pédagogique} \\
&& Supplementary course for Parcoursup OUI-SI candidates. \\
&& SI: 10h TD \\[\teachingskip]
\end{tabularx}
\vspace{-6mm}
\subsection{Other courses}
\label{sec:teaching-other}
\cvsecrule
\begin{tabularx}{\textwidth}{>{\leavevmode\color{Prune}}ll X}
2020 & Open online class & \textbf{Introduction to Membrane Computing}\chargeshared \\
&& SI: 4h CM online + 4h TD online,\\
&& David \textsc{Orellana-Martín}: 6h CM online + 4h TD online \\[\teachingskip]
2017--2024 & Popular science & \textbf{Fête de la Science --- Science Days}\chargeshared \\
&& SI: 2 full days on the stand + organization
\end{tabularx}
\vspace{-3mm}
\subsection{Teaching and research}
\label{sec:teaching-research}
\cvsecrule
All Master's level courses I teach link directly to my
research. In the course \textbf{Computational DNA nanotechnology}, we
introduce the students to DNA self-assembly and its potential
applications, including applications in biology and medicine.
We typically overview the state of the project I share with Damien
\textsc{Regnault} to build a functioning pipeline for self-assembly of
DNA nanostructures, spanning the entire spectrum from theoretical
design to actual wet-lab production.
Both the courses \textbf{Computational Systems Biology \& Network
Medicine} and \textbf{Network Systems: Modelling and Analysis} focus
on another major pillar of my research: approaching the complexity of
biological systems using the tools of network science and discrete
dynamical systems. More concretely, in these classes we introduce the
students to the basics of graph theory, and then extensively discuss
two formal models of discrete dynamical networks---Boolean networks
and Petri nets---as well as show concrete applications for therapy
inference or setting up formal frameworks for thinking about the
origins of Life.
Finally, I use the course \textbf{Systèmes multi-agents}
(\textit{Multi-agent systems}) as an opportunity to introduce the
students to emergent complexity of the living systems, made up of
simple entities interacting in complex ways. In this course, we
discuss different tools which can formalize multi-agent systems---in
particular membrane (P) systems---and propose several practical
assignments to help the students better understand the connection
between abstract objects and concrete systems.
Outside my normal teaching activity, I particularly appreciate
\textbf{Science Days} (\textit{Fêtes de la Science}), which are always
an excellent opportunity to illustrate the hallmarks of my research to
school students and the general public. I have taken part in Science
Days every year, including during the pandemic when we held online
stands, and I have consistently invested a considerable effort in
organizing the stands.
Finally, even though my bachelor level courses are not in direct
connection to my research, I always bring in discussions
of complexity and even theoretical biology, to illustrate some
abstract concepts on the one hand, and to challenge the students and
push them out of their comfort zone on the other hand.
\vspace{-2mm}
\section{Organization of scientific events}
\label{sec:management}
\cvsecrule
\newcommand{\eventskip}{.5mm}
\noindent
\begin{tabularx}{\textwidth}{>{\leavevmode\color{Prune}}p{22mm} X}
2022 & \textbf{IBISC Laboratory Day} \\
& coorganization with Guillaume \textsc{Postic} \\[\eventskip]
\end{tabularx}
\pagebreak
\noindent
\begin{tabularx}{\textwidth}{>{\leavevmode\color{Prune}}p{22mm} X}
2022 & Seminar \textbf{Workshop on the Atavistic Theory of Cancer --- ATAC2022} \\
& coorganization with Nicolas \textsc{Glade} and Angélique \textsc{Stéphanou} \\[\eventskip]
2020 & Online \textbf{Conference on Membrane Computing --- CMC 2020} \\
& coorganization with Rudolf \textsc{Freund} \\[\eventskip]
2018 & Seminar of the \textbf{French-speaking Society for Theoretical Biology (SFBT)} \\
& coorganization with Nicolas \textsc{Glade} and Angélique \textsc{Stéphanou} \\[\eventskip]
2018 & Joint conferences \textbf{Unconventional Computation, Natural Computation ---\newline UCNC2018} and \textbf{Machines, Computations, and Universality --- MCU 2018} \\
& main organizer: Sergey \textsc{Verlan} \\[\eventskip]
2018 & \textbf{Workshop on Membrane Computing} \\
& conference \textit{Unconventional Computation, Natural Computation --- UCNC 2018} \\
& coorganization with Rudolf \textsc{Freund} \\[\eventskip]
2017 & \textbf{IBISC Laboratory Day} \\
& coorganization with Najett \textsc{Neji} \\[\eventskip]
\end{tabularx}
\vspace{-2mm}
\section{Scientific roles}
\label{sec:roles}
\cvsecrule
\newcommand{\roleskip}{1mm}
\begin{tabularx}{\textwidth}{>{\leavevmode\color{Prune}}p{22mm} X}
2022--2026 & Elected member of the \textbf{Research Commission} of Université d'Évry Paris-Saclay \\[\roleskip]
2021--2023 & Elected member of the \textbf{IBISC Laboratory Council} \\[\roleskip]
2019--2021 & Appointed member of the \textbf{IBISC Laboratory Council} \\[\roleskip]
2020-- & Manager of the \textbf{work group on personalized medicine} of IBISC \\
& coorganization with Farida \textsc{Zehraoui} \\[\roleskip]
2017-- & IBISC representative to the group \textbf{Méthodes
Formelles pour les Systèmes Logiciels et Matériels --- MeFoSyLoMa}
(\textit{Formal Methods for Software and Hardware systems}) \\[\roleskip]
\end{tabularx}
\vspace{-2mm}
\section{Projects and grants}
\label{sec:projects}
\cvsecrule
\newcommand{\projectskip}{1mm}
\begin{tabularx}{\textwidth}{>{\leavevmode\color{Prune}}l p{17mm} X}
2022 & FRR\footnote{\href{https://www.univ-evry.fr/recherche/commission-de-la-recherche/campagnes.html}{FRR} = project-based competitive local funding of Université d'Évry Paris-Saclay.} & \textit{Setting up experimental projects in DNA self-assembly} \\
& \textbf{3 k€} & Role: \textbf{Principal Investigator} \\
&& Other Principal investigator: Damien \textsc{Regnault} \\[\projectskip]
2021 & IXXI\footnote{\href{http://www.ixxi.fr/}{IXXI} = Institute of Complex Systems of the Auvergne-Rhône-Alpes region.}\newline \textbf{4~k€} &
\textit{Exploration of evolutivity and robustness of biological
networks — Characterisation of structural and dynamic connected
components of sign Boolean networks, as well as of viability
constraints} \\
&& Role: \textbf{Investigator} \\
&& Principal investigator: Nicolas \textsc{Glade} \\[\projectskip]
2018--2019 & DIM RFSI & \textit{Computer Science Models for Cellular Reprogramming} \\
& \textbf{11 k€} & Role: \textbf{Principal investigator} \\
&& Other investigators: Franck \textsc{Delaplace}, Loïc \textsc{Paulevé} \\
\end{tabularx}
\vspace{-2mm}
\section{Distinctions}
\label{sec:distinctions}
\cvsecrule
\begin{tabularx}{\textwidth}{>{\leavevmode\color{Prune}}p{22mm} X}
2023--2025 & \textbf{RIPEC C3 for scientific activity} \\
& 3-year monthly ministerial premium for outstanding research work \\[1mm]
2023--2024 & \textbf{Congé de Recherche ou de Conversion Thématique --- CRCT} \\
& Leave for research or thematic conversion \\
\end{tabularx}
\section{Reviews and editorial activity}
\label{sec:reviews}
\cvsecrule
\subsection{Program and scientific committees}
\label{sec:program-committees}
\vspace{-2mm}
\newcommand{\reviewEmph}[1]{#1}
\newcommand{\pcskip}{0mm}
\noindent
\begin{tabularx}{\textwidth}{>{\leavevmode\color{Prune}}p{22mm} X}
2023 & \reviewEmph{Non-Classical Models of Automata and Applications} (NCMA) \\
& Member of the Program Committee \\[\pcskip]
2022--2023 & \reviewEmph{Conference on Membrane Computing} (CMC) \\
& Member of the Program Committee \\[\pcskip]
2022-- & \reviewEmph{Computer Science Journal of Moldova} \\
& Member of the Editorial Board \\[\pcskip]
2020 & \reviewEmph{International Conference on Membrane Computing} (ICMC) \\
& Co-chair of the Program Committee \\[\pcskip]
2018 & \reviewEmph{Unconventional Computation and Natural Computation} (UCNC) \\
& Member of the Program Committee \\[\pcskip]
2018--2019 & \reviewEmph{Acta Biotheoretica} \\
& Guest editor after the seminar of the \textit{Société Francophone de la Biology Théorique} \\[\pcskip]
\end{tabularx}
\vspace{-2mm}
\subsection{Journal reviews}
\label{sec:journal-reviews}
\vspace{-2mm}
I have reviewed and regularly review papers for the
following journals.
\vspace{1mm}
{\renewcommand{\arraystretch}{1.05}
\noindent
\begin{tabularx}{\textwidth}{XcX}
\reviewEmph{Theoretical Computer Science} & \hspace{5mm}  & \reviewEmph{Fundamenta Informaticae}\\[0pt]
\reviewEmph{Lecture Notes for Computer Science} & & \reviewEmph{Journal of Cellular Automata}\\[0pt]
\reviewEmph{Swarm and Evolutionary Computation} & & \reviewEmph{Socio-Ecological Practice Research}\\[0pt]
\reviewEmph{Journal of Symbolic Computation} & & \reviewEmph{Journal of Membrane Computing}\\[0pt]
\reviewEmph{International Journal of Foundations of\newline Computer Science} & & \reviewEmph{Indian Journal of Pure and Applied Mathematics}\\[0pt]
\reviewEmph{Concurrency and Computation: Practice\newline and Experience} & & \reviewEmph{Journal of Automata, Languages, and Combinatorics}\\[0pt]
\reviewEmph{Computer Science Journal of Moldova} & & \reviewEmph{Natural Computing}\\[0pt]
\end{tabularx}
}
\noindent
I am a recommender for \reviewEmph{Peer Community In Mathematical and
Computational Biology}.
\vspace{-2mm}
\subsection{Conference reviews}
\label{sec:conference-reviews}
I reviewed papers for the following conferences multiple times,
without being on the Program Committee: \reviewEmph{Conference on Membrane
Computing} (CMC), \reviewEmph{Machines, Computations, and Universality}
(MCU), \reviewEmph{Developments in Language Theory} (DLT),
\reviewEmph{Unconventional Computation and Natural Computation} (UCNC).
\section{Jurys}
\label{sec:jurys}
\cvsecrule
\subsection{PhD defences}
\label{sec:phd-defences}
\subsubsection{Sara \textsc{Riva}}
\label{sec:sara-riva}
\begin{tabularx}{\textwidth}{>{\leavevmode\color{Prune}}lX}
Title: & \textbf{Factorization of Discrete Dynamic Systems} \\
Director: & Enrico \textsc{Formenti}, Université Côte d'Azur \\
Co-director: & Alberto \textsc{Dennunzio}, Università degli Studi di Milano-Bicocca \\
Duration: & 2019--2022 \\
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{19mm} 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*{Louison \textsc{Crépin}}
\label{sec:louison-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{25mm} 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) \\
& Sergiu \textsc{Ivanov} 75\%, Damien \textsc{Regnault} 25\% \\[\internskip]
Sep 2022 --\newline Jan 2023 & \textbf{Ai-Ling \textsc{Nguyen Bonnet}} --- \textit{Efficient exploration strategies in the evolutionary mille-feuille}, CentraleSupélec 4th year intern \\
& Sergiu \textsc{Ivanov} 50\%, Nicolas \textsc{Glade} 50\%\\[\internskip]
Jun-Jul 2022 & \textbf{Vincent \textsc{Ferrari-Dominguez}} --- \textit{Controllability of complex systems} \\
& ENS Paris 3rd year intern \\
& Sergiu \textsc{Ivanov} 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) \\
& Sergiu \textsc{Ivanov} 100\% \\[\internskip]
Apr--Jun 2022 & \textbf{Idriss \textsc{Ben Saïd}} --- \textit{Software simulation of DNA self-assembly models} \\
& UEVE 3rd year intern (L3) \\
& Sergiu \textsc{Ivanov} 100\% \\[\internskip]
Apr--Jun 2022 & \textbf{Mustapha \textsc{Si Kaddour}} --- \textit{DNA self-assembly and array grammars} \\
& UEVE 3rd year intern (L3) \\
& Sergiu \textsc{Ivanov} 100\% \\[\internskip]
Jun--Aug 2021 & \textbf{Rémy \textsc{Défossez}} --- \textit{Evolutionary mille-feuille: a new formalization of evolution} \\
& ENS Paris 3rd year intern \\
& Sergiu \textsc{Ivanov} 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) \\
& Sergiu \textsc{Ivanov} 75\%, Nicolas \textsc{Glade} 25\%\\[\internskip]
Feb--Apr 2020 & \textbf{Yacine \textsc{Hadjar}},\hspace{-.5mm} \textbf{Imad \textsc{Bouzgou}} \hspace{-.5mm}--\hspace{-.5mm} \textit{Multi-agent modelling of rheumatoid arthritis} \\
& UEVE 4th year research project (M1 TER) \\
& Sergiu \textsc{Ivanov} 75\%, Anna \textsc{Niarakis} 25\%\\[\internskip]
Apr--Jun 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) \\
& Sergiu \textsc{Ivanov} 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}
\newcommand{\researchSep}{0mm}
\vspace{-2mm}
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. My work falls into the following 2 broad
categories:
\begin{enumerate}[itemsep=0mm]
\item deepening the knowledge about complex biological systems and
suggesting improvements for health-related applications,
\item setting up formal frameworks for better conceiving of 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 works and publications.
\vspace{-1mm}
\subsection{Bioinformatics}
\label{sec:bioinformatics}
\vspace{-1mm}
\begin{itemize}[itemsep=\researchSep]
\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{Nia\-ra\-kis} which fell victim to the
Covid19 pandemic (Yacine \textsc{Hadjar} and Imad \textsc{Bouzgou}'s
internship in 2020)
\end{itemize}
\vspace{-2mm}
\subsection{Theoretical biology}
\label{sec:theoretical-biology}
\vspace{-1mm}
\begin{itemize}[itemsep=\researchSep]
\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}
\vspace{-2mm}
\subsection{Natural computing}
\label{sec:tcs}
\vspace{-1mm}
\begin{itemize}[itemsep=\researchSep]
\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}
\vspace{-2mm}
\subsection{DNA computing}
\label{sec:dna}
\vspace{-1mm}
\begin{itemize}[itemsep=\researchSep]
\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
\end{itemize}
I carry out this work in collaboration with Damien \textsc{Regnault}.
\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{\href{https://www.siana.eu/}{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.''} 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-de\-le\-tion 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
An\-dru\-na\-chie\-vici'' (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 \\
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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