Publications by authors named "Robert Castelo"

27Publications

Genome-wide postnatal changes in immunity following fetal inflammatory response.

FEBS J 2020 Oct 2. Epub 2020 Oct 2.

Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1111/febs.15578DOI Listing
October 2020

The BIOMEPOC Project: Personalized Biomarkers and Clinical Profiles in Chronic Obstructive Pulmonary Disease.

Arch Bronconeumol 2019 02 19;55(2):93-99. Epub 2018 Oct 19.

Centro de Investigación Biomédica en Red, Área de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, España; Servicio de Neumología (Instituto Clínic de Respiratorio) y Dispositivo Transversal de Hospitalización a Domicilio (Dirección Médica y de Enfermería), Hospital Clínic - Fundació Clínic per la Recerca Biomèdica, Universitat de Barcelona, IDIBAPS, Barcelona, España.

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S03002896183032
Publisher Site
http://dx.doi.org/10.1016/j.arbres.2018.07.026DOI Listing
February 2019

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

Bioinformatics 2018 09;34(18):3208-3210

Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/bty311DOI Listing
September 2018

The propagation of perturbations in rewired bacterial gene networks.

Nat Commun 2015 Dec 16;6:10105. Epub 2015 Dec 16.

EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003 Barcelona, Spain.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/ncomms10105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4703840PMC
December 2015

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

Pediatr Res 2016 Mar 5;79(3):473-81. Epub 2015 Nov 5.

Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/pr.2015.233DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4823644PMC
March 2016

Mapping eQTL networks with mixed graphical Markov models.

Genetics 2014 Dec 29;198(4):1377-93. Epub 2014 Sep 29.

Department of Experimental and Health Sciences, Universitat Pompeu Fabra, E-08003 Barcelona, Spain Research Programme on Biomedical Informatics, Institut Hospital del Mar d'Investigacions Mèdiques, E-08003 Barcelona, Spain

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1534/genetics.114.169573DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4256758PMC
December 2014

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

BMC Bioinformatics 2013 Aug 21;14:254. Epub 2013 Aug 21.

Center for Research in Environmental Epidemiology (CREAL), Barcelona, Spain.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2105-14-254DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3849762PMC
August 2013

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

BMC Bioinformatics 2013 Jan 16;14. Epub 2013 Jan 16.

Research Program on Biomedical Informatics, Hospital del Mar Medical Research Institute, Barcelona, Catalonia, Spain.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2105-14-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3618321PMC
January 2013

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

Methods Mol Biol 2012 ;802:215-33

Research Program on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/978-1-61779-400-1_14DOI Listing
April 2012

Evolution of primate orphan proteins.

Biochem Soc Trans 2009 Aug;37(Pt 4):778-82

Biomedical Informatics Research Programme (GRIB), Universitat Pompeu Fabra, Barcelona Biomedical Research Park , Barcelona 08003, Spain.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1042/BST0370778DOI Listing
August 2009

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

Genome Biol 2009 29;10(1):R11. Epub 2009 Jan 29.

Centre de Regulació Genòmica, Parc de Recerca Biomèdica de Barcelona, Dr Aiguader 88, Barcelona, Spain.

View Article

Download full-text PDF

Source
http://genomebiology.biomedcentral.com/articles/10.1186/gb-2
Publisher Site
http://dx.doi.org/10.1186/gb-2009-10-1-r11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2687788PMC
September 2009

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

J Comput Biol 2009 Feb;16(2):213-27

Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1089/cmb.2008.08TTDOI Listing
February 2009

Origin of primate orphan genes: a comparative genomics approach.

Mol Biol Evol 2009 Mar 8;26(3):603-12. Epub 2008 Dec 8.

Evolutionary Genomics Group, Biomedical Informatics Research Programme, Fundació Institut Municipal d'Investigació Mèdica, Barcelona, Spain.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/molbev/msn281DOI Listing
March 2009

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

Authors:
Ewan Birney John A Stamatoyannopoulos Anindya Dutta Roderic Guigó Thomas R Gingeras Elliott H Margulies Zhiping Weng Michael Snyder Emmanouil T Dermitzakis Robert E Thurman Michael S Kuehn Christopher M Taylor Shane Neph Christoph M Koch Saurabh Asthana Ankit Malhotra Ivan Adzhubei Jason A Greenbaum Robert M Andrews Paul Flicek Patrick J Boyle Hua Cao Nigel P Carter Gayle K Clelland Sean Davis Nathan Day Pawandeep Dhami Shane C Dillon Michael O Dorschner Heike Fiegler Paul G Giresi Jeff Goldy Michael Hawrylycz Andrew Haydock Richard Humbert Keith D James Brett E Johnson Ericka M Johnson Tristan T Frum Elizabeth R Rosenzweig Neerja Karnani Kirsten Lee Gregory C Lefebvre Patrick A Navas Fidencio Neri Stephen C J Parker Peter J Sabo Richard Sandstrom Anthony Shafer David Vetrie Molly Weaver Sarah Wilcox Man Yu Francis S Collins Job Dekker Jason D Lieb Thomas D Tullius Gregory E Crawford Shamil Sunyaev William S Noble Ian Dunham France Denoeud Alexandre Reymond Philipp Kapranov Joel Rozowsky Deyou Zheng Robert Castelo Adam Frankish Jennifer Harrow Srinka Ghosh Albin Sandelin Ivo L Hofacker Robert Baertsch Damian Keefe Sujit Dike Jill Cheng Heather A Hirsch Edward A Sekinger Julien Lagarde Josep F Abril Atif Shahab Christoph Flamm Claudia Fried Jörg Hackermüller Jana Hertel Manja Lindemeyer Kristin Missal Andrea Tanzer Stefan Washietl Jan Korbel Olof Emanuelsson Jakob S Pedersen Nancy Holroyd Ruth Taylor David Swarbreck Nicholas Matthews Mark C Dickson Daryl J Thomas Matthew T Weirauch James Gilbert Jorg Drenkow Ian Bell XiaoDong Zhao K G Srinivasan Wing-Kin Sung Hong Sain Ooi Kuo Ping Chiu Sylvain Foissac Tyler Alioto Michael Brent Lior Pachter Michael L Tress Alfonso Valencia Siew Woh Choo Chiou Yu Choo Catherine Ucla Caroline Manzano Carine Wyss Evelyn Cheung Taane G Clark James B Brown Madhavan Ganesh Sandeep Patel Hari Tammana Jacqueline Chrast Charlotte N Henrichsen Chikatoshi Kai Jun Kawai Ugrappa Nagalakshmi Jiaqian Wu Zheng Lian Jin Lian Peter Newburger Xueqing Zhang Peter Bickel John S Mattick Piero Carninci Yoshihide Hayashizaki Sherman Weissman Tim Hubbard Richard M Myers Jane Rogers Peter F Stadler Todd M Lowe Chia-Lin Wei Yijun Ruan Kevin Struhl Mark Gerstein Stylianos E Antonarakis Yutao Fu Eric D Green Ulaş Karaöz Adam Siepel James Taylor Laura A Liefer Kris A Wetterstrand Peter J Good Elise A Feingold Mark S Guyer Gregory M Cooper George Asimenos Colin N Dewey Minmei Hou Sergey Nikolaev Juan I Montoya-Burgos Ari Löytynoja Simon Whelan Fabio Pardi Tim Massingham Haiyan Huang Nancy R Zhang Ian Holmes James C Mullikin Abel Ureta-Vidal Benedict Paten Michael Seringhaus Deanna Church Kate Rosenbloom W James Kent Eric A Stone Serafim Batzoglou Nick Goldman Ross C Hardison David Haussler Webb Miller Arend Sidow Nathan D Trinklein Zhengdong D Zhang Leah Barrera Rhona Stuart David C King Adam Ameur Stefan Enroth Mark C Bieda Jonghwan Kim Akshay A Bhinge Nan Jiang Jun Liu Fei Yao Vinsensius B Vega Charlie W H Lee Patrick Ng Atif Shahab Annie Yang Zarmik Moqtaderi Zhou Zhu Xiaoqin Xu Sharon Squazzo Matthew J Oberley David Inman Michael A Singer Todd A Richmond Kyle J Munn Alvaro Rada-Iglesias Ola Wallerman Jan Komorowski Joanna C Fowler Phillippe Couttet Alexander W Bruce Oliver M Dovey Peter D Ellis Cordelia F Langford David A Nix Ghia Euskirchen Stephen Hartman Alexander E Urban Peter Kraus Sara Van Calcar Nate Heintzman Tae Hoon Kim Kun Wang Chunxu Qu Gary Hon Rosa Luna Christopher K Glass M Geoff Rosenfeld Shelley Force Aldred Sara J Cooper Anason Halees Jane M Lin Hennady P Shulha Xiaoling Zhang Mousheng Xu Jaafar N S Haidar Yong Yu Yijun Ruan Vishwanath R Iyer Roland D Green Claes Wadelius Peggy J Farnham Bing Ren Rachel A Harte Angie S Hinrichs Heather Trumbower Hiram Clawson Jennifer Hillman-Jackson Ann S Zweig Kayla Smith Archana Thakkapallayil Galt Barber Robert M Kuhn Donna Karolchik Lluis Armengol Christine P Bird Paul I W de Bakker Andrew D Kern Nuria Lopez-Bigas Joel D Martin Barbara E Stranger Abigail Woodroffe Eugene Davydov Antigone Dimas Eduardo Eyras Ingileif B Hallgrímsdóttir Julian Huppert Michael C Zody Gonçalo R Abecasis Xavier Estivill Gerard G Bouffard Xiaobin Guan Nancy F Hansen Jacquelyn R Idol Valerie V B Maduro Baishali Maskeri Jennifer C McDowell Morgan Park Pamela J Thomas Alice C Young Robert W Blakesley Donna M Muzny Erica Sodergren David A Wheeler Kim C Worley Huaiyang Jiang George M Weinstock Richard A Gibbs Tina Graves Robert Fulton Elaine R Mardis Richard K Wilson Michele Clamp James Cuff Sante Gnerre David B Jaffe Jean L Chang Kerstin Lindblad-Toh Eric S Lander Maxim Koriabine Mikhail Nefedov Kazutoyo Osoegawa Yuko Yoshinaga Baoli Zhu Pieter J de Jong
June 2007

Tandem chimerism as a means to increase protein complexity in the human genome.

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

Grup de Recerca en Informàtica Biomèdica, Institut Municipal d'Investigació Mèdica-Universitat Pompeu Fabra, and Programa de Bioinformàtica i Genòmica, Centre de Regulació Genòmica, E08003 Barcelona, Catalonia, Spain.

View Article

Download full-text PDF

Source
http://www.genome.org/cgi/doi/10.1101/gr.4145906
Publisher Site
http://dx.doi.org/10.1101/gr.4145906DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1356127PMC
January 2006

Gene finding in the chicken genome.

BMC Bioinformatics 2005 May 30;6:131. Epub 2005 May 30.

Institut Municipal d'Investigacio Medica, Universitat Pompeu Fabra, Centre de Regulacio Genomica, E08003 Barcelona, Catalonia, Spain.

View Article

Download full-text PDF

Source
http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
Publisher Site
http://dx.doi.org/10.1186/1471-2105-6-131DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1174864PMC
May 2005

Comparative gene finding in chicken indicates that we are closing in on the set of multi-exonic widely expressed human genes.

Nucleic Acids Res 2005 4;33(6):1935-9. Epub 2005 Apr 4.

Research Unit on Biomedical Informatics, Institut Municipal d'Investigació Mèdica/Universitat Pompeu Fabra, Centre de Regulació Genòmica E08003 Barcelona, Spain.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gki328DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1074396PMC
April 2005

Comparison of splice sites in mammals and chicken.

Genome Res 2005 Jan 8;15(1):111-9. Epub 2004 Dec 8.

Grup de Recerca en Informàtica Biomèdica, Institut Municipal d'Investigació Mèdica, Universitat Pompeu Fabra, and Programa de Bioinformàtica i Genòmica, Centre de Regulació Genòmica, C/ Dr. Aiguader 80, E-08003 Barcelona, Catalonia, Spain.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.3108805DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC540285PMC
January 2005

Splice site identification by idlBNs.

Bioinformatics 2004 Aug;20 Suppl 1:i69-76

Grup de Recerca en Informàtica Biomèdica, Institut Municipal d'Investigació Mèdica, Universitat Pompeu Fabra, Centre de Regulació Genòmica, Psg. Marítim 37-49, Barcelona, Spain.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/bth932DOI Listing
August 2004