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Evolution of primate orphan proteins.
Toll-Riera M, Castelo R, Bellora N, Albà MM. Toll-Riera M, et al. Biochem Soc Trans. 2009 Aug;37(Pt 4):778-82. doi: 10.1042/BST0370778. Biochem Soc Trans. 2009. PMID: 19614593 Review.
The propagation of perturbations in rewired bacterial gene networks.
Baumstark R, Hänzelmann S, Tsuru S, Schaerli Y, Francesconi M, Mancuso FM, Castelo R, Isalan M. Baumstark R, et al. Among authors: castelo r. Nat Commun. 2015 Dec 16;6:10105. doi: 10.1038/ncomms10105. Nat Commun. 2015. PMID: 26670742 Free PMC article.
Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions.
Denoeud F, Kapranov P, Ucla C, Frankish A, Castelo R, Drenkow J, Lagarde J, Alioto T, Manzano C, Chrast J, Dike S, Wyss C, Henrichsen CN, Holroyd N, Dickson MC, Taylor R, Hance Z, Foissac S, Myers RM, Rogers J, Hubbard T, Harrow J, Guigó R, Gingeras TR, Antonarakis SE, Reymond A. Denoeud F, et al. Genome Res. 2007 Jun;17(6):746-59. doi: 10.1101/gr.5660607. Genome Res. 2007. PMID: 17567994 Free PMC article.
EGASP: the human ENCODE Genome Annotation Assessment Project.
Guigó R, Flicek P, Abril JF, Reymond A, Lagarde J, Denoeud F, Antonarakis S, Ashburner M, Bajic VB, Birney E, Castelo R, Eyras E, Ucla C, Gingeras TR, Harrow J, Hubbard T, Lewis SE, Reese MG. Guigó R, et al. Genome Biol. 2006;7 Suppl 1(Suppl 1):S2.1-31. doi: 10.1186/gb-2006-7-s1-s2. Epub 2006 Aug 7. Genome Biol. 2006. PMID: 16925836 Free PMC article. Review.
Gene finding in the chicken genome.
Eyras E, Reymond A, Castelo R, Bye JM, Camara F, Flicek P, Huckle EJ, Parra G, Shteynberg DD, Wyss C, Rogers J, Antonarakis SE, Birney E, Guigo R, Brent MR. Eyras E, et al. BMC Bioinformatics. 2005 May 30;6:131. doi: 10.1186/1471-2105-6-131. BMC Bioinformatics. 2005. PMID: 15924626 Free PMC article.
Comparative gene finding in chicken indicates that we are closing in on the set of multi-exonic widely expressed human genes.
Castelo R, Reymond A, Wyss C, Câmara F, Parra G, Antonarakis SE, Guigó R, Eyras E. Castelo R, et al. Nucleic Acids Res. 2005 Apr 4;33(6):1935-9. doi: 10.1093/nar/gki328. Print 2005. Nucleic Acids Res. 2005. PMID: 15809229 Free PMC article.
Origin of primate orphan genes: a comparative genomics approach.
Toll-Riera M, Bosch N, Bellora N, Castelo R, Armengol L, Estivill X, Albà MM. Toll-Riera M, et al. Mol Biol Evol. 2009 Mar;26(3):603-12. doi: 10.1093/molbev/msn281. Epub 2008 Dec 8. Mol Biol Evol. 2009. PMID: 19064677
Tandem chimerism as a means to increase protein complexity in the human genome.
Parra G, Reymond A, Dabbouseh N, Dermitzakis ET, Castelo R, Thomson TM, Antonarakis SE, Guigó R. Parra G, et al. Genome Res. 2006 Jan;16(1):37-44. doi: 10.1101/gr.4145906. Epub 2005 Dec 12. Genome Res. 2006. PMID: 16344564 Free PMC article.
Reverse engineering molecular regulatory networks from microarray data with qp-graphs.
Castelo R, Roverato A. Castelo R, et al. J Comput Biol. 2009 Feb;16(2):213-27. doi: 10.1089/cmb.2008.08TT. J Comput Biol. 2009. PMID: 19178140
An R package, called qpgraph implementing this method is part of the Bioconductor project and can be downloaded from ( ...
An R package, called qpgraph implementing this method is part of the Bioconductor project and can be downloaded from (www.bioconducto …
Distinct regulatory programs establish widespread sex-specific alternative splicing in Drosophila melanogaster.
Hartmann B, Castelo R, Miñana B, Peden E, Blanchette M, Rio DC, Singh R, Valcárcel J. Hartmann B, et al. RNA. 2011 Mar;17(3):453-68. doi: 10.1261/rna.2460411. Epub 2011 Jan 13. RNA. 2011. PMID: 21233220 Free PMC article.
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