People - Robert Castelo

Robert Castelo
Dr. Aiguader 88
E-08003 Barcelona
telf: +34.933.160.514
fax: +34.933.160.550
robert.castelo at
Google Author Profile

1991-1994BSc Computer Science.
University of Lleida (UdL), Spain.
1994-1997MSc Computer Science.
Technical University of Catalonia (UPC), Barcelona, Spain.
1997-2002PhD Computer Science.
National Research Institute for Mathematics and Computer Science (CWI) and University of Utrecht (UU), The Netherlands.
2002-2006Lecturer and postdoc at Roderic Guigo's research group.
Pompeu Fabra University (UPF) and Centre for Genomic Regulation (CRG), Barcelona, Spain.
2006-2012Ramon y Cajal fellow.
Pompeu Fabra University (UPF), Barcelona, Spain.
2012-...Associate Professor.
Pompeu Fabra University (UPF), Barcelona, Spain.



  1. P. Puigdevall and R. Castelo. GenomicScores: seamless access to genomewide position-specific scores from R and Bioconductor. Bioinformatics, in pres, 2018. [full text].


  2. A. Roverato and R. Castelo. The networked partial correlation and its application to the analysis of genetic interactions. Journal of the Royal Statistical Society Series C -Applied Statistics, 66:647-665, 2017. [full text, preprint].


  3. L. Kannan, M. Ramos, A. Re, N. El-Hachem, Z. Safikhani, D.M.A. Gendoo, S. Davis, D. Gomez-Cabrero, R. Castelo, K.D. Hansen, V.J. Carey, M. Morgan, A.C. Culhane, B. Haibe-Kains and L. Waldron. Public data and open source tools for multi-assay genomic investigation of disease. Briefings in Bioinformatics, 17(4):603-615, 2016. [full text].
  4. D. Costa and R. Castelo. Umbilical cord gene expression reveals the molecular architecture of the fetal inflammatory response in extremely preterm newborns. Pediatric Research, 79:473-481, 2016. [full text, supplement].


  5. R. Baumstark, S. Hänzelmann, S. Tsuru, Y. Schaerli, M. Francesconi, F.M. Mancuso, R. Castelo and M. Isalan. The propagation of perturbations in rewired bacterial gene networks. Nature Communications, 6:10105, 2015. [full text]
  6. S. Hänzelmann, J. Wang, E. Güney, Y. Tang, E. Zhang, A.S. Axelsson, H. Nenonen, A.S. Salehi, C.B. Wollheim, E. Zetterberg, E. Berntorp, I.G. Costa, R. Castelo and A.H. Rosengren. Thrombin stimulates insulin secretion via protease-activated receptor-3. Islets, 7(4):e1118195, 2015. [full text]


  7. I. Tur, A. Roverato and R. Castelo. Mapping eQTL networks with mixed graphical Markov models. Genetics, 198(4):1377-1383, 2014. [abstract, preprint & comments, supplement].


  8. M. Esnaola, P. Puig, D. Gonzalez, R. Castelo and J.R. Gonzalez. A flexible count data model to fit the wide diversity of expression profiles arising from extensively replicated RNA-seq experiments. BMC Bioinformatics, 14:254, 2013. [full text, Bioconductor package].
  9. S. Hänzelmann, R. Castelo and J. Guinney. GSVA: gene set variation analysis for microarray and RNA-Seq data. BMC Bioinformatics, 14:7, 2013. [full text, Bioconductor package].


  10. I. Tur and R. Castelo. Learning high-dimensional mixed graphical models with missing values. In Proceedings of the Sixth European Workshop on Probabilistic Graphical Models (PGM 2012), A. Cano, M. Gómez-Olmedo and T.D. Nielsen, Eds., pp. 323-330, University of Granada, ISBN 978-84-15536-57-4, Granada, 2012. [PDF].
  11. A. Roverato and R. Castelo. Learning undirected graphical models from multiple datasets with the generalized non-rejection rate. International Journal of Approximate Reasoning, 53(9):1326-1335, 2012. [abstract].
  12. R. Castelo. Comments on: Sequences of regressions and their independences. Test, 21(2):253-254, 2012. [abstract].
  13. R. Castelo and A. Roverato. Inference of regulatory networks from microarray data with R and the Bioconductor package qpgraph. In Next Generation Microarray Bioinformatics, J. Wang, A.C. Tan and T. Tian, Eds., pp. 215-233, Methods in Molecular Biology Series, Humana Press, USA, ISBN 978-1-61779-399-8, 2012. [publisher, preprint, Bioconductor package].


  14. I. Tur and R. Castelo. Learning mixed graphical models from data with p larger than n. In Proceedings 27th Conference on Uncertainty in Artificial Intelligence (UAI 2011), F.G. Cozman and A. Pfeffer, Eds., pp. 689-697, AUAI Press, ISBN 978-0-9749039-7-2, Barcelona, 2011. [PDF].
  15. B. Hartmann, R. Castelo, B. Miñana, E. Peden, M. Blanchette, D.C. Rio, R. Singh and J. Valcarcel. Distinct regulatory programs establish widespread sex-specific alternative splicing in Drosophila melanogaster. RNA, 17:453-468, 2011. [abstract].


  16. A. Roverato and R. Castelo. Learning undirected graphical models from multiple datasets with the generalized non-rejection rate. In Proceedings of the Fifth European Workshop on Probabilistic Graphical Models (PGM 2010), P. Myllymäki, T. Roos and T. Jaakkola, Eds., pp. 249-256, HIIT Publications, Helsinki, 2010. [PDF].


  17. M. Toll-Riera, R. Castelo, N. Bellora and M.M. Albà. Evolution of primate orphan proteins. Biochem. Soc. Trans., 37(Pt 4):778-782, 2009. [full text]
  18. B. Hartmann, R. Castelo, M. Blanchette, S. Boue, D.C. Rio and J. Valcarcel. Global analysis of alternative splicing regulation by insulin and wingless signalling in Drosophila cells. Genome Biology, 10:R11, 2009. [full text, supplement].
  19. M. Toll-Riera, N. Bosch, N. Bellora, R. Castelo, L. Armengol, X. Estivill and M.M. Albà. Origin of primate orphan genes: a comparative genomics approach. Mol. Biol. Evol., 26(3):603-612, 2009. [abstract]
  20. R. Castelo and A. Roverato. Reverse engineering molecular regulatory networks from microarray data with qp-graphs, Journal of Computational Biology, 16(2):213-227, 2009. [preprint, supplement, Bioconductor package].


  21. R. Lyle, P. Prandini, K. Osoegawa, B. ten Hallers, S. Humphray, B. Zhu, E. Eyras, R. Castelo, C.P. Bird, S. Cagos, C. Scott, A. Cox, S. Deutsch, C. Ucla, M. Cruts, S. Dahoun, X. She, F. Bena, S-Y Wang, C. Van Broeckhoven, E.E. Eichler, R. Guigó, J. Rogers, P.J. de Jong, A. Reymond and S.E. Antonarakis. Islands of euchromatin-like sequence and expressed polymorphic sequences within the short arm of human chromosome 21. Genome Research, 17:1690-1696, 2007. [abstract].
  22. J. Segura, C. Fillat, D. Andreu, J. Llop, O. Millan, B.G. de la Torre, Z. Nikolovski, V. Gomez, N. Andreu, A. Pinyot, R. Castelo, J.D. Gispert and J.A. Pascual. Monitoring gene therapy by external imaging of mRNA: pilot study on murine Erythropoietin, Therapeutic Drug Monitoring, 29(5):612-618, 2007. [abstract].
  23. The ENCODE Project Consortium (including R. Castelo). Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 447:799-816, 2007. [abstract].
  24. F. Denoeud, P. Kapranov, C. Ucla, A. Frankish, R. Castelo, J. Drenkow, J. Lagarde, T. Alioto, C. Manzano, J. Chrast, S. Dike, C. Wyss, C.N. Henrichsen, N. Holroyd, M.C. Dickson, R. Taylor, Z. Hance, S. Foissac, R.M. Myers, J. Rogers, T. Hubbard, J. Harrow, R. Guigó, T.R. Gingeras, S.E. Antonarakis and A. Reymond. Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions. Genome Research, 17:746-759, 2007. [abstract].
  25. 2006

  26. R. Castelo and A. Roverato. A robust procedure for Gaussian graphical model search from microarray data with p larger than n. Journal of Machine Learning Research, 7(Dec):2621-2650, 2006. [abstract and PDF, R package]
  27. R. Guigó, P. Flicek, J.F. Abril, A. Reymond, J. Lagarde, F. Denoeud, S.E. Antonarakis, M. Ashburner, V.B. Bajic, E. Birney, R. Castelo, E. Eyras, C. Ucla, T.R. Gingeras, J. Harrow, T. Hubbard, S. Lewis and M.G. Reese. EGASP: The human ENCODE genome annotation assessment project. Genome Biology, 7(Suppl 1):S2, 2006. [full text].
  28. G. Parra, A. Reymond, N. Dabbouseh, E.T. Dermitzakis, R. Castelo, T.M. Thomson, S.E. Antonarakis and R. Guigó. Tandem chimerism as a means to increase protein complexity in the human genome. Genome Research, 16:37-44, 2006. [abstract]
  29. 2005

  30. J.M. Izquierdo, N. Majós, S. Bonnal, C. Martínez, R. Castelo, R. Guigó, D. Bilbao and J. Valcárcel. Regulation of Fas alternative splicing by antagonistic effects of TIA-1 and PTB on exon definition. Molecular Cell, 19:475-484, 2005. [abstract].
  31. E. Eyras, A. Reymond, R. Castelo, J.M. Bye, F. Câmara, P. Flicek, E.J. Huckle, G. Parra, D.D. Shteynberg, C. Wyss, J. Rogers, S.E. Antonarakis, E. Birney, R. Guigó and M. Brent. Gene finding in the chicken genome. BMC Bioinformatics, 6:131, 2005. [full text].
  32. R. Castelo, A. Reymond, C. Wyss, F. Câmara, G. Parra, S.E. Antonarakis, R. Guigó and E. Eyras. Comparative gene finding in chicken indicates that we are closing in on the set of multi-exonic widely expressed human genes. Nucleic Acids Research, 33(6):1935-1939, 2005. [abstract, supplementary information].
  33. J.F. Abril, R. Castelo and R. Guigó. Comparison of splice sites in mammals and chicken. Genome Research, 15:111-119, 2005. [abstract].
  34. 2004

  35. International Chicken Genome Sequencing Consortium (including R. Castelo). Sequencing and comparative analysis of the chicken genome. Nature, 432:695-716, 2004. [abstract].
  36. The ENCODE Project Consortium (including R. Castelo). The ENCODE (ENCyclopedia Of DNA Elements). Science, 306(5696):636-640, 2004. [abstract].
  37. R. Castelo and R. Guigó. Splice Site Identification by idlBNs. Bioinformatics, 20(1):i69-i76, 2004. [abstract, supplementary information].
  38. 2003

  39. R. Castelo and N. Wormald. Enumeration of P4-free chordal graphs. Journal of Graphs and Combinatorics, 19(4):467-474, 2003. [abstract]
  40. R. Castelo and T. Kocka. On inclusion-driven learning of Bayesian Networks. Journal of Machine Learning Research, 4(Sep):527-574, 2003. [abstract and PDF]
  41. R. Castelo and A. Siebes. A characterization of moral transitive acyclic directed graph Markov models as labeled trees. Journal of Statistical Planning and Inference, 115(1):235-259, 2003 [abstract].
  42. P. Giudici and R. Castelo. Improving Markov Chain Monte Carlo model search for data mining. Machine Learning, 50(1-2):127--158, January 2003 [abstract].
  43. 2002

  44. Z.R. Struzik, W.J. van Wijngaarden and R. Castelo. Reasoning from non-stationarity. Physica A: Statistical Mechanics and its Applications, 314(1-4):246-255, November 2002. [abstract]
  45. 2001

  46. T. Kocka and R. Castelo. Improved learning of Bayesian networks. In Proceedings 17th Conference on Uncertainty in Artificial Intelligence, Seattle, Morgan Kauffman, pp. 269-276, August 2001. [PDF].
  47. P. Giudici and R. Castelo. Association models for web mining. Journal of Data Mining and Knowledge Discovery, 5:183-196, July 2001. [abstract].
  48. 2000

  49. R. Castelo and A. Siebes. Priors on network structures. Biasing the search for Bayesian Networks. International Journal of Approximate Reasoning , 24(1):39-57, March 2000. [abstract].


Research Program on Biomedical Informatics (GRIB)
Dept. of Health & Experimental Sciences (CEXS) Universitat
Pompeu Fabra
Barcelona Biomedical Research Park (PRBB)