Pre-prints submitted

  1. C. H. Bernabé, N. Queralt-Rosinach, V. Souza, L. Santos, A. Jacobsen, B. Mons, M. Roos, “The use of Foundational Ontologies in Bioinformatics”, Research Square, 2022. [DOI]

Peer-reviewed journal articles

  1. N. Matentzoglu, J. P. Balhoff, S. M. Bello et al., “A Simple Standard for Sharing Ontological Mappings (SSSOM)”, Database, Volume 2022, baac035, 2022. [arXiv][DOI]
  2. J.O.B. Jacobsen, M. Baudis, G. S. Baynam et al. “The GA4GH Phenopacket schema defines a computable representation of clinical data”, Nat Biotechnol 40, 817–820, 2022. [medrXiv][DOI]
  3. M. Mayers, R. Tu, D. Steinecke, T. S. Li, N. Queralt-Rosinach, A. I. Su, “Design and application of a knowledge network for automatic prioritization of drug mechanisms”, Bioinformatics, 38, 10, 2880–2891, 2022. [DOI]
  4. N Queralt-Rosinach, R. Kaliyaperumal, C. H. Bernabé, Q. Long, S. A. Joosten, H. J. van der Wijk, E. L. A. Flikkenschild, K. Burger, A. Jacobsen, B. Mons, M. Roos, BEAT-COVID Group, COVID-19 LUMC Group, “Applying the FAIR principles to data in a hospital: challenges and opportunities in a pandemic”, J Biomed Semant 13, 12, 2022. [medrXiv][DOI]
  5. R. Kaliyaperumal, M. Wilkinson, P. Alarcón Moreno et al., “Semantic modelling of Common Data Elements for Rare Disease registries, and a prototype workflow for their deployment over registry data”, J Biomed Semant 13, 9, 2022. [medrXiv][DOI]
  6. A. Yamaguchi and N. Queralt-Rosinach, “A proof-of-concept study of extracting patient histories for rare/intractable diseases from social media”, Genomics & Informatics, 2020. [Genomics & Informatics][DOI]
  7. A. Waagmeester, G. Stupp, S. Burgstaller-Muehlbacher, B. M. Good, M. Griffith, O. Griffith, K. Hanspers, H. Hermjakob, K. Hybiske, S. M. Keating, M. Manske, M. Mayers, E. Mitraka, A. R. Pico, T. Putman, A. Riutta, N. Queralt-Rosinach, L. M. Schriml, D. Slenter, G. Tsueng, R. Tu, E. Willighagen, C. Wu, A. I. Su, “Wikidata as a FAIR knowledge graph for the life sciences”, eLife, 2020. [bioRxiv][eLife]
  8. N. Queralt-Rosinach, G. S. Stupp, T. S. Li, M. Mayers, M. E. Hoatlin, M. Might, B. M. Good, A. I. Su, “Structured Reviews for Data and Knowledge Driven Research”,  Database, 2020. [bioRxiv][Database]
  9. R. A. Vos, T. Katayama, H. Mishima, S. Kawano, S. Kawashima, J.-D. Kim, Y. Moriya, T. Tokimatsu, A. Yamaguchi, Y. Yamamoto, H. Wu, P. Amstutz, E. Antezana, N. Aoki, K. Arakawa, J. Bolleman, E. Bolton, R. J. P. Bonnal, H. Bono, K. Burger, H. Chiba, K. Cohen, E. Deutsch, J. Fernández-Breis, G. Fu, T. Fujisawa, A. Fukushima, A. García, N. Goto, T. Groza, C. Hercus, R. Hoehndorf, K. Itaya, N. Juty, T. Kawashima, J.-H. Kim, A. Kinjo, M. Kotera, K. Kozaki, S. Kumagai, T. Kushida, T. Lütteke, M. Matsubara, J. Miyamoto, A. Mohsen, H. Mori, Y. Naito, T. Nakazato, J. Nguyen-Xuan, K. Nishida, N. Nishida, H. Nishide, S. Ogishima, T. Ohta, S. Okuda, B. Paten, J.-L. Perret, P. Prathipati, P. Prins, N. Queralt-Rosinach, D. Shinmachi, S. Suzuki, T. Tabata, T. Takatsuki, K. Taylor, M. Thompson, I. Uchiyama, B. Vieira, C.-H. Wei, M. Wilkinson, I. Yamada, R. Yamanaka, K. Yoshitake, A. C. Yoshizawa, M. Dumontier, K. Kosaki, T. Takagi, “BioHackathon 2015: Recent developments pertaining to Linked Open Data for the Life Sciences”, F1000Research, 2020.
  10. M. D. Mayers, T. S. Li, N. Queralt-Rosinach, A. I. Su, “Time-resolved evaluation of compound repositioning predictions on a text-mined knowledge network“, BMC Bioinformatics, 2019. [bioRxiv][BMC Bioinformatics][DOI]
  11. J. L. Oliveira, P. Sernadela, L. González-Castro, C. Carta, E. v. d. Horst, P. Lopes, R. Kaliyaperumal, R. Thompson, N. Queralt-Rosinach, E. Lopez, L. Wood, C. Lamanna, M. Gilling, M. Orth, R. Martinez, M. Posada, D. Taruscio, P. Robinson, M. Roos, and A. Robertson, “Linked Registries: connecting rare diseases patient registries through a semantic web layer”, BioMed Research International, 2017. [BMRI][DOI]
  12. R. Hoehndorf and N. Queralt-Rosinach, “Data Science and Symbolic AI: Synergies, challenges and opportunities”, Data Science, 2017. [DataScience][DOI]
  13. M. Alshahrani, M. A. Khan, O. Maddouri, A. R. Kinjo, N. Queralt-Rosinach, R. Hoehndorf, “Neuro-symbolic representation learning on biological knowledge graphs”, Bioinformatics, 2017. [Bioinformatics][DOI]
  14. J. Piñero, À. Bravo, N. Queralt-Rosinach, A. Gutiérrez-Sacristán, J. Deu-Pons, E. Centeno, J. García-García, F. Sanz, L. I. Furlong, “DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants”, NAR, 2017. [NAR][DOI]
  15. T. Kuhn, C. Chichester, M. Krauthammer, N. Queralt-Rosinach, R. Verborgh, G. Giannakopoulos, A-C. N. Ngomo, R. Viglianti, M. Dumontier, “Decentralized Provenance-Aware Publishing with Nanopublications”, PeerJ CompSci, 2016. [PeerJ CompSci][DOI]
  16. D. Digles, B. Zdrazil, J.-M. Neefs, H. Van Vlijmen, C. Herhaus, A. Caracoti, J. Brea, B. Roibás, M. Loza, N. Queralt-Rosinach, L. I. Furlong, A. Gaulton, L. Bartek, S. Senger, C. Chichester, O. Engkvist, C. Evelo, G. F. Ecker and E. Jacoby, “Open PHACTS Computational Protocols for in silico Target Validation of Cellular Phenotypic Screens: Knowing the Knowns”, MedChemCommun, 2016. [HTML][PubMed][DOI]
  17. N. Queralt-Rosinach, J. Piñero, À. Bravo, F. Sanz, and L. I. Furlong, “DisGeNET-RDF: Harnessing the Innovative Power of the Semantic Web  to Explore the Genetic Basis of Diseases”, Bioinformatics, 2016. [HTML][PubMed][DOI]
  18. N. Queralt-Rosinach, T. Kuhn, C. Chichester, M. Dumontier, F. Sanz, and L.I. Furlong, “Publishing DisGeNET as Nanopublications”, Semantic Web, 2016. [HTML][IOSPress][DOI]
  19. J. Piñero, N. Queralt-Rosinach, À. Bravo, J. Deu-Pons, A. Bauer-Mehren, M. Baron, F. Sanz, and L.I. Furlong, “DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes”, Database (Oxford), 2015. [HTML][pdf]
  20. À. Bravo, J. Piñero, N. Queralt-Rosinach, M. Rautschka, and L.I. Furlong, “Extraction of relations between genes and diseases from text and large-scale data analysis: implications for translational research”, BMC Bioinformatics, 2015. [HTML][DOI]
  21. À. Bravo, M. Cases, N. Queralt-Rosinach, F. Sanz, and L.I. Furlong, “A Knowledge-Driven Approach to Extract Disease-Related Biomarkers from the Literature”, BioMed Research International, 2014. [HTML][pdf]
  22. M. Dumontier et al., “The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery”, Journal of Biomedical Semantics, 2014. [HTML][pdf]
  23. N. Queralt-Rosinach and J. Mestres, “A canonical cation-π interaction stabilizes the agonist conformation of estrogen-like nuclear receptors”, European Biophysics Journal, 2010. [HTML]
  24. I. Negodaev, N. Queralt-Rosinach, R. Caballol, and C. de Graaf, “Theoretical study of the magnetic exchange interaction in catena-μ-Tris[oxalato(2-)-O1,O2;O3,O4]-dicopper complex with interlocked helical chains”, Chemical Physics, 379, 109-115, 2011. [pdf]
  25. N. Queralt, D. Taratiel, C. de Graaf, R. Caballol, R. Cimiraglia, and C. Angeli, “On the applicability of multireference second-order perturbation theory to study weak magnetic coupling in molecular complexes”, Journal of Computational Chemistry, 29, 994-1003, 2008. [pdf]
  26. N. Queralt, C. de Graaf, J. Cabrero, and R. Caballol, “Ferrimagnetic coupling in oxamido-bridged Mn(II)Cu(II) compounds: a combined CASPT2 and DDCI study”, Molecular Physics, 101, 2095-2102, 2003. [pdf]
Conference presentations
  1. N. Queralt-Rosinach, P. N. Schofield, M. Roos, R. Hoehndorf, “Updating the CEMO ontology for future epidemiological challenges”, SWAT4HCLS 2023, 2023. [abstract][poster]
  2. K. Cremers, M. Roos, K. Wolstencroft, E. Mina, N. Queralt-Rosinach, “Structured review on Huntington’s disease iron hypothesis”, SWAT4HCLS 2023, 2023. [abstract][poster]
  3. P. Perdomo-Quinteiro, S. Siminiuc, E. Sakellariou, M. Roos, P. Spitali, N. Queralt-Rosinach, “FAIRification and semantic modelling for Duchenne and Becker Muscular Dystrophy rare diseases”, SWAT4HCLS 2023, 2023. [abstract][poster]
  4. P. Perdomo-Quinteiro, K. Wolstencroft, M. Roos, N. Queralt-Rosinach, “Knowledge graphs and Explainable AI for Drug Repurposing on Rare Diseases”, ICBO 2022 Role of Ontologies in Biomedical AI workshop, 2022. [abstract][talk]
  5. N. Queralt-Rosinach, R. Kaliyaperumal, V. Emonet, M. Wilkinson, M. Hanauer, M. Roos, “Rare disease specific FAIR Maturity Indicators”, ECCB 2022, 2022. [abstract][talk]
  6. N. Benis, R. de Groot, P. Alarcón, R. Kaliyaperumal, M. Roos, R. Cornet, N. Queralt-Rosinach, “EJP RD meets OHDSI: enabling interoperability for rare disease research”, ISMB 2022 Bio-Ontologies COSI, 2022. [abstract][talk]
  7. R. de Groot, N. Benis, P. Alarcón, R. Kaliyaperumal, M. Roos, R. Cornet, N. Queralt-Rosinach, “OMOP CDM for European rare disease registrires”, 2022 OHDSI European Symposium, 2022. [abstract][poster]
  8. R. Kaliyaperumal, G. Singh, N. Queralt-Rosinach, J. Bayjanov, P. B. T. Hoen, M. Roos, “Phenopackets for the Semantic Web”, SWAT4HCLS 2022, 2022. [short paper][talk]
  9. C. H. Bernabé, N. Queralt-Rosinach, V. E. Silva Souza, L. O. Bonino da Silva Santos, A. Jacobsen, B. Mons, M. Roos, “The use of Foundational Ontologies in Bioinformatics”, SWAT4HCLS 2022, 2022. [research paper][talk]
  10. N. Queralt-Rosinach, C. H. Bernabé, Q. Long, R. Kaliyaperumal, M. Roos, “LUMC Clinical Ontology for Biomedical Research”, ICBO 2021, 2021. [abstract][talk]
  11. N. Queralt-Rosinach, M. Wilkinson, R. Kaliyaperumal, C. H. Bernabé,Q. Long, M. Dumontier, P. N. Schofield, M. Roos, “Reuse of Design Pattern Measurements for Health Data”, FOIS 2021 – Demonstrations, 2021. [abstract][IOS Press site][demonstration]
  12. C. H. Bernabé, A. Jacobsen, N. Queralt-Rosinach, L. O. Bonino da Silva Santos, V. E. Silva Souza, B. Mons, M. Roos, “Goal-models to support communication, planning and guiding of FAIRification”, ISMB/ECCB 2021 Bio-ontologies COSI, 2021. [abstract][poster]
  13. N. Queralt-Rosinach, P. N. Schofield, R. Hoehndorf, C. Weiland, E. Schultes, C. H. Bernabé, M. Roos, “COVID-19 epidemiology and monitoring ontology”, ISMB/ECCB 2021 Bio-ontologies COSI, 2021. [abstract][talk][poster]
  14. C. H. Bernabé, A. Jacobsen, N. Queralt-Rosinach, L. O. Bonino da Silva Santos, V. E. Silva Souza, B. Mons, M. Roos, “Goal-models to support communication, planning and guiding of FAIRification”, BioSB 2021, 2021. [abstract][talk]
  15. R. Kaliyaperumal, N. Queralt-Rosinach, K. Burger, L. O. Bonino da Silva Santos, M. Hanauer, M. Roos, “Enabling FAIR discovery of Rare Disease digital resources”, dHealth Conference, 2021. [abstract][talk]
  16. N. Queralt-Rosinach, R. Kaliyaperumal, C. Bernabé, Q. Long, H. J. van der Wijk, B. Mons, M. Roos, “FAIR Data Management to Access Patient Data”, ISWC2020 DaMaLOS workshop, 2020. [abstract][slides][talk]
  17. N. Queralt-Rosinach, S. M. Bello, R. Hoehndorf, C. Weiland, P. Rocca-Serra, P. N. Schofield, “Modeling quantitative traits for COVID-19 case reports”, ISMB2020 Bio-Ontologies COSI, 2020. [abstract][medRxiv][talk][poster]
  18. T. Kuhn, A. Meroño-Peñuela, A. Malic, J. H. Poelen, A. H. Hurlbert, E. Centeno Ortiz, L. I. Furlong, N. Queralt-Rosinach, C. Chichester, J. M. Banda, E. Willighagen, F. Ehrhart, C. Evelo, T. B. Malas, and M. Dumontier, “Nanopublications: A Growing Resource of Heterogeneous Provenance-Centric Linked Data”, eScience 2018, 2018. [arXiv][talk]
  19. T. Kuhn, E. Willighagen, C. Evelo, N. Queralt-Rosinach, E. Centeno, L. I. Furlong, “Reliable Granular References to Changing Linked Data”, ISWC2017, 2017. [preprint][talk]
  20. A. Waagmeester, E. Willighagen, N. Queralt-Rosinach, E. Mitraka, S. Burgstaller-Muehlbacher, T. E. Putman, J. Turner, L. M. Schriml, P. Pavlidis, A. I. Su, B. M. Good, “Linking Wikidata to the rest of the Semantic Web”, SWAT4LS 2016 proceedings, 2016. [pdf][talk]
  21. G. Fu, E. Bolton, N. Queralt-Rosinach, L. I. Furlong, V. Nguyen, A. Sheth, O. Bodenreider, and M. Dumontier, “Exposing Provenance Metadata Using Different RDF Models”, SWAT4LS 2015 proceedings, 2015. [arXiv][talk]
  22. N. Queralt-Rosinach and L.I. Furlong, “DisGeNET RDF: A Gene-Disease Association Linked Open Data Resource”, SWAT4LS 2013, 2013. [pdf][poster]
  23. N. Queralt-Rosinach and L.I. Furlong, “DisGeNET: from MySQL to Nanopublication, Modelling Gene-Disease Associations for the Semantic Web”, SWAT4LS 2012, 2012. [pdf][poster]
  1. DisGeNET: a discovery platform for translational bioinformatics, Semantic Web Applications and Tools for Life Sciences International Conference (SWAT4LS), December 2015
  2. DisGeNET: a discovery platform for translational bioinformatics, Swiss Institute of Bioinformatics, Bioinformatics course, November 2015
BioHackrXiv papers
  1. N. Queralt-Rosinach, P. Alarcón Moreno, T. Callahan, et al., “Mapping OHDSI OMOP Common Data Model and GA4GH Phenopackets for COVID-19 disease epidemics and analytics”, BioHackathon-Europe 2021, 2021. [BioHackrXiv]
  2. N. Queralt-Rosinach, P. N. Schofield, R. Hoehndorf, C. Weiland, E. Schultes, C. H. Bernabé, M. Roos, “The COVID-19 epidemiology and monitoring ontology”, BioHackathon-Europe 2020, 2020. [BioHackrXiv]
  1. V. Nguyen, O. Bodenreider, K. Thirunarayan, G. Fu, E. Bolton, N. Queralt-Rosinach, L. I. Furlong, Michel Dumontier, and Amit Sheth, “On Reasoning with RDF Statements about Statements using Singleton Property Triples”, 2015. [arXiv]

PhD Thesis