About the Authors
- Sarah Djebali
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Contributed equally to this work with: Sarah Djebali, Julien Lagarde, Philipp Kapranov, Vincent Lacroix
Affiliation Bioinformatics and Genomics, Centre for Genomic Regulation and Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
- Julien Lagarde
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Contributed equally to this work with: Sarah Djebali, Julien Lagarde, Philipp Kapranov, Vincent Lacroix
Affiliation Bioinformatics and Genomics, Centre for Genomic Regulation and Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
- Philipp Kapranov
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Contributed equally to this work with: Sarah Djebali, Julien Lagarde, Philipp Kapranov, Vincent Lacroix
Current address: Helicos BioSciences Corporation, Cambridge, Massachusetts, United States of America
Affiliation Affymetrix Inc., Santa Clara, California, United States of America
- Vincent Lacroix
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Contributed equally to this work with: Sarah Djebali, Julien Lagarde, Philipp Kapranov, Vincent Lacroix
Current address: Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, INRIA BAMBOO, Villeurbanne, France
Affiliation Bioinformatics and Genomics, Centre for Genomic Regulation and Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
- Christelle Borel
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Affiliation Department of Genetic Medicine and Development, University of Geneva Medical School, University Hospitals of Geneva, Geneva, Switzerland
- Jonathan M. Mudge
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Affiliation Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
- Cédric Howald
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Affiliation The Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
- Sylvain Foissac
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Current address: Integromics, S.L., Grisolía, Tres Cantos, Madrid, Spain
Affiliations Bioinformatics and Genomics, Centre for Genomic Regulation and Universitat Pompeu Fabra, Barcelona, Catalonia, Spain, Affymetrix Inc., Santa Clara, California, United States of America
- Catherine Ucla
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Affiliation Department of Genetic Medicine and Development, University of Geneva Medical School, University Hospitals of Geneva, Geneva, Switzerland
- Jacqueline Chrast
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Affiliation The Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
- Paolo Ribeca
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Affiliation Bioinformatics and Genomics, Centre for Genomic Regulation and Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
- David Martin
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Affiliation Bioinformatics and Genomics, Centre for Genomic Regulation and Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
- Ryan R. Murray
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Affiliation Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Xinping Yang
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Affiliation Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Lila Ghamsari
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Affiliation Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Chenwei Lin
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Affiliation Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Ian Bell
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Affiliation Affymetrix Inc., Santa Clara, California, United States of America
- Erica Dumais
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Affiliation Affymetrix Inc., Santa Clara, California, United States of America
- Jorg Drenkow
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Affiliation Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
- Michael L. Tress
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Affiliation Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre, Madrid, Spain
- Josep Lluís Gelpí
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Affiliation Institute of Research in Biomedicine and Barcelona Supercomputer Center, Joint Program on Computational Biology. Parc Científic de Barcelona, Universitat de Barcelona, Facultat de Biologia, Barcelona, Catalonia, Spain
- Modesto Orozco
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Affiliation Institute of Research in Biomedicine and Barcelona Supercomputer Center, Joint Program on Computational Biology. Parc Científic de Barcelona, Universitat de Barcelona, Facultat de Biologia, Barcelona, Catalonia, Spain
- Alfonso Valencia
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Affiliation Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre, Madrid, Spain
- Nynke L. van Berkum
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Affiliation Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Bryan R. Lajoie
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Affiliation Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Marc Vidal
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Affiliation Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- John Stamatoyannopoulos
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Affiliation University of Washington, Seattle, Washington, United States of America
- Philippe Batut
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Affiliation Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
- Alex Dobin
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Affiliation Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
- Jennifer Harrow
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Affiliation Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
- Tim Hubbard
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Affiliation Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
- Job Dekker
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Affiliation Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Adam Frankish
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Affiliation Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
- Kourosh Salehi-Ashtiani
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Affiliations Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates, and Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America
- Alexandre Reymond
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Affiliation The Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
- Stylianos E. Antonarakis
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* E-mail: gingeras@cshl.edu (TG); roderic.guigo@crg.ca (RG); Stylianos.Antonarakis@unige.ch (SA)
Affiliation Department of Genetic Medicine and Development, University of Geneva Medical School, University Hospitals of Geneva, Geneva, Switzerland
- Roderic Guigó
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* E-mail: gingeras@cshl.edu (TG); roderic.guigo@crg.ca (RG); Stylianos.Antonarakis@unige.ch (SA)
Affiliations Bioinformatics and Genomics, Centre for Genomic Regulation and Universitat Pompeu Fabra, Barcelona, Catalonia, Spain, Departament de Ciènces Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
- Thomas R. Gingeras
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* E-mail: gingeras@cshl.edu (TG); roderic.guigo@crg.ca (RG); Stylianos.Antonarakis@unige.ch (SA)
Affiliations Affymetrix Inc., Santa Clara, California, United States of America, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
Competing Interests
The study was partially funded by Affymetrix Inc. PK, SF, IB, ED, J.Drenkow, AD and TG were employees of Affymetrix Inc. at the time of the study. There are no patents, products in development or marketed products to declare. This does not alter the authors' adherence to all the PLoS ONE policies on sharing data and materials, as detailed online in the guide for authors.
Author Contributions
Conceived and designed the experiments: TG RG SA AR KS-A J.Dekker SD JL SF MV JS. Performed the experiments: PK CB CH CU JC RM XY LG CL IB ED J.Drenkow NvB PB. Analyzed the data: SD JL VL JM SF PR DM MT JLG BL AD AF MO AV JH TH. Contributed reagents/materials/analysis tools: PK CB CH CL. Wrote the paper: TG RG SD VL JL.