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  2020 (5)
Dynamic simulations of microbial communities under perturbations: opportunities for microbiome engineering. García-Jiménez, B.; Carrasco, J.; Medina, J.; and Wilkinson, M., D. Research Square - Preprint, (Version 1). 2 2020.
Dynamic simulations of microbial communities under perturbations: opportunities for microbiome engineering [link]Website   bibtex   2 downloads
Data-driven classification of the certainty of scholarly assertions. Prieto, M.; Deus, H.; de Waard, A.; Schultes, E.; García-Jiménez, B.; and Wilkinson, M. PeerJ, 2020(4). 2020.
bibtex   abstract   1 download
Predicting microbiomes through a deep latent space. García-Jiménez, B.; Muñoz, J.; Cabello, S.; Medina, J.; and Wilkinson, M., D. bioRxiv,2020.04.27.063974. 2020.
Predicting microbiomes through a deep latent space [link]Website   bibtex   abstract
MEMOTE for standardized genome-scale metabolic model testing. Lieven, C.; Beber, M.; Olivier, B.; Bergmann, F.; Ataman, M.; Babaei, P.; Bartell, J.; Blank, L.; Chauhan, S.; Correia, K.; Diener, C.; Dräger, A.; Ebert, B.; Edirisinghe, J.; Faria, J.; Feist, A.; Fengos, G.; Fleming, R.; García-Jiménez, B.; Hatzimanikatis, V.; van Helvoirt, W.; Henry, C.; Hermjakob, H.; Herrgård, M.; Kaafarani, A.; Kim, H.; King, Z.; Klamt, S.; Klipp, E.; Koehorst, J.; König, M.; Lakshmanan, M.; Lee, D.; Lee, S.; Lee, S.; Lewis, N.; Liu, F.; Ma, H.; Machado, D.; Mahadevan, R.; Maia, P.; Mardinoglu, A.; Medlock, G.; Monk, J.; Nielsen, J.; Nielsen, L.; Nogales, J.; Nookaew, I.; Palsson, B.; Papin, J.; Patil, K.; Poolman, M.; Price, N.; Resendis-Antonio, O.; Richelle, A.; Rocha, I.; Sánchez, B.; Schaap, P.; Malik Sheriff, R.; Shoaie, S.; Sonnenschein, N.; Teusink, B.; Vilaça, P.; Vik, J.; Wodke, J.; Xavier, J.; Yuan, Q.; Zakhartsev, M.; and Zhang, C. Nature Biotechnology, 38(3). 2020.
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Metabolic Modelling Approaches for Describing and Engineering Microbial Communities. García-Jiménez, B.; Torres, J.; and Nogales, J. . 9 2020.
Metabolic Modelling Approaches for Describing and Engineering Microbial Communities [link]Website   bibtex
  2019 (4)
Robust and automatic definition of microbiome states. García-Jiménez, B.; and Wilkinson, M., D. PeerJ, 7: e6657. 3 2019.
Robust and automatic definition of microbiome states [link]Website   bibtex   abstract   1 download
Data-driven classification of the certainty of scholarly assertions. Prieto, M.; Deus, H.; Waard, A., D.; Schultes, E.; García-Jiménez, B.; and Wilkinson, M., D. . 6 2019.
Data-driven classification of the certainty of scholarly assertions [link]Website   bibtex
Modeling recovery of Crohn's disease, by simulating microbial community dynamics under perturbations. Carrasco Muriel, J.; García-Jiménez, B.; and Wlikinson, M., D. In Intelligent Systems for Molecular Biology and European Conference on Computational Biology, 2019.
Modeling recovery of Crohn's disease, by simulating microbial community dynamics under perturbations [link]Website   bibtex   abstract
Condensed Microbiome Representation using Transfer and Deep Learning to Promote Microbial Composition Prediction. Cabello, S.; Garcia-Jimenez, B.; and Wilkinson, M., D. In Advances in Computational Biology Conference, 11 2019.
Condensed Microbiome Representation using Transfer and Deep Learning to Promote Microbial Composition Prediction [link]Website   bibtex   abstract
  2018 (2)
MDPbiome: microbiome engineering through prescriptive perturbations. García-Jiménez, B.; de la Rosa, T.; and Wilkinson, M., D. Bioinformatics, 34(17): i838-i847. 9 2018.
MDPbiome: microbiome engineering through prescriptive perturbations [link]Website   bibtex   abstract
FLYCOP: metabolic modeling-based analysis and engineering microbial communities. García-Jiménez, B.; García, J., L.; and Nogales, J. Bioinformatics, 34(17): i954-i963. 9 2018.
FLYCOP: metabolic modeling-based analysis and engineering microbial communities [link]Website   bibtex   abstract
  2016 (2)
Temporal microbiome road-maps guided by perturbations. García-Jiménez, B.; and Wilkinson, M. Technical Report 4 2016.
Temporal microbiome road-maps guided by perturbations [link]Website   bibtex
MDPbiome: Predicting temporal microbiome dynamics influenced by external perturbations. García-Jiménez, B.; and Wilkinson, M., D. In XIII Symposium on Bioinformatics. JBI 2016. Poster, 2016.
MDPbiome: Predicting temporal microbiome dynamics influenced by external perturbations [link]Website   bibtex
  2014 (4)
Predicting Protein Relationships to Human Pathways through a Relational Learning Approach based on Simple Sequence Features. García-Jiménez, B.; Pons, T.; Sanchis, A.; and Valencia, A. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 11(4): 753-765. 2014.
Predicting Protein Relationships to Human Pathways through a Relational Learning Approach based on Simple Sequence Features [link]Website   bibtex
Automatic annotation of bioinformatics workflows with biomedical ontologies. García-Jiménez, B.; and Wilkinson, M., D. In Margaria, T.; and Steffen, B., editor(s), ISoLA2014: Proceedings of the 6th International Symposium On Leveraging Applications of Formal Methods, Verification and Validation, volume 8803, of Lecture Notes in Computer Science, pages 464-478, 2014. Springer-Verlag Heidelberg
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Identifying Bioinformatics Sub-Workflows using Automated Biomedical Ontology Annotations. García-Jiménez, B.; and Wilkinson, M., D. In XII Symposium on Bioinformatics. JBI 2014. Poster, 2014.
Identifying Bioinformatics Sub-Workflows using Automated Biomedical Ontology Annotations [link]Website   bibtex
Minería de Datos. García-Jiménez, B.; and Fernández, J., M. Bioinformática con Ñ, pages 119-156. Sebastián, Á.; and Pascual-García, A., editor(s). CreateSpace, (In press) edition, 2014.
Bioinformática con Ñ [link]Website   bibtex
  2013 (1)
The relevance of systems biology in relational learning to annotate human protein with Reactome pathways. García-Jiménez, B.; and Sanchis, A. In 21st International Conference on Intelligent Systems for Molecular Biology and 12th European Conference on Computational Biology, ISMB/ECCB 2013, volume 4, of Protein Structure and Function Prediction and Analysis, poster L059, pages 986, 7 2013. F1000Posters
The relevance of systems biology in relational learning to annotate human protein with Reactome pathways [link]Website   bibtex
  2012 (1)
Relational Learning-based Extension for Reactome Pathways with Sequence Features and Interactions. García-Jiménez, B.; Pons, T.; Sanchis, A.; and Valencia, A. In 11th Spanish Symposium on Bioinformatics. JBI 2012. Talk., 1 2012. Spanish Institute of Bioinformatics and Portuguese Bioinformatics Network
Relational Learning-based Extension for Reactome Pathways with Sequence Features and Interactions [link]Website   bibtex
  2011 (1)
MMRF for Proteome Annotation Applied to Human Protein Disease Prediction. García-Jiménez, B.; Ledezma, A.; and Sanchis, A. In Frasconi, P.; and Lisi, F., editor(s), Proceedings of the 20th International Conference on Inductive Logic Programming, ILP 2010. Revised Papers., volume 6489, of Lecture Notes in Computer Science, pages 67-75, 6 2011. Springer Berlin Heidelberg
MMRF for Proteome Annotation Applied to Human Protein Disease Prediction [link]Website   bibtex
  2010 (2)
Inference of Functional Relations in Predicted Protein Networks with a Machine Learning Approach. García-Jiménez, B.; Juan, D.; Ezkurdia, I.; Andrés-León, E.; and Valencia, A. PLoS ONE, 5(4): e9969. 1 2010.
Inference of Functional Relations in Predicted Protein Networks with a Machine Learning Approach [link]Website   bibtex   abstract
S.cerevisiae Complex Function Prediction with Modular Multi-Relational Framework. García-Jiménez, B.; Ledezma Espino, A.; and Sanchis de Miguel, A. In Trends in Applied Intelligent Systems: Proceedings of the 23rd International Conference on Industrial, Engineering & Other Applications of Applied Intelligent Systems (IEA-AIE 10), volume 6098, of Lecture Notes in Artificial Intelligence, pages 82-91, 6 2010. Springer
S.cerevisiae Complex Function Prediction with Modular Multi-Relational Framework [link]Website   bibtex   abstract
  2009 (2)
EcID. A Database for the Inference of Functional Interactions in E. coli. León, E., A.; Ezkurdia, I.; García-Jiménez, B.; Valencia, A.; and Juan, D. Nucleic acids research, 37(suppl 1): 629-635. 2009.
EcID. A Database for the Inference of Functional Interactions in E. coli [link]Website   bibtex   abstract
Modular Multi-Relational Framework for Gene Group Function Prediction. García-Jiménez, B.; Ledezma, A.; and Sanchis, A. In ILP '09: 19th International Conference on Inductive Logic Programming, 7 2009. Springer
Modular Multi-Relational Framework for Gene Group Function Prediction. [pdf]Website   bibtex   abstract
  2008 (2)
Protein-protein functional association prediction using genetic programming. García-Jiménez, B.; Aler, R.; Ledezma, A.; and Sanchis, A. In Proceedings of the 10th annual conference on Genetic and Evolutionary Computation - GECCO '08, pages 347-348, 7 2008. ACM Press
Protein-protein functional association prediction using genetic programming [link]Website   bibtex
Genetic Programming for Predicting Protein Networks. García-Jiménez, B.; Aler, R.; Ledezma, A.; and Sanchis, A. In Geffner, H., editor(s), Proceedings of the 11th Ibero-American Conference on Artificial Intelligence (IBERAMIA'08), volume 5290, of Lecture Notes in Artificial Intelligence. Advances in Artificial Intelligence, pages 432-441, 10 2008. Springer
Genetic Programming for Predicting Protein Networks [link]Website   bibtex
  2003 (1)
Studying the Capacity of Grammatical Encoding to Generate FNN Architectures. Gutiérrez, G.; García-Jiménez, B.; Molina, J., M.; and Sanchis, A. In Mira, J.; and Álvarez, J., R., editor(s), Computational Methods in Neural Modeling Proceedings of the 7th Work-Conference on Artificial and Natural Neuronal Networks (IWANN 2003), of Lecture Notes in Computer Science, pages 478-485, 6 2003. Springer
Studying the Capacity of Grammatical Encoding to Generate FNN Architectures [link]Website   bibtex