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Sergiu Ivanov e46e131ce5 Add the book chapter on network modelling methods.
2022-12-04 00:30:16 +01:00

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2022

  1. Elio Nushi, Victor-Bogdan Popescu, José Ángel Sánchez Martín, Sergiu Ivanov, Eugen Czeizler, Ion Petre: Book chapter Network modeling methods for precision medicine in Systems Biology Modelling and Analysis: Formal Bioinformatics Methods and Tools, Elisabetta De Maria, editor. In press, Wiley 2022.
  2. Artiom Alhazov, Rudolf Freund et Sergiu Ivanov: P versus B: P Systems as a Formal Framework for Controllability of Boolean Networks. Proceedings 12th International Workshop on Non-Classical Models of Automata and Applications, Debrecen, Hungary, August 26-27, 2022.
  3. Artiom Alhazov, Rudolf Freund, Sergiu Ivanov et Sergey Verlan: Regulated Insertion-Deletion Systems. Journal of Automata, Languages and Combinatorics 27.1–3 (2022), p. 15-45.
  4. Artiom Alhazov, Rudolf Freund, Sergiu Ivanov, Sergey Verlan: Tissue P Systems with Vesicles of Multisets. Int. J. Found. Comput. Sci. 33(3&4): 179-202 (2022)
  5. Artiom Alhazov, Rudolf Freund, Sergiu Ivanov, Marion Oswald: Variants of derivation modes for which purely catalytic P systems are computationally complete. Theor. Comput. Sci. 920: 95-112 (2022)
  6. Artiom Alhazov, Rudolf Freund, Sergiu Ivanov, Sergey Verlan: Prescribed Teams of Rules Working on Several Objects. MCU 2022: 27-41

2021

  1. Artiom Alhazov, Rudolf Freund, Sergiu Ivanov, Sergey Verlan: Variants of derivation modes for which catalytic P systems with one catalyst are computationally complete.

    1. Membr. Comput. 3(4): 233-245 (2021)
  2. Sergiu Ivanov, Sergey Verlan: Single semi-contextual insertion-deletion systems. Nat. Comput. 20(4): 703-712 (2021)
  3. Rémi Segretain, Laurent Trilling, Nicolas Glade, Sergiu Ivanov: Who Plays Complex Music? On the Correlations Between Structural and Behavioral Complexity Measures in Sign Boolean Networks. Proceedings of the 21th IEEE International Conference on BioInformatics and BioEngineering BIBE 2021: 1-6.
  4. Artiom Alhazov, Rudolf Freund, Sergiu Ivanov, Marion Oswald: Relations between Control Mechanisms for Sequential Grammars. Fundam. Informaticae 181(2-3): 239-271 (2021)
  5. Artiom Alhazov, Rudolf Freund, Sergiu Ivanov: P systems with limited number of objects. J. Membr. Comput. 3(1): 1-9 (2021)

  6. Artiom Alhazov, Rudolf Freund, Sergiu Ivanov: When catalytic P systems with one catalyst can be computationally complete.

    1. Membr. Comput. 3(3): 170-181 (2021)
  7. Jérémie Pardo, Sergiu Ivanov, Franck Delaplace: Sequential reprogramming of biological network fate. Theor. Comput. Sci. 872: 97-116 (2021)
  8. Rémi Segretain, Sergiu Ivanov, Laurent Trilling, Nicolas Glade: A Methodology for Evaluating the Extensibility of Boolean Networks’ Structure and Function. In: Benito R.M., Cherifi C., Cherifi H., Moro E., Rocha L.M., Sales-Pardo M. (eds) Complex Networks & Their Applications IX. COMPLEX NETWORKS 1. Studies in Computational Intelligence, vol 944. Springer, Cham. (2021)
  9. Elio Nushi, Victor-Bogdan Popescu, José Ángel Sánchez Martín, Sergiu Ivanov, Eugen Czeizler, Ion Petre: Network modeling methods for precision medicine. CoRR abs/2104.09206 (2021)

2020

  1. Franck Delaplace, Sergiu Ivanov: Bisimilar Booleanization of multivalued networks. Biosyst. 197: 104205 (2020)

  2. Sergiu Ivanov, Ion Petre: Controllability of reaction systems.

    1. Membr. Comput. 2(4): 290-302 (2020)
  3. Artiom Alhazov, Rudolf Freund, Sergiu Ivanov, Linqiang Pan, Bosheng Song: Time-freeness and clock-freeness and related concepts in P systems. Theor. Comput. Sci. 805: 127–143 (2020)
  4. Artiom Alhazov, Rudolf Freund, Sergiu Ivanov: P systems with randomized right-hand sides of rules. Theor. Comput. Sci. 805: 144–160 (2020)
  5. Franck Delaplace, Sergiu Ivanov: Bisimilar Conversion of Multi-valued Networks to Boolean Networks. CoRR abs/2001.07371 (2020)
  6. Sergiu Ivanov, Ion Petre: Controllability of reaction systems. CoRR abs/2007.09461 (2020)
  7. Urvan Christen, Sergiu Ivanov, Rémi Segretain, Laurent Trilling, Nicolas Glade: On Computing Structural and Behavioral Complexities of Threshold Boolean Networks. Acta Biotheoretica 68 119–138 (2020)
  8. Rémi Segretain, Sergiu Ivanov, Laurent Trilling, Nicolas Glade: Implementation of a Computing Pipeline for Evaluating the Extensibility of Boolean Networks’ Structure and Function. bioRxiv 2020.10.02.323949 (2020)

2019

  1. Artiom Alhazov, Rudolf Freund, Sergiu Ivanov: Variants of P systems with activation and blocking of rules. Nat. Comput. 18(3): 593–608 (2019)
  2. Jérémie Pardo, Sergiu Ivanov, Franck Delaplace: Sequential Reprogramming of Biological Network Fate. CMSB 2019: 20–41
  3. Artiom Alhazov, Rudolf Freund, Sergiu Ivanov: Register machines over groups. NCMA 2019: 31–46

2018

  1. Artiom Alhazov, Rudolf Freund, Sergiu Ivanov, Marion Oswald, Sergey Verlan: Extended spiking neural P systems with white hole rules and their red-green variants. Nat. Comput. 17(2): 297–310 (2018)
  2. Artiom Alhazov, Rudolf Freund, Sergiu Ivanov, Marion Oswald, Sergey Verlan: Chocolate P Automata. Enjoying Natural Computing 2018: 1–20
  3. Sergiu Ivanov, Vladimir Rogojin, Sepinoud Azimi, Ion Petre: WEBRSIM: A Web-Based Reaction Systems Simulator. Enjoying Natural Computing 2018: 170–181
  4. Artiom Alhazov, Rudolf Freund, Sergiu Ivanov: Sequential Grammars with Activation and Blocking of Rules. MCU 2018: 51–68
  5. Artiom Alhazov, Rudolf Freund, Sergiu Ivanov, Sergey Verlan: Tissue P Systems with Point Mutation Rules. Int. Conf. on Membrane Computing 2018: 33–56
  6. Artiom Alhazov, Rudolf Freund, Sergiu Ivanov: P Systems with Activation and Blocking of Rules. UCNC 2018: 1–15

2017

  1. Sergiu Ivanov, Sergey Verlan: Universality and Computational Completeness of Controlled Leftist Insertion-Deletion Systems. Fundam. Informaticae 155(1-2): 163–185 (2017)
  2. Aaron Meurer, Christopher P. Smith, Mateusz Paprocki, Ondrej Certík, Sergey B. Kirpichev, Matthew Rocklin, Amit Kumar, Sergiu Ivanov, Jason Keith Moore, Sartaj Singh, Thilina Rathnayake, Sean Vig, Brian E. Granger, Richard P. Muller, Francesco Bonazzi, Harsh Gupta, Shivam Vats, Fredrik Johansson, Fabian Pedregosa, Matthew J. Curry, Andy R. Terrel, Stepán Roucka, Ashutosh Saboo, Isuru Fernando, Sumith Kulal, Robert Cimrman, Anthony M. Scopatz: SymPy: symbolic computing in Python. PeerJ Comput. Sci. 3: e103 (2017)
  3. Artiom Alhazov, Henning Fernau, Rudolf Freund, Sergiu Ivanov, Rani Siromoney, K. G. Subramanian: Contextual array grammars with matrix control, regular control languages, and tissue P systems control. Theor. Comput. Sci. 682: 5–21 (2017)
  4. Quoc-Trung Vuong, Roselyne Chauvin, Sergiu Ivanov, Nicolas Glade, Laurent Trilling: A Logical Constraint-based Approach to Infer and Explore Diversity and Composition in Thresholded Boolean Automaton Networks. COMPLEX NETWORKS 2017: 567–579
  5. Artiom Alhazov, Rudolf Freund, Sergiu Ivanov: Hierarchical P Systems with Randomized Right-Hand Sides of Rules. Int. Conf. on Membrane Computing 2017: 15–39
  6. Artiom Alhazov, Rudolf Freund, Sergiu Ivanov, Sergey Verlan: (Tissue) P Systems with Vesicles of Multisets. AFL 2017: 11–25

2016

  1. Rudolf Freund, Sergiu Ivanov, Ludwig Staiger: Going Beyond Turing with P Automata: Regular Observer ω-Languages and Partial Adult Halting. Int. J. Unconv. Comput. 12(1): 51-69 (2016)

  2. Artiom Alhazov, Sergiu Ivanov, Elisabeth Pelz, Sergey Verlan: Small Universal Deterministic Petri Nets with Inhibitor Arcs.

    1. Autom. Lang. Comb. 21(1-2): 7-26 (2016)
  3. Sepinoud Azimi, Cristian Gratie, Sergiu Ivanov, Luca Manzoni, Ion Petre, Antonio E. Porreca: Complexity of model checking for reaction systems. Theor. Comput. Sci. 623: 103-113 (2016)
  4. Artiom Alhazov, Bogdan Aman, Rudolf Freund, Sergiu Ivanov: Simulating R Systems by P Systems. Int. Conf. on Membrane Computing 2016: 51-66
  5. Artiom Alhazov, Omar Belingheri, Rudolf Freund, Sergiu Ivanov, Antonio E. Porreca, Claudio Zandron: Purely Catalytic P Systems over Integers and Their Generative Power. Int. Conf. on Membrane Computing 2016: 67-82

  6. Aaron Meurer, Christopher P. Smith, Mateusz Paprocki, Ondrej Certík, Matthew Rocklin, Amit Kumar, Sergiu Ivanov, Jason Keith Moore, Sartaj Singh, Thilina Rathnayake, Sean Vig, Brian

    1. Granger, Richard P. Muller, Francesco Bonazzi, Harsh Gupta,

    Shivam Vats, Fredrik Johansson, Fabian Pedregosa, Matthew

    1. Curry, Ashutosh Saboo, Isuru Fernando, Sumith Kulal, Robert

    Cimrman, Anthony M. Scopatz: SymPy: Symbolic computing in Python. PeerJ Prepr. 4: e2083 (2016)

  7. Artiom Alhazov, Rudolf Freund, Sergiu Ivanov: Polymorphic P Systems: A Survey. Bulletin of the International Membrane Computing Society (IMCS). Number 2, December 2016: 79–101.

2015

  1. Sergiu Ivanov: On the Power and Universality of Biologically-inspired Models of Computation. (Étude de la puissance d'expression et de l'universalité des modèles de calcul inspirés par la biologie). University of Paris-Est, France, 2015
  2. Sergiu Ivanov: Annotation on PhD Thesis. Comput. Sci. J. Moldova 23(3): 386-388 (2015)
  3. Sergiu Ivanov, Sergey Verlan: Random Context and Semi-conditional Insertion-deletion Systems. Fundam. Informaticae 138(1-2): 127-144 (2015)
  4. Sepinoud Azimi, Cristian Gratie, Sergiu Ivanov, Ion Petre: Dependency graphs and mass conservation in reaction systems. Theor. Comput. Sci. 598: 23-39 (2015)
  5. Sergiu Ivanov, Sergey Verlan: Universality of Graph-controlled Leftist Insertion-deletion Systems with Two States. MCU 2015: 79-93
  6. Sergiu Ivanov, Sergey Verlan: On the Lower Bounds for Leftist Insertion-Deletion Languages. Annals of the University of Bucharest (Informatics) LXII(2): 77–88 (2015)
  7. Rudolf Freund, Sergiu Ivanov, Sergey Verlan: P Systems with Generalized Multisets Over Totally Ordered Abelian Groups. Int. Conf. on Membrane Computing 2015: 117-136
  8. Rudolf Freund, Sergiu Ivanov, Ludwig Staiger: Going Beyond Turing with P Automata: Partial Adult Halting and Regular Observer ω-Languages. UCNC 2015: 169-180
  9. Artiom Alhazov, Rudolf Freund, Sergiu Ivanov, Marion Oswald: Observations on P Systems with States. Multidisciplinary Creativity, Marian Gheorghe, Ion Petre, Mario J. Pérez-Jiménez, Grzegorz Rozenberg, and Arto Salomaa, eds. p. 17-28, Editura Spandugino, 2015.

2014

  1. Artiom Alhazov, Rudolf Freund, Sergiu Ivanov: Length P Systems. Fundam. Informaticae 134(1-2): 17-37 (2014)

  2. Sergiu Ivanov, Yurii Rogozhin, Sergey Verlan: Small Universal Networks of Evolutionary Processors.

    1. Autom. Lang. Comb. 19(1-4): 133-144 (2014)
  3. Sergiu Ivanov, Elisabeth Pelz, Sergey Verlan: Small Universal Non-deterministic Petri Nets with Inhibitor Arcs. DCFS 2014: 186-197
  4. Sergiu Ivanov: Polymorphic P Systems with Non-cooperative Rules and No Ingredients. Int. Conf. on Membrane Computing 2014: 258-273

2013

  1. Sergiu Ivanov: A formal framework for clock-free networks of cells. Int. J. Comput. Math. 90(4): 776-788 (2013)
  2. Sergiu Ivanov, Sergey Verlan: About One-Sided One-Symbol Insertion-Deletion P Systems. Int. Conf. on Membrane Computing 2013: 225-237

  3. Henning Fernau, Rudolf Freund, Sergiu Ivanov, Markus L. Schmid,

      1. Subramanian: Array Insertion and Deletion P Systems. UCNC

    2013: 67-78

  4. Rudolf Freund, Sergiu Ivanov, Marion Oswald, K. G. Subramanian: One-dimensional Array Grammars and P Systems with Array Insertion and Deletion Rules. MCU 2013: 62-75
  5. Sergiu Ivanov, Elisabeth Pelz, Sergey Verlan: Small Universal Petri Nets with Inhibitor Arcs. CoRR abs/1312.4414 (2013)

2012

  1. Sergiu Ivanov: Static and Dynamic Membrane Structures. Comput. Sci. J. Moldova 20(3): 374-402 (2012)

2011

  1. Sergiu Ivanov, Artiom Alhazov, Vladimir Rogojin, Miguel

    1. Gutiérrez-Naranjo: /Forward and Backward Chaining with P

    Systems./ Int. J. Nat. Comput. Res. 2(2): 56-66 (2011)

  2. Sergiu Ivanov: Basic Concurrency Resolution in Clock-Free P Systems. Int. Conf. on Membrane Computing 2011: 226-242
  3. Sergiu Ivanov, Sergey Verlan: Random Context and Semi-Conditional Insertion-Deletion Systems. CoRR abs/1112.5947 (2011)

2010

  1. Artiom Alhazov, Elena Boian, Liudmila Burtseva, Constantin Ciubotaru, Svetlana Cojocaru, Alexandru Colesnicov, Valentina Demidova, Sergiu Ivanov, Veaceslav Macari, Galina Magariu, Ludmila Malahova, Vladimir Rogojin, Yurii Rogozhin, Tatiana Tofan, Sergey Verlan, Tatiana Verlan: Investigations on Natural Computing in the Institute of Mathematics and Computer Science. Comput. Sci. J. Moldova 18(2): 101-138 (2010)
  2. Artiom Alhazov, Constantin Ciubotaru, Sergiu Ivanov, Yurii Rogozhin: Membrane Systems Languages Are Polynomial-Time Parsable. Comput. Sci. J. Moldova 18(2): 139-148 (2010)
  3. Artiom Alhazov, Constantin Ciubotaru, Sergiu Ivanov, Yurii Rogozhin: The Family of Languages Generated by Non-cooperative Membrane Systems. Int. Conf. on Membrane Computing 2010: 65-80
  4. Artiom Alhazov, Sergiu Ivanov, Yurii Rogozhin: Polymorphic P Systems. Int. Conf. on Membrane Computing 2010: 81-94