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Artificial Intelligence Lab (LIA-UPM) www.lia.upm.es is a research group in UPM formed by researchers and professors working in Synthetic Biology and Evolutionary Computation with different backgrounds: computer scientists, physicists, mathematicians, and biotechnologists.

 

RESEARCH

Synthetic Biology (the engineering of biology) is the application of the engineering principles to biology in order to build synthetic biological systems. This is a new and fascinating interdisciplinary field (born in 2000 in MIT Artificial Intelligence Lab), where engineers, physicists, and computer scientists have a new opportunity to apply their engineering concepts and tools: Biology is the new hardware that can be programmed.

In our group we address the following research questions:

  1. Biological information processing: how cells communicate, process biological signals and take decisions?
  2. Synthetic Biology and DNA Computing confluence: how to engineer and program new biological systems (based on DNA, RNA or proteins) that can interact with cell and/or can sense and respond to biological signals?  How can we design new DNA/RNA Computing devices able to operate in vivo
  3. Artificial Intelligence in vivo: How to use algorithmic ideas developed in Artificial Intelligence field to program smart cellular computers? Or, how to apply evolutionary computing ideas in the design of new biocircuits?
  4. Multicellular computing and non-digital SynBio: Most biocircuits developed so far are based on Boolean algebra and use a digital/binary abstraction to operate with biological signals. How could we design new robust analog and multicellular biocircuits?
  5. Bio-design automation and Programmable Biology: We produce software to simulate multicellular genetic circuits and to automatize biology protocols.

Our FP7 EU FET-Proactive research projects:

PLASWIRESwww.plaswires.eu 

EVOPROG: www.evoprog.eu

PhD positions available in LIA group. If you are a great programmer (an engineer or physicist) that likes biology and wants to program cells and DNA, code biology or engineer life contact us (candidates should send by email: CV, academic transcripts and a motivation letter). We love people passionate about research that wants to deep into the unknown.

Introduction to Synthetic Biology

You may find some documents in this section to introduce the reader to Synthetic Biology:

Description of PLASWIRES synthetic biology FP7 FET research project. Report included in UPM Journal, n.28, June 2014. Spanish version: http://www.upm.es/institucional/UPM/CanalUPM/Revista

English version (in pdf): Report on PLASWIRES and LIA research group

Some introductory material to Synthetic Biology

If you prefer to read:

If you prefer to watch:

Videos:

PROJECTS


 

PLASWIRES

We are coordinating the European project funded under FP7 – FET Proactive area and titled PLASWIRES:”Engineering Multicellular Biocircuits: Programming Cell-Cell Communication Using PLASmids as WIRES.

Duration of the project: 36 months. Start: October, 2013.

Additional information in: www.plaswires.eu

EVOPROG

We are also partners in the project on synthetic biology called EVOPROG: “General-Purpose Programmable Evolution Machine on a Chip.  Start: October, 2013. Duration of the project: 36 months. 

Additional information: www.evoprog.eu

TIN2012-36992

Spanish Project TIN2012-36992 titled: “ENGINEERING and PROGRAMMING BIOCIRCUITS: DESIGN and IN SILICO MODELING”. “PROGRAMACIÓN E INGENIERÍA DE BIOCIRCUITOS: DISEÑO Y MODELADO IN SILICO.” This project will start in January 2013 and finish in December 2015. Duration: 3 years.

TIN2016- 81079-R

Our new 3-years research project from the Spanish Plan Estatal de I+D+i will begin in January 2017

MTM2014-54053-P

We are participating in the Spanish funded research project “Ecuaciones en diferencias y aproximación constructiva: teoría y aplicaciones”, Ref. MTM2014-54053-P. Duration of the project: 36 mothns. Start: January, 2015.

Past Research Projects

  • Bacterial Computing with Engineered Populations (BACTOCOM): LIA Group has participated also in the European Synthetic Biology project called BACTOCOM. www.bactocom.eu
  • Modelling of biological processes using P Systems and designing new biomolecular computing devices: Proyecto TIN2009-14421. Financiado por el MICINN. Fechas: enero de 2010 a diciembre de 2012. Investigador principal: Alfonso Rodríguez-Patón.

SOFTWARE


BioBlocks

BioBlocks is a web-based visual editor for describing experiments in Biology. It is based on Google’s Blockly and MIT Scratch. Experiments described in BioBlocks are automatically translated to machine specific code of a compatible hardware platform for automated execution of the experiment. An English translation and a graphical protocol workflow of the experiment are also generated. BioBlocks aims to remove the programming bottleneck so that biologists (non-programmers) can take advantage of automation in their work. Our goal in LIA is to make programming of Biological protocols simpler and fun!

To try BioBlocks, please click the logo!

 

Please find below some tutorials video which explain BioBlocks.

 

TUTORIAL 1: Bioblocks Library Description

TUTORIAL 2: Bioblocks Interface Explanation

TUTORIAL 3: BioBlocks Example Protocol

See the attention BioBlocks is getting using Altmetrics:  

A pre-print of BioBlocks on biorXiv is available here.  (accepted in ACS Synthetic Biology). 

BioBlocks is under continuous development as we try to add more features to it. If you are interested to collaborate with us fork us on GitHub (LIA UPM GitHub). We would appreciate any feedback through email (contactliaupm@gmail.com) or in the BioBlocks forum.

Gro

LIA group is developing a new faster and improved version of the open-source multicellular simulator Gro. Check out our developer’s version in Bitbucket.

Preprint available on Biorxiv:  A new improved and extended version of the multicell bacterial simulator gro

BactoSIM

BactoSIM is mainly focused on in silico simulation of computational biology and ecology of bacterial conjugation. It is based on spatially explicit individual-based (or agent based) models.

Fork us on GitHub

PUBLICATIONS

JOURNALS

Martín Eduardo Gutiérrez, Paula Gregorio-Godoy, Guillermo Pérez del Pulgar, Luis Enrique Muñoz, Sandra Sáez, Alfonso Rodríguez-Patón  A new improved and extended version of the multicell bacterial simulator gro. Biorxiv, December 2016

Vishal Gupta, Jesús Irimia, Iván Pau, Alfonso Rodríguez-Patón  Bioblocks: Programming protocols in biology made easier. BioRxiv, October 2016   (ACCEPTED IN ACS SYNTHETIC BIOLOGY).

Beneš, D., Rodríguez-Patón, A. & Sosík, P.  Directed evolution of biocircuits using conjugative plasmids and CRISPR-Cas9: design and in silico experiments.  Natural Computing (2016).

A Prestes García, A Rodríguez‐Patón. Sensitivity analysis of Repast computational ecology models with R/Repast.Ecology and Evolution (2016)  (free full-text).

Antonio Prestes García, Alfonso Rodríguez-Patón:
EvoPER – An R package for applying evolutionary computation methods in the parameter estimation of individual-based models implemented in Repast. PeerJ PrePrints 4: e2279 (2016).

X Zeng, N Ding, A Rodríguez-Patón, Z Lin, Y Ju. Prediction of MicroRNA–disease Associations by Matrix Completion. Current Proteomics 13 (2), 151-157. 

Antonio Prestes García, Alfonso Rodríguez-Patón. Analyzing Repast Symphony models in R with RRepast package. BioRxiv, 047985

CONFERENCES

Font, J.M., Izquierdo, R. Manrique, D., Togelius, J. Constrained Level Generation Through Grammar-Based Evolutionary Algorithms. G. Squillero and P. Burelli (Eds.): EvoApplications 2016, Part I, Lecture Notes in Computer Science Vol. 9597, pp. 558-573. Porto, Portugal, 30 March – 1 April. DOI: 10.1007/978-3-319-31204-0_36

JOURNALS

Font, J.M., Manrique, D., Ramos Criado, P. del Rio, D. Partition Based Real-Valued Encoding Scheme for Evolutionary Algorithms. Natural Computing, Springer. May 2015. DOI: 10.1007/s11047-015-9505-6

Amos, M., Axmann, I., Bluethgen, N., de la Cruz, F., Jaramillo, A., Rodríguez-Patón, A. & Simmel, F.Bacterial computing with engineered populations. Philosophical Transactions of the Royal Society A. 15 June 2015. http://dx.doi.org/10.1098/rsta.2014.0218 (free full-text).

Alonso, F, Manrique D, Martinez, L Viñes, J.M. Study of the Influnce of Social Relationships among Students on Knowledge Building Using a Moderately Constructivist Learning Model. J. Educational Computing Research, Vol. 51, No. 4, Jan 2015, pp. 417-439. doi: 10.2190/EC.51.4.c

Beneš D1, Sosík P, Rodríguez-Patón A. An Autonomous In Vivo Dual Selection Protocol for Boolean Genetic Circuits. Artificial Life, MIT, Vol. 21, No. 2, Spring 2015.

Barrios Rolanía, D.; Manrique, D. On the Existence of Darboux Transformations for Banded Matrices. Applied Mathematics and Computation, Vol 253, Feb. 2015, pp. 116-125.doi:10.1016/j.amc.2014.12.053

CONFERENCES

Antonio Prestes García, Alfonso Rodríguez-Patón: BactoSim – An Individual-Based Simulation Environment for Bacterial Conjugation. PAAMS 2015: 275-279

Antonio Prestes García, Alfonso Rodríguez-Patón: A Preliminary Assessment of Three Strategies for the Agent-Based Modeling of Bacterial Conjugation. PACBB 2015: 1-9

JOURNALS

Barrios Rolanía, D.; Font, J.M.; Manrique, D. Bacterially Inspired Evolution of Intelligent Systems under Constantly Changing Environments. Int. J. of Soft Computing. DOI 10.1007/s00500-014-1319-4. June, 2014.

Rodríguez-Patón, A.; Sainz de Murieta, I.; Sosík, DNA strand displacement system running logic programs.BioSystems, 115 ( 1 ) pp. 5 – 12 (2014).

CONFERENCES

Alonso, F.; Font, J.; Lopez, G.; Manrique, D. Study of the Evolution of the Underlying Social Network of Discussion and Generation of New Ideas Apllying an Instructional and Learning Model. 4th International Conference on Methodologies and Intelligent Systems for Technology Enhanced Learning. Advances in Intelligent Systems and Computing, 292, 1-8, 2014. Springer. Salamanca, 4-6 junio 2014.

JOURNALS

Iñaki Sainz de Murieta, Alfonso Rodríguez-Patón: Probabilistic reasoning with a Bayesian DNA device based on strand displacement. Natural Computing, 2013.

Petr Sosík,  Andrei Păun, Alfonso Rodríguez-Patón: P systems with proteins on membranes characterize PSPACE. Theoretical Computer Science. 488, 78-95 (2013).

Petr Sosík, Alfonso Rodríguez-Patón, Lucie Ciencialová: Polynomial time bounded computations in spiking P systems. Neural Network World 1/13, 2013, 31-48.

CONFERENCES

Font, J.M., Mahlmann, T., Manrique, D., Togelius, J. Towards the Automatic Generation of Card Games through Grammar-Guided Genetic Programming. Foundations of Digital Games 2013, 360-363 (2013).

Font, J.M., Mahlmann, T., Manrique, D., Togelius, J. A Card Game Description Language. EvoApplications, 2013. Lecture Notes in Computer Science. 7835, 254-263, (2013).

Saínz de Murieta, I., Rodríguez-Patón, A. Probabilistic Reasoning with an Enzyme-Driven DNA Device. In proceedings of the 19th International Conference, DNA 19, Tempe, AZ, USA, September 22-27, 2013, pp. 160-173.

PhD Theses

Sainz de Murieta, I. Inference models in DNA Computing. PhD Thesis, Departamento de Inteligencia Artificial, Facultad de Informática, Universidad Politécnica de Madrid. Supervisor: Rodríguez-Patón A (2013).

PATENTS

Alfonso Rodríguez-Patón, José María Larrea, and Iñaki Sainz de Murieta. Dispositivos de ácidos nucleicos para la realización de inferencia lógica. Patent publication number 2383651 granted on October 26, 2012.

JOURNALS

Barrios Rolania, D.; Font, J. M; Manrique, D. Bacterially Inspired Evolving System with an Application to Times Series Prediction. Applied Softcomputing, 13, 2: 1136-1146 (2012).

Sainz de Murieta, I; Rodríguez-Patón, A. DNA biosensors that reason. BioSystems, 109, 2: 91-104 (2012).

CONFERENCES

Sainz de Murieta I, Rodríguez-Patón A. Probabilistic Reasoning with a Bayesian DNA Device Based on Strand Displacement. DNA Computing and Molecular Programming. Lecture Notes in Computer Science. 7433, 110-122, (2012)

Murphy N, Rodríguez-Patón A. Distributed Computing with Prokaryotic Immune Systems. Artificial Immune Systems. Lecture Notes in Computer Science. 7597, 286-288, (2012)

Miró-Bueno JM, Rodríguez-Patón A. One-gene oscillators with a positive transcriptional feedback and a negative interaction. enGENEious, University of Oxford, June 25-26 (2012)

Murphy N, Rodríguez-Patón A. Reprogrammable, modular Boolean logic bio-sensors using conjugative plasmids. International Society of Plasmid Biology Conference (ISPB), Santander (Spain), September 12-16 (2012).

Murphy N, Rodríguez-Patón A.. Programmed removal and exclusion of plasmid sets. International Society of Plasmid Biology Conference (ISPB), Santander (Spain), September 12-16 (2012).

Glaschick R, Neary T, Woods D,  Murphy N. Hasenjaeger’s electromechanical small universal Turing machine is time efficient. Turing in context II, 10-12th October 2012, Brussels, Belgium.

Porreca AE, Murphy N, Pérez-Jiméz MJ. An Optimal Frontier of the Efficiency of Tissue P Systems with Cell Division. In Proceedings of the 10th Brainstorming Week on Membrane Computing (2012).

Pérez-Jiméz MJ, Sosík, P. Improving the Efficiency of Tissue P Systems with Cell Separation. In Proceedings of the 10th Brainstorming Week on Membrane Computing(2012).

PhD Theses

Miró-Bueno, JM. Oscillatory genetic circuits: new designs and mathematical models. PhD Thesis, Departamento de Inteligencia Artificial, Facultad de Informática, Universidad Politécnica de Madrid. Supervisor: Rodríguez-Patón A (2012).

Font, J.M. Sistema Evolutivo Bio-Inspirado en el Comportamiento Bacteriano. PhD Thesis, Departamento de Inteligencia Artificial, Facultad de Informática, Universidad Politécnica de Madrid, Febrero 2012. Supervisors: Barrios-Rolanía, D.; Manrique, D

JOURNALS

Miró-Bueno JM, Rodríguez-Patón A (2011) A Simple Negative Interaction in the Positive Transcriptional Feedback of a Single Gene Is Sufficient to Produce Reliable Oscillations. PLoS ONE 6(11): e27414. doi:10.1371/journal.pone.0027414 (pdf)

Manrique, D.; Rodríguez-Patón, A; Sosík, P. On the scalability of biocomputing algorithms: The case of the maximum clique problem. Theoretical Computer science. 412, 7075-7086 (2011).

Sainz de Murieta, I; Miró-Bueno, JM; Rodríguez-Patón, A. Biomolecular computers. Current Bioinformatics, 6, 173-184 (2011)

Ionescu M., Păun G., Pérez-Jiménez M.J., Rodríguez-Patón A. Spiking Neural P Systems with Several Types of Spikes. International Journal of Computers Communications & Control, 6, 648-656 (2011).

Paun, A; Rodríguez-Patón, A;  Paun, M; Sidoroff, M. P systems with proteins on membranes: a survey.International Journal of Foundations of Computer Science, 22 (1), 39-53 (2011) .

Sosík, P; Rodríguez-Patón, A;  Cienciala, L. On the power of families of recognizer spiking neural P systems.International Journal of Foundations of Computer Science, 22 (1), 75-88 (2011) .

Jack, J; Paun, A; Rodríguez-Patón, A. A review of the nondeterministic waiting time algorithm. Natural Computing, 10, 139-149 (2011)

CONFERENCES

Rodríguez-Patón, A; Sainz de Murieta, I; Sosík, P. Autonomous resolution based on DNA strand displacement.17th International Conference on DNA Computing and Molecular Programming. September 19-23th, 2011. Pasadena, California, USA.

Gómez Esteban, P and Rodríguez-Patón, A. Simulating a Rock-Scissors-Paper Bacterial Game with a Discrete Cellular AutomatonNew Challenges on Bioinspired Applications. Lecture Notes in Computer Science. 6687, 363-370, (2011)

Font, J. M., Manrique, D., and Pascual E. Grammar-Guided Evolutonary Construction of Bayesian Networks.IWINAC 2011, Part I, Lecture Notes in Computer Science, 6686, 60-69, (2011)

Jack, J; Rodríguez-Patón, A; Paun, A. Poster:Biochemical Signaling: a discrete simulation with Memory Enhancement. IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2011, Orlando, FL, USA, February 3-5, ISBN 978-1-61284-851-8, (2011)

JOURNALS

Miró-Bueno, JM; Rodríguez-Patón, A. Biomolecular computing devices in Synthetic Biology. International Journal of Nanotechnology and Molecular Computation, 2 (2), 47-64, 2010.

Javier Andrade Garda, Juan Ares Casal, María A. Martínez, Juan Pazos, Santiago Rodríguez Yánez, Sonia Suárez:A fuzzy approach for solving a critical benchmarking problem. Knowl. Inf. Syst. 24(1): 59-75 (2010)

Mihaela Paun, Nichamon Naksinehaboon, Raja Nassar, Chokchai Leangsuksun, Stephen L. Scott, Narate Taerat:Incremental Checkpoint Schemes for Weibull Failure Distribution. Int. J. Found. Comput. Sci. 21(3): 329-344 (2010)

Narasimha Raju Gottumukkala, Raja Nassar, Mihaela Paun, Chokchai Leangsuksun, Stephen L. Scott:Reliability of a System of k Nodes for High Performance Computing Applications. IEEE Transactions on Reliability 59(1): 162-169 (2010)

CONFERENCES

Petr Sosík, Alfonso Rodríguez-Patón, Lucie Ciencialová. Polynomial Complexity Classes in Spiking Neural P Systems. Int. Conf. on Membrane Computing 2010: 348-360

José M. Font, Daniel Manrique. Grammar-Guided Evolutionary Automatic System for Autonomously Building Biological Oscillators. WCCI 2010 IEEE World Congress on Computational Intelligence, Barcelona, Spain, pp 2742-2748 (Jul. 2010).

Carrascal, A., Font, J. M., and Pelta, D. Evolutionary Physical Model Design. In Research and Development in Intelligent Systems XXVI, Proceedings of the AI 2009, part 12, pp. 487-492, 2010, Cambridge, UK.

Alfonso Rodríguez-Patón, José María Larrea, and Iñaki Sainz de Murieta. Inference with DNA molecules. Poster.9th International Conferences UNCONVENTIONAL COMPUTATION (UC). June 2010. Tokyo. Japan.

Fernando Alonso, Genoveva López, José M. Font, Daniel Manrique. Learner Satisfaction when Applying an Instructional Model in E-Learning. An Experimental Study. 2nd International Conference on Computer Supported Education, Valencia, Spain, pp 141-146 (Apr. 2010).

OTHER PUBLICATIONS

Petr Sosík: Catalytic P systems. Scholarpedia 5(1): 9336 (2010)

JOURNALS

Fernando Alonso, Daniel Manrique, José María Viñes: A moderate constructivist e-learning instructional model evaluated on computer specialists. Computers & Education, 2009, Vol. 53(1), pp. 57-65.

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  1. García-Arnau, D. Pérez, A. Rodríguez-Patón, P. Sosík: Spiking neural P systems: Stronger normal forms. Intern. J. of Unconventional Computing, 2009, vol. 5(5), p. 411-425

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Adleman, LM; Kari, J; Kari, L; Reishus, D; Sosík, P. The Undecidability of the Infinite Ribbon Problem: Implications for Computing by Self-Assembly. SIAM Journal on Computing, 38, (6), 2356-2381 (2009). © SIAM

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Ibarra, OH; Paun, A; Rodríguez-Patón, A. Sequential SNP systems based on min/max spike numbers.Theoretical Computer science, 410, 2982-2991 (2009). © Elsevier

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Paun, A; Paun, M; Rodríguez-Patón, A. On the Hopcroft’s minimization technique for DFA and DFCA.Theoretical Computer science, 410, 2424-2430 . © Elsevier

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John Jack, Andrei Paun: The Nondeterministic Waiting Time Algorithm: A Review CoRR abs/0907.4554: (2009)

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Petr Sosík: Preface. Int. J. Found. Comput. Sci. 20(3): 379-380 (2009)

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CONFERENCES
Jack, J.; Paun, A. Discrete Modeling of Biochemical Signaling with Memory EnhancementTransactions on Computational Systems Biology XI – Lecture Notes in Computer Science, 5750, 200-215 (2009)

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Petr Sosík, Andrei Paun, Alfonso Rodríguez-Patón, David Pérez. On the Power of Computing with Proteins on Membranes. Membrane Computing – Lecture Notes in Computer Science, 5957, 448-460 (2009)

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Carrascal, A.; Díez, A.; Font, J.M.; Manrique D. Evolutionary Generation of Fuzzy Knowledge Bases for Diagnosing Monitored Railway Systems. 22nd International Congress Condition Monitoring and Diagnostic Engineering Management (COMADEM), San Sebastián, Spain, 9-11 june, 2009, pp 191-198.

Couchet, J.; Font, J.M.; Manrique, D. Rule Evolving System for Knee Lesion Prognosis from Medical Isokinetic Curves. Bioinspired Applications in Artificial and Natural Computation – Lecture Notes in Computer Science, 5602, 188-197 (2009). © Springer-Verlag

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Miró-Bueno, JM; Rodríguez-Patón, A. A new model of synthetic genetic oscillator based on trans-acting repressor ribozyme Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living – Lecture Notes in Computer Science, 5518, 1170-1177 (2009). © Springer-Verlag

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Jack, J; Paun, A; Rodríguez-Patón, A. Effects of HIV-1 Proteins on the Fas-Mediated Apoptotic Signalling Cascade: A Computational Study of Latent CD4+ T Cell Activation.Membrane Computing – Lecture Notes in Computer Science, 391, 246-259 (2009). © Springer-Verlag

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BOOKS

Ashish Goel, Friedrich C. Simmel, Petr Sosík. 14th International Meeting on DNA Computing, DNA 14, Prague, Czech Republic, June 2-9, 2008. Revised Selected PaperDNA Computing – Lecture Notes in Computer Science, 5347, (2009).

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Font, J. M., Manrique, D., and Ríos, J. Redes de Neuronas Artificiales y Computación Evolutiva. Fundación General de la UPM, Facultad de Informática, Universidad Politécnica de Madrid, 2009, ISBN: 978-84-96737-61-7, Depósito legal: M-39181-2009.

JOURNALS

Ibarra, OH; Woodworth, S; Yu, F; Paun, A. On spiking neural P systems and partially blind counter  machines.Natural Computing, 7, (1), 3-19 (2008). © Springer-Verlag

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Kari, L; Sosík, P. On the weight of universal insertion grammars. Theoretical Computer science, 396, (1-3), 264-270 (2008). © Elsevier

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Chen, H; Ionescu, M; Ishdorj, TO; Paun, A; Paun, G; Pérez-Jiménez, MJ. Spiking neural P systems with extended rules: universality and languages. Natural Computing, 7, (2), 147-166 (2008). © Springer-Verlag

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Ibarra, OH; Paun, A. Computing with cells: membrane systems – some complexity issues. International Journal of Parallel, Emergent and Distributed Systems, 3, (5), 347-365 (2008). © Taylor & Francis

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Jack, J; Rodríguez-Patón, A; Ibarra, OH; Paun, A. Discrete Nondeterministic Modeling of the Fas Pathway.International Journal of Foundations of Computer Science, 19, 1147-1162 (2008). © World Scientific

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García-Arnau, M; Pérez, D; Rodríguez-Patón, A; Sosík, P. On the power of elementary features in spiking neural P systems. Natural Computing, 7, 471-483 (2008). © Springer-Verlag

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CONFERENCES

Couchet, J.; Font, J.M.; Manrique, D. Using Evolved Fuzzy Neural Networks for Injury Detection from Isokinetic Curves. International Conference on Artificial Intelligence, Dec. 9-11, 2008, Cambridge, UK.

Miró-Bueno JM, Rodríguez-Patón, A. Design, analysis and simulation of a synthetic genetic oscillator. ESF-UB Conference in Biomedicine: Systems Biology. Sant Feliu de Guixols (Spain), April 12-17, 2008.

Ibarra, OH; Paun, A; Rodríguez-Patón, A. Sequentiality Induced by Spike Number in SNP Systems. DNA Computing – Lecture Notes in Computer Science, 5347, 179-190 (2008).

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Paun, A; Paun, M; Rodríguez-Patón, A. Hopcroft’s Minimization Technique: Queues or Stacks?.Implementation and Application of Automata – Lecture Notes in Computer Science, 5148, 78-91 (2008). © Springer-Verlag

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García-Arnau, M; Manrique, D; Rodríguez-Patón, A; Sosík, P. Towards a Robust Biocomputing Solution of Intractable Problems. DNA Computing – Lecture Notes in Computer Science, 4848, 221-230 (2008). © Springer-Verlag

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BOOK CHAPTERS

Miró-Bueno, JM; Rodríguez-Patón, A. Biomolecular computing devices in Synthetic Biology, in Porto, A; Pazos, A; Buño, W (Eds.), Advancing Artificial Intelligence through Biological Process Applications (pp. 250-267). Medical Information Science Reference (2008). © IGI Global

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Abstract

Manrique, D.; Ríos, J.; Rodríguez-Patón, A. Grammar-Guided Genetic Programming, in Rabuñal, J.R.; Dorado, J.; Pazos, A. (Eds.), Encyclopedia of Artificial Intelligence. Information Science Reference (2008). © IGI Global

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JOURNAL PUBLICATIONS

Sosík, P; Rodríguez-Patón, A. Membrane computing and complexity theory: A characterization of PSPACE.Journal of Computer and System Science, 73, 137-152 (2007)
© Elsevier

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Andrade, J; Ares, J; Garcia, R; Pazos, J; Rodriguez, S; Rodriguez-Paton, A; Silva, A. Towards a lessons learned system for critical software. Reliability Engineering & System Safety, 92, 902-913 (2007)
© Elsevier

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Couchet, J; Manrique, D; Ríos, J; Rodriguez-Paton, A. Crossover and Mutation Operators for Grammar-Guided Genetic Programming. Soft Computing, 11, 943-955 (2007)
© Springer-Verlag

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García-Arnau, M; Manrique, D; Rodríguez-Patón, A; Sosík, P. A P System and a Constructive Membrane-Inspired DNA Algorithm for Solving the Maximum Clique Problem.BioSystems, 90, 687-697 (2007)
© Elsevier

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García-Arnau, M; Manrique, D; Ríos, J; Rodríguez-Patón, A. Initialization method for grammar-guided genetic programming. Knowledge-Based Systems, 20, 127-133 (2007)
© Elsevier

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Ibarra, OH; Paun, A; Paun, G; Rodríguez-Patón, A; Sosík, P; Woodworth, S. Normal forms for spiking neural P systems. Theoretical Computer Science, 372, 196-217 (2007)
© Elsevier

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Paun, A; Paun, G. Small universal spiking neural P systems. Biosystems, 90, 46-60 (2007)
© Elsevier

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Cheruku, S; Paun, A; Romero-Campero, FJ; Perez-Jimenez, MJ; Ibarra, OH. Simulating FAS-induced apoptosis by using P systems. Progress in Natural Science, 17, 424-431 (2007)
© Taylor & Francis

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Cienciala, L; Ciencialova, L; Frisco, P; Sosik, P. On the power of deterministic and sequential communicating P systems. International Journal of Foundations of Computer Science, 18, 414-431 (2007)
© World Scientific

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Sebestyen, P; Sosik, P. Modelling multiple robots in space: An adaptive eco-grammar system.Fundamenta Informaticae, 76, 367-381 (2007)
© IOS press

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CONFERENCE PROCEEDINGS

García-Arnau, M; Manrique, D; Rodríguez-Patón, A. A Parallel DNA Algorithm Using a Microfluidic Device to Build Scheduling Grids. Bio-inspired Modeling of Cognitive Tasks – Lecture Notes in Computer Science, 4527, 193-202 (2007)
© Springer-Verlag

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Paun, A; Rodríguez-Patón, A. On Flip-Flop Membrane Systems with Proteins. Membrane Computing – Lecture Notes in Computer Science, 4860, 414-427 (2007)
© Springer-Verlag

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Couchet, J; Ferreira, E; Fonseca, A; Manrique, D. A Novel Architecture for the Classification and Visualization of Sequential Data. Adaptive and Natural Computing Algorithms – Lecture Notes in Computer Science, 4431 ,730-738 (2007)
© Springer-Verlag

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Couchet, J; Manrique, D; Porras, L. Grammar-Guided Neural Architecture Evolution. Bio-inspired Modeling of Cognitive Tasks – Lecture Notes in Computer Science, 4527, 437-446 (2007)
© Springer-Verlag

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Alonso, F; Lopez, G; Manrique, D; Soriano, FJ. E-learning instructional approach with learning objects.E-Activities: Networking the world – Electrical and Computer Engineering Series, 242-247 (2007)

JOURNAL PUBLICATIONS

Domaratzki, M; Sosik, P; Rodríguez-Patón, A. Algebraic properties of substitution on trajectories.Theoretical Computer Science, 369, 183-196 (2006)
© Elsevier

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Manrique, D; Ríos, J; Rodríguez-Patón, A. Evolutionary system for automatically constructing and adapting radial basis function networks. Neurocomputing, 69, 2268-2283 (2006)
© Elsevier

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Paun, A, Popa, B. P Systems with Proteins on Membranes. Fundamenta Informaticae, 72, 467-483 (2006)
© IOS press

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Kari, L; Losseva, E; Konstantinidis, S; Sosik, P; Thierrin, G. A formal language analysis of DNA hairpin structures.Fundamenta Informaticae, 71, 453-475 (2006)
© IOS press

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Campeanu, C; Paun, A; Smith, JR. Incremental construction of minimal deterministic finite cover automata.Theoretical Computer Science, 363, 135-148 (2006)
© Elsevier

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Andrade, J; Ares, J; Garcia, R; Pazos, J; Rodriguez, S; Silva, A. Definition of a problem-sensitive conceptual modelling language: foundations and application to software engineering. Information and Software Technology, 48, 517-531 (2006)
© Elsevier

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CONFERENCE PROCEEDINGS

Sosík, P; Rodríguez-Patón, A. P Systems with Active Membranes Characterize PSPACE. DNA Computing – Lecture Notes in Computer Science, 4287, 33-46 (2006)
© Springer-Verlag

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Ionescu, M; Paun, A; Paun, G; Perez-Jimenez, M. Computing with spiking neural P systems: Traces and small universal systems. DNA Computing – Lecture Notes in Computer Science, 4287, 1-16 (2006)
© Springer-Verlag

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Nagda, H; Paun, A; Rodríguez-Patón, A .P Systems with Symport/Antiport and Time. Membrane Computing – Lecture Notes in Computer Science, 4361, 463-476 (2006)
© Springer-Verlag

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Carrascal, A; Couchet, J; Ferreira, E; Manrique, D. Anomaly Detection using prior knowledge: application to TCP/IP traffic. Artificial Intelligence in Theory and Practice – IFIP International Federation for Information Processing, 217, 139-148 (2006)
© Springer-Verlag

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Ibarra, OH; Paun, A. Counting Time in Computing with Cells. DNA Computing – Lecture Notes in Computer Science, 3892, 112-128 (2006)
© Springer-Verlag

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Kari, L; Konstantinidis, S; Losseva, E; Sosik, P; Thierrin, G. Hairpin structures in DNA words. DNA Computing – Lecture Notes in Computer Science, 3892, 158-170 (2006)
© Springer-Verlag

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Sosik, P; Valik, O. On evolutionary lineages of membrane systems. Membrane Computing – Lecture Notes in Computer Science, 3850, 67-78 (2006)
© Springer-Verlag

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Paun, A; Popa, B. P systems with proteins on membranes and membrane division. Developments in Language Theory – Lecture Notes in Computer Science, 4036, 292-303 (2006)
© Springer-Verlag

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Campeanu, C; Paun, A; Smith, JR. An incremental algorithm for constructing minimal deterministic finite cover automata. Implementation and Application of Automata – Lecture Notes in Computer Science,3845, 90-103 (2006)
© Springer-Verlag

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Paun, A; Perez-Jimenez, MJ; Romero-Campero, FJ. Modeling signal transduction using P systems.Membrane Computing – Lecture Notes in Computer Science, 4361, 100-122 (2006)
© Springer-Verlag

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Ibarra, OH; Woodworth, S; Yu, F; Paun, A. On spiking neural P systems and partially blind counter machines.Unconventional Computation – Lecture Notes in Computer Science, 4135, 113-129 (2006)
© Springer-Verlag

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JOURNAL PUBLICATIONS

Ledesma, L; Manrique, D; Rodriguez-Paton, A. A tissue P system and a DNA microfluidic device for solving the shortest common superstring problem. Soft Computing, 9, 679-685 (2005)
© Springer-Verlag

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Alonso, F; Lopez, G; Manrique, D; Vines, JM. An instructional model for web-based e-learning education with a blended learning process approach. British Journal of Educational Technology, 36, 217-235 (2005)

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Paun, G; Perez-Jimenez, MJ; Pazos, J; Rodriguez-Paton, A. Symport/antiport P systems with three objects are universal. Fundamenta Informaticae, 64, 353-367 (2005)
© IOS press

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Kari, L; Konstantinidis, S; Sosik, P. Bond-free languages: Formalizations, maximality and construction methods.International Journal of Foundations of Computer Science, 16, 1039-1070 (2005)
© World Scientific

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Kari, L; Konstantinidis, S; Sosik, P. Operations on trajectories with applications to coding and bioinformatics.International Journal of Foundations of Computer Science, 16, 531-546 (2005)
© World Scientific

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Kari, L; Konstantinidis, S; Sosik, P. On properties of bond-free DNA languages. Theoretical Computer Science,334, 131-159 (2005)
© Elsevier

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Kari, L; Sosik, P. Aspects of shuffle and deletion on trajectories. Theoretical Computer Science, 332, 47-61 (2005)
© Elsevier

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Freund, R; Kari, L; Oswald, M; Sosik, P. Computationally universal P systems without priorities: two catalysts are sufficient. Theoretical Computer Science, 330, 251-266 (2005)
© Elsevier

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Freund, R; Oswald, M; Paun, A. Optimal results for the computational completeness of gemmating (tissue) P systems. International Journal of Foundations of Computer Science, 16, 929-942 (2005)
© World Scientific

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Freund, R; Paun, A. P systems with active membranes and without polarizations. Soft Computing, 9, 657-663 (2005)
© Springer-Verlag

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Campeanu, C; Kari, L; Paun, A. Results on transforming NFA into DFCA. Fundamenta Informaticae, 64, 53-63 (2005)
© IOS press

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CONFERENCE PROCEEDINGS

Manrique, D; Marquez, F; Rios, J; Rodriguez-Paton, A. Grammar based crossover operator in genetic programming. Artificial Intelligence and Knowledge Engineering Applications: A Bioinspired Approach – Lecture Notes in Computer Science, 3562, 252-261 (2005)
© Springer-Verlag

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Kari, L; Konstantinidis, S; Sosik, P. Bond-free languages: Formalizations, maximality and construction methods.DNA Computing – Lecture Notes in Computer Science, 3384, 169-181 (2005)
© Springer-Verlag

MEMBERS


Associate Professors

Alfonso Rodríguez-Patón
Alfonso Rodríguez-PatónDirector - IP
Daniel Manrique Gamo
Daniel Manrique Gamo

Associate Researchers

Andrei Paun
Andrei Paun

Postdoctoral Researchers

Xianxiang Zeng
Xianxiang Zeng

Ph.D Students

Guillermo Pérez del Pulgar Frowein
Guillermo Pérez del Pulgar Frowein
Martín Gutierrez Pescarmona
Martín Gutierrez Pescarmona
Paula Gregorio Godoy
Paula Gregorio Godoy
Vishal Gupta
Vishal Gupta
Marcos Rodríguez Regueira
Marcos Rodríguez Regueira
Pablo Ramos Criado
Pablo Ramos Criado
Antonio Prestes García
Antonio Prestes García
Iván Pau
Iván Pau
Guillermo Delgado Martínez
Guillermo Delgado Martínez

Past Members

Jesús María Miró Bueno
Jesús María Miró Bueno
Niall Murphy
Niall Murphy
Iñaki Sainz de Murieta Fuentes
Iñaki Sainz de Murieta Fuentes
José María Font Fernández
José María Font Fernández
Petr Sosik
Petr Sosik
David Pérez Pérez
David Pérez Pérez

Visiting Researchers

2016 – 2017 

  • Xiangxiang Zeng (Xiamen University, China)
  • Tao Song (China University of Petroleum)

2014-2015

  • Petr Sosík (Opava University)

2013

  • Fernando de la Cruz (Univ. de Cantabria, Spain).

2012

  • Joao B Xavier (Memorial Sloan-Kettering Cancer Center, New York, USA.)

2011

  • Martyn Amos (Manchester Metropolitan University)

2010

  • Christof Teuscher (Portland State University and University of New Mexico)
  • Friedrich Simmel (Technische Universität München)

2009

  • Gheorghe Paun (Academia de Ciencias, Rumania)
  • Alfonso Jaramillo (Ecole Polytechnique. CNRS Francia)
  • Milan Stojanovic (Columbia University, USA)
  • Matteo Cavaliere (Microsooft Research – Trento)
  • Friedrich Simmel (Technische Universität München)

2008

2007

  • Yaakov Benenson (Harvard University)
  • George Paun (Romanian Academy)
  • Oscar H. Ibarra (California University)
  • Grzegorz Rozenberg ( Universiteit Leiden)
  • Rudolf Freund (Technische Universität Wien)

OPEN POSITIONS


PhD positions available in LIA group. If you are a great programmer (an engineer or physicist) that likes biology and wants to program cells and DNA, code biology or engineer life contact us (candidates should send by email: CV, academic transcripts and a motivation letter). We love people passionate about research that wants to deep into the unknown.

CONTACT US


Cómo llegar: http://www.fi.upm.es/es/comollegar 

La ETSI INF – UPM en Google Maps: https://goo.gl/maps/NhLnAofm1uo 

Laboratorio de Inteligencia Artificial: Bloque 5, planta 1.

Twitter: @LIA_UPM

email: arpaton@fi.upm.es