Song, T., Ren, Y., Wang, S., Han, P., Wang, L., Li, X., & Rodriguez-Patón, A. (2023). DNMG: Deep molecular generative model by fusion of 3D information for de novo drug design. Methods, 211, 10-22.

Ma, T., Méndez-Merino, D., Uría-Regojo, G., Sánchez-Fernández, C., Giner-Sánchez, L., Guerrero-Aspizua, S., … & Rodríguez-Patón, A. (2023). BioBlocksLab: A Portable DIY Bio Lab Using BioBlocks language. Methods.

Li, X., Han, P., Chen, W., Gao, C., Wang, S., Song, T., … & Rodriguez-Patón, A. (2023). MARPPI: boosting prediction of protein–protein interactions with multi-scale architecture residual network. Briefings in Bioinformatics, 24(1), bbac524.


Tao Song, Xudong Zhang, MaoDing, Alfonso Rodriguez-Paton, Shudong Wang, Gan Wang. DeepFusion: A deep learning based multi-scale feature fusion method for predicting drug-target interactions. Methods, 2022, 204: 269-277.

Xudong Zhang, Gan Wang, Xiangyu Meng, Shuang Wang, Ying Zhang, Alfonso Rodriguez-Paton, Jianmin Wang, Xun Wang. Molormer: a lightweight self-attention-based method focused on spatial structure of molecular graph for drug–drug interactions prediction. Briefings in Bioinformatics, 2022.

Tao Song, Gan Wang, Mao Ding, Alfonso Rodriguez-Paton, Xun Wang, Shudong Wang. Network‐Based Approaches for Drug Repositioning. Molecular Informatics, 2022, 41(5): 2100200.

Daniel García-Lojo, David Méndez-Merino, Ignacio Pérez-Juste, Ángel Acuña, Luís García-Río, Alfonso Rodriguez-Paton, Isabel Pastoriza-Santos, Jorge Pérez-Juste. Bolaform Surfactant‐Induced Au Nanoparticle Assemblies for Reliable Solution‐Based Surface‐Enhanced Raman Scattering Detection. Advanced Materials Technologies, 2022: 2101726.

Shanchen Pang, Ying Zhang, Tao Song, Xudong Zhang, Xun Wang, Alfonso Rodriguez-Paton. AMDE: A novel attention-mechanism-based multidimensional feature encoder for drug–drug interaction prediction. Briefings in Bioinformatics, 2022, 23(1): bbab545.

Wang Shudong, Du Zhenzhen, Ding Mao, Alfonso Rodriguez-Paton,Song Tao. KG-DTI: a knowledge graph based deep learning method for drug-target interaction predictions and Alzheimer’s disease drug repositions. Applied Intelligence, 2022, 52(1): 846-857.


Francis George C. Cabarle, Xiangxiang Zeng, Niall Murphy, Tao Song, Alfonso Rodriguez-Paton, Xiangrong Liu. “Neural-like P systems with plasmids.” Information and Computation. 2021, 104766, ISSN 0890-5401.

Wang, Shudong, Zhenzhen Du, Mao Ding, Alfonso Rodriguez-Paton, and Tao Song. “KG-DTI: a knowledge graph based deep learning method for drug-target interaction predictions and Alzheimer’s disease drug repositions.” Applied Intelligence (2021): 1-12.

Wang, Xun, Dayan Liu, Jinfu Zhu, Alfonso Rodriguez-Paton, and Tao Song. “CSConv2d: A 2-D Structural Convolution Neural Network with a Channel and Spatial Attention Mechanism for Protein-Ligand Binding Affinity Prediction.” Biomolecules 11, no. 5 (2021): 643.

David Ruano-Gallego, Julia Sanchez-Garrido, Zuzanna Kozik, Elena Núñez-Berrueco, Massiel Cepeda-Molero, Caroline Mullineaux-Sanders, Jasmine Naemi-Baghshomali Clark, Sabrina L. Slater, Naama Wagner, Izabela Glegola-Madejska, Theodoros I. Roumeliotis, Tal Pupko, Luis Ángel Fernández, Alfonso Rodríguez-Patón, Jyoti S. Choudhary, Gad Frankel. Type III secretion system effectors form robust and flexible intracellular virulence networks. SCIENCE. Vol. 371, Issue 6534. 12 Mar 2021.
To know more details about the article, there is a video on YouTube.

Song, Bosheng, Xiangxiang Zeng, and Alfonso Rodríguez-Patón. “Monodirectional tissue P systems with channel states.” Information Sciences 546 (2021): 206-219.

Amărioarei, Alexandru, Frankie Spencer, Gefry Barad, Ana-Maria Gheorghe, Corina Iţcuş, Iris Tuşa, Ana-Maria Prelipcean, Andrei Păun, Mihaela Păun, Alfonso Rodriguez-Paton, Romică Trandafir, and Eugen Czeizler. 2021. “DNA-Guided Assembly for Fibril Proteins.” Mathematics 9, no. 4: 404. https://doi.org/10.3390/math9040404

Juan Perianez-Rodriguez, Marcos Rodriguez, Marco Marconi, Estefano Bustillo-Avendaño, Guy Wachsman, Alvaro Sanchez-Corrionero, Hugues De Gernier, Javier Cabrera, Pablo Perez-Garcia, Inmaculada Gude, Angela Saez, Laura Serrano-Ron, Tom Beeckman, Philip N. Benfey, Alfonso Rodríguez-Patón, Juan Carlos del Pozo, Krzysztof Wabnik, Miguel A. Moreno-Risueno. An auxin-regulable oscillatory circuit drives the root clock in Arabidopsis. SCIENCE ADVANCES, 2021.


Wang, Shudong, Zhenzhen Du, Mao Ding, Renteng Zhao, Alfonso Rodriguez-Paton, and Tao Song. “LDCNN-DTI: A Novel Light Deep Convolutional Neural Network for Drug-Target Interaction Predictions.” In 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 1132-1136. IEEE, 2020.

García, Antonio Prestes, and Alfonso Rodríguez-Patón. “Applying Evolutionary Metaheuristics for Parameter Estimation of Individual-Based Models.” arXiv preprint arXiv:2005.12841 (2020).

Liu, Xiangrong, Zengyan Hong, Juan Liu, Yuan Lin, Alfonso Rodríguez-Patón, Quan Zou, and Xiangxiang Zeng. “Computational methods for identifying the critical nodes in biological networks.” Briefings in bioinformatics 21, no. 2 (2020): 486-497.


Rocío López-Igual, Joaquín Bernal-Bayard, Alfonso Rodríguez-Patón, Jean-Marc Ghigo, and Didier Mazel. Engineered toxin-intein antimicrobials can selectively target and kill antibiotic-resistant bacteria in mixed populations. Nature Biotechnology, 2019. DOI: 10.1038/s41587-019-0105-3.
Free full-text access to a view-only version: https://rdcu.be/bw1w7.
The gif below is an animation describing the programmable antibiotic presented in our Nature Biotechnology paper.

Marcos Rodríguez Regueira, Jesús Daza García & Alfonso Rodríguez-Patón. The multicellular incoherent feedforward loop motif generates spatial patterns. BioRxiv, 2019: 579342.

Liu X, Hong Z, Liu J, Lin Y, Rodríguez-Patón A, Zou Q, Zeng X. Computational methods for identifying the critical nodes in biological networks. Brief Bioinform. 2019 Feb 12. doi: 10.1093/bib/bbz011.

Song T, Pan L, Wu T, Zheng P, Wong MLD, Rodriguez-Paton A.Spiking Neural P Systems with Learning Functions. IEEE Trans Nanobioscience. 2019 Feb 1. doi: 10.1109/TNB.2019.2896981.

Goñi-Moreno A, de la Cruz F, Rodríguez-Patón A, Amos M. Dynamical Task Switching in Cellular Computers. Life (Basel). 2019 Jan 26;9(1). pii: E14. doi: 10.3390/life9010014.

Zhang X, Zou Q, Rodríguez-Patón A, Zeng X. Meta-Path Methods for Prioritizing Candidate Disease miRNAs. IEEE/ACM Trans Comput Biol Bioinform. 2019 Jan-Feb; 16(1): 283-291. doi: 10.1109/TCBB.2017.2776280. Epub 2017 Nov 22.

Ma Tongmao, Hao Shaohua, Wang Xun, Alfonso Alfonso Rodríguez-Patón, Wang Shudong, Song Tao. Double layers self-organized spiking neural P systems with anti-spikes for fingerprint recognition. IEEE Access, 2019, 7: 177562-177570.


Xiangxiang Zeng, Jiawei Lin, Chen Lin, Xiangrong Liu, Alfonso Rodríguez-Patón “Structural Hole Spanner in HumanNet Identifies Disease Gene and Drug targets”  IEEE Access ( Early Access ), 27 June 2018, ISSN: 2169-3536, DOI: 10.1109/ACCESS.2018.2849216

T Song, A Rodríguez-Patón, P Zheng, X Zeng.Spiking Neural P Systems With Colored Spikes. IEEE Transactions on Cognitive and Developmental Systems, 2018, 10(4): 1106-1115.

Tao Song, Xiangxiang Zeng, Pan Zheng, Min Jiang, Alfonso Rodríguez-Patón.A Parallel Workflow Pattern Modeling Using Spiking Neural P Systems With Colored Spikes. IEEE transactions on nanobioscience, 2018, 17(4): 474-484.

A Goni-Moreno, F de la Cruz, A Rodriguez-Paton, M Amos.Dynamical Task Switching in Cellular Computers. bioRxiv, 2018: 479998.

X Yan, X Liu, X Zeng, A Rodríguez-Patón. An Implementation of Elementary Arithmetic with Virus Machine. Enjoying Natural Computing. Springer, Cham, 2018: 304-317.

Shanchen Pang, Tong Ding, Alfonso Rodríguez-Patón, Tao Song, Zhen Phen. A Parallel Bioinspired Framework for Numerical Calculations Using Enzymatic P System With an Enzymatic Environment. IEEE Access, 2018, 6: 65548-65556.

T Song, S Pang, S Hao, A Rodríguez-Patón, P Zheng. A Parallel Image Skeletonizing Method Using Spiking Neural P Systems with Weights. Neural Processing Letters, 2018: 1-18.

Paula Gregorio-Godoy, Guillermo Perez del Pulgar, Marcos Rodriguez-Regueira, Alfonso Rodríguez-Patón. Deriving general conditions and mechanisms for division of labor using the cell-based simulator gro. bioRxiv, 2018: 363093.


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.   ACS Synth. Biol., 6 (8), pp 1496–1508 DOI: 10.1021/acssynbio.7b00003 Publication Date (Web): April 24, 2017

Andrei Paun, Alfonso Rodríguez-Patón. P Systems Simulating Bacterial Conjugation: Universality and Properties. Fundamenta Informaticae,  vol. 153, no. 1-2, pp. 87-103, 2017  DOI: 10.3233/FI-2017-1532

Vishal Gupta, Jesús Irimia, Iván Pau, Alfonso Rodríguez-Patón  Bioblocks: Programming protocols in biology made easier.   ACS Synth. Biol., 6 (7), pp 1230–1232  DOI: 10.1021/acssynbio.6b00304  Publication Date (Web): January 4, 2017

Xin Li, Li Hong, Tao Song, Alfonso Rodríguez-Patón, Congzhou Chen, Haiyan Zhao, Xiaolong Shi.  Highly Biocompatible Drug-Delivery Systems Based on DNA Nanotechnology. Journal of Biomedical Nanotechnology, Volume 13, Number 7, July 2017, pp. 747-757(11) DOI: https://doi.org/10.1166/jbn.2017.2383
David Beneš, Alfonso Rodríguez-Patón, Petr Sosík. Directed evolution of biocircuits using conjugative plasmids and CRISPR-Cas9: design and in silico experiments. Natural Computing. September 2017, Volume 16, Issue 3, pp 497–505. DOI: 10.1007/s11047-016-9595-9
Xiangyi Meng, Quan Zou, Alfonso Rodríguez-Patón, Xiangxiang Zeng. Iteratively collective prediction of disease-gene associations through the incomplete network. IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2017. pp 1324-1330 DOI: 10.1109/BIBM.2017.8217854

Xuan Zhang, Quan Zou, Alfonso Rodriguez-Paton. Meta-path methods for prioritizing candidate disease miRNAsIEEE/ACM Transactions on Computational Biology and Bioinformatics, 2017.  DOI: 10.1109/TCBB.2017.2776280

Xiangxiang Zeng, Ningxiang Ding, Alfonso Rodríguez-Patón, Quan Zou. Probability-based collaborative filtering model for predicting gene–disease associations. BMC medical genomics 2017 10(Suppl 5):76. DOI: https://doi.org/10.1186/s12920-017-0313-y

Tao Song, Alfonso Rodríguez-Patón, Pan Zheng, Xiangxiang Zeng.  Spiking Neural P Systems with Colored Spikes. IEEE Transactions on Cognitive and Developmental Systems, 2017.  DOI: 10.1109/TCDS.2017.2785332

Martín Eduardo GutiérrezAlfonso Rodríguez-Patón  Simulating multicell populations with an accelerated gro simulator.   The MIT Press, In Proceedings of the 14th European Conference on Artificial Life, pp. 186-188, Lyon, France, 4-8 September 2017.


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
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


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
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


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).

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.


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.
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.