People - Robert Castelo


Robert Castelo
MELIS-UPF-PRBB
Doctor Aiguader 88
E-08003 Barcelona
Spain
telf: +34.933.160.514
robert.castelo[at]upf.edu
 Google Author Profile
Web of Science 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

    2024

  1. J. Drnevich, F.J. Tan, F. Almeida-Silva, R. Castelo, A.C. Culhane, S. Davis, M.A. Doyle, S. Holmes, L. Lahti, A. Mahmoud, K. Nishida, M. Ramos, K. Rue-Albrecht, D.J.H. Shih, L. Gatto, C. Soneson. Learning and teaching biological data science in the Bioconductor community. arXiv, 2410.01351, 2024. [preprint]
  2. L.M. Boll, S. Vázquez Montes de Oca, M.E. Camarena, R. Castelo, J. Bellmunt, J. Perera-Bel, M.M. Albà. Predicting immunotherapy response in advanced bladder cancer: a meta-analysis of six independent cohorts. bioRxiv, 2024. [preprint]
  3. M.E. Camarena, P. Theunissen, M. Ruiz, J. Ruiz-Orera, B. Calvo-Serra, R. Castelo, C. Castro, P. Sarobe, P. Fortes, J. Perera-Bel and M.M. Albà. Microproteins encoded by noncanonical ORFs are a major source of tumor-specific antigens in a liver cancer patient meta-cohort. Science Advances, 10:eadn3628, 2024. [full text, preprint]

    2023

  4. R. Castelo. Teaching computational skills with GitHub Classroom. Revista del Congrés Internacional de Docència Universitària i Innovació (CIDUI), Núm. 6, 2023. [full text].

    2021

  5. D. Costa, N. Bonet, A. Solé, J.M. González de Aledo-Castillo, E. Sabidó, F. Casals, C. Rovira, A. Nadal, J.L. Marín, T. Cobo and R. Castelo. Genome-wide postnatal changes in immunity following fetal inflammatory response. FEBS Journal, 288:2311-2331, 2021. [full text, preprint, Raw and processed RNA-seq expression data, Raw proteomics expression data].

    2020

  6. A. Roverato and R. Castelo. Path weights in concentration graphs. Biometrika, 107:705-722, 2020. [abstract, preprint].

    2019

  7. P. Puigdevall, L. Piccari, I. Blanco, J.A. Barberà, D. Geiger, C. Badenas, M. Milà, R. Castelo and I. Madrigal. Genetic linkage analysis of a large family identifies FIGN as a candidate modulator of reduced penetrance in heritable pulmonary arterial hypertension. Journal of Medical Genetics, 56:481-490, 2019. [full text, Raw and processed microarray genotyping data].
  8. J. Gea, S. Pascual, A. Castro-Acosta, C. Hernández-Carcereny, R. Castelo, E. Márquez-Martín, C. Montón, A. Palou, R. Faner, L.I. Furlong, L. Seijo, F. Sanz, M. Torà, C. Vilaplana, C. Casadevall, J.L. López-Campos, E. Monsó, G. Peces-Barba, B.G. Cosío, A. Agustí, on behalf of the BIOMEPOC group. The BIOMEPOC project: personalized biomarkers and clinical profiles in chronic obstructive pulmonary disease. Archivos de Bronconeumología, 55:93-99, 2019. [abstract].

    2018

  9. P. Puigdevall and R. Castelo. GenomicScores: seamless access to genomewide position-specific scores from R and Bioconductor. Bioinformatics, 18:3208-3210, 2018. [full text, R/Bioconductor package].
  10. A. Roverato and R. Castelo. Differential networking with path weights in Gaussian trees. In Proceedings of the Ninth International Conference on Probabilistic Graphical Models (PGM 2018), M. Studený and V. Kratochvíl, Eds., PMLR, 72:404-415, 2018. [abstract and PDF].

    2017

  11. 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, supplement].

    2016

  12. 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].
  13. 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

  14. 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]
  15. 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

  16. I. Tur, A. Roverato and R. Castelo. Mapping eQTL networks with mixed graphical Markov models. Genetics, 198(4):1377-1383, 2014. [full text, arXiv preprint, supplement, R/Bioconductor package].

    2013

  17. 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, R/Bioconductor package].

    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, R/Bioconductor package].

    2012

  18. 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].
  19. 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, R/Bioconductor package].
  20. R. Castelo. Comments on: Sequences of regressions and their independences. Test, 21(2):253-254, 2012. [abstract].
  21. 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, R/Bioconductor package].

    2011

  22. 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, F.G. Cozman and A. Pfeffer, Eds., pp. 689-697, AUAI Press, ISBN 978-0-9749039-7-2, Barcelona, 2011. [PDF, R/Bioconductor package].
  23. 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

  24. 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, R/Bioconductor package].

    2009

  25. 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]
  26. 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].
  27. 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]
  28. 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. [abstract and PDF, supplement, R/Bioconductor package].

    2007

  29. 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].
  30. 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].
  31. 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, raw and processed data].
  32. 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].

    2006

  33. 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/Bioconductor package]
  34. 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].
  35. 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]

    2005

  36. 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].
  37. 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].
  38. 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, GenBank sequences (AY947523, AY947524, AY947525, AY947526, AY947527, AY947528)].
  39. J.F. Abril, R. Castelo and R. Guigó. Comparison of splice sites in mammals and chicken. Genome Research, 15:111-119, 2005. [abstract].

    2004

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

    2003

  43. R. Castelo and N. Wormald. Enumeration of P4-free chordal graphs. Journal of Graphs and Combinatorics, 19(4):467-474, 2003. [abstract, integer sequences (A058862, A058863, A058864, A058865)].
  44. R. Castelo and T. Kocka. On inclusion-driven learning of Bayesian Networks. Journal of Machine Learning Research, 4:527-574, 2003. [abstract and PDF].
  45. 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, integer sequences (A000169, A000272)].
  46. P. Giudici and R. Castelo. Improving Markov Chain Monte Carlo model search for data mining. Machine Learning, 50(1-2):127--158, 2003. [abstract].

    2002

  47. 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, 2002. [abstract].

    2001

  48. 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, 2001. [PDF].
  49. P. Giudici and R. Castelo. Association models for web mining. Journal of Data Mining and Knowledge Discovery, 5:183-196, 2001. [abstract].

    2000

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


Links

Research Program on Biomedical Informatics (GRIB)
 		Dept. of Medicine and Life Sciences (MELIS) Universitat
Pompeu Fabra
(UPF)
 		Barcelona Biomedical Research Park (PRBB)