Illueca-Fernández E, Jara Valera A, Fernández-Breis JT. Improving Air Quality Zoning through Deep Learning and Hyperlocal Measurements. IEEE Access vol. 12, pp. 38700-38716 (IF 2022:3.9)
Illueca-Fernández E, Fernández-Breis JT, Jara Valera A. Embedded machine learning of IoT streams to promote early detection of unsafe environments. Internet of Things Volume 25, April 2024, 101128 (IF 2022: 5.9)
Illueca-Fernández E, Cuevas-Martínez I, Fernández-Breis JT, Jara Valera A. Design and Evaluation of a Dryer System for IoT Hyperlocal Particulate Matter Monitoring Device, IEEE Sensors 24(7): 11152-11165 (IF 2022: 4.3)
Redondo-Aniorte FJ, Abad-Navarro F, Fernández-Breis JT. Analysis of the impact of orthogonality in the readability of the OBO Foundry ontologies. WorldCIST 2024
Cuenca-Guardiola J, de la Morena-Barrio B, Navarro-Manzano E, Stevens J, Ouwehand WH, Gleadall NS, Corral J, Fernández-Breis JT,
Detection and annotation of transposable element insertions and deletions on the human genome using nanopore sequencing, iScience 26(11):108214 (IF 2022:5.8)
Abad-Navarro F., Martínez-Costa M, Fernández-Breis JT. HURON: A quantitative framework for assessing human readability in ontologies, IEEE Access 11: 101833 - 101851 (IF 2022:3.9)
Illueca-Fernández E, Fernández-Llatas C, Jara-Valera AJ, Fernández-Breis JT, Seoane F. Sequence-Oriented Sensitive Analysis for PM2.5 exposure and risk assessment using Interactive Process Mining, PLoS ONE 18(8): e0290372(IF 2022:3.7)
Cuenca-Guardiola J, de la Morena-Barrio B, García JL, Sanchis-Juan A, Corral J, Fernández-Breis JT , Improvement of large copy number variant detection by whole genome nanopore sequencing, Journal of Advanced Research Volume 50, August 2023, Pages 145-158 (IF 2022: 10.7)
Miñarro-Giménez JA, Fernández-Llatas C, Martínez-Salvador B, Martínez-Costa C, Marcos M, Fernández-Breis JT, Ontology Model for Supporting Process Mining on Healthcare-Related Data, International Conference on Artificial Intelligence in Medicine (AIME), 352-356
Alcantud R, Weiss J, Terry MI, Bernabé N, Verdú-Navarro F, Fernández-Breis JT, Egea-Cortines M. Flower transcriptional response to long term hot and cold environments in Antirrhinum majus" Frontiers in Plant Science 14, 1120183(IF 2022: 5.6)
Castell-Díaz J, Abad-Navarro J, de la Morena-Barrio ME, Corral J , Fernández-Breis JT, "Using Machine Learning for Predicting the Effect of Mutations in the Initiation Codon," in IEEE Journal of Biomedical and Health Informatics, 2022, 26(11):5750-5756 (IF 2022: 7.7)
van Damme P, Fernández-Breis JT, Benis N, Miñarro-Gimenez JA, de Keizer NF, Cornet R. Performance assessment of ontology matching systems for FAIR data. Journal of Biomedical Semantics 13:19(IF 2022:1.9)
Mulero-Hernández J, Fernández-Breis JT. Analysis of the landscape of human enhancer sequences in biological databases, Computational and Structural Biotechnology Journal, Volume 20,2022,Pages 2728-2744 (IF 2022: 6.0)
Fuensanta Navarro-Lafuente, Evdochia Adoamnei, Julián J. Arense-Gonzalo, María T. Prieto-Sánchez, María L. Sánchez-Ferrer, Antonio Parrado, Mariana F. Fernández, Beatriz Suarez, Antonia López-Acosta, Antonio Sánchez-Guillamón, Luis García-Marcos, Eva Morales, Jaime Mendiola, Alberto M. Torres-Cantero, M.E. Candel-Torralba, L. Garcia-Marcos, M.J. Gimenez-Banon, A. Martinez-Torres, E. Morales, V. Perez-Fernandez, M. Sanchez-Solis, A. Nieto, M.T. Prieto-Sanchez, M. Sanchez-Ferrer, L. Fernanez-Palacios, V.P. Gomez-Gomez, C. Martinez-Gracia, P. Peso-Echarri, G. Ros-Berruezo, M. Santaella-Pacual, A. Gazquez, E. Larque, M.T. Pastor-Fajardo, M. Sanchez-Campillo, A. Serrano-Munuera, M. Zornoza-Moreno, P. Jimenez-Guerrero, E. Adoamnei, J.J. Arense-Gonzalo, J. Mendiola, F. Navarro-Lafuente, A.M. Torres-Cantero, C. Salvador-Garcia, M. Segovia-Hernández, G. Yagüe-Guirao, P.L. Valero-Guillén, F.V. Aviles-Plaza, J. Cabezas-Herrera, A. Martinez-Lopez, M. Martinez-Villanueva, J.A. Noguera-Velasco, A. Franco-Garcia, A.M. Garcia-Serna, T. Hernandez-Caselles, E. Martin-Orozco, M. Norte-Muñoz, M. Canovas, E. Cantero-Cano, T. de Diego, J.M. Pastor, R.A. Sola-Martínez, A. Esteban-Gil, J.T. Fernández-Breis, M.V. Alcántara, S. Hernández, C. López-Soler. Maternal urinary concentrations of bisphenol a during pregnancy are associated with global Dna methylation in cord blood of newborns in the “Nela” birth cohort, Science of the Total Environment (IF 2022: 9.8)
Bernabé-Díaz JA, Franco M, Vivo JM, Quesada-Martínez M, Fernández-Breis JT. An automated process for supporting decisions in clustering-based data analysis. Computer Methods and Programs in Biomedicine 219, June 2022, 106765 (IF 2022: 6.1)]]
Kuiper M, Bonello J, Fernández-Breis JT, Bucher P, Futschik ME, Gaudet P, Kulakovskiy IV, Licata L, Logie C, Lovering RC, Makeev VJ, Orchard S, Panni S, Perfetto L, Sant D, Schulz S, Vercruysse S, Zerbino DR, Lægreid A, The GRECO Consortium. The Gene Regulation Knowledge Commons,The Action Area of GREEKC. Biochimica et Biophysica Acta - Gene Regulatory Mechanisms 1865, Issue 1, January 2022, 194768 (IF 2022: 4.7)
García-Serna AM, Martín-Orozco E, Jiménez-Guerrero P, Hernández-Caselles T, Pérez-Fernández V, Cantero-Cano E, Muñoz-García M, Molina-Ruano MD, Rojo-Atenza E, García-Marcos L, Morales E; NELA Study Group. Cytokine profiles in cord blood in relation to prenatal traffic-related air pollution: The NELA cohort.
Pediatric Allergy and Immunology 2022 Feb;33(2):e13732 (listed as member of the NELA Study Group) (IF 2022: 4.4)
Almagro-Hernández, G.; Vivo, J.-M.; Franco, M.; Fernández-Breis, J.T. Analysing the Protein-DNA Binding Sites in Arabidopsis thaliana from ChIP-seq Experiments. Mathematics 2021, 9, 3239 (IF 2021:2.592)
Juanes Cortés B, Vera-Ramos JA, Lovering R, Gaudet P, Laegreid A, Logie C, Schulz S, Roldán-García MM, Kuiper M, Fernández-Breis JT. Formalization of gene regulation knowledge using ontologies and Gene Ontology Causal Activity Models. Biochimica et Biophysica Acta - Gene Regulatory Mechanisms Volume 1864, Issues 11–12, November–December 2021, 194766 (IF 2021: 6.304)
Castell Díaz J, Abad-Navarro F, Fernández-Breis JT, de la Morena Barrio ME, Corral de la Calle J. Using Machine Learning for the prediction of mutations in the initiation codon. II workshop IA-Biomed.
Maldonado JA, Marcos M, Fernández-Breis JT, Giménez-Solano VM, Legaz-García MC, Martínez-Salvador B. A platform for the design and execution of clinical data transformation and reasoning workflows. II workshop IA-Biomed.
Abad-Navarro F, Martínez-Costa C, Fernández-Breis, JT. Semankey: a semantics-driven approach for querying RDF repositories using keywords, IEEE Access (2021) 9:91282-91302 (IF 2021:3.476)
Linard, B., Ebersberger, I., Mcglynn, S., Glover, N., Mochizuki, T., Patricio, M., ... & Uchiyama, I. (2021). Ten years of collaborative progress in the Quest for Orthologs. Molecular biology and evolution 2021 Jul 29;38(8):3033-3045 (IF 2021: 8.800) (listed as member of the QfO)
García-Serna, Azahara M., et al. "Air pollution from traffic during pregnancy impairs newborn's cord blood immune cells: The NELA cohort." Environmental Research (2021): 198:110468 (IF 2021: 8.431 (listed as member of the NELA group)
Sola-Martínez, R. A., Lozano-Terol, G., Gallego-Jara, J., Morales, E., Cantero-Cano, E., Sanchez-Solis, M., García-Marcos L., Jiménez-Guerrero P., Noguera-Velasco J.A., Cánovas Díaz M., de Diego Puente T., and the NELA study group (2021). Exhaled volatilome analysis as a useful tool to discriminate asthma with other coexisting atopic diseases in women of childbearing age. Scientific Reports, 11(1), 1-17 (IF 2021: 4.996 (listed as member of the NELA group)
Franco M, Vivo JM, Quesada-Martínez M, Duque-Ramos A, Fernández-Breis JT. Evaluation of ontology structural metrics based on public repository data, Briefings in Bioinformatics 21(2):473-485 (impact factor 2020: 11,622)
Abad-Navarro F, Quesada-Martínez M, Duque-Ramos A, Fernández-Breis JT. Analysis of readability and structural accuracy in SNOMED CT. BMC Medical Informatics and Decision Making (2020) 20:284(IF 2020: 2.796)
Bernabé-Díaz JA, Franco-Nicolás M, Vivo-Molina JM, Quesada-Martínez M, Duque-Ramos A, Fernández-Breis JT. An automated process for the repository-based analysis of ontology structural metrics, IEEE Access 8: 148722-148743 (IF 2020:3.367)
Maldonado JA, Marcos M, Fernández-Breis JT, Giménez-Solano VM, Legaz-García MC, Martínez-Salvador B. CLIN-IK-LINKS: A platform for the design and execution of clinical data transformation and reasoning workflows, Computer Methods and Programs in Biomedicine 197: 105616 (IF 2020: 5.428)
Almagro-Hernández G., Fernández-Breis J.T. (2020) Discovering the Most Characteristic Motif from a Set of Peak Sequences. In: Rojas I., Valenzuela O., Rojas F., Herrera L., Ortuño F. (eds) Bioinformatics and Biomedical Engineering. IWBBIO 2020. Lecture Notes in Computer Science, vol 12108. Springer, Cham
Abad-Navarro, F.; Bernabé-Diaz, J.A.; García-Castro, A.; Fernandez-Breis, J.T. Semantic Publication of Agricultural Scientific Literature Using Property Graphs. Appl. Sci. 2020, 10, 861. (IF 2020:2,679)
Vos RA, Katayama T, Mishima H et al. BioHackathon 2015: Semantics of data for life sciences and reproducible research. F1000Research 2020, 9:136
Esteban-Gil A, Pérez-Sanz F, García-Solano J, Alburquerque-González B, Parreño-González M, Legaz-García MC, Fernandez-Breis JT, Rodríguez-Braun E, Pimentel P, Mäkinen M, Tuomisto A, Slaby O, Conesa-Zamora P, ColPortal, an integrative multiomic platform for analysing epigenetic interactions in colorectal cancer, Scientific Data 6, 255(impact factor 2019: 5,541)
Gómez-Gil E, Franco A, Madrid M, Vázquez-Marín B, Gacto G, Fernández-Breis JT, Vicente-Soler J, Soto T, Cansado J. Quorum sensing and stress-activated MAPK signaling repress yeast to hypha transition in the fission yeast Schizosaccharomyces japonicus. PLOS Genetics 15(5):
e1008192 (impact factor 2019: 5,174)
Katayama T, Kawashima S, Micklem G et al. BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services . F1000Research 2019, 8:1677
Bernabé-Díaz JA, Legaz-García MC, García JM, Fernández-Breis JT Efficient, semantics-rich transformation and integration of large datasets, Expert Systems with Applications 133(1):198-214(impact factor 2019: 5,452)
Martinez Soriano I, Castro Peña JL, Fernández-Breis JT, San Roman I, Alonso Barriuso A, Guevara Baraza D.Snomed2Vec: representation of SNOMED CT terms using Word2Vec, CMBS 2019
Vera-Ramos JA, Juanes-Cortés B, Fernández-Breis JT, Gaudet P, Kuiper M, Lægreid A, Logie C, Roldán García MM, Schulz S, An Example of Multimodal Biological Knowledge Representation, ODLS 2019 – Ontologies and Data in Life Sciences
Noussair L, Fernández-Breis JT, Zahir J, Mousannif H,Towards distributed learning in Internet of things. Air Quality monitoring use case, Workshop on Data Science for Social Good in Africa (DSSGA), MEDI 2019
De la Morena-Barrio B, De la Morena-Barrio ME, EMartinez, Sanchis-Juan A, Garcia-Hernandez JL, Padilla J, Abad-Navarro F, Minano A, Bernabe-Diaz JA, Bravo C, Esteban-Gil A, Fernandez-Breis JT, Velasco F, Rodriguez-Alen A, Ouwenhand WH, Vidal F, Hernandez-Rivas JM, Vicente V, Corral J, 2019, October. Repetitive sequences in genomics and its role in the dean-tithrombin deficiency. HAEMATOLOGICA (Vol. 104, pp. 103-104).
B De la Morena-Barrio, E Martinez, J Padilla, F Abad-Navarro, JL Garcia-Hernandez, ME De la Morena-Barrio, JA Bernabe-Diaz, A Esteban-Gil, F Perez, A Minano, C Bravo, F Vidal, JT Fernandez-Breis, JM Hernandez-Rivas, V Vicente. Sequencing for nanopores for the identification of structural variants: strengths and weaknesses. HAEMATOLOGICA (Vol. 104, pp. 74-75)
de la Morena-Barrio B, Martínez E, Padilla J, Abad-Navarro F, García-Hernández JL, de la Morena-Barrio ME, Bernabé-Díaz JA; Esteban-Gil A, Pérez F, Miñano A; Bravo C, Vidal F , Fernández-Breis JT, Hernández-Rivas JM, Vicente V, Corral J.(2019) Secuenciación por nanoporos para la identificación de variantes estructurales: fortalezas y debilidades, presented at LXI Congreso Nacional de la Sociedad Española de Hematología y Hemoterapia (SEHH) y XXXV Congreso Nacional de la Sociedad Española de Trombosis y Hemostasia (SETH), Valencia, 2019.
de la Morena-Barrio B, de la Morena-Barrio ME, Martínez E, Sanchís-Juan A, García-Hernández JL, Padilla J; Abad-Navarro F, Miñano A, Bernabé-Díaz JA, Bravo C,Esteban-Gil A, Fernández-Breis JT, Velasco F, Rodríguez-Alen A, Ouwenhand WH,Vidal F, Hernández-Rivas JM ,Vicente V, Corral J. Secuencias repetitivas en el genoma y su papel en la deficiencia de antitrombina, presented at Congreso Nacional de la Sociedad Española de Hematología y Hemoterapia (SEHH) y XXXV Congreso Nacional de la Sociedad Española de Trombosis y Hemostasia (SETH), Valencia, 2019.
López-Cascales MT, Fernández-Breis JT, Marín F. Genoarchitecture of the mouse brain according to genome-wide expression data. 8th National Meeting of the Spanish Society of Neuroscience
Quesada-Martínez M, Marcos M, Abad-Navarro F, Martínez-Salvador B, Fernández-Breis JT, Towards the semantic enrichment of Computer Interpretable Guidelines: a method for the identification of relevant ontological terms, AMIA 2018
Fernández-Breis JT, Menárguez-Tortosa R, Martínez-Costa C, Miñarro-Giménez JA, Legaz-García MC, Quesada-Martínez MC, Duque-Ramos A, Esteban-Gil A, Castellanos-Nieves D. Tecnologías para el Modelado, Procesamiento y Gestión de Conocimiento, IA-Biomed, CAEPIA 2018
Ayllón-Benítez A, Mougin F, Quesada-Martínez M, Fernández-Breis JT, Bourqui R, Thébault P, Deciphering functional annotation of multiple gene sets with MOTVIS, JOBIM 2018
Abad-Navarro F, Fernández-Breis JT. Getting answers from semantic repositories: a keywords-based approach, Procesamiento de Lenguaje Natural 61:39-46
van Damme P, Quesada-Martínez M, Cornet R, Fernández-Breis JT. From Lexical Regularities to Axiomatic Patterns for the Quality Assurance of Biomedical Terminologies and Ontologies, Journal of Biomedical Informatics 84:59-74 (IF 2018:2,950)
Abad-Navarro F, De la Morena Bario ME, Fernández-Breis JT, Corral de la Calle J. Lost In Translation: Bioinformatic analysis of variations affecting the translation initiation codon in the Human Genome, Bioinformatics 34(22):3788-3794 (IF 2018: 4,531)
Bernabé-Díaz JA, Legaz-García MC, García JM, Fernández-Breis JT. Application of High Performance Computing Techniques to the Semantic Data Transformation, Trends and Advances in Information Systems and Technologies (745):691-700
Forslund K, Pereira C, Capella-Gutierrez S, Sousa da Silva A, Altenhoff A, Huerta-Cepas J, Muffato M, Patricio M, Vandepoele K, Ebersberger I, Blake J, Fernández-Breis JT, the Quest for Orthologs Consortium, Boeckmann B, Gabaldón T, Sonnhammer E, Dessimoz C, and Lewis S, Gearing up to handle the mosaic nature of life, Bioinformatics, Volume 34, Issue 2, 15 January 2018, Pages 323–329 (IF 2018: 4,531)
Bernabé-Díaz JA, Legaz-García MC, García JM, Fernández-Breis JT. Optimizing Semantic Data Transformation using High Performance Computing Techniques, SWAT4LS
Farias T, Chiba H, Fernández-Breis JT, Leveraging logical rules for efficacious representation of large orthology datasets,SWAT4LS
Esteban-Gil A, Fernández-Breis JT, Boeker M, Analysis and visualization of disease courses in a semantically-enabled cancer registry, Journal of Biomedical Semantics 8:46(impact factor 2016:1,845)
Quesada-Martínez M, Castellanos-Nieves D., Fernández-Breis JT. OntoEnrich: Una plataforma para el análisis léxico de ontologías orientado a su enriquecimiento axiomático, Procesamiento de Lenguaje Natural 59:171-174
Fernández-Breis, JT. La Historia Clínica Electrónica en el Learning Health System. Revista Española de Informática de la Salud 124:7-13
Ayllon-Benitez A, Thébault P, Fernández-Breis JT, Quesada-Martínez M, Mougin F, Bourqui R. Deciphering gene sets annotations with Ontology based visualization, IV2017: 19th International Conference Information Visualisation
Quesada-Martínez M, Fernández-Breis JT. Studying the reuse of content in biomedical ontologies: An axiom-based approach. AIME 2017, Lecture Notes in Computer Science 10259:3-13
Almagro-Hernández G, Fernández-Breis JT. Angel: A multi-level approach for the analysis of variants in individual genomes. Congreso Nacional de Biotecnología 2017
Quesada-Martínez M, Duque-Ramos A, Iniesta-Moreno M, Fernández-Breis JT, Preliminary analysis of the OBO Foundry ontologies and their evolution using OQuaRE, Studies in Health Technology and Informatics 235: 426 - 430
Legaz-García MC, Dentler K, Fernández-Breis JT, Cornet R, Combining archetypes, ontologies and formalization enables automated computation of quality indicators, Studies in Health Technology and Informatics 235: 416 - 420
Fernández-Breis JT, Quesada-Martínez M, Duque-Ramos A, Can existing biomedical ontologies be more useful for EHR and CDS? Lecture Notes in Computer Science 10096:3-20
Esteban-Gil A, Fernández-Breis JT .Case Report Form based on semantic Web technologies. SWAT4LS 2016, Amsterdam
Maldonado JA, Marcos M, Fernández-Breis JT, Parcero E, Boscá D, Legaz-García MC, Martínez-Salvador B, Robles M, A platform for exploration into chaining of web services for clinical data transformation and reasoning, AMIA Annual Symposium 2016
Astrid Duque-Ramos, Manuel Quesada-Martinez, Miguela Iniesta-Moreno, Jesualdo Tomas Fernandez-Breis, Robert Stevens, Supporting the analysis of ontology evolution processes through the combination of static and dynamic scaling functions in OQuaRE, Journal of Biomedical Semantics 7:63 (impact factor 2016:1,845)
Quesada-Martínez M, Fernández-Breis JT, Karlsson, D. Suggesting missing relations in biomedical ontologies based on lexical regularities, HEC 2016/MIE 2016, Studies in Health Technology and Informatics 228:384-388
Miñarro-Giménez JA, Quesada Martínez M, Fernández-Breis JT, Schulz S.Publishing biomedical predication repository about MeSH co-occurrences in MEDLINE,HEC 2016/MIE 2016, Studies in Health Technology and Informatics 228:765-769
Fernandez-Breis JT, Chiba H, Legaz-García MC, Uchiyama I, The Orthology Ontology: development and applications, Journal of Biomedical Semantics 2016, 7:34 (impact factor 2016:1,845)
Legaz-García MC, Miñarro-Giménez JA, Menárguez-Tortosa M., Fernández-Breis JT. Generation of Open Biomedical Datasets through Ontology-Driven Transformation and Integration Processes, Journal of Biomedical Semantics 2016,7:32(impact factor 2016:1,845)
Legaz-García MC, Martínez-Costa C, Menárguez-Tortosa M., Fernández-Breis JT. A Semantic Web based Framework for the Interoperability and Exploitation of Clinical Models and EHR Data, Knowledge-based Systems 105 (2016):175-189 (impact factor 2016:4,529)
Quesada-Martínez M, Fernández-Breis JT, Stevens R, Aussenac-Gilles N, Karlsson D. The OntoEnrich platform: using workflows for quality assurance and axiomatic enrichment of ontologies, UK Ontology Network Meeting 2016
Almagro-Hernández G, García-Sánchez F, de la Morena ME, Corral J, Fernández-Breis JT, Angel: Towards a multilevel method for the analysis of variants in individual genomes. IWBBIO 2016, Lecture Notes in Computer Science 9656:47-58
Jesualdo Tomás Fernández-Breis, María Del Carmen Legaz-García, Hirokazu Chiba and Ikuo Uchiyama, Towards the semantic standardization of orthology content, SWAT4LS
Angel Esteban-Gil, Jesualdo Tomás Fernandez-Breis and Clara Miranda-Lopez, Performance evaluation of human resources in a hospital, SWAT4LS, poster
Angel Esteban-Gil and Jesualdo Tomas Fernandez-Breis, Semantically-enhanced Electronic Case Report Forms, International Semantic Web Conference, Industry Track
Manuel Quesada-Martínez, Eleni Mikroyannidi, Jesualdo Tomás Fernández-Breis, Robert Stevens. Approaching the axiomatic enrichment of the Gene Ontology from a lexical perspective. Artificial Intelligence in Medicine 65 (2015), pp. 35-48 (impact factor 2015:2,142)
Manuel Quesada-Martínez, Astrid Duque-Ramos and Jesualdo Tomás Fernández-Breis, Analysis of the evolution of ontologies using OQuaRE: application to EDAM, ICBO 2015
Legaz-García, MC, Menárguez-Tortosa, M., Fernández-Breis, J.T., Chute, C., Tao, C. Transformation of Standardized Clinical Models based on OWL technologies: from CEM to OpenEHR archetypes, Journal of the American Medical Informatics Association (JAMIA) 22 (3): 536-544(impact factor 2015: 3,428)
Mari Carmen Legaz-García, José Antonio Miñarro-Giménez, Marcos Menárguez-Tortosa, Jesualdo Tomás Fernández-Breis, Lessons learned in the generation of biomedical research datasets using Semantic Open Data technologies, Medical Informatics Europe 2015, Studies in Health Technology and Informatics 2010:165-169
Manuel Quesada-Martínez, Jesualdo Tomás Fernández-Breis and Robert Stevens, Lexical Characterisation of Bio-ontologies by the Inspection of Regularities in Labels, Current Bioinformatics 10(2):165-176(impact factor 2015:0,770)
Manuel Quesada-Martínez, Jesualdo Tomás Fernández-Breis, Robert Stevens, Nathalie Aussenac-Gilles. OntoEnrich: A Platform for the Lexical Analysis of Ontologies, Knowledge Engineering and Knowledge Management, Lecture Notes in Computer Science Volume 8982, 2015, pp 172-176
Manuel Quesada-Martínez, Jesualdo Tomás Fernández-Breis, Robert Stevens, Eleni Mikroyannidi. Prioritising lexical patterns for further axiomatisation by inspecting their localisation and modularity in biomedical ontologies. Methods of Information in Medicine 54 1: 56-64, (impact factor 2014: 2,248)
Erik Sonnhammer,Toni Gabaldón, Alan Wilter Sousa da Silva,Maria Martin,Marc Robinson-Rechavi,Brigitte Boeckmann,Paul Thomas,Christophe Dessimoz, and
the Quest for Orthologs consortium (Jesualdo Tomás Fernández-Breis) Big Data and Other Challenges in the Quest for Orthologs, Bioinformatics (2014) 30(21):2993-2998, (impact factor 2014:4,981)
Angel Esteban-Gil, Jesualdo Tomas Fernandez-Breis and Martin Boeker. Analysis and visualization of disease courses in a semantic enabled cancer registry, SWAT4LS 2014, Berlin, Germany
Eleni Mikroyannidi, Manuel Quesada-Martínez, Dmitry Tsarkov, Jesualdo Tomás Fernández-Breis, Robert Stevens, Ignazio Palmisano, A Quality Assurance Workflow for Ontologies based on Semantic Regularities,
Knowledge Engineering and Knowledge Management, Lecture Notes in Computer Science Volume 8876, 2014, pp 288-303
Astrid Duque-Ramos, Martin Boeker, Ludger Jansen, Stefan Schulz, Miguela Iniesta, Jesualdo Tomás Fernández-Breis, Evaluating the Good Ontology Design guideline (GoodOD) with the Ontology Quality Requirements and Evaluation method and metrics (OQuaRE). PLOS One 9(8), e104463 (impact factor 2014:3.234)
Legaz-García M.C, Martínez-Costa C., Miñarro-Giménez JA,Fernández-Breis, J.T., Schulz, S. Menárguez-Tortosa, M. Ontology patterns-based transformation of clinical information, Studies in Health Technology and Informatics
205 (MIE 2014): e-Health – For Continuity of Care:1018-1022
Martínez-Costa C., Legaz-García M.C., Schulz S., Fernández-Breis, J.T. Ontology-based Infrastructure for a Meaningful EHR Representation and Use, EEE-EMBS International Conferences on Biomedical and Health Informatics (BHI)
Martínez-Costa C., Menárguez-Tortosa, M., Fernández-Breis, J.T. Interoperability of EHR Systems Based on Semantic Representation and Transformation Models. In Sicilia and Serrano (eds). Interoperability in Healthcare Information Systems: Standards, Management, and Technology, pp 59-81
Mikel Egaña Aranguren, Jesualdo Tomás Fernández-Breis, Michel Dumontier, Special issue on Linked Data for Health Care and the Life Sciences, Editorial, Semantic Web Journal 5(2);99-100
José Antonio Miñarro-Giménez, Mikel Egaña Aranguren, Boris Villazón Terrazas, Jesualdo Tomás Fernández-Breis, Translational research combining orthologous genes and human diseases with the OGOLOD dataset, Semantic Web journal 5(2);145-149
Jesualdo Tomás Fernández-Breis, José Alberto Maldonado, Mar Marcos, María del Carmen Legaz-García, David Moner, Joaquín Torres-Sospedra, Angel Esteban-Gil, Begoña Martínez-Salvador, Montserrat Robles. Leveraging Electronic Healthcare Record Standards and Semantic Web Technologies for the Identification of Patient Cohorts. Journal of the American Medical Informatics Association (JAMIA)(2013) 20:e288-e296 (impact factor 2013: 3,932)
Alejandro Rodríguez González, Miguel Angel Mayer; Jesualdo Tomas Fernandez Breis, Guest Editorial Special Section on Biomedical Information through the Implementation of Social Media Environments, Journal of Biomedical Informatics 46 (2013), pp. 955-956 (impact factor 2013: 2,482)
Catalina Martínez-Costa, Diego Bosca, Mari Carmen Legaz-García, Cui Tao,
Jesualdo Tomás Fernández Breis, Stefan Schulz, Christopher G. Chute, Isosemantic rendering of clinical information using formal ontologies and RDF, Medinfo 2013
Manuel Quesada-Martínez, Jesualdo Tomás Fernández-Breis and Robert Stevens, Lexical Analysis and Characterization of the OBOFoundry Ontologies, Bio-ontologies 2013 (link to Bio-ontologies SIG 2013 papers)
María del Mar Sánchez Vera, María Paz Prendes Espinosa, Jesualdo Tomás Fernández Breis. Tecnologías semánticas para la evaluación en red: análisis de una experiencia con la herramienta OeLE. Revista de Investigación Educativa 31(2):464-482
Manuel Quesada-Martínez, Jesualdo Tomás Fernández-Breis, Robert Stevens, Lexical characterization and analysis of the BioPortal ontologies, AIME 2013, Lecture Notes in Computer Science Volume 7885, 2013, pp 206-215
Marcos Menárguez-Tortosa, Jesualdo Tomás Fernández Breis. OWL-based Reasoning Methods for Validating Archetypes. Journal of Biomedical Informatics 46 (2013) pp. 304-317(impact factor 2013: 2,482)
Mari Carmen Legaz-García, Cui Tao, Marcos Menárguez-Tortosa, Jesualdo Tomás Fernández-Breis, Christopher G. Chute.An Approach for the Mapping of CEM and OpenEHR Archetypes. AMIA CRI 2013, poster
Manuel Quesada-Martínez, Jesualdo Tomás Fernández-Breis, and Robert Stevens. Analysis and classification of bio-ontologies by the structure of their labels. International Work-Conference on Bioinformatics and Biomedical Engineering 2013, pp 713-720. Copicentro Granada S.L.
Edgar Alan Calvillo Moreno, Alejandro Padilla, Jaime Muñoz Arteaga, Julio Ponce, Jesualdo Tomás Fernández Breis, Searching Research Papers Using Clustering and Text Mining, CONIELECOMP 2013
Astrid Duque Ramos, Jesualdo Tomás Fernández-Breis, Miguela Iniesta, Michel Dumontier, Mikel Egaña Aranguren, Stefan Schulz, Nathalie Aussenac-Gilles, Robert Stevens.Evaluation of the OQuaRE framework for ontology quality, Expert Systems with Applications 40 (2013) pp. 2696-2703(impact factor 2013:1,965)
María del Mar Sánchez Vera, Mari Paz Prendes Espinosa, Jesualdo Tomás Fernández Breis, José Luis Serrano Sánchez. Practical experiences for the development of educational semantic web systems. Journal of New Approaches in Educational Research 2(1):23-31
Mikel Egaña Aranguren, Jesualdo Tomás Fernández-Breis, Erick Antezana, Chris Mungall, Alejandro Rodríguez González, Mark D Wilkinson. OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows, Journal of Biomedical Semantics 2013, 4:2
Chunguo Wu, Gaoyang Li, Xiaozhou Wu, Xiaosong Han, Binghong Wang, Jesualdo Tomás Fernández Breis, Fei Wang, and Yanchun Liang. An Hidden Markov Model-Based Transcription Factor Mining Method. Journal of Bionanoscience 7:66-71
Jesualdo Tomás Fernández-Breis, Francisco Frutos-Morales, Angel Esteban Gil, Dagoberto Castellanos-Nieves, Rafael Valencia-García, Francisco García-Sánchez, and María del Mar Sánchez-Vera. Recommendation of personalized learning contents supported by semantic web technologies, Communications in Computer and Information Science series 278, pp. 540–545. Springer, Heidelberg
Angel Esteban-Gil, Francisco García-Sanchez, Rafael Valencia-García, Jesualdo Tomás Fernández-Breis. A Social-Empowered Platform for Gathering Semantic Information Communications in Computer and Information Science series 278, pp. 534–539. Springer, Heidelberg
María del Carmen Legaz-García,José Antonio Miñarro-Giménez, Marisa Madrid, Marcos Menárguez-Tortosa, Santiago Torres Martínez, Jesualdo Tomás Fernández-Breis. Linking Genome Annotation Projects with Genetic Disorders using Ontologies, Journal of Medical Systems Volume 36 Supplement 1:11-23 (impact factor 2012:1,783)
Manuel Quesada-Martínez, Jesualdo Tomás Fernández-Breis and Robert Stevens. Extraction and analysis of the structure of labels in biomedical ontologies, Second International Workshop on Managing Interoperability and compleXity in Health Systems MIX-HS’12
Manuel Quesada-Martínez, Jesualdo Tomás Fernández-Breis and Robert Stevens, Enrichment of OWL Ontologies: a method for defining axioms from labels, K-MED 2012 - International Workshop on Capturing and Refining Knowledge in the Medical Domain
Chunguo Wu, Xiaozhou Wu, Xiaosong Han, Binghong Wang, Jesualdo Tomás Fernández Breis, Fei Wang, Yanchun Liang.An HMM-Based Transcription Factor Mining Method, Poster, Joint Workshops on IWSIS2012 & IWMWC2012, Taiyuan, China.
Sánchez Vera M, Fernández Breis JT (editors). Web semántica. Aplicaciones prácticas para la educación , Dykinson, ISBN: 978-84-9031-001-4
Marcos Menárguez-Tortosa, Catalina Martínez-Costa, Jesualdo Tomás Fernández-Breis, A Generative tool for building health applications driven by ISO 13606 archetypes, Journal of Medical Systems 36:3063–3075(impact factor 2012:1,783)
José Alberto Maldonado, Catalina Martínez-Costa, David Moner, Marcos Menárguez-Tortosa, Diego Boscá, Jose Antonio Miñarro-Giménez, Jesualdo Tomás Fernández-Breis, Montserrat Robles-Viejo. Using the ResearchEHR platform to facilitate the practical application of the EHR standards, Journal of Biomedical Informatics 45:746-762, Special Issue on Standards in Practice (impact factor 2012:2,131)
María del Carmen Legaz García, Catalina Martínez-Costa, Marcos Menárguez-Tortosa, Jesualdo Tomás Fernandez-Breis. Recommendation of Standardized Health Learning Contents using Archetypes and Semantic Web Technologies, MIE 2012, Studies in Health Technology and Informatics 180:963-967
Jose Antonio Miñarro-Giménez, Mikel Egaña-Aranguren, Boris Villazón-Terrazas and Jesualdo Tomás Fernández-Breis. Publishing Orthology and Diseases Information in the Linked Open Data cloud. Current Bioinformatics 7(3):255-266 (impact factor 2012:2,017)
Rafael Valencia-García, Francisco García-Sánchez, Cristina Casado-Lumbreras, Dagoberto Castellanos-Nieves, Jesualdo Tomás Fernández-Breis. Informal learning through expertise mining in the social web, Behaviour and Information Technology 31,8:757-766 (impact factor 2012:0,856)
María del Carmen Legaz-García, Catalina Martínez-Costa, Marcos Menárguez-Tortosa, Jesualdo Tomás Fernández-Breis. Exploitation of ontologies for the management of clinical archetypes in ArchMS, ICBO 2012
Jose Antonio Miñarro Giménez, Mikel Egaña Aranguren, Jesualdo Tomás Fernández-Breis and Erick Antezana. NCBO-Galaxy: bridging the BioPortal web services and the Galaxy platform, Software demo, ICBO 2012
María del Mar Sánchez-Vera, Jesualdo Tomás Fernández-Breis, Dagoberto Castellanos-Nieves, Francisco Frutos-Morales, María Paz Prendes-Espinosa.Semantic Web Technologies for Generating Feedback in Online Assessment Environments. Knowledge-Based Systems 33 152–165 (impact factor 2012:4,104)
Angel Esteban-Gil, Francisco Garcia-Sanchez, Rafael Valencia-Garcia, Jesualdo T. Fernandez-Breis. SocialBROKER: A collaborative social space for gathering semantically-enhanced financial information, Expert Systems with Applications 39(12) 9715-22 (impact factor 2012:1,854)
Jesualdo Tomás Fernández-Breis, Dagoberto Castellanos-Nieves, José Hernández-Franco, Celia Soler-Segovia, María del Carmen Robles-Redondo, Rodrigo González-Martínez, María Paz Prendes-Espinosa, A semantic platform for the management of the educative curriculum, Expert Systems with Applications 39 (2012) 6011–6019(impact factor 2012:2,203)
Astrid Duque-Ramos, Jesualdo Tomás Fernández-Breis, Robert Stevens, Nathalie Aussenac-Gilles. OQuaRE: a SQuaRE-based approach for evaluating the quality of ontologies, Journal of Research and Practice in Information Technology, vol 43 No 2:159-173 (impact factor 2010:0,205)
M.M. Sánchez Vera, M.P. Prendes Espinosa, J.T. Fernández-Breis. Diseño y desarrollo de exámenes a partir de herramientas de web semántica. @tic. revista d'innovació educativa, 7(2011):1-11
Mikel Egaña Aranguren, Jesualdo Tomás Fernández Breis, Erick Antezana. OPPL-Galaxy: Enhancing ontology exploitation in Galaxy with OPPL,4th International SWAT4LS Workshop, London, UK.
José Antonio Miñarro-Giménez, Mikel Egaña-Aranguren, Rodrigo Martínez-Béjar, Jesualdo Tomás Fernández-Breis, Marisa Madrid. Semantic integration of information about orthologs and diseases: The OGO system. Journal of Biomedical Informatics 44 (2011) 1020–1031 (impact factor 2011:1,792)
María del Carmen Legaz-García, Catalina Martínez-Costa, Marcos Menárguez-Tortosa, Jesualdo Tomás Fernández-Breis, Towards semantic platforms for archetype management: ArchMS, OpenHealth 2011, Barcelona, Spain.
José Antonio Miñarro-Giménez, Jesualdo Tomás Fernández-Breis, Ontology-driven Method for Integrating Biomedical Repositories, AI Health 2011, CAEPIA 2011, Lecture Notes in Computer Science 7023:473-482
C.Martínez-Costa, M. Menárguez-Tortosa, J.T. Fernández-Breis. Clinical Data Interoperability based on Archetype Transformation. Journal of Biomedical Informatics 44(2011):869-880(impact factor 2011:1,792)
Eduardo J. Cepas, Ginés D. Guerrero, José M. Cecilia, José M. García y J.T. Fernández-Breis, Estrategias de Paralelización de Algoritmos de Razonamiento para Ontologías Biomédicas, XXII Jornadas de Paralelismo
Jose Antonio Miñarro-Giménez, Teddy Miranda-Mena, Rodrigo Martínez Béjar, and Jesualdo Tomás Fernández-Breis. Exploitation of Translational Bioinformatics for Decision-Making on Cancer Treatments. Christian Böhm, Sami Khuri, Lenka Lhotská, Nadia Pisanti (Eds.): Information Technology in Bio- and Medical Informatics - Second International Conference, ITBAM 2011, Toulouse, France, August 29 - September 2, 2011Lecture Notes in Computer Science 6865:1-15
Eduardo Lupiani-Ruiz, Ignacio García-Manotas, Rafael Valencia García, Francisco García-Sánchez, Dagoberto Castellanos-Nieves, Jesualdo Tomás Fernández Breis, Juan Bosco Camón Herrero. Financial News Semantic Search Engine, Expert Systems with Applications 38:15565–15572(impact factor 2011:2,203)
M. Menárguez-Tortosa, J.T. Fernández Breis. Validation of the openEHR Archetype Library by using OWL Reasoning, Medical Informatics Europe 2011., Studies in Health Technology and Informatics 169:789-793
Jesualdo Tomás Fernández Breis. Enrichment of biomedical ontologiesl: challenges and opportunities. SATBI 2011, keynote.
Maria del Carmen Legaz Garcia, Jose Antonio Miñarro Giménez, Marisa Madrid, Santiago Torres Martinez and Jesualdo Tomás Fernández-Breis. Using Ontologies for Supporting Genomic Sequence Annotation Project. SATBI 2011
J.T. Fernández-Breis, M.Madrid, J.A. Miñarro-Giménez, M.C. Legaz-García, M. Egaña Aranguren, R. Stevens. Exploitation of Semantic Gene Ontology Annotations for Schizosaccharomyces Pombe. 6th International Fission Yeast Meeting. Poster.
J.M. Ruiz-Martínez, R. Valencia-García, J. T. Fernández-Breis, F. García-Sánchez and R. Martínez-Béjar. Ontology learning from biomedical natural language documents using UMLS, Expert Systems with Applications 38(10):12365-12378 (impact factor 2011:2,203)
D. Castellanos Nieves, J. T. Fernández-Breis, R. Valencia-García, R. Martínez-Béjar, M. Iniesta. Semantic Web Technologies for Supporting Learning Assessment, Information Sciences 181(9):1517-1537 (impact factor 2011:2,833).
R. Valencia-García, F. García-Sánchez, D. Castellanos-Nieves, J.T. Fernández-Breis. OWLPath: an OWL ontology-guided query editor, IEEE Transactions on Systems, Man, Cybernetics: Part A 41(1):121-136 (impact factor 2011:2,123)
R. Valencia-García, F. García-Sánchez, D. Castellanos-Nieves, J.T. Fernández-Breis and A. Toval. Exploitation of Social Semantic Technology for Software Development Team Configuration, IET Software, Special Issue on Social Semantic Web Support for Software Development, December 2010 -- Volume 4, Issue 6, p.373–385 (impact factor 2010:0,671)
J.T. Fernandez-Breis, L. Iannone, I. Palmisano, A. Rector, R. Stevens. Enriching the Gene Ontology via the Dissection of Labels using the Ontology Pre-Processor Language. EKAW 2010, Lecture Notes in Computer Science 6317, 59-73 **BEST RESEARCH PAPER AWARD**
M. Menárguez-Tortosa, C. Martínez-Costa, J.T. Fernández-Breis. Validating Archetypes using OWL Reasoning. II OpenHealth Spain Symposium, Fuenlabrada, Madrid, Spain.
C. Martínez-Costa, M. Menárguez-Tortosa, P. D. López López, M. M. Rubio González, J. T. Fernández-Breis. ArchForms: Automatic generation of applications based on ISO 13606 archetypes. II OpenHealth Spain Symposium, Fuenlabrada, Madrid, Spain.
M.M Sánchez-Vera, M.P. Prendes-Espinosa, J.T. Fernández-Breis. Una aplicación de Web Semántica para la evaluación en línea de aprendizajes de los alumnos. EDUTEC 2010
A. Duque Ramos, U. López, J.T. Fernández-Breis and R. Stevens. Towards a SQuaRE based Quality Evaluation Framework for Ontologies, Workshop on Ontology Quality, EKAW 2010
M. Menárguez-Tortosa, J.T. Fernandez-Breis. OWL-based Reasoning Methods for Validating Archetyped Clinical Knowledge, EKAW 2010, Poster, Lisbon, Portugal, CEUR WS Proceedings vol 674:21
J.A. Miñarro-Giménez, M. Egaña Aranguren, F. García-Sánchez, J. T. Fernández-Breis. A Semantic Query Interface for the OGO Platform. ITBAM 2010, Lecture Notes in Computer Science 6266:128-142
C. Martínez-Costa, J.A. Miñarro-Giménez, M. Menárguez-Tortosa, R. Valencia-García, J. T. Fernández-Breis. Flexible Semantic Querying of Clinical Archetypes. KES 2010, Part I, Lecture Notes in Artificial Intelligence 6276:597-606
C.Martínez-Costa, M. Menárguez-Tortosa, J.T. Fernández-Breis. An Approach for the Semantic Interoperability of ISO 13606 and OpenEHR archetypes. Journal of Biomedical Informatics 43:736-746 (impact factor 2010:1,719)
I. García-Manotas, R. Valencia-García, J.T. Fernández-Breis, F. García-Sánchez, D. Castellanos-Nieves. Retrieval and Integration of Audiovisual Contents for TV using Semantic Web Technologies. ICNIT 2010
M. Robles, J.T. Fernández-Breis, J.A. Maldonado, D. Moner, C. Martínez-Costa, D. Bosca, M. Menárguez-Tortosa. ResearchEHR: Use of semantic web technologies and archetypes for the description of EHRs. EFMI STC 2010, Studies in Health Technology and Informatics vol 155:129-135
J.A. Maldonado, D. Moner, D. Boscá, L. Marco, J.T. Fernández-Breis,E. Reig, M. Robles. LinkEHR-Ed: A Tool for the Description and Normalization of Legacy Clinical Data. EFMI STC 2010, Poster
Mikel Egaña Aranguren, Robert Stevens, Erick Antezana, Jesualdo Tomás Fernández-Breis, Martin Kuiper, Vladimir Mironov. Technologies and best practices for building bio-ontologies. In Marco Ramoni and Gil Alterovitz (Eds), Knowledge-based Bioinformatics: From Analysis to Interpretation, 68-86. ISBN: 978-0-470-74831-2
Torralba-Rodríguez F.J., Bixquert-Montagud V., Fernández-Breis J.T., Martínez-Béjar R. An incremental knowledge acquisition-based system for supporting decisions in biomedical domains. Computer Methods and Programs in Biomedicine, 98:161-171 (impact factor 2010:1,238)
M. Sánchez-Vera, F. Frutos- Morales, M, D. Castellanos-Nieves, C. Cruz, M.P. Prendes-Espinosa, J.T. Fernández-Breis. Generation of useful semantic feedback for students and teachers. CSEDU 2010
Rico, M., Garcia-Sanchez, F., Gomez,J.M., Valencia-Garcia, R. and Fernandez-Breis, J.T. Enabling Intelligent Service Discovery with GGODO, Journal of Information Science and Engineering, vol 6(4):1 (impact factor 2010:0,265)
Martinez-Costa, C., Menarguez Tortosa, M., Maldonado, J.A., Fernandez Breis, J.T.. Semantic Web technologies for managing EHR-related clinical knowledge. Semantic Web,201-219 ISBN 978-953-7619-33-6.
Miranda-Mena, T., Martínez-Costa, D., Moner, D., Menárguez-Tortosa, M., Maldonado, J.A., Robles-Viejo, M., Fernández-Breis, J.T. MIURAS 2: Motor de integración universal para aplicaciones sanitarias avanzadas, Inforsalud 2010, Madrid, Spain.
Martínez-Costa, C., Menárguez-Tortosa, M., Fernández-Breis, J.T. ARCHFORMS: Generación automática de aplicaciones ISO 13606. Inforsalud 2010, Madrid, Spain.
Frutos-Morales, F., Sánchez-Vera, M.M., Castellanos-Nieves, D., Esteban-Gil,A., Cruz-Corona, C. Prendes-Espinosa, M.P., Fernández-
Breis, J.T. An extension of the OeLE platform for generating semantic feedback for students and teachers.Procedia - Social and Behavioral Sciences, Volume 2, Issue 2, 2010, Pages 527-531
Castellanos-Nieves, D., González-Martínez, G., Soler-Segovia, C., Robles M.C., Hernández-Franco, J., Prendes-Espinosa, M.P., Fernández-Breis, J.T. Semantic Web-based system for managing the educative curriculum. Procedia - Social and Behavioral Sciences, Volume 2, Issue 2, 2010, Pages 521-526
Torralba-Rodríguez F.J., Fernández-Breis J.T., Martínez-Béjar R., Bixquert-Montagud V. An incremental knowledge acquisition-based system for critical domains. Expert Systems with Applications 37 (2010), pp. 2838-2847 (impact factor 2010:1,924)
Miñarro-Gimenez, J.A., Madrid, M., Fernández-Breis, J.T. Semantic integration and exploitation of orthology information and genetic disorders. Proceedings of 2nd Workshop Semantic Web Applications and Tools for Life Sciences, Amsterdam, Netherlands, November 20.
Miñarro-Gimenez, J.A., Madrid, M., Fernández-Breis, J.T. OGO: an ontological approach for integrating knowledge about orthology. BMC Bioinformatics vol 10:S10:S13(impact factor 2009: 3,43)
Martínez-Costa, C., Menárguez-Tortosa,M., Fernández-Breis, J.T. Towards UNE-EN 13606 and OpenEHR Archetype-based semantic interoperability. XXII International Conference of the European Federation for Medical Informatics, Studies in Health Technology and Informatics, volume 150:260-264
Fernández-Breis, J.T., Egaña Aranguren, M., Stevens, R. Quality evaluation framework for bio-ontologies. International Conference on Biomedical Ontology, 127-130
Lasheras, J., Valencia-García, R., Fernández-Breis, J.T., Toval, A., Modelling Reusable Security Requirements based on an Ontology Framework, Journal of Research and Practice in Information Technology 41(2):119-133 (impact factor 2009: 0,500)
Maldonado, JA, Moner, D, Bosca, D., Fernández-Breis, J.T., Angulo, C., Robles, M. LinkEHR-Ed: A multi-reference model archetype editor based on formal semantics. International Journal of Medical Informatics,78(8), pp. 559-570 (impact factor 2009: 3,126)
Martínez-Costa, C., Menárguez-Tortosa, M., Fernández Breis, J.T. Ontology-based archetype interoperability and management. First Spanish OpenHealth Symposium, Alcalá de Henares, Spain.
Ruiz-Martínez, J.M., Castellanos-Nieves, D., Valencia-Garcia, R., Fernández-Breis,J.T., Garcia-Sanchez, F., Vivancos-Vicente, P.J., Castejón-Garrido, J.S., Bosco Camón, J. and Martínez-Béjar, R. Accessing Touristic Knowledge Bases through a Natural Language Interface, Lecture Notes on Artificial Intelligence 5465:147-160
Sánchez-Peral, I., García-Sánchez, F., Valencia-García, R., Fernández-Breis, J.T., and Martínez-Béjar, R. Towards Adaptable Semantic Grid Services Execution Environments. Fifth International Conference on Networking and Services.
Garcia-Sanchez, F., Vidoni,R., Martínez-Béjar, R., Gasparetto, A., Valencia-Garcia,R., Fernández-Breis, J.T. Bridging the gap between the logical and the physical worlds. 7th International Conference on Practical Applications of Agents and Multi-Agent Systems, Salamanca, Spain
Martínez-Costa, C., Menárguez-Tortosa, M., Valencia-García, R., Maldonado,J.A.,Fernández Breis, J.T. Transformación automática de arquetipos UNE-EN 13606 y openEHR para facilitar la interoperabilidad semántica. Inforsalud 2009, 16-18 Marzo, Madrid.
Eduardo Lupiani, Rafael Valencia-García, Dagoberto Castellanos-Nieves, Francisco García-Sánchez, and Jesualdo Tomás Fernández-Breis (2009) Semantic Technologies-based Financial News Search Engine. EUROCAST 2009
Ignacio García-Manotas, Rafael Valencia-García, Francisco García-Sánchez,Dagoberto Castellanos-Nieves, and Jesualdo Tomás Fernández-Breis (2009) Ontology Population from Semi-structured Financial Texts. EUROCAST 2009
Juan Luis Chirlaque, Rafael Valencia-García, Francisco García-Sánchez, Dagoberto Castellanos-Nieves, and Jesualdo Tomás Fernández-Breis (2009) OWL-Path: an ontology-guided natural language query editor. EUROCAST 2009
Martínez-Costa, C., Menárguez-Tortosa, M., Fernández-Breis, J.T., Maldonado, J.A. A Model-driven Approach for Representing Clinical Archetypes for Semantic Web Environments. Journal of Biomedical Informatics, 42 (2009) pp. 150-164 (impact factor 2009: 2,432)
Esteban-Gil, A., Fernandez-Breis, J.T., Castellanos-Nieves, D., Valencia-Garcia, R., Garcia-Sanchez, F. Semantic enrichment of SCORM metadata for efficient management of educative contents (2009) Procedia - Social and Behavioral Sciences, Volume 1, Issue 1, Pages 927-932
Fernández-Breis, J.T., Castellanos-Nieves, D., Valencia-García, R. Measuring Individual Learning Performance in Group Work from a Knowledge Integration perspective. Information Sciences 179 (339–354)
(impact factor 2009: 3,291)
Gladun, A., Rogushina, J.;García-Sánchez, F., Martínez-Béjar, R.,Fernández-Breis, J.T. An application of Intelligent Techniques and Semantic Web Technologies in E-Learning Environments. Expert Systems with Applications 36(2)Part 1:1922-1931 (impact factor 2009: 2,908)
García-Sánchez, F., Valencia-García, R., Martínez-Béjar, R., Fernández-Breis, J.T. An ontology, intelligent agent-based framework for the provision of semantic web services. Expert Systems with Applications 36(2)Part 2:3167–3187(impact factor 2009: 2,908)
Ruíz-Martínez J.M., Valencia-García, R., Fernández-Breis, J.T., Martínez-Bejar, R. La anotación semántica para la consulta de ontologías en lenguaje natural. En Felisa Verdejo Maíllo,Ana García Serrano (Eds) Acceso y visibilidad de información multilingüe en la red: el rol de la semántica:249-258.ISBN: 978-84-362-5609-3
Ruiz-Martínez, J.M., Castellanos-Nieves, D., Valencia-Garcia, R., Fernández-Breis,J.T., Garcia-Sanchez, F., Vivancos-Vicente, P.J., Castejón-Garrido, J.S., Bosco Camón, J. and Martínez-Béjar, R. Querying ontology-based systems in natural language in the e-Tourism domain. PKAW 2008, Hanoi, Vietnam
Ruiz Martínez, J.M., Miñarro Giménez, J.A., Guillén Cárceles, L., Valencia García, R., García Sánchez, F., Fernández Breis, J.T. and Martínez Béjar, R. Populating Ontologies in the eTourism domain, Workshop on Natural Language Processing and Ontology Engineering, IEEE/WIC/ACM International Conference on Web Intelligence and Intelligent Agent Technology, 2008, Sydney, Australia
Miñarro-Giménez, J.A., Madrid, M., Fernández-Breis, J.T. An integrated ontological knowledge base about orthologous genes and proteins,Proceedings of 1st Workshop SWAT4LS08, Edinburgh, United Kingdom, November 28, 2008, CEUR Workshop Proceedings vol 435, ISSN 1613-0073
Castellanos-Nieves, D., Fernandez-Breis, J.T., Valencia-Garcia, R., Cruz, C., Prendes-Espinosa, M.P. ,Martinez-Bejar, R. Using Semantic Web Technologies for the Assessment of Open Questions. Lecture Notes on Artificial Intelligence 5351, 42-53, PRICAI, 2008, Hanoi, Vietnam
García-Sánchez, F., Fernández-Breis, J.T., Valencia-García, R., Gómez, J.M., Martínez-Béjar, R. Combining Semantic Web Technologies with Multi-Agent Systems for Integrated Access to Biological Resources. Journal of Biomedical Informatics 41(5) 848-859(impact factor: 1,92)
Jesualdo Tomás Fernández-Breis, Marcos Menárguez-Tortosa, Catalina Martinez-Costa, Eneko Fernandez Breis, Jose Herrero, Jesús Sánchez Cuadrado, David Moner, Rafael Valencia-García, Montserrat Robles.A Semantic Web-based System for Managing Clinical Archetypes.30th Annual International Conference of the IEEE Engineering in Medicine and Biology Society:1482-1485.
José Alberto Maldonado, David Moner, Diego Bosca, Jesualdo Tomás Fernández-Breis, Carlos Angulo, Montserrat Robles. Semantic Upgrade and Normalization of Existing EHR Extracts. 30th Annual International Conference of the IEEE Engineering in Medicine and Biology Society:1466-1469.
Valencia-García,R. Fernández-Breis, J.T., Ruiz-Martínez, J.M., García-Sánchez, F. and Martínez-Béjar, R. A knowledge acquisition methodology to ontology construction for information retrieval from medical documents. Expert Systems: The Knowledge Engineering Journal 25(3):314-334 (impact factor: 0,717)
García-Sánchez, F., Martínez-Béjar, R., Valencia-García, R. Fernández-Breis, J.T. Knowledge Technologies-based Multi-Agent System for Semantic Web Services Environments. Lecture Notes on Artificial Intelligence 5097:1222-1233
Amorós-Póveda, L., Prendes-Espinosa, M.P., Fernández-Breis, J.T. (2008) Web Semántica: Aportaciones sobre evaluación. TICEMUR'2008
Lasheras, J., Valencia-García, F., Fernández-Breis, J.T., Toval, A. An Ontology-Based Framework for Modelling Security Requirements. The 6th International Workshop on Security In Information Systems (WOSIS 2008)
García-Sánchez, F., Fernández-Breis, J.T., Martínez-Béjar, R. Ontological Knowledge Capture From Databases.Problems in Programming vol 2-3:431,437
Miranda-Mena, T.G., Marco-Verdú, L., González-Olalla,J.,Fernández-Breis, J.T., Moner-Cano, D., Robles-Viejo,M.,
López-Perán, I.A., García-Martos, A. MIURAS: motor de integración universal para aplicaciones sanitarias. INFORSALUD 2008
Fernández Breis, J.T. ,Prendes-Espinosa. M.P., Castellanos-Nieves, D.,Martínez-Sánchez, F., Valencia-García, R., Ruiz-Martínez, J.M. (2007) Evaluación en e-learning basada en tecnologías de la web semántica y el procesamiento del lenguaje natural. ISBN:978-84-8425-601-4
Prendes-Espinosa, M.P., Fernández-Breis, J.T., Hernández-Franco, J., Martínez-Sánchez, F. (2007) Objetos de aprendizaje para enseñar matemáticas. X Congreso Internacional sobre inclusión digital en la educación superior. Desafios y oportunidades en la sociedad de la información, Buenos Aires, Argentina.
Fernández-Breis, J.T., Valencia-García, R., Moner,D., Maldonado, J.A., Menárguez-Tortosa, M., Vivancos-Vicente, P.J. (2007) From ADL to OWL: The POSEACLE approach. CAEPIA,Salamanca, España
Castellanos-Nieves, D., Fernández-Breis, J.T., Valencia-García, R., Martínez-Béjar, R. (2007) The OeLE Platform for Assisting the Assessment of Open Questions..SINTICE Zaragoza, España.
Fernández-Breis, J.T., Martínez-Béjar, R., Martín-Rubio, F.(2007) El Desarrollo de Memorias Corporativas. La Gestión Tecnológica del Conocimiento,228-259. ISBN 978-84-8371-661-8
Castellanos-Nieves, D., Fernández-Breis, JT, Valencia-García ,R., Martínez-Béjar, R. (2007) A Semantic Web Technologies-based System for Students Assessment in E-Learning Environments. IADIS E-Learning Conference.
Maldonado, JA, Moner,F, Tomás, D., Ángulo,C., Robles,M, Fernández-Breis, JT(2007) Framework for clinical data standardization based on archetypes.12th International Health (Medical) Informatics Congress, Medinfo.
Fernández-Breis, J.T., Menárguez-Tortosa, M., Vivancos-Vicente, PJ, Valencia-García,R., Moner, D., Maldonado, J.A. (2007) Poseacle: An Ontological Infrastructure for Managing Clinical Archetypes in Semantic Web Environments . 12th International Health (Medical) Informatics Congress, Medinfo.
Fernández-Breis, J.T., Valencia-García, R. Menárguez-Tortosa,M., Vivancos-Vicente,PJ (2007) Approaching Electronic Healthcare Records Management from a Semantic Web perspective. 4th European Semantic Web Conference. Póster
Fernández-Breis, J.T. Menarguez-Tortosa, M., Moner, D., Valencia-García, R., Maldonado, J.A., Vivancos-Vicente P.J. ,Miranda-Mena, T., Martínez-Béjar, R. (2006) An Ontological Infrastructure for the Semantic Integration of Clinical Archetypes.Lecture Notes in Computer Science: 4303:156-167.
Vivancos-Vicente, P.J. Fernández-Breis, J.T., Martínez-Béjar,R. and Valencia-García, R. (2006) Visual Knowledge Annotation and Management by Using Qualitative Spatial Information. Lecture Notes in Computer Science: 4303:1-12
Moner Cano, D.; Fernández Breis, J.T.; Maldonado Segura, J.A.; Boscá Tomás, D.; Valencia García, R.; Angulo Fernández, C.; Menárguez Tortosa, M.; Robles Viejo, M. ; Vivancos Vicente, P.J. (2006) Plataforma basada en tecnologías de la web semántica para la gestión de Historias Clínicas Electrónicas federadas estandarizadas. Póster.XI Congreso Nacional de Informática Médica (INFORMED 2006). ISBN: 690-0102-7. Páginas 241 – 244, Murcia, Noviembre 2006.
Moner,D., Maldonado,J.A., Boscá,D., Fernández-Breis, J.T., Angulo,C., Vivancos, P.J., Robles, M. (2006) Integración semántica y estandarización de datos clínicos basada en arquetipos. XXIV Congreso Anual de la Sociedad Española de Ingeniería Biomédica, Pamplona, Spain.
Vivancos-Vicente, P.J., Fernández-Breis, J.T., Martínez-Béjar, R. ,Valencia-García, R. (2006) A methodology for visual knowledge annotation and management. Pacific Rim Knowledge Acquisition Workshop, Guilin, China.
Fernández-Breis, J.T.,Vivancos-Vicente, P.J., Menarguez-Tortosa, M., Moner, D., Maldonado, J.A., Valencia-García, R., Miranda-Mena, T., Martínez-Béjar, R. (2006) Towards the semantic interoperability of EHR information systems. Pacific Rim Knowledge Acquisition Workshop,Guilin, China.
Fernández-Breis, J.T.,Vivancos-Vicente, P.J., Menarguez-Tortosa, M., Moner, D., Maldonado, J.A., Valencia-García, R., Miranda-Mena, T.(2006) Using semantic technologies to promote interoperability between electronic healthcare records' information models. 28th Anual International Conference IEEE Engineering in Medicine and Biology, New York, EEUU.
Moner, D., Maldonado, J.A., Bosca, D., Fernández-Breis, J.T., Angulo,C., Crespo, P., Vivancos-Vicente, P.J., Robles,M. (2006) Archetype-Based Semantic Integration and Standardization of Clinical Data. 28th Anual International Conference IEEE Engineering in Medicine and Biology, New York, EEUU.
Fernández-López, L.M., Fernández-Breis, J.T., Martínez-Sánchez, F., Prendes-Espinosa, M.P. (2006) Modelos de evaluación en e-learning: posibilidades de la Web Semántica y el Procesamiento del Lenguaje Natural. EDUTEC 2006
Valencia-García, R., Castellanos-Nieves, D.,Fernández-Breis, J.T., Vivancos-Vicente, P.J. (2006)A methodology for extracting ontological knowledge from Spanish documents. Lecture Notes in Computer Science 3878,71-80
Miranda-Mena, T,G. Benítez-Uzcategui, S.L., Ochoa, J.L. Martínez-Béjar, R:, Fernández-Breis, J.T., Salinas, J. (2006): A knowledge-based approach to assign breast cancer treatments in oncology units. Expert Systems with Applications 31(3):451-457. (impact factor 2006: 0,957)
García-Sánchez, F., Martínez-Béjar, R., Fernández-Breis, J.T., Contreras-Albornoz, L., Castellanos-Nieves, D. (2006) An ontology-based intelligent system for recruitment. Expert Systems with Applications 31(2):248-263 (impact factor 2006: 0,957)
Fernández-Breis, J.T.,Menárguez-Tortosa, M., Valencia-García, R.,Vivancos-Vicente, P.J. (2005) WI-ONTO: A web tool for the automatic integration of ontologies. CAEPIA'05
Fernández-Breis, J.T., Cañavate-Cañavate, D., Castellanos-Nieves, D., Valencia-García, R., Vivancos-Vicente, P. J., (2005) OeLE: Applying ontologies to support the evaluation of open questions-based test. International Workshop on Applications of Semantic Web Technologies for E-Learning, Third International Conference on Knowledge Capture, Banff, Canada
Fernández-Breis, J.T., Martínez-Béjar, R., Valencia-García, R.,Compton, P.(2005) Ontology-Driven Methodology for Knowledge Modeling in Functional Genomics. International Workshop on Genomic Signal Processing, Bucarest, Romania
Fernández-Breis, J.T. (2005) Tecnologías Semánticas para facilitar la integración de datos e interoperabilidad de sistemas de información sanitarios. Jornadas sobre Normalización e Integración de Sistemas de Información Sanitarios, Mayo, Valencia, España
Beydoun, G., Hoffmann, A., Fernández-Breis, J.T., Martínez-Béjar, R., Valencia-García, R., Aurum, A. (2005) Cooperative Modelling Evaluated. International Journal of Cooperative Information Systems, 14(1):45-71 (impact factor 2005: 1,371)
Valencia-García, R., Fernández-Breis, J.T., Cantos-Gómez, P. Martínez-Béjar, R. (2004) An Approach for Acquiring Structures Knowledge from Text TEXT TECHNOLOGY, VOL. NOVEMBER, Nº 2, 27–53
Castellanos-Nieves, D., Fernández-Breis, J.T. (2004) Using Semantic Web Technologies to Support Evaluation Processes in E-learning. AIS SIGSEMS Bulletin 1(3):61-64
Fernández-Breis, J.T., Martínez-Béjar, R. Valencia-García, R.,Vivancos-Vicente, P.J., García-Sánchez, F. (2004) Towards Cooperative Frameworks for Modeling and Integrating Biological Processes Knowledge. IEEE Transactions on NanoBioscience 3(3):164-171 (impact factor 2007: 1,899)
Vivancos Vicente, P.J., Valencia-Garcia, R. Fernandez Breis, J.T., Martinez Bejar, R. (2004) An approach for multirelational ontology modelling. Lecture Notes in Computer Science 3157:997-998 (impact factor:0,513)
Valencia-García, R., Ruiz-Sánchez, J.M., Vivancos-Vicente, P.J., Fernández-Breis, J.T., Martínez-Béjar, R. (2004) An incremental approach for discovering medical knowledge from texts. Expert Systems with Applications 26(3):291-299 (impact factor 2004: 1,247)
Valencia-García, R., Castellanos-Nieves, D., Vivancos-Vicente, P.J., Fernández-Breis, J.T., Martínez-Béjar, R., García-Sánchez, F. (2004) An approach for Ontology Building from text supported by NLP techniques. Lecture Notes in Computer Science 3040: 126-135
Fernández-Breis, J.T. (2003) Un entorno para Integrar Ontologías para el Desarrollo de Sistemas de Gestión de Conocimiento. Tesis Doctoral, Universidad de Murcia, ISBN: 84-689-5048-3.
Ruiz-Sánchez, J. M., Valencia-García, R., Fernández-Breis, J. T., Martínez-Béjar, R. and Compton, P. (2003) An approach for incremental knowledge acquisition from text Expert Systems with Applications 25(2): 77-86. (impact factor 2003: 1,067)
Torralba-Rodríguez,F.J. Fernández-Breis, J.T. Valencia-García, R., Ruíz-Sánchez, J.M., Martínez-Béjar, R., Gómez-Rubí, J.A. (2003) An Ontological Framework for Representing and Exploiting Medical Knowledge. Expert Systems with Applications 25(2): 211-230. (impact factor 2003: 1,067)
Vivancos-Vicente, P.J., Valencia-García, R., Fernández-Breis, J.T., Martínez-Béjar, R., Castellanos-Nieves, D. (2003) An ontology-based approach for evaluating e-learning courses. Second International Conference on Multimedia and Information & Communication Technologies in Education, Badajoz, Spain
Martínez-Béjar, R., Vivancos-Vicente, P.J., Fernández-Breis, J.T., Valencia-García, R., Martín-Rubio, F. (2003) An ontological user-driven approach for modelling biological processes. 4th Spanish Symposium on Bioinformatics. La Coruña, Spain
Beydoun, G., Fernández-Breis, J.T., Martínez-Béjar, R., Hoffmann, A., Valencia-García, R. (2002) Statistical Monitoring of Ontology Integration for Corporate Memory. Pacific Knowledge Acquisition Workshop, Tokyo, Japan.
Fernández-Breis, J. T., and Martínez-Béjar, R. (2002) A Cooperative Framework for Integrating Ontologies. International Journal of Human-Computer Studies, 56(6):662-717. (impact factor 2002: 0,918)
Fernández-Breis, J.T., Campoy-Gómez, L., Martínez-Béjar, R., Martín-Rubio, F. , and García-Martínez, J.J.(2002). A cooperative approach to corporate memory modelling. European Conference on Artificial Intelligence, Workshop on Knowledge Management and Organizational Memories , Lyon, France.
Fernández-Breis, J.T., Martínez-Béjar, R., and Martín-Rubio, F. (2002) A framework for collaborative construction of molecular biology ontologies. International Joint Conference on Autonomous Agents and Multi-Agent Systems, Bologna, Italy.
Fernández-Breis, J.T., Campoy-Gómez, L., Martínez-Béjar, R., and Martín-Rubio, F. (2002) Towards Knowledge Management in Intensive Care Units. I Congreso Internacional Sociedad de la Información, Las Palmas de Gran Canaria, Spain
Fernández-Breis, J.T., Campoy-Gómez, L., Martínez-Béjar, R., and Martín-Rubio, F. (2002) An Approach to Corporate Memory Modelling. I Congreso Internacional Sociedad de la Información, Las Palmas de Gran Canaria, Spain.
Fernandez-Breis, J.T., Castellanos D., Valencia-Garcia, R., Vivancos-Vicente, P.J., Martinez-Bejar, R., De las Heras-Gonzalez, M. (2001). Towards Scott domains-based topological ontology models. An application to a cancer domain. Formal Ontology in Information Systems.
Rodrigo Martínez-Béjar, Francisca Ibáñez-Cruz, Paul Compton, Jesualdo Tomás Fernández-Breis, Manuel De las Heras-González: Integrating Ripple Down Rules with Ontologies in an Oncology Domain. Lecture Notes in Computer Science 2101: 324-327 (impact factor 2001:0,415)
Fernández Breis, J.T., Valencia García R., Martínez Béjar, R., Cantos Gómez, P. (2001) A context-driven approach for knowledge acquisition: application to a leukemia domain. Lecture Notes in Computer Science. Springer-Verlag. Berlin. Vol 2116: 445-448 (impact factor 2001:0,415)
Fernández Breis, J.T., Martínez Béjar, R. (2001) An ontology-based approach for integrating molecular biology knowledge. II Jornadas de Bioinformática. Málaga
Gutiérrez-Casorrán, C., Fernández-Breis, J.T., Martínez-Béjar, R. (2001) Ontological modelling of Natural Categories: an Ant Colony. Workshop on Ontologies in Agent Systems. 5th International Conference on Autonomous Agents. Montreal (Canada)
Fernández-Breis, J. T., Padilla-Díaz, F., and Martínez-Béjar, R. (2001) An ontology-based system for monitoring patients in Intensive Care Units. CIMAF'2001. La Habana, Cuba
Fernández-Breis, J. T., and Martínez-Béjar, R. (2000) A web-based framework for integrating knowledge. Industrial Knowledge Management - A Micro Level Approach,123-138.
Sánchez-Carreño, R., Fernández-Breis, J. T., Martínez-Béjar, R., and Cantos-Gómez, P. (2000). An Ontology-based Approach to Knowledge Acquisition From Text. Cuadernos de Filología Inglesa. Vol 9(1): 191-212.
Fernández-Breis, J. T., and Martínez-Béjar, R. (2000). A cooperative tool for facilitating Knowledge Management. Expert Systems with Applications. Vol 18(4): 315-330 (impact factor 2000: 0,405)
Fernández-Breis, J.T., Paniagua-Arís, E., Martín-Rubio, F. (2000) Analysis of Multi-Agent Systems for representing human organisations (in Spanish). Simposio Español de Informática Distribuida, Orense (Spain)
Campoy-Gómez, L., Fernandez-Breis, J. T., Martínez-Béjar, R. and Martín-Rubio, F. (1999) A Prototype of Knowledge based system applied to tasks of Environmental Engineering. An approach based on gradual rules of knowledge (in Spanish). Terceras Jornadas sobre Transferencia Tecnológica de Inteligencia Artificial. Universidad de Murcia. Murcia (Spain)
Research Projects and Contracts
| Institution | Year | Weeks | Topic |
| University of Manchester (United Kingdom) | 2009 | 17 | Semantic Web and Bioinformatics |
| University of Manchester (United Kingdom) | 2008 | 9 | Semantic Web and Bioinformatics |
| University of Koblenz (Germany) | 2005 | 17 | Semantic Web and Multimedia |
| IRIT (France) | 2002 | 13 | Ontology Engineering |
| University of Aberdeen (United Kingdom) | 2001 | 13 | Ontology Engineering |
| Universidad Autónoma de Aguascalientes (México) | 2000 | 4 | Knowledge Engineering |