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Items: 1 to 20 of 28

1.

GenomicScores: seamless access to genomewide position-specific scores from R and Bioconductor.

Puigdevall P, Castelo R.

Bioinformatics. 2018 Apr 26. doi: 10.1093/bioinformatics/bty311. [Epub ahead of print]

PMID:
29718111
2.

Thrombin stimulates insulin secretion via protease-activated receptor-3.

Hänzelmann S, Wang J, Güney E, Tang Y, Zhang E, Axelsson AS, Nenonen H, Salehi AS, Wollheim CB, Zetterberg E, Berntorp E, Costa IG, Castelo R, Rosengren AH.

Islets. 2015;7(4):e1118195. doi: 10.1080/19382014.2015.1118195.

3.

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.

Nat Commun. 2015 Dec 16;6:10105. doi: 10.1038/ncomms10105.

4.

Umbilical cord gene expression reveals the molecular architecture of the fetal inflammatory response in extremely preterm newborns.

Costa D, Castelo R.

Pediatr Res. 2016 Mar;79(3):473-81. doi: 10.1038/pr.2015.233. Epub 2015 Nov 5.

5.

Public data and open source tools for multi-assay genomic investigation of disease.

Kannan L, Ramos M, Re A, El-Hachem N, Safikhani Z, Gendoo DM, Davis S, Gomez-Cabrero D, Castelo R, Hansen KD, Carey VJ, Morgan M, Culhane AC, Haibe-Kains B, Waldron L.

Brief Bioinform. 2016 Jul;17(4):603-15. doi: 10.1093/bib/bbv080. Epub 2015 Oct 12. Review.

6.

Mapping eQTL networks with mixed graphical Markov models.

Tur I, Roverato A, Castelo R.

Genetics. 2014 Dec;198(4):1377-93. doi: 10.1534/genetics.114.169573. Epub 2014 Sep 29.

7.

A flexible count data model to fit the wide diversity of expression profiles arising from extensively replicated RNA-seq experiments.

Esnaola M, Puig P, Gonzalez D, Castelo R, Gonzalez JR.

BMC Bioinformatics. 2013 Aug 21;14:254. doi: 10.1186/1471-2105-14-254.

8.

GSVA: gene set variation analysis for microarray and RNA-seq data.

Hänzelmann S, Castelo R, Guinney J.

BMC Bioinformatics. 2013 Jan 16;14:7. doi: 10.1186/1471-2105-14-7.

9.

Inference of regulatory networks from microarray data with R and the bioconductor package qpgraph.

Castelo R, Roverato A.

Methods Mol Biol. 2012;802:215-33. doi: 10.1007/978-1-61779-400-1_14.

PMID:
22130883
10.

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.

RNA. 2011 Mar;17(3):453-68. doi: 10.1261/rna.2460411. Epub 2011 Jan 13.

11.

Evolution of primate orphan proteins.

Toll-Riera M, Castelo R, Bellora N, Albà MM.

Biochem Soc Trans. 2009 Aug;37(Pt 4):778-82. doi: 10.1042/BST0370778. Review.

PMID:
19614593
12.

Global analysis of alternative splicing regulation by insulin and wingless signaling in Drosophila cells.

Hartmann B, Castelo R, Blanchette M, Boue S, Rio DC, Valcárcel J.

Genome Biol. 2009;10(1):R11. doi: 10.1186/gb-2009-10-1-r11. Epub 2009 Jan 29.

13.

Reverse engineering molecular regulatory networks from microarray data with qp-graphs.

Castelo R, Roverato A.

J Comput Biol. 2009 Feb;16(2):213-27. doi: 10.1089/cmb.2008.08TT.

PMID:
19178140
14.

Origin of primate orphan genes: a comparative genomics approach.

Toll-Riera M, Bosch N, Bellora N, Castelo R, Armengol L, Estivill X, Albà MM.

Mol Biol Evol. 2009 Mar;26(3):603-12. doi: 10.1093/molbev/msn281. Epub 2008 Dec 8.

PMID:
19064677
15.

Monitoring gene therapy by external imaging of mRNA: pilot study on murine erythropoietin.

Segura J, Fillat C, Andreu D, Llop J, Millan O, de la Torre BG, Nikolovski Z, Gomez V, Andreu N, Pinyot A, Castelo R, Gispert JD, Pascual JA.

Ther Drug Monit. 2007 Oct;29(5):612-8.

PMID:
17898652
16.

Islands of euchromatin-like sequence and expressed polymorphic sequences within the short arm of human chromosome 21.

Lyle R, Prandini P, Osoegawa K, ten Hallers B, Humphray S, Zhu B, Eyras E, Castelo R, Bird CP, Gagos S, Scott C, Cox A, Deutsch S, Ucla C, Cruts M, Dahoun S, She X, Bena F, Wang SY, Van Broeckhoven C, Eichler EE, Guigo R, Rogers J, de Jong PJ, Reymond A, Antonarakis SE.

Genome Res. 2007 Nov;17(11):1690-6. Epub 2007 Sep 25.

17.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA; NISC Comparative Sequencing Program; Baylor College of Medicine Human Genome Sequencing Center; Washington University Genome Sequencing Center; Broad Institute; Children's Hospital Oakland Research Institute, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ.

Nature. 2007 Jun 14;447(7146):799-816.

18.

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.

Genome Res. 2007 Jun;17(6):746-59.

19.

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.

Genome Biol. 2006;7 Suppl 1:S2.1-31. Epub 2006 Aug 7. Review.

20.

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.

Genome Res. 2006 Jan;16(1):37-44. Epub 2005 Dec 12.

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