Roderic Guigó

Roderic Guigó

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Roderic Guigó

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Integrative transcriptomic analysis suggests new autoregulatory splicing events coupled with nonsense-mediated mRNA decay.

Nucleic Acids Res 2019 06;47(10):5293-5306

Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain.

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http://dx.doi.org/10.1093/nar/gkz193DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6547761PMC
June 2019

Recent advances in functional genome analysis.

F1000Res 2018 21;7. Epub 2018 Dec 21.

RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.

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http://dx.doi.org/10.12688/f1000research.15274.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6305211PMC
March 2019

Using geneid to Identify Genes.

Curr Protoc Bioinformatics 2018 12 17;64(1):e56. Epub 2018 Oct 17.

Centre de Regulació Genòmica (CRG), Barcelona, Spain.

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http://dx.doi.org/10.1002/cpbi.56DOI Listing
December 2018

Damage-responsive elements in regeneration.

Genome Res 2018 12 20;28(12):1852-1866. Epub 2018 Nov 20.

Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona 08028, Catalonia, Spain.

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http://dx.doi.org/10.1101/gr.233098.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6280756PMC
December 2018

Towards a complete map of the human long non-coding RNA transcriptome.

Nat Rev Genet 2018 09;19(9):535-548

Department of Medical Oncology, Inselspital, University Hospital and University of Bern, Bern, Switzerland.

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http://dx.doi.org/10.1038/s41576-018-0017-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6451964PMC
September 2018

Comparative transcriptomics across 14 Drosophila species reveals signatures of longevity.

Aging Cell 2018 08 19;17(4):e12740. Epub 2018 Apr 19.

Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.

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http://dx.doi.org/10.1111/acel.12740DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6052463PMC
August 2018

ggsashimi: Sashimi plot revised for browser- and annotation-independent splicing visualization.

PLoS Comput Biol 2018 08 17;14(8):e1006360. Epub 2018 Aug 17.

Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.

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http://dx.plos.org/10.1371/journal.pcbi.1006360
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http://dx.doi.org/10.1371/journal.pcbi.1006360DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6114895PMC
August 2018

Selenoprofiles: A Computational Pipeline for Annotation of Selenoproteins.

Methods Mol Biol 2018 ;1661:17-28

Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.

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http://dx.doi.org/10.1007/978-1-4939-7258-6_2DOI Listing
May 2018

The discovery potential of RNA processing profiles.

Nucleic Acids Res 2018 02;46(3):e15

Pompeu Fabra University (UPF), E08003 Barcelona, Spain.

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http://dx.doi.org/10.1093/nar/gkx1115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5814818PMC
February 2018

High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing.

Nat Genet 2017 Dec 6;49(12):1731-1740. Epub 2017 Nov 6.

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.

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http://dx.doi.org/10.1038/ng.3988DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5709232PMC
December 2017

LncATLAS database for subcellular localization of long noncoding RNAs.

RNA 2017 07 6;23(7):1080-1087. Epub 2017 Apr 6.

Department of Clinical Research, University of Bern, 3008 Bern, Switzerland.

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http://dx.doi.org/10.1261/rna.060814.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5473142PMC
July 2017

Comparative transcriptomics in human and mouse.

Nat Rev Genet 2017 07 8;18(7):425-440. Epub 2017 May 8.

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain.

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http://dx.doi.org/10.1038/nrg.2017.19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6413734PMC
July 2017

Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletion.

PLoS Comput Biol 2017 03 2;13(3):e1005341. Epub 2017 Mar 2.

Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, Barcelona, Spain.

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http://dx.doi.org/10.1371/journal.pcbi.1005341DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5333799PMC
March 2017

Brain Transcriptome Sequencing of a Natural Model of Alzheimer's Disease.

Front Aging Neurosci 2017 20;9:64. Epub 2017 Mar 20.

Laboratory of Molecular Neuropsychiatry, Institute of Cognitive and Translational Neuroscience (INCyT), INECO Foundation, Favaloro University, National Scientific and Technical Research CouncilBuenos Aires, Argentina; GeN.DDI LtdLondon, UK.

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http://dx.doi.org/10.3389/fnagi.2017.00064DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5357652PMC
March 2017

Ten Simple Rules on How to Organize a Scientific Retreat.

PLoS Comput Biol 2017 02 2;13(2):e1005344. Epub 2017 Feb 2.

Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain.

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http://dx.doi.org/10.1371/journal.pcbi.1005344DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5289491PMC
February 2017

Computational identification of the selenocysteine tRNA (tRNASec) in genomes.

PLoS Comput Biol 2017 02 13;13(2):e1005383. Epub 2017 Feb 13.

Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.

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http://dx.doi.org/10.1371/journal.pcbi.1005383DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5330540PMC
February 2017

Data Resources for Human Functional Genomics.

Curr Opin Syst Biol 2017 Feb 22;1:75-79. Epub 2017 Feb 22.

Center for Genomic Regulation (CRG), Barcelona, Catalonia, Spain.

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http://dx.doi.org/10.1016/j.coisb.2016.12.019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5625631PMC
February 2017

ChimPipe: accurate detection of fusion genes and transcription-induced chimeras from RNA-seq data.

BMC Genomics 2017 01 3;18(1). Epub 2017 Jan 3.

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.

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http://dx.doi.org/10.1186/s12864-016-3404-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5209911PMC
January 2017

Discovery of Cancer Driver Long Noncoding RNAs across 1112 Tumour Genomes: New Candidates and Distinguishing Features.

Sci Rep 2017 01 27;7:41544. Epub 2017 Jan 27.

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain.

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http://dx.doi.org/10.1038/srep41544DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5269722PMC
January 2017

Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells.

Cell 2016 11;167(5):1398-1414.e24

Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK; Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK; British Heart Foundation Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK; The National Institute for Health Research Blood and Transplant Unit (NIHR BTRU) in Donor Health and Genomics at the University of Cambridge, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge CB1 8RN, UK. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00928674163144
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http://dx.doi.org/10.1016/j.cell.2016.10.026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5119954PMC
November 2016

The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease.

Cell 2016 11;167(5):1415-1429.e19

Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK; Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK; The National Institute for Health Research Blood and Transplant Unit (NIHR BTRU) in Donor Health and Genomics at the University of Cambridge, University of Cambridge, Strangeways Research Laboratory, Wort's Causeway, Cambridge CB1 8RN, UK; British Heart Foundation Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2016.10.042DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5300907PMC
November 2016

Lokiarchaeota Marks the Transition between the Archaeal and Eukaryotic Selenocysteine Encoding Systems.

Mol Biol Evol 2016 09 12;33(9):2441-53. Epub 2016 Jul 12.

Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA

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http://dx.doi.org/10.1093/molbev/msw122DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4989117PMC
September 2016

Gene-specific patterns of expression variation across organs and species.

Genome Biol 2016 07 8;17(1):151. Epub 2016 Jul 8.

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.

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http://dx.doi.org/10.1186/s13059-016-1008-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937605PMC
July 2016

Cytoplasmic long noncoding RNAs are frequently bound to and degraded at ribosomes in human cells.

RNA 2016 06 18;22(6):867-82. Epub 2016 Apr 18.

Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), 08003 Barcelona, Spain.

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http://dx.doi.org/10.1261/rna.053561.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4878613PMC
June 2016

Erratum to: 'DECKO: Single-oligo, dual-CRISPR deletion of genomic elements including long non-coding RNAs'.

BMC Genomics 2016 Mar 9;17:215. Epub 2016 Mar 9.

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain.

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http://dx.doi.org/10.1186/s12864-016-2544-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4784307PMC
March 2016

Erratum to: Promoter-like epigenetic signatures in exons displaying cell type-specific splicing.

Genome Biol 2016 Mar 18;17:52. Epub 2016 Mar 18.

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader, 88, Barcelona, 08003, Catalonia, Spain.

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http://dx.doi.org/10.1186/s13059-016-0890-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4799591PMC
March 2016

Identification of a selenium-dependent glutathione peroxidase in the blood-sucking insect Rhodnius prolixus.

Insect Biochem Mol Biol 2016 Feb 25;69:105-14. Epub 2015 Sep 25.

Laboratório de Bioquímica de Artrópodes Hematófagos, Instituto de Bioquímica Médica, Programa de Biologia Molecular e Biotecnologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular (INCT-EM), Brazil. Electronic address:

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http://dx.doi.org/10.1016/j.ibmb.2015.08.007DOI Listing
February 2016

Spatiotemporal Control of Forkhead Binding to DNA Regulates the Meiotic Gene Expression Program.

Cell Rep 2016 Feb 21;14(4):885-895. Epub 2016 Jan 21.

Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona 08003, Spain. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2015.12.074DOI Listing
February 2016

Genome of Rhodnius prolixus, an insect vector of Chagas disease, reveals unique adaptations to hematophagy and parasite infection.

Authors:
Rafael D Mesquita Raquel J Vionette-Amaral Carl Lowenberger Rolando Rivera-Pomar Fernando A Monteiro Patrick Minx John Spieth A Bernardo Carvalho Francisco Panzera Daniel Lawson André Q Torres Jose M C Ribeiro Marcos H F Sorgine Robert M Waterhouse Michael J Montague Fernando Abad-Franch Michele Alves-Bezerra Laurence R Amaral Helena M Araujo Ricardo N Araujo L Aravind Georgia C Atella Patricia Azambuja Mateus Berni Paula R Bittencourt-Cunha Gloria R C Braz Gustavo Calderón-Fernández Claudia M A Carareto Mikkel B Christensen Igor R Costa Samara G Costa Marilvia Dansa Carlos R O Daumas-Filho Iron F De-Paula Felipe A Dias George Dimopoulos Scott J Emrich Natalia Esponda-Behrens Patricia Fampa Rita D Fernandez-Medina Rodrigo N da Fonseca Marcio Fontenele Catrina Fronick Lucinda A Fulton Ana Caroline Gandara Eloi S Garcia Fernando A Genta Gloria I Giraldo-Calderón Bruno Gomes Katia C Gondim Adriana Granzotto Alessandra A Guarneri Roderic Guigó Myriam Harry Daniel S T Hughes Willy Jablonka Emmanuelle Jacquin-Joly M Patricia Juárez Leonardo B Koerich Angela B Lange José Manuel Latorre-Estivalis Andrés Lavore Gena G Lawrence Cristiano Lazoski Claudio R Lazzari Raphael R Lopes Marcelo G Lorenzo Magda D Lugon David Majerowicz Paula L Marcet Marco Mariotti Hatisaburo Masuda Karine Megy Ana C A Melo Fanis Missirlis Theo Mota Fernando G Noriega Marcela Nouzova Rodrigo D Nunes Raquel L L Oliveira Gilbert Oliveira-Silveira Sheila Ons Ian Orchard Lucia Pagola Gabriela O Paiva-Silva Agustina Pascual Marcio G Pavan Nicolás Pedrini Alexandre A Peixoto Marcos H Pereira Andrew Pike Carla Polycarpo Francisco Prosdocimi Rodrigo Ribeiro-Rodrigues Hugh M Robertson Ana Paula Salerno Didier Salmon Didac Santesmasses Renata Schama Eloy S Seabra-Junior Livia Silva-Cardoso Mario A C Silva-Neto Matheus Souza-Gomes Marcos Sterkel Mabel L Taracena Marta Tojo Zhijian Jake Tu Jose M C Tubio Raul Ursic-Bedoya Thiago M Venancio Ana Beatriz Walter-Nuno Derek Wilson Wesley C Warren Richard K Wilson Erwin Huebner Ellen M Dotson Pedro L Oliveira

Proc Natl Acad Sci U S A 2015 Dec 16;112(48):14936-41. Epub 2015 Nov 16.

Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, Rio de Janeiro 21941-591, Brazil; Programa de Biologia Molecular e Biotecnologia, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-591, Brazil;

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http://dx.doi.org/10.1073/pnas.1506226112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4672799PMC
December 2015

Active transcription without histone modifications.

Oncotarget 2015 Dec;6(39):41401

Universitat de Barcelona and Institut de Biomedicina de la Universitat de Barcelona, Barcelona, Catalonia, Spain.

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http://dx.doi.org/10.18632/oncotarget.6437DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4747162PMC
December 2015

Absence of canonical marks of active chromatin in developmentally regulated genes.

Nat Genet 2015 Oct 17;47(10):1158-1167. Epub 2015 Aug 17.

Centre for Genomic Regulation. Barcelona, Catalonia, Spain.

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http://dx.doi.org/10.1038/ng.3381DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4625605PMC
October 2015

DECKO: Single-oligo, dual-CRISPR deletion of genomic elements including long non-coding RNAs.

BMC Genomics 2015 Oct 23;16:846. Epub 2015 Oct 23.

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain.

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http://dx.doi.org/10.1186/s12864-015-2086-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4619085PMC
October 2015

Promoter-like epigenetic signatures in exons displaying cell type-specific splicing.

Genome Biol 2015 Oct 23;16:236. Epub 2015 Oct 23.

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08003, Barcelona, Catalonia, Spain.

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http://dx.doi.org/10.1186/s13059-015-0797-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4619081PMC
October 2015

Evolution of selenophosphate synthetases: emergence and relocation of function through independent duplications and recurrent subfunctionalization.

Genome Res 2015 Sep 20;25(9):1256-67. Epub 2015 Jul 20.

Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), 08003 Barcelona, Catalonia, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Catalonia, Spain; Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), 08003 Barcelona, Catalonia, Spain;

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http://dx.doi.org/10.1101/gr.190538.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4561486PMC
September 2015

Role of six single nucleotide polymorphisms, risk factors in coronary disease, in OLR1 alternative splicing.

RNA 2015 Jun 22;21(6):1187-202. Epub 2015 Apr 22.

Centre de Regulació Genòmica, 08003 Barcelona, Spain Universitat Pompeu Fabra, 08003 Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats, 08020 Barcelona, Spain.

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http://dx.doi.org/10.1261/rna.049890.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4436670PMC
June 2015

Human genomics. The human transcriptome across tissues and individuals.

Science 2015 May;348(6235):660-5

Center for Genomic Regulation (CRG), Barcelona, Catalonia, Spain. Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain. Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Catalonia, Spain. Joint CRG-Barcelona Super Computing Center (BSC)-Institut de Recerca Biomedica (IRB) Program in Computational Biology, Barcelona, Catalonia, Spain.

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http://dx.doi.org/10.1126/science.aaa0355DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4547472PMC
May 2015

Genomic analysis of a migratory divide reveals candidate genes for migration and implicates selective sweeps in generating islands of differentiation.

Mol Ecol 2015 Apr 3;24(8):1873-88. Epub 2015 Apr 3.

Department of Zoology, University of British Columbia, 6270 University Blvd, Vancouver, BC, Canada, V6T1Z4.

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http://dx.doi.org/10.1111/mec.13150DOI Listing
April 2015

The genomes of two key bumblebee species with primitive eusocial organization.

Authors:
Ben M Sadd Seth M Barribeau Guy Bloch Dirk C de Graaf Peter Dearden Christine G Elsik Jürgen Gadau Cornelis J P Grimmelikhuijzen Martin Hasselmann Jeffrey D Lozier Hugh M Robertson Guy Smagghe Eckart Stolle Matthias Van Vaerenbergh Robert M Waterhouse Erich Bornberg-Bauer Steffen Klasberg Anna K Bennett Francisco Câmara Roderic Guigó Katharina Hoff Marco Mariotti Monica Munoz-Torres Terence Murphy Didac Santesmasses Gro V Amdam Matthew Beckers Martin Beye Matthias Biewer Márcia M G Bitondi Mark L Blaxter Andrew F G Bourke Mark J F Brown Severine D Buechel Rossanah Cameron Kaat Cappelle James C Carolan Olivier Christiaens Kate L Ciborowski David F Clarke Thomas J Colgan David H Collins Andrew G Cridge Tamas Dalmay Stephanie Dreier Louis du Plessis Elizabeth Duncan Silvio Erler Jay Evans Tiago Falcon Kevin Flores Flávia C P Freitas Taro Fuchikawa Tanja Gempe Klaus Hartfelder Frank Hauser Sophie Helbing Fernanda C Humann Frano Irvine Lars S Jermiin Claire E Johnson Reed M Johnson Andrew K Jones Tatsuhiko Kadowaki Jonathan H Kidner Vasco Koch Arian Köhler F Bernhard Kraus H Michael G Lattorff Megan Leask Gabrielle A Lockett Eamonn B Mallon David S Marco Antonio Monika Marxer Ivan Meeus Robin F A Moritz Ajay Nair Kathrin Näpflin Inga Nissen Jinzhi Niu Francis M F Nunes John G Oakeshott Amy Osborne Marianne Otte Daniel G Pinheiro Nina Rossié Olav Rueppell Carolina G Santos Regula Schmid-Hempel Björn D Schmitt Christina Schulte Zilá L P Simões Michelle P M Soares Luc Swevers Eva C Winnebeck Florian Wolschin Na Yu Evgeny M Zdobnov Peshtewani K Aqrawi Kerstin P Blankenburg Marcus Coyle Liezl Francisco Alvaro G Hernandez Michael Holder Matthew E Hudson LaRonda Jackson Joy Jayaseelan Vandita Joshi Christie Kovar Sandra L Lee Robert Mata Tittu Mathew Irene F Newsham Robin Ngo Geoffrey Okwuonu Christopher Pham Ling-Ling Pu Nehad Saada Jireh Santibanez DeNard Simmons Rebecca Thornton Aarti Venkat Kimberly K O Walden Yuan-Qing Wu Griet Debyser Bart Devreese Claire Asher Julie Blommaert Ariel D Chipman Lars Chittka Bertrand Fouks Jisheng Liu Meaghan P O'Neill Seirian Sumner Daniela Puiu Jiaxin Qu Steven L Salzberg Steven E Scherer Donna M Muzny Stephen Richards Gene E Robinson Richard A Gibbs Paul Schmid-Hempel Kim C Worley

Genome Biol 2015 Apr 24;16:76. Epub 2015 Apr 24.

Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, TX, 77030, USA.

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http://dx.doi.org/10.1186/s13059-015-0623-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4414376PMC
April 2015

RNA. Prescribing splicing.

Science 2015 Jan;347(6218):124-5

Center for Genomic Regulation, 08003 Barcelona, Spain. Universitat Pompeu Fabra, 08003 Barcelona, Spain. Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain.

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http://dx.doi.org/10.1126/science.aaa4864DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4772402PMC
January 2015

A comparative encyclopedia of DNA elements in the mouse genome.

Authors:
Feng Yue Yong Cheng Alessandra Breschi Jeff Vierstra Weisheng Wu Tyrone Ryba Richard Sandstrom Zhihai Ma Carrie Davis Benjamin D Pope Yin Shen Dmitri D Pervouchine Sarah Djebali Robert E Thurman Rajinder Kaul Eric Rynes Anthony Kirilusha Georgi K Marinov Brian A Williams Diane Trout Henry Amrhein Katherine Fisher-Aylor Igor Antoshechkin Gilberto DeSalvo Lei-Hoon See Meagan Fastuca Jorg Drenkow Chris Zaleski Alex Dobin Pablo Prieto Julien Lagarde Giovanni Bussotti Andrea Tanzer Olgert Denas Kanwei Li M A Bender Miaohua Zhang Rachel Byron Mark T Groudine David McCleary Long Pham Zhen Ye Samantha Kuan Lee Edsall Yi-Chieh Wu Matthew D Rasmussen Mukul S Bansal Manolis Kellis Cheryl A Keller Christapher S Morrissey Tejaswini Mishra Deepti Jain Nergiz Dogan Robert S Harris Philip Cayting Trupti Kawli Alan P Boyle Ghia Euskirchen Anshul Kundaje Shin Lin Yiing Lin Camden Jansen Venkat S Malladi Melissa S Cline Drew T Erickson Vanessa M Kirkup Katrina Learned Cricket A Sloan Kate R Rosenbloom Beatriz Lacerda de Sousa Kathryn Beal Miguel Pignatelli Paul Flicek Jin Lian Tamer Kahveci Dongwon Lee W James Kent Miguel Ramalho Santos Javier Herrero Cedric Notredame Audra Johnson Shinny Vong Kristen Lee Daniel Bates Fidencio Neri Morgan Diegel Theresa Canfield Peter J Sabo Matthew S Wilken Thomas A Reh Erika Giste Anthony Shafer Tanya Kutyavin Eric Haugen Douglas Dunn Alex P Reynolds Shane Neph Richard Humbert R Scott Hansen Marella De Bruijn Licia Selleri Alexander Rudensky Steven Josefowicz Robert Samstein Evan E Eichler Stuart H Orkin Dana Levasseur Thalia Papayannopoulou Kai-Hsin Chang Arthur Skoultchi Srikanta Gosh Christine Disteche Piper Treuting Yanli Wang Mitchell J Weiss Gerd A Blobel Xiaoyi Cao Sheng Zhong Ting Wang Peter J Good Rebecca F Lowdon Leslie B Adams Xiao-Qiao Zhou Michael J Pazin Elise A Feingold Barbara Wold James Taylor Ali Mortazavi Sherman M Weissman John A Stamatoyannopoulos Michael P Snyder Roderic Guigo Thomas R Gingeras David M Gilbert Ross C Hardison Michael A Beer Bing Ren

Nature 2014 Nov;515(7527):355-64

Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA.

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http://dx.doi.org/10.1038/nature13992DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4266106PMC
November 2014

The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima.

Authors:
Ariel D Chipman David E K Ferrier Carlo Brena Jiaxin Qu Daniel S T Hughes Reinhard Schröder Montserrat Torres-Oliva Nadia Znassi Huaiyang Jiang Francisca C Almeida Claudio R Alonso Zivkos Apostolou Peshtewani Aqrawi Wallace Arthur Jennifer C J Barna Kerstin P Blankenburg Daniela Brites Salvador Capella-Gutiérrez Marcus Coyle Peter K Dearden Louis Du Pasquier Elizabeth J Duncan Dieter Ebert Cornelius Eibner Galina Erikson Peter D Evans Cassandra G Extavour Liezl Francisco Toni Gabaldón William J Gillis Elizabeth A Goodwin-Horn Jack E Green Sam Griffiths-Jones Cornelis J P Grimmelikhuijzen Sai Gubbala Roderic Guigó Yi Han Frank Hauser Paul Havlak Luke Hayden Sophie Helbing Michael Holder Jerome H L Hui Julia P Hunn Vera S Hunnekuhl LaRonda Jackson Mehwish Javaid Shalini N Jhangiani Francis M Jiggins Tamsin E Jones Tobias S Kaiser Divya Kalra Nathan J Kenny Viktoriya Korchina Christie L Kovar F Bernhard Kraus François Lapraz Sandra L Lee Jie Lv Christigale Mandapat Gerard Manning Marco Mariotti Robert Mata Tittu Mathew Tobias Neumann Irene Newsham Dinh N Ngo Maria Ninova Geoffrey Okwuonu Fiona Ongeri William J Palmer Shobha Patil Pedro Patraquim Christopher Pham Ling-Ling Pu Nicholas H Putman Catherine Rabouille Olivia Mendivil Ramos Adelaide C Rhodes Helen E Robertson Hugh M Robertson Matthew Ronshaugen Julio Rozas Nehad Saada Alejandro Sánchez-Gracia Steven E Scherer Andrew M Schurko Kenneth W Siggens DeNard Simmons Anna Stief Eckart Stolle Maximilian J Telford Kristin Tessmar-Raible Rebecca Thornton Maurijn van der Zee Arndt von Haeseler James M Williams Judith H Willis Yuanqing Wu Xiaoyan Zou Daniel Lawson Donna M Muzny Kim C Worley Richard A Gibbs Michael Akam Stephen Richards

PLoS Biol 2014 Nov 25;12(11):e1002005. Epub 2014 Nov 25.

Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America.

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http://dx.doi.org/10.1371/journal.pbio.1002005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4244043PMC
November 2014

Identification of genetic variants associated with alternative splicing using sQTLseekeR.

Nat Commun 2014 Aug 20;5:4698. Epub 2014 Aug 20.

1] Center for Genomic Regulation, Universitat Pompeu Fabra, C/ Dr Aiguader 88 08003, Barcelona, Catalonia, Spain [2] Department of Experimental and Health Sciences, Universitat Pompeu Fabra 08003, Barcelona, Catalonia, Spain.

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http://dx.doi.org/10.1038/ncomms5698DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4143934PMC
August 2014

Comparative analysis of the transcriptome across distant species.

Nature 2014 Aug;512(7515):445-8

1] Department of Genome Sciences and University of Washington School of Medicine, William H. Foege Building S350D, 1705 Northeast Pacific Street, Box 355065 Seattle, Washington 98195-5065, USA [2].

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http://dx.doi.org/10.1038/nature13424DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4155737PMC
August 2014

The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs.

RNA 2014 Jul 21;20(7):959-76. Epub 2014 May 21.

Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), 08003 Barcelona, Spain.

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http://dx.doi.org/10.1261/rna.044560.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114693PMC
July 2014

ASPic-GeneID: a lightweight pipeline for gene prediction and alternative isoforms detection.

Biomed Res Int 2013 7;2013:502827. Epub 2013 Nov 7.

Centre Nacional d'Anàlisi Genòmica (CNAG), Parc Científic de Barcelona, 08028 Barcelona, Spain.

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http://dx.doi.org/10.1155/2013/502827DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3838850PMC
June 2014

SelenoDB 2.0: annotation of selenoprotein genes in animals and their genetic diversity in humans.

Nucleic Acids Res 2014 Jan 4;42(Database issue):D437-43. Epub 2013 Nov 4.

Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain and Department of Medicine, Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.

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http://dx.doi.org/10.1093/nar/gkt1045DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965025PMC
January 2014

Systematic evaluation of spliced alignment programs for RNA-seq data.

Nat Methods 2013 Dec 3;10(12):1185-91. Epub 2013 Nov 3.

1] European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK. [2].

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http://dx.doi.org/10.1038/nmeth.2722DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4018468PMC
December 2013

Assessment of transcript reconstruction methods for RNA-seq.

Nat Methods 2013 Dec 3;10(12):1177-84. Epub 2013 Nov 3.

European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK.

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http://dx.doi.org/10.1038/nmeth.2714DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3851240PMC
December 2013

Topoisomerase II regulates yeast genes with singular chromatin architectures.

Nucleic Acids Res 2013 Nov 9;41(20):9243-56. Epub 2013 Aug 9.

Molecular Biology Institute of Barcelona, CSIC, 08028 Barcelona, Spain, Department of Biology, University of Crete, 71409 Heraklion, Greece, Department of Genetics and ERI Biotecmed, University of Valencia, 46100 Burjassot, Spain, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain and Department of Biochemistry and Molecular Biology and ERI Biotecmed, University of Valencia, 46100 Burjassot, Spain.

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http://dx.doi.org/10.1093/nar/gkt707DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3814376PMC
November 2013

Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories.

Nat Biotechnol 2013 Nov 15;31(11):1015-22. Epub 2013 Sep 15.

1] Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands. [2] Netherlands Bioinformatics Centre, Leiden, The Netherlands.

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http://dx.doi.org/10.1038/nbt.2702DOI Listing
November 2013

Unravelling the hidden DNA structural/physical code provides novel insights on promoter location.

Nucleic Acids Res 2013 Aug 12;41(15):7220-30. Epub 2013 Jun 12.

Institute for Research in Biomedicine (IRB Barcelona), Barcelona 08028, Spain, Joint IRB-BSC Research Program on Computational Biology, Barcelona 08028, Spain, Bioinformatics and Genomics Group, Center for Genomic Regulation and Universitat Pompeu Fabra, Barcelona 08003, Spain, Barcelona Supercomputing Center, Barcelona 08034, Spain and Department of Biochemistry and Molecular Biology, University of Barcelona, Barcelona 08028, Spain.

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http://dx.doi.org/10.1093/nar/gkt511DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3753636PMC
August 2013

SECISearch3 and Seblastian: new tools for prediction of SECIS elements and selenoproteins.

Nucleic Acids Res 2013 Aug 19;41(15):e149. Epub 2013 Jun 19.

Division of Genetics, Department of Medicine, Brigham and Womens Hospital and Harvard Medical School, 77 Avenue Louis Pasteur, 02115, Boston, MA, USA and Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain and Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain.

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http://dx.doi.org/10.1093/nar/gkt550DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3753652PMC
August 2013

Grape RNA-Seq analysis pipeline environment.

Bioinformatics 2013 Mar 17;29(5):614-21. Epub 2013 Jan 17.

Bioinformatics and Genomics Group, Centre for Genomic Regulation (CRG) and Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Spain.

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http://bioinformatics.oxfordjournals.org/content/early/2013/
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March 2013

CPEB1 coordinates alternative 3'-UTR formation with translational regulation.

Nature 2013 Mar 24;495(7439):121-5. Epub 2013 Feb 24.

Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, 08028 Barcelona, Spain.

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http://dx.doi.org/10.1038/nature11901DOI Listing
March 2013

Intron-centric estimation of alternative splicing from RNA-seq data.

Bioinformatics 2013 Jan 21;29(2):273-4. Epub 2012 Nov 21.

Centre de Regulació Genòmica, 08003 Barcelona, Spain.

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http://dx.doi.org/10.1093/bioinformatics/bts678DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3546801PMC
January 2013

The GEM mapper: fast, accurate and versatile alignment by filtration.

Nat Methods 2012 Dec 28;9(12):1185-8. Epub 2012 Oct 28.

Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain.

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http://www.nature.com/articles/nmeth.2221
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December 2012

Modelling and simulating generic RNA-Seq experiments with the flux simulator.

Nucleic Acids Res 2012 Nov 7;40(20):10073-83. Epub 2012 Sep 7.

Bioinformatics and Genomics Program, Centre de Regulació Genòmica (CRG), 08003 Barcelona, Spain.

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http://dx.doi.org/10.1093/nar/gks666DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3488205PMC
November 2012

The Long Non-Coding RNAs: A New (P)layer in the "Dark Matter".

Front Genet 2011 9;2:107. Epub 2012 Jan 9.

Bioinformatics and Genomics, Centre for Genomic Regulation, Universitat Pompeu Fabra Barcelona, Spain.

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http://dx.doi.org/10.3389/fgene.2011.00107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3266617PMC
October 2012

Landscape of transcription in human cells.

Nature 2012 Sep;489(7414):101-8

Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain.

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http://dx.doi.org/10.1038/nature11233DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3684276PMC
September 2012

Composition and evolution of the vertebrate and mammalian selenoproteomes.

PLoS One 2012 30;7(3):e33066. Epub 2012 Mar 30.

Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3316567PMC
August 2012

An encyclopedia of mouse DNA elements (Mouse ENCODE).

August 2012

The genome of melon (Cucumis melo L.).

Proc Natl Acad Sci U S A 2012 Jul 2;109(29):11872-7. Epub 2012 Jul 2.

Institut de Recerca i Tecnologia Agroalimentàries, Centre for Research in Agricultural Genomics Consejo Superior de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universitat Autònoma de Barcelona-Universitat de Barcelona, 08193 Barcelona, Spain.

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http://dx.doi.org/10.1073/pnas.1205415109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3406823PMC
July 2012

Modeling gene expression using chromatin features in various cellular contexts.

Genome Biol 2012 Jun 13;13(9):R53. Epub 2012 Jun 13.

Program in Bioinformatics and Integrative Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.

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http://dx.doi.org/10.1186/gb-2012-13-9-r53DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3491397PMC
June 2012