Publications

(Only journal publications including Springer’s Lecture Notes from 2008 on)

2024
  • Practical Design and Implementation of Virtual Chatbot Assistants for Bioinformatics Based ib a NLU Open Framework. (2024) A.A. Elsayed A.I. Hafez, R. Ceprián, G. Martínez, A. Granados, B. Soriano, C. Llorens, J.M. Sempere. Big Data and Cognitive Computing  8(11):163.
  • Membrane computing simulation of sexually transmitted bacterial infections in hotspots of individuals with various risk behaviors. (2024) Marcelino Campos, Juan Carlos Galán, Mario Rodríguez-Domínguez, José M. Sempere, Carlos Llorens, Fernando Baquero.  Microbiology Spectrum Vol.12 Issue 2  e02728-23
2023
  • Modeling Markov sources and hidden Markov models by P systems. (2023) José M. Sempere. Journal of Membrane Computing Vol. 5 Issue 3, pp 161-169.
  • A Solidity implementation of TAVS (2023) A. Larriba-Flor, D. López Rodríguez.  Frontiers in Block Chain. Vol. 6:1105119.
  • Applications and Server-Side Docker for Management of RNASeq and/or VariantSeq Workflows and Pipelines of the GPRO Suite. (2023) A.I. Hafez, B. Soriano, A.A. Elsayed, R. Futami, R. Ceprian, R. Ramos-Ruiz, G. Martinez, F.J. Roig, M.A. Torres-Font, F. Naya-Catala, J.A. Calduch-Giner, L. Trilla-Fuertes, A. Gamez-Pozo, V. Arnau, J.M. Sempere-Luna, J. Perez-Sanchez, T. Gabaldon, C. Llorens. Genes 14(2):267.
  • How to grant anonymous access (2023). Antonio M. Larriba, Damián López. IEEE Transactions on Information Forensics and Security Vol. 18. pp 613-625.
2022
  • SUVS: Secure Unencrypted Voting Scheme (2022) Antonio Larriba-Flor,  Damián López Rodríguez. Informatica Vol. 33 Issue 4, pp. 749-769. 
  • Simulating the efficacy of vaccines on the epidemiological dynamics of SARS-CoV-2 in a membrane computing model (2022) Marcelino Campos, José M Sempere, Juan C Galán, Andrés Moya, Rafael Cantón, Carlos Llorens, Fernando Baquero. microLife Vol. 3, uqac018.
  • Simulating epidemics by membrane computing (2022)  José M. Sempere, Marcelino Campos. Bulletin of The International Membrance Computing Society, Number 13, pp 91-97.
  • Generating networks of genetic processors (2022) Marcelino Campos &  José M. Sempere. Genetic Programming and Evolvable Machines  Vol. 23,  Issue 1, pp 133-155.
2021
  • P systems in the time of COVID-19 (2021) Fernando Baquero, Marcelino Campos, Carlos Llorens & José M. Sempere. Journal of Membrane Computing Vol. 3, Issue 4, pp 246-257.
  • Simulating the impact of non-pharmaceutical interventions limiting transmission in COVID-19 epidemics using a membrane computing model (2021) M.Campos, J.M. Sempere, J.C. Galán, A. Moya, C. Llorens, C. de los Ángeles, F. Baquero-Artigao, R. Cantón, F. Baquero. microLife Vol.2, uqab011.
  • Distributed Trust, a Blockchain Election Scheme  (2021) Antonio M. Larriba , Aleix Cerdà i Cucó, José M. Sempere and Damián López. Informatica 32(2), pp. 321–355.
  • On the Languages Accepted by Watson-Crick Finite Automata with Delays  (2021).   José M. Sempere. Mathematics  9(8), 813. 
2020
  • A two authorities electronic vote scheme  (2020).  Antonio Larriba, José M. Sempere, Damián López. Computers and Security  Vol. 97, October 2020, 101940.
  • Simulating the Influence of Conjugative-Plasmid Kinetic Values on the Multilevel Dynamics of Antimicrobial Resistance in a Membrane Computing Model (2020).  Marcelino Campos, Álvaro San Millán, José M. Sempere, Val F. Lanza, Teresa M. Coque, Carlos Llorens, Fernando Baquero. Antimicrobial Agents and Chemotherapy  August 2020, 64(8) e00593-20.
  • On Compensation Loops in Genomic Duplications (2020). José M. Sempere. International Journal of Foundations of Computer Science  Vol. 31, No.1, pp 133-142.
2019
  • Modeling of Decision Trees Through P Systems (2019). José M. Sempere. New Generation Computing 37, pp 325-337.
  • Simulating Multilevel Dynamics of Antimicrobial Resistance in a Membrane Computing Model (2019). Marcelino Campos, Rafael Capilla, Fernando Naya, Ricardo Futami, Teresa Coque, Andrés Moya, Val Fernandez-Lanza, Rafael Cantón, José M. Sempere, Carlos Llorens, Fernando Baquero. mBio Jan 2019, 10 (1) e02460-18.
2018
  • Families of Languages Encoded by SN P Systems (2018). José M. Sempere. In Proceedings of the 18th International Conference on Membrane Computing (CMC 2017) (Bradford, UK). Marian Gheorghe, Grzegorz Rozenberg, Arto Salomaa, Claudio Zandron (eds.), LNCS Vol.10725, pp 262-269, Springer.
  • A Model of Antibiotic Resistance Evolution Dynamics Through P Systems with Active Membranes and Communication Rules (2018). Fernando Baquero, Marcelino Campos, Carlos Llorens, José M. Sempere. In Enjoying Natural Computing. Essays Dedicated to Mario de Jesús Pérez-Jiménez on the Occasion of His 70th Birthday. Carmen Graciani, Agustín Riscos-Núñez, Gheorghe Păun, Grzegorz Rozenberg (eds.), LNCS Vol.11270, pp 33-44, Springer.
  • Grammatical inference of directed acyclic graph languages with polynomial time complexity (2018). Javier Gallego, Damián López, Jorge Calera-Rubio. Journal of Computer and System Science 95 pp 19-34.
2017
  • Networks of Genetic Processors: From Universality to a Formal Language Characterization (2017). José M. Sempere. In 15th International Conference on Automata and Formal Languages (AFL 2017) (Debrecen, HU). Electronic Proceedings in Theoretical Computer Science, EPTCS (E. Csuhaj-Varjú, P. Dömösi, Gy. Vaszil, eds.) Vol. 252, pp 7-8.
  • A View of P Systems from Information Theory (2017). José M. Sempere. In Proceedings of the 17th International Conference on Membrane Computing (CMC 2016) (Milano, Italy). Alberto Leporati, Grzegorz Rozenberg, Arto Salomaa, Claudio Zandron (eds.), LNCS Vol.10105, pp 352-362, Springer. 
2016
  • Families of Languages Associated with SN P Systems: Preliminary Ideas, Open Problems (2016). Gh. Păun, José M. Sempere. Bulletin of The International Membrane Computing Society, Number 2, pp 161-164.
  • Minimal consistent DFA revisited (2016).  Manuel Vázquez de Parga, Pedro García, Damián López. Theoretical Computer Science Vol. 647, pp 43-49. 
  • A sufficient condition to polynomially compute a minimum separating DFA (2016). Manuel Vázquez de Parga, Pedro García, Damián López. Information Sciences Vol. 370-371, pp 204-220. 
  • Topics in Grammatical Inference (2016). Jeffrey Heinz, José M. Sempere (eds.) Springer. ISBN: 978-3-662-48393-0.
2015
  • Membrane Computing. Revised Selected Papers of the 16th International Conference CMC2015 (2015) Grzegorz. Rozenberg, Arto Salomaa, José M. Sempere, Claudio Zandron (eds.) LNCS Vol. 9504. Springer. ISBN: 978-3-319-28474-3.
  • A membrane computing simulator of trans-hierarchical antibiotic resistance evolution dynamics in nested ecological compartments (ARES) (2015). Marcelino Campos, Carlos Llorens, José M. Sempere, Ricardo Futami, Irene Rodríguez, Purificación Carrasco, Rafael Capilla, Amparo Latorre, Teresa M. Coque, Andrés Moya and Fernando Baquero. Biology Direct Vol. 10(41).
  • A Split-Based Incremental Deterministic Automata Minimization Algorithm (2015). Pedro García, Manuel Vázquez de Parga, Jairo A. Velasco and Damián López. Theory of Computing Systems Vol. 57 pp 319-336.
  • DFA minimization: Double reversal versus split minimization algorithms (2015). Pedro García, Damián López and Manuel Vázquez de Parga. Theoretical Computer Science Vol. 583 pp 78-85.
2014
  • Efficient Deterministic Finite Automata Split-Minimization Derived from Brzozowski’s Algorithm (2014). Pedro García, Damián López and Manuel Vázquez de Parga. International Journal of Foundations of Computer Science Vol.25, No.6 pp 679-696. 
2013
  • Regular languages and partial commutations (2013). Antonio Cano, Giovanna Guaiana, Jean-Éric Pin. Information and Computation Vol. 230, pp 76-96. 
  • Solving Combinatorial Problems with Networks of Genetic Processors (2013). Marcelino Campos, José M. Sempere. International Journal “Information Technologies and Knowledge” Vol.7 No. 1, pp 65-71.
  • A polynomial double reversal minimization algorithm for deterministic finite automata (2013). Manuel Vázquez de Parga, Pedro García, Damián López. Theoretical Computer Science Vol. 487, pp 17-22. 
2012
  • Networks of Bio-inspired Processors (2012). Fernando Arroyo Montoro, Juan Castellanos, Victor Mitrana, Eugenio Santos, José M. Sempere. Triangle Vol. 7, pp 3-22.
  • Accepting Networks of Genetic Processors are computationally complete (2012). Marcelino Campos, José M. Sempere. Theoretical Computer Science Vol. 456, pp 18-29.
  • Polynomial characteristic sets for DFA identification (2012). Pedro García, Damián López, Manuel Vázquez de Parga. Theoretical Computer Science Vol. 448, pp 41-46. 
  • Structural Graph Extraction from Images (2012). Antonio Javier Gallego Sánchez, Jorge Calera Rubio, Damián López. Proceedings of the 9th International Conference on Distributed Computing and Artificial Intelligence. S. Omatu, J.F. De Paz Santana, S. Rodríguez González, J.M. Molina, A.M. Bernardos, J.M. Corchado Rodríguez, (eds.) Series of Advances in Intelligent and Soft Computing Vol. 151, pp 717-724, Springer-Verlag.
2011
  • HyRPNI Algorithm and an Application to Bioinformatics (2011). Gloria Inés Álvarez, Jorge Hernán Victoria, Enrique Bravo, Pedro García. Revista de Ingeniería 33 pp 44-52; Enero/Junio.
  • GyDB mobilomics: LTR retroelements and integrase-related transposons of the pea aphid Acyrthosiphon pisum genome (2011).  P. Bernet, Alfonso Muñoz Pomer, Laura Domínguez-Escribá, Laura Covelli, Lucía Bernad, Sukanya Ramasamy, Ricardo Futami, Jose M. Sempere, Andrés Moya and Carlos Llorens. Mobile Genetic Elements 1:2, 97-102; July/August.
  • From regular expressions to smaller NFAs (2011). Pedro García, Damián López, José Ruiz and Gloria I. Álvarez. Theoretical Computer Science Vol. 412, Issue 41, pp 5802-5807.
  • Simulating Accepting Networks of Evolutionary Processors with Filtered Connections by Accepting Evolutionary P Systems (2011). Juan Castellanos, Victor Mitrana, Eugenio Santos, José M. Sempere. Proceedings of the 4th International Work-Conference on the Interplay between Natural and Artificial Computation (IWINAC 2011). LNCS Vol.6686, pp 295-302, Springer-Verlag.
  • The Spanish Network on Biomolecular and Biocellular Computing: Bio-inspired Natural Computing in Spain (2011). Mario de J. Pérez-Jiménez, Alfonso Ortega de la Puente, José M. Sempere. ERCIM News, No. 85, pp 25.
  • The Gypsy Database (GyDB) of mobile genetic elements: release 2.0 (2011).  Llorens, Ricardo Futami, Laura Covelli, Laura Dominguez-Escriba, Jose M. Viu, Daniel Tamarit, Jose Aguilar-Rodriguez, Miguel Vicente-Ripolles, Gonzalo Fuster, Guillermo P. Bernet, Florian Maumus, Alfonso Muñoz-Pomer, José M. Sempere, Amparo Latorre, Andres Moya. Nucleic Acids Research Vol. 39, Database issue, D70-D74.
  • Complexity-preserving simulations among three variants of accepting networks of evolutionary processors (2011). Paolo Bottoni, Anna Labella, Florin Manea, Victor Mitrana, Ion Petre, Jose M. Sempere. Natural Computing, Vol. 10, No. 1, pp 429-445.
  • Filter Position in Networks of Substitution Processors does not matter (2011). F. Arroyo, J. Castellanos, V. Mitrana, E. Santos, J.M. Sempere. International Journal of Foundations of Computer Science, Vol. 22, No. 1, pp 155-165.
2010
  • Grammatical Inference: Theoretical Results and Applications. Proceedings of the 10th International Colloquium on Grammatical Inference (2010). José M. Sempere, Pedro García (eds.) LNAI Vol. 6339 Springer. ISBN: 3-642-15487-5.
  • A Non-deterministic Grammar Inference Algorithm Applied to the Cleavage Site Prediction Problem in Bioinformatics (2010).Gloria Inés Álvarez, Jorge Hernán Victoria, Enrique Bravo, Pedro García. Proceedings of the 10th International Colloquium on Grammatical Inference (ICGI 2010). LNAI Vol. 6339, pp 267-270, Springer.
  • Transducer Inference by Assembling Specific Languages (2010).  Piedachu Peris, Damián López. Proceedings of the 10th International Colloquium on Grammatical Inference (ICGI 2010) LNAI Vol. 6339, pp 178-188, Springer. 
  • Learning Automata Teams (2010). Pedro García, Manuel Vázquez de Parga, Damián López, José Ruiz. Proceedings of the 10th International Colloquium on Grammatical Inference (ICGI 2010). LNAI Vol. 6339, pp 52-65, Springer. 
  • Inferring Regular Trace Languages from Positive and Negative Samples (2010). Antonio Cano. Proceedings of the 10th International Colloquium on Grammatical Inference (ICGI 2010). LNAI Vol. 6339, pp 11-23, Springer.
  • Dogmatic P Systems (2010) José M. Sempere.  Eigth Brainstorming Week on Membrane Computing, pp 291-300, Fénix Editora. 
  • Antioxidant N-Acetyl-Cysteine Protects Retinal Pigmented Epithelial Cells from Long-Term Hypoxia Changes in Gene Expression (2010). Guillermo Gerona, Damián López, Mercedes Palmero, Victoria Maneu. Journal of Ocular Pharmacology and Therapeutics. August 2010, Vol. 26, No. 4, pp 309-314. 
2009
  • On locally reversible languages (2009). P. García, M. Vázquez de Parga, A. Cano, D. López. Theoretical Computer Science. Vol. 410, Issues 47-49, pp 4961-4974.
  • Networks of Evolutionary Picture Processors With Filtered Connections (2009).  Paolo Bottoni, Anna Labella, Florin Manea, Victor Mitrana, José M. Sempere. Proceedings of the  8th International Conference on Unconventional Computation (UC09). LNCS Vol. 5715, pp 70-84. Springer.
  • Filter Position in Networks of Evolutionary Processors Does Not Matter: A Direct Proof (2009). Paolo Bottoni, Anna Labella, Florin Manea, Victor Mitrana, José M. Sempere. Proceedings of the 15th International Meeting on DNA Computing and Molecular Programming (DNA15). LNCS Vol. 5877, pp 1-11. Springer.
  • Some Remarks on Superposition Based on Watson-Crick-like Complementarity (2009) Florin Manea, Victor Mitrana, José M. Sempere. Proceedings of the 13th International Conference on Developments in Language Theory (DLT 2009). LNCS Vol. 5583, pp 372-383. Springer.
2008
  • IgTM: An algorithm to predict transmembrane domains and topology in proteins (2008).  P. Peris, Damián López and Marcelino Campos. BMC Bioinformatics 9:367.
  • Universal automata and NFA learning (2008). Pedro García, Manuel Vázquez de Parga, Gloria I. Álvarez and José Ruiz. Theoretical Computer Science Vol. 407, Issues 1-3, pp 192-202.
  • On the efficient construction of quasi-reversible automata for reversible languages (2008). Pedro García, Manuel Vázquez de Parga, Damián López. Information Processing Letters, Vol. 107 Issue 1, pp 13-17.
  • When Does Partial Commutative Closure Preserve Regularity ? (2008) Antonio Cano Gómez, Giovanna Guaiana, Jean-Eric Pin. Proceedings of the 35th International Colloquium on Automata, Languages and Programming (ICALP 2008).  LNCS Vol. 5126 pp. 209-220. Springer.
  • A Robust Class of Regular Languages (2008). Antonio Cano Gómez, Jean-Eric Pin. Proceedings of the 33rd International Symposium on Mathematical Foundations of Computer Science (MFCS 2008)  LNCS Vol. 5162 pp. 36-51. Springer.
  • Learning Context-Sensitive Languages from Linear Structural Information (2008).  José M. Sempere. Proceedings of the 9th International Colloquium on Grammatical Inference (ICGI 2008) LNAI Vol. 5278  pp. 175-186. Springer.
  • Learning Commutative Regular Languages (2008). Antonio Cano Gómez, Gloria I. Álvarez. Proceedings of the 9th International Colloquium on Grammatical Inference (ICGI 2008). LNAI Vol. 5278  pp. 71-83. Springer.
  • Translating Multiset Tree Automata into P systems (2008). José M. Sempere.  Proceedings of the  9th Workshop on Membrane Computing (WMC9). LNCS Vol.5391 pp 394-402. Springer.
  • Learning Regular Languages Using Nondeterministic Finite automata (2008).  Pedro García, Manuel Vázquez de Parga, Gloria I. Álvarez, José Ruiz. Proceedings of the 13th International Conference CIAA 2008  LNCS Vol. 5148 pp 92-101. Springer.

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