People - Robert Castelo


Robert Castelo
GRIB-UPF-PRBB
Dr. Aiguader 88
E-08003 Barcelona
Spain
telf: +34.933.160.514
fax: +34.933.160.550
robert.castelo at upf.edu
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.

Publications

    2017

  1. 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].

    2016

  2. 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].
  3. 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].

    2015

  4. 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]
  5. 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]

    2014

  6. 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].

    2013

  7. 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].
  8. 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].

    2012

  9. 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].
  10. 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].
  11. R. Castelo. Comments on: Sequences of regressions and their independences. Test, 21(2):253-254, 2012. [abstract].
  12. 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].

    2011

  13. 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].
  14. 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].

    2010

  15. 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].

    2009

  16. 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]
  17. 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].
  18. 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]
  19. 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].

    2007

  20. 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].
  21. 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].
  22. 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].
  23. 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].
  24. 2006

  25. 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]
  26. 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].
  27. 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]
  28. 2005

  29. 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].
  30. 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].
  31. 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].
  32. J.F. Abril, R. Castelo and R. Guigó. Comparison of splice sites in mammals and chicken. Genome Research, 15:111-119, 2005. [abstract].
  33. 2004

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

  38. R. Castelo and N. Wormald. Enumeration of P4-free chordal graphs. Journal of Graphs and Combinatorics, 19(4):467-474, 2003. [abstract]
  39. 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]
  40. 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].
  41. 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].
  42. 2002

  43. 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]
  44. 2001

  45. 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].
  46. P. Giudici and R. Castelo. Association models for web mining. Journal of Data Mining and Knowledge Discovery, 5:183-196, July 2001. [abstract].
  47. 2000

  48. 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].


Links

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