Publications 1994 - 2022

Theoretical Computer Science, Mathematical Logic, Cryptography,
Computational Methods in Systems Biology, Algorithmic Number Theory, Logic in Computer Science

List of Publications.

This list is organised by years and by topics.



  • Marco Cianfriglia, Elia Onofri, Silvia Onofri, Marco Pedicini Ten years of cube attacks In IACR e-print archive n.137/2022. [bibtex|pdf].
  • Lorenzo Grassi, Silvia Onofri, Marco Pedicini, Luca Sozzi Invertible Quadratic Non-Linear Layers for MPC-/FHE-/ZK-Friendly Schemes over $\mathbb F_{p^n}$ In IACR e-print archive n.1695/2021. [bibtex|pdf].
  • Elia Onofri, Marco Pedicini Novel notation on Cube Attacks In De Cifris Cryptanalysis Selected papers from the ITASEC2020 Workshop De Cifris Cryptanalysis: Cryptanalysis a Key Tool in Securing and Breaking Ciphers, (in press). [bibtex].
  • Marco Cianfriglia, Marco Pedicini Unboxing the Kite Attack In De Cifris Cryptanalysis Selected papers from the ITASEC2020 Workshop De Cifris Cryptanalysis: Cryptanalysis a Key Tool in Securing and Breaking Ciphers. (in press). [bibtex].
  • Marco Cianfriglia, Stefano Guarino, Massimo Bernaschi, Flavio Lombardi, Marco Pedicini Kite attack: reshaping the cube attack for a flexible GPU-based maxterm search In Journal of Cryptographic Engineering, Springer, (Online first May 2019) [bibtex|doi].
  • M. Cianfriglia, S. Guarino, M. Bernaschi, F. Lombardi and M. Pedicini A Novel GPU-Based Implementation of the Cube Attack - In: Gollmann D., Miyaji A., Kikuchi H. (eds) Applied Cryptography and Network Security. ACNS 2017. Lecture Notes in Computer Science, vol 10355. Springer, Cham [bibtex|doi].

Logic in Computer Science:

  • Marco Pedicini, Mario Piazza, Quentijn W.Q. Puite, On the number of provable formulas in L. Bellotti, G. Turbanti (eds), Fourth Pisa Colloquium in Logic, Language and Epistemology. Essays in Honour of E. Moriconi, Edizioni ETS, 2021, pp. 145-166. [bibtex|pdf].
  • A. C. Lai, M. Pedicini, M. Piazza Abstract Machines, Optimal Reduction, and Streams, Mathematical Structures in Computer Science (2019). [bibtex|doi].

Computational Methods in Systems Biology:

  • F. Castiglione, C. Nardini, E. Onofri, M. Pedicini, P. Tieri Explainable Drug Repurposing Approach from Biased Random Walks (submitted). [bibtex].
  • F. Castiglione, E. Mancini, M. Pedicini, A. S. Jarrah Quantitative Modelling Approaches In book: Reference Module in Life Sciences, Elsevier (2018) [bibtex|link|doi].
  • M. Pedicini, M. C. Palumbo, F. Castiglione. Computing Hierarchical Transition Graphs of Asynchronous Genetic Regulatory Networks Communications in Computer and Information Science, (2018), Springer-Verlag. [bibtex|link].

Number Theory and Automata:

  • V. Komornik, M. Pedicini, A. Pethö. Multiple common expansions in non-integer bases, Acta Sci. Math. (Szeged) 83 (2017), 51-60. [bibtex|doi]
  • V. Komornik, M. Pedicini. Critical bases for ternary alphabets, Acta Math. Hungar, June 2017, Volume 152, Issue 1, pp 25-57. [bibtex|doi]


Logic in Computer Science:

  • D. Canavese, E. Cesena, R. Ouchary, M. Pedicini, L. Roversi. Light combinators for finite fields arithmetics, Science of Computer Programming 111 (2015) 365--394 [bibtex|doi].
  • D. Canavese, E. Cesena, R. Ouchary, M. Pedicini, L. Roversi. Can a Light Typing Discipline be compatible with efficient implementation of finite fields inversion ?, in Foundational and Practical Aspects of Resource Analysis Third International Workshop, FOPARA 2013, Bertinoro, Italy, August 29-31, 2013, Revised Selected Papers, LNCS 8552, pp. 38 - 57 (2014) [bibtex|doi].
  • M. Pedicini, G. Pellitta, M. Piazza. Sequential and Parallel Abstract Machines for Optimal Reduction, presented at Trends in Functional Programming (2014) [bibtex|pdf].

Quantum Computing:

  • A.C. Lai, M. Pedicini, S. Rognone. Quantum Entanglement and the Bell matrix, Quantum Information Processing, July 2016, Volume 15, Issue 7, pp 2923-2936 (2016). [bibtex|pdf| arxiv|doi].


Computational Methods in Systems Biology:

  • T. Clancy, M. Pedicini, F. Castiglione, D. Santoni, V. Nygaard, T. J. Lavelle, M. Benson, E. Hovig. Immunological network signatures of cancer progression and survival BMC Medical Genomics, 4:28 (2011) [bibtex|doi].


  • A. Agnesse, M. Pedicini. Cube attack in finite fields of higher order. In Conferences in Research and Practice in Information Technology (CRPIT), Vol. 116, Colin Boyd and Josef Pieprzyk, Eds. Australian Computer Society, Inc. Conference Proceedings of the 9th Australasian Information Security Conference (AISC 2011), Perth, Australia, (January 2011) [bibtex|acm|pdf].

Number Theory and Automata:

  • V. Komornik, A.C. Lai, M. Pedicini. Generalized golden ratios of ternary alphabets, in Journal of the European Mathematical Society, Volume 13, Issue 4, pp. 1113--1146 (2011) [bibtex|doi].

Logic in Computer Science:

  • E. Cesena, M. Pedicini, L. Roversi. Typing a Core Binary Field Arithmetic in a Light Logic, contributed paper at FOPARA2011, Madrid (2011), [bibtex|doi].


Mathematical Logic:

  • M. Pedicini, M. Piazza. Elementary Complexity and von Neumann Algebras, CoRR abs/0912.5342, submitted (2009) [bibtex|pdf].
  • M. Pedicini, M. Piazza, An application of von Neumann algebras to computational complexity, in M. D'Agostino et alii (editors), New Essays In Logic and Philosophy of Science, College Publications, London, pp. 183-194, November 2010 [bibtex].

Computational Methods in Systems Biology:

  • M. Pedicini, F. Barrenas, T. Clancy, F. Castiglione, E. Hovig, K. Kanduri, D. Santoni, M. Benson. Combining network modeling and gene expression microarray analysis to explore the dynamics of Th1 and Th2 cell regulation, PLOS Computational Biology 6(12): e1001032 (2010) [bibtex|doi].
  • F. Castiglione, D. Santoni and M. Pedicini. Implementing agent's rules with gene regulatory networks in mesoscopic-level models of cellular interactions. In A practical guide to bioinformatics analysis : pp. 57--68, Editor Gabriel P.C. Fung, iConcept Press (2010) [bibtex].
  • D. Santoni, M. Pedicini, F. Castiglione. Implementation of a regulatory gene network to simulate the TH1/2 differentiation in an agent-based model of hypersensitivity reactions. Bioinformatics 24(11): 1374-1380 (2008) [bibtex|doi].

Logic in Computer Science:

  • M. Pedicini, M. Piazza, Elementary Complexity into the Hyperfinite \(\mathrm{II}_1\) Factor contributed paper at CiE07 Computation and Logic in the Real World 2007, Siena, (2007) [bibtex].
  • P. Baillot and M. Pedicini. An embedding of the BSS model of computation in light affine lambda-calculus. contributed paper at FLOC - LCC'06, 8th International Workshop on Logic and Computational Complexity Seattle, (2006) [bibtex|arxiv].
  • M. Pedicini and F. Quaglia. PELCR: Parallel Environment for Optimal Lambda Calculus Reduction. ACM Transactions on Computational Logic, 8:3, pp. 1--14 (2007) [bibtex|doi].


Logic in Computer Science:

  • A. Cosentino, M. Pedicini and F. Quaglia. Supporting Function Calls within PELCR Electronic Notes in Theoretical Computer Science Volume 135, Issue 3 , 3 March 2006, Pages 107-117 Proceedings of the First International Workshop on Developments in Computational Models (DCM 2005) [bibtex|doi].
  • M. Pedicini and F. Quaglia. Scheduling vs Communication in PELCR, Proc. Euro-Par'02, Paderborn (Germany), LNCS, Spinger-Verlang, August (2002) [bibtex|doi].
  • M. Pedicini and F. Quaglia. A parallel implementation for optimal lambda-calculus reduction Proceedings of the 2nd International Conference on Principles and Practice of Declarative Programming, pages 3-14. ACM Press, (2000) [bibtex|doi].
  • P. Baillot and M. Pedicini. Elementary complexity and geometry of interaction. Annales Societatis Mathematicae Polonae. Series IV. Fundamenta Informaticae 45(1-2):1-31, (2000) [bibtex|url].

Idempotent Analysis:

  • P. Loreti and M. Pedicini. An Object-Oriented Approach to Idempotent Analysis: Integral Equations as Optimal Control Problems. Contemporary Mathematics, vol. 377, AMS. Proceedings of the Conference on Idempotent Mathematics and Mathematical Physics. Editors G.L. Litvinov and V.P. Maslov (2005) [bibtex].
  • P. Loreti and M. Pedicini. An idempotent analogue of resolvent kernels for a deterministic optimal control problem. (traduzione dal russo), Matematicheskie Zametki, vol. 69, no. 2, pp. 235-244 (2001) [bibtex|doi].

Number Theory and Automata:

  • M. Pedicini. Greedy expansions and sets with deleted digits. Theoretical Computer Science, 332 pp. 313-336. Elsevier, Amsterdam, The Netherlands, (2005) [bibtex|doi].
  • V. Komornik, P. Loreti, and M. Pedicini. An approximation property of Pisot numbers. Journal of Number Theory, vol. 80 n. 2, 218-237 Academic Press, (2000) [bibtex|doi].

Before 2000

Logic in Computer Science:

  • P. Baillot and M. Pedicini. Elementary complexity and geometry of interaction (extended abstract). In J.-Y. Girard, editor, 4th International Conference, TLCA'99, L'Aquila, number 1581 in Lecture Notes in Computer Science, pages 25-39. Springer Verlag, Berlin, (1999) [bibtex|doi].
  • G. F. Mascari and M. Pedicini. Types and dynamics in partially additive categories. In J. Gunawardena, editor, Idempotency, volume 11 of Publications of the Isaac Newton Institute, pages 112-132, Cambridge, UK. Cambridge University Press, (1998) [bibtex].
  • V. Danos, M. Pedicini, and L. Regnier. Directed virtual reductions. In M. Bezem and D. van Dalen, editors, Computer Science Logic, 10th International Workshop, CSL '96, volume 1258 of Lecture Notes in Computer Science, pages 76-88. EACSL, Springer Verlag, Berlin, DE (1997) [bibtex|doi].
  • M. Pedicini. Remarks on elementary linear logic. In A Special Issue on the ``Linear Logic 96, Tokyo Meeting'', volume 3 of Electronic Notes in Theoretical Computer Science, Elsevier, Amsterdam, The Netherlands (1996) [bibtex|doi].
  • G. F. Mascari and M. Pedicini. Head linear reduction and pure proof net extraction. Theoret. Comput. Sci., 135(1):111-137, Amsterdam, The Netherlands, Elsevier (1994) [bibtex|doi].

Projects 1994 - 2014

National and International Research Projects.

Running Projects

Expired Projects

In charge of the following research projects :

  • PRINCIPAL INVESTIGATOR of the Roma Tre University Unit of PRIN 2010-2011: Metodi Logici per il trattamento dell'informazione (other members of the Unit: Prof. V.M. Abrusci, Prof. L. Tortora de Falco, Prof. R. Maieli)
  • PRINCIPAL INVESTIGATOR "INT.P01.007.006 Applied cryptography: analysis and performance of cryptographic primitives", Istituto per le Applicazioni del Calcolo (2010 - 2012) under the topic "INT.P01.007 Trustworthy and Secure Future Internet" of the CNR national project "INT.P01 Security".
  • PRINCIPAL INVESTIGATOR of the Unit of Research "Interaction models in parallel non-deterministic computation" at Istituto per le Applicazioni del Calcolo of the Project MIUR-PRIN2007 "CONCERTO: Controllo e certificazione dell'uso delle risorse" (2008 - 2009).
  • PRINCIPAL INVESTIGATOR CNR activity "Dynamics of Computational Processes", Istituto per le Applicazioni del Calcolo (2000 - 2004).
  • PRINCIPAL INVESTIGATOR (for the italian part) of the CNR/CNRS Project "Interazione e Complessità " (2006-2007, O. Laurent was the french principal investigator).
  • PRINCIPAL INVESTIGATOR (for the italian part) of the CNR/CNRS Project "Interazione e Complessità " (2004-2005, P. Baillot was the french principal investigator).
  • PRINCIPAL INVESTIGATOR (for the italian part) of the CNR/CNRS Project "Valutazioni Ottimali e Parallele del lambda-calcolo" (1996-1997, V. Danos was the french principal investigator).

Participant to the following international research projects:

  • Project UE Strep FP7-ICT-2011-9 (MISSION-T2D) Multiscale Immune System SImulator for the Onset of Type 2 Diabetes integrating genetic, metabolic and nutritional data other members of the Unit: see Digital Biology Unit at IAC-CNR and the project site.
  • Project UE FP6/2005/NEST-PATH Contract No IST-2006-043241 (Complexdis) - "Unravelling complex diseases with complexity theory: from networks to the bedside" (2007-2009);
  • Project UE FP6/2004/IST/Call4 Proposal No IST-2004-028069 (ImmunoGrid) - "The European Virtual Human Immune System Project" (2005-2007);
  • Project UE TMR (Linear Logic in Theoretical Computer Science) (1998-2002);
  • Project UE INTAS (Analisi Idempotente Lineare e non Lineare) (1997-1998);
  • Project CEE HCM - Network (Lambda Calculs Typé es) (1992-1998);
  • Project CEE ESPRIT BRA 3272 (Gentzen) (1993-1996).

Participant to the following italian research projects:

  • MIUR-COFIN2005, "FOLLIA: Fondazioni Logiche di Linguaggi Astratti di Programmazione" (2005-2006), coordinator Prof. Simonetta Ronchi della Rocca;
  • MIUR-COFIN2003, "PROTOCOLLO: dalla prova alla computazione con la logica lineare" (2003-2004), coordinator Prof. Simonetta Ronchi della Rocca;
  • MURST-COFIN2001, "Logica Lineare e oltre" (2001-2002) coordinator Prof. Andrea Asperti.

Events 2002 - 2018

tracks of research activities, communications, workshops and conferences


Dynamics of Arithmetics

  • One World Numeration (OWN) Seminar This is an online seminar on the topics of the series of Numeration conferences, in the spirit of other One World Seminars. If you want to participate, please contact Wolfgang Steiner with an email to


  • Eurocrypt 2020, Tel Aviv, Israel, April 29-May 3 Notification: 15 January 2018. Due to the coronavirus spread, Eurocrypt 2020 will be virtual. The dates of this event are (close to) the original dates: May 11-15 2020. We suggest you read the participation guidelines to see what it will be like.
  • FSE2018 Fast Software Encryption (FSE), Bruges, Belgium, March 5-March 7 Submission: 23 November 2017; Notification: 23 January 2018.
  • Crypto 2018 (Crypto), Santa Barbara, USA, August 19-August 23

Computational Methods in Systems Biology

Logic and Theoretical Computer Science


Participation to Events:

Teaching 2002 - 2020

Lectures, Courses, Thesis
office hours: on Monday 12.00 - 13.00 at Room 308 (3rd floor) - Building C - Largo San Leonardo Murialdo 1









Dipartimento di Matematica e Fisica, Università degli Studi Roma Tre
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