Nuria Lopez-Bigas

Nuria Lopez-Bigas

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Nuria Lopez-Bigas

Nuria Lopez-Bigas

Publications by authors named "Nuria Lopez-Bigas"

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100Publications

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OncodriveCLUSTL: a sequence-based clustering method to identify cancer drivers.

Bioinformatics 2019 Nov;35(22):4788-4790

Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.

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http://dx.doi.org/10.1093/bioinformatics/btz501DOI Listing
November 2019

Local Determinants of the Mutational Landscape of the Human Genome.

Cell 2019 Mar;177(1):101-114

Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain; Research Program on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2019.02.051DOI Listing
March 2019

Somatic and Germline Mutation Periodicity Follow the Orientation of the DNA Minor Groove around Nucleosomes.

Cell 2018 11;175(4):1074-1087.e18

Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain; Research Program on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2018.10.004DOI Listing
November 2018

A Pan-cancer Landscape of Interactions between Solid Tumors and Infiltrating Immune Cell Populations.

Clin Cancer Res 2018 08 17;24(15):3717-3728. Epub 2018 Apr 17.

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

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http://dx.doi.org/10.1158/1078-0432.CCR-17-3509DOI Listing
August 2018

Author Correction: Reduced mutation rate in exons due to differential mismatch repair.

Nat Genet 2018 08;50(8):1196

Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.

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http://dx.doi.org/10.1038/s41588-018-0123-yDOI Listing
August 2018

Cancer Genome Interpreter annotates the biological and clinical relevance of tumor alterations.

Genome Med 2018 03 28;10(1):25. Epub 2018 Mar 28.

Research Program on Biomedical Informatics (GRIB), IMIM Hospital del Mar Medical, Research Institute and Pompeu Fabra University, Barcelona, Spain.

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http://dx.doi.org/10.1186/s13073-018-0531-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5875005PMC
March 2018

Reduced mutation rate in exons due to differential mismatch repair.

Nat Genet 2017 Dec 6;49(12):1684-1692. Epub 2017 Nov 6.

Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.

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http://dx.doi.org/10.1038/ng.3991DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5712219PMC
December 2017

Comparison of algorithms for the detection of cancer drivers at subgene resolution.

Nat Methods 2017 Aug 17;14(8):782-788. Epub 2017 Jul 17.

Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA.

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http://dx.doi.org/10.1038/nmeth.4364DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5935266PMC
August 2017

Rational design of cancer gene panels with OncoPaD.

Genome Med 2016 10 3;8(1):98. Epub 2016 Oct 3.

Research Program on Biomedical Informatics, IMIM Hospital del Mar Medical Research Institute and Universitat Pompeu Fabra, Doctor Aiguader 88, 08003, Barcelona, Catalonia, Spain.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047348PMC
http://dx.doi.org/10.1186/s13073-016-0349-1DOI Listing
October 2016

OncodriveFML: a general framework to identify coding and non-coding regions with cancer driver mutations.

Genome Biol 2016 06 16;17(1):128. Epub 2016 Jun 16.

Research Program on Biomedical Informatics, IMIM Hospital del Mar Medical Research Institute and Universitat Pompeu Fabra, Doctor Aiguader 88, 08003, Barcelona, Catalonia, Spain.

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http://dx.doi.org/10.1186/s13059-016-0994-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4910259PMC
June 2016

Altered oncomodules underlie chromatin regulatory factors driver mutations.

Oncotarget 2016 May;7(21):30748-59

Research Program on Biomedical Informatics, IMIM Hospital del Mar Medical Research Institute and Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain.

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http://dx.doi.org/10.18632/oncotarget.8752DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5058714PMC
May 2016

Nucleotide excision repair is impaired by binding of transcription factors to DNA.

Nature 2016 Apr;532(7598):264-7

Research Program on Biomedical Informatics, IMIM Hospital del Mar Medical Research Institute and Universitat Pompeu Fabra, Doctor Aiguader 88, 08003 Barcelona, Spain.

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http://biorxiv.org/content/biorxiv/early/2015/10/13/028886.f
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http://www.nature.com/doifinder/10.1038/nature17661
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http://dx.doi.org/10.1038/nature17661DOI Listing
April 2016

Increased mitochondrial function downstream from KDM5A histone demethylase rescues differentiation in pRB-deficient cells.

Genes Dev 2015 Sep 27;29(17):1817-34. Epub 2015 Aug 27.

Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois 60607, USA;

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http://dx.doi.org/10.1101/gad.264036.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4573855PMC
September 2015

In silico prescription of anticancer drugs to cohorts of 28 tumor types reveals targeting opportunities.

Cancer Cell 2015 Mar;27(3):382-96

Biomedical Genomics Lab, Research Program on Biomedical Informatics, IMIM Hospital del Mar Medical Research Institute and Universitat Pompeu Fabra, Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2015.02.007DOI Listing
March 2015

NF-κB directly mediates epigenetic deregulation of common microRNAs in Epstein-Barr virus-mediated transformation of B-cells and in lymphomas.

Nucleic Acids Res 2014 8;42(17):11025-39. Epub 2014 Sep 8.

Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Spain

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http://dx.doi.org/10.1093/nar/gku826DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4176189PMC
February 2015

Chromatin-wide profiling of DYRK1A reveals a role as a gene-specific RNA polymerase II CTD kinase.

Mol Cell 2015 Feb 22;57(3):506-20. Epub 2015 Jan 22.

Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Spain; Centre for Biomedical Network Research on Rare Diseases (CIBERER), Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2014.12.026DOI Listing
February 2015

Identification of Cdca7 as a novel Notch transcriptional target involved in hematopoietic stem cell emergence.

J Exp Med 2014 Nov 10;211(12):2411-23. Epub 2014 Nov 10.

Program de Recerca en Càncer, Institut Hospital del Mar d'Investigacions Mèdiques, Parc de Recerca Biomèdica de Barcelona, 08003 Barcelona, Spain

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http://dx.doi.org/10.1084/jem.20131857DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4235648PMC
November 2014

Independent component analysis uncovers the landscape of the bladder tumor transcriptome and reveals insights into luminal and basal subtypes.

Cell Rep 2014 Nov 13;9(4):1235-45. Epub 2014 Nov 13.

Institut Curie, Centre de Recherche, 75248 cedex 05 Paris, France; CNRS, UMR 144, Oncologie Moléculaire, Equipe Labellisée Ligue Contre le Cancer, Institut Curie, 75248 cedex 05 Paris, France. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2014.10.035DOI Listing
November 2014

OncodriveROLE classifies cancer driver genes in loss of function and activating mode of action.

Bioinformatics 2014 Sep;30(17):i549-55

Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, E08003 Barcelona and Institució Catalana de Recerca i Estudis Avançats (ICREA), E08010 Barcelona, Spain Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, E08003 Barcelona and Institució Catalana de Recerca i Estudis Avançats (ICREA), E08010 Barcelona, Spain.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btu467DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4147920PMC
September 2014

Fast randomization of large genomic datasets while preserving alteration counts.

Bioinformatics 2014 Sep;30(17):i617-23

Fondazione Bruno Kessler, I-38100 Povo (Trento), Italy, European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge CB10 1SD, UK, Wellcome Trust Sanger Institute, Cambridge CB10 1SD, UK and Universitat Pompeu Fabra, Barcelona 08003, Spain.

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http://dx.doi.org/10.1093/bioinformatics/btu474DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4147926PMC
September 2014

Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation.

Genome Med 2012 26;4(11):89. Epub 2012 Nov 26.

Research Programme on Biomedical Informatics - GRIB. Universitat Pompeu Fabra - UPF, Hospital del Mar Medical Research Institute - IMIM. Parc de Recerca Biomèdica de Barcelona (PRBB). Dr. Aiguader, 88, E-08003 Barcelona, Spain ; Institució Catalana de Recerca i Estudis Avançats (ICREA). Passeig Lluís Companys, 23, E-08010, Barcelona, Spain.

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http://dx.doi.org/10.1186/gm390DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4064314PMC
August 2014

Regulation of plant stem cell quiescence by a brassinosteroid signaling module.

Dev Cell 2014 Jul 26;30(1):36-47. Epub 2014 Jun 26.

Department of Molecular Genetics, Center for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S15345807140034
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http://dx.doi.org/10.1016/j.devcel.2014.05.020DOI Listing
July 2014

An intronic microRNA links Rb/E2F and EGFR signaling.

PLoS Genet 2014 Jul 24;10(7):e1004493. Epub 2014 Jul 24.

Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1004493DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4109884PMC
July 2014

Visualizing multidimensional cancer genomics data.

Genome Med 2013 31;5(1). Epub 2013 Jan 31.

Research Program on Biomedical Informatics - GRIB, Universitat Pompeu Fabra (UPF), Parc de Recerca Biomèdica de Barcelona (PRBB), Dr. Aiguader 88, E-08003 Barcelona, Spain ; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.

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http://link.springer.com/content/pdf/10.1186%2Fgm413.pdf
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http://genomemedicine.com/content/5/1/9
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http://dx.doi.org/10.1186/gm413DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3706894PMC
June 2014

jHeatmap: an interactive heatmap viewer for the web.

Bioinformatics 2014 Jun 23;30(12):1757-8. Epub 2014 Feb 23.

Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Dr. Aiguader 88, Barcelona, Spain and Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23, Barcelona, SpainResearch Unit on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Dr. Aiguader 88, Barcelona, Spain and Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23, Barcelona, Spain.

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http://dx.doi.org/10.1093/bioinformatics/btu094DOI Listing
June 2014

Mapping of six somatic linker histone H1 variants in human breast cancer cells uncovers specific features of H1.2.

Nucleic Acids Res 2014 Apr 29;42(7):4474-93. Epub 2014 Jan 29.

Department of Molecular Genomics, Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Barcelona, E-08028 Spain, Research Programme on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, E-08003 Spain, Department of Genetic Engineering, Biotechnology, University of Dhaka, Dhaka-1000, Bangladesh, Centro de Investigación Príncipe Felipe, Valencia, E-46012 Spain and Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, E-08010 Spain.

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http://dx.doi.org/10.1093/nar/gku079DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3985652PMC
April 2014

IntOGen-mutations identifies cancer drivers across tumor types.

Nat Methods 2013 Nov 15;10(11):1081-2. Epub 2013 Sep 15.

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

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http://dx.doi.org/10.1038/nmeth.2642DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5758042PMC
November 2013

Loss of dE2F compromises mitochondrial function.

Dev Cell 2013 Nov;27(4):438-51

Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA.

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http://dx.doi.org/10.1016/j.devcel.2013.10.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3866969PMC
November 2013

Expression of polycomb targets predicts breast cancer prognosis.

Mol Cell Biol 2013 Oct 5;33(19):3951-61. Epub 2013 Aug 5.

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

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http://dx.doi.org/10.1128/MCB.00426-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3811872PMC
October 2013

Comprehensive identification of mutational cancer driver genes across 12 tumor types.

Sci Rep 2013 Oct 2;3:2650. Epub 2013 Oct 2.

1] Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Dr. Aiguader 88, Barcelona, Spain [2].

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http://dx.doi.org/10.1038/srep02650DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3788361PMC
October 2013

Oncodrive-CIS: a method to reveal likely driver genes based on the impact of their copy number changes on expression.

PLoS One 2013 8;8(2):e55489. Epub 2013 Feb 8.

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

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0055489PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3568145PMC
September 2013

OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes.

Bioinformatics 2013 Sep 24;29(18):2238-44. Epub 2013 Jul 24.

Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona and Institució Catalana de Recerca i Estudis Avançats ICREA, Passeig Lluis Companys, 23, 08010 Barcelona, Spain.

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http://dx.doi.org/10.1093/bioinformatics/btt395DOI Listing
September 2013

Identification of novel markers in rheumatoid arthritis through integrated analysis of DNA methylation and microRNA expression.

J Autoimmun 2013 Mar 8;41:6-16. Epub 2013 Jan 8.

Chromatin and Disease Group, Cancer Epigenetics and Biology Programme, Bellvitge Biomedical Research Institute, 08907 L'Hospitalet de Llobregat, Barcelona, Spain.

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https://linkinghub.elsevier.com/retrieve/pii/S08968411120015
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http://dx.doi.org/10.1016/j.jaut.2012.12.005DOI Listing
March 2013

Functional impact bias reveals cancer drivers.

Nucleic Acids Res 2012 Nov 16;40(21):e169. Epub 2012 Aug 16.

Research Programme on Biomedical Informatics - GRIB, Universitat Pompeu Fabra - UPF, Parc de Recerca Biomèdica de Barcelona. Dr. Aiguader, 88, E-08003 Barcelona, Spain.

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http://dx.doi.org/10.1093/nar/gks743DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3505979PMC
November 2012

Drosophila GAGA factor is required for full activation of the dE2f1-Yki/Sd transcriptional program.

Cell Cycle 2012 Nov 15;11(22):4191-202. Epub 2012 Oct 15.

Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA.

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http://dx.doi.org/10.4161/cc.22486DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3524215PMC
November 2012

Coordinated repression of cell cycle genes by KDM5A and E2F4 during differentiation.

Proc Natl Acad Sci U S A 2012 Nov 23;109(45):18499-504. Epub 2012 Oct 23.

Department of Biochemistry and Molecular Genetics, University of Illinois, Chicago, IL 60607, USA.

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http://dx.doi.org/10.1073/pnas.1216724109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3494949PMC
November 2012

PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis.

Bioinformatics 2012 Sep;28(18):i640-i646

Department of Biomolecular Engineering and CBSE, University of California Santa Cruz, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1093/bioinformatics/bts402DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3436829PMC
September 2012

Oncogenomics methods and resources.

Cold Spring Harb Protoc 2012 May 1;2012(5). Epub 2012 May 1.

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http://dx.doi.org/10.1101/pdb.top069229DOI Listing
May 2012

Sample-level enrichment analysis unravels shared stress phenotypes among multiple cancer types.

Genome Med 2012 Mar 29;4(3):28. Epub 2012 Mar 29.

Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Dr, Aiguader 88, Barcelona, Spain.

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http://genomemedicine.biomedcentral.com/articles/10.1186/gm3
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http://dx.doi.org/10.1186/gm327DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3446278PMC
March 2012

Co-regulation of histone-modifying enzymes in cancer.

PLoS One 2011 23;6(8):e24023. Epub 2011 Aug 23.

Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0024023PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3160334PMC
February 2012

SVGMap: configurable image browser for experimental data.

Bioinformatics 2012 Jan 27;28(1):119-20. Epub 2011 Oct 27.

Department of Experimental and Health Sciences, Research Unit on Biomedical Informatics (GRIB), Universitat Pompeu Fabra-IMIM, Dr Aiguader 88, Barcelona, Spain.

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http://dx.doi.org/10.1093/bioinformatics/btr581DOI Listing
January 2012

Integrative cancer genomics (IntOGen) in Biomart.

Database (Oxford) 2011 7;2011:bar039. Epub 2011 Sep 7.

Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona, Spain.

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http://dx.doi.org/10.1093/database/bar039DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3169995PMC
December 2011

Gitools: analysis and visualisation of genomic data using interactive heat-maps.

PLoS One 2011 13;6(5):e19541. Epub 2011 May 13.

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

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019541PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3094337PMC
October 2011

mir-11 limits the proapoptotic function of its host gene, dE2f1.

Genes Dev 2011 Sep 19;25(17):1820-34. Epub 2011 Aug 19.

Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois 60607, USA.

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http://dx.doi.org/10.1101/gad.16947411DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3175718PMC
September 2011

Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, Condel.

Am J Hum Genet 2011 Apr 31;88(4):440-9. Epub 2011 Mar 31.

Research Programme on Biomedical Informatics, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona.

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http://dx.doi.org/10.1016/j.ajhg.2011.03.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3071923PMC
April 2011

Selective targeting of histone methylation.

Cell Cycle 2011 Feb 1;10(3):413-24. Epub 2011 Feb 1.

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

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3115016PMC
http://dx.doi.org/10.4161/cc.10.3.14705DOI Listing
February 2011

Cooperation between dE2F1 and Yki/Sd defines a distinct transcriptional program necessary to bypass cell cycle exit.

Genes Dev 2011 Feb;25(4):323-35

Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois 60607, USA.

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http://dx.doi.org/10.1101/gad.1999211DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3042156PMC
February 2011

Genome-wide analysis using ChIP to identify isoform-specific gene targets.

J Vis Exp 2010 Jul 7(41). Epub 2010 Jul 7.

Department of Biochemistry and Molecular Genetics, University of Illinois Chicago - UIC, USA.

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http://dx.doi.org/10.3791/2101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3156076PMC
July 2010

International network of cancer genome projects.

Authors:
Thomas J Hudson Warwick Anderson Axel Artez Anna D Barker Cindy Bell Rosa R Bernabé M K Bhan Fabien Calvo Iiro Eerola Daniela S Gerhard Alan Guttmacher Mark Guyer Fiona M Hemsley Jennifer L Jennings David Kerr Peter Klatt Patrik Kolar Jun Kusada David P Lane Frank Laplace Lu Youyong Gerd Nettekoven Brad Ozenberger Jane Peterson T S Rao Jacques Remacle Alan J Schafer Tatsuhiro Shibata Michael R Stratton Joseph G Vockley Koichi Watanabe Huanming Yang Matthew M F Yuen Bartha M Knoppers Martin Bobrow Anne Cambon-Thomsen Lynn G Dressler Stephanie O M Dyke Yann Joly Kazuto Kato Karen L Kennedy Pilar Nicolás Michael J Parker Emmanuelle Rial-Sebbag Carlos M Romeo-Casabona Kenna M Shaw Susan Wallace Georgia L Wiesner Nikolajs Zeps Peter Lichter Andrew V Biankin Christian Chabannon Lynda Chin Bruno Clément Enrique de Alava Françoise Degos Martin L Ferguson Peter Geary D Neil Hayes Thomas J Hudson Amber L Johns Arek Kasprzyk Hidewaki Nakagawa Robert Penny Miguel A Piris Rajiv Sarin Aldo Scarpa Tatsuhiro Shibata Marc van de Vijver P Andrew Futreal Hiroyuki Aburatani Mónica Bayés David D L Botwell Peter J Campbell Xavier Estivill Daniela S Gerhard Sean M Grimmond Ivo Gut Martin Hirst Carlos López-Otín Partha Majumder Marco Marra John D McPherson Hidewaki Nakagawa Zemin Ning Xose S Puente Yijun Ruan Tatsuhiro Shibata Michael R Stratton Hendrik G Stunnenberg Harold Swerdlow Victor E Velculescu Richard K Wilson Hong H Xue Liu Yang Paul T Spellman Gary D Bader Paul C Boutros Peter J Campbell Paul Flicek Gad Getz Roderic Guigó Guangwu Guo David Haussler Simon Heath Tim J Hubbard Tao Jiang Steven M Jones Qibin Li Nuria López-Bigas Ruibang Luo Lakshmi Muthuswamy B F Francis Ouellette John V Pearson Xose S Puente Victor Quesada Benjamin J Raphael Chris Sander Tatsuhiro Shibata Terence P Speed Lincoln D Stein Joshua M Stuart Jon W Teague Yasushi Totoki Tatsuhiko Tsunoda Alfonso Valencia David A Wheeler Honglong Wu Shancen Zhao Guangyu Zhou Lincoln D Stein Roderic Guigó Tim J Hubbard 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Nature 2010 Apr;464(7291):993-8

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2902243PMC
April 2010

Jagged1 is the pathological link between Wnt and Notch pathways in colorectal cancer.

Proc Natl Acad Sci U S A 2009 Apr 26;106(15):6315-20. Epub 2009 Mar 26.

Institut d'Investigació Biomèdica de Bellvitge Gran Via km 2.7, Hospitalet and Institut Municipal d'Investigacions Mèdiques-Hospital del Mar, Dr. Aiguader 88, 08003 Barcelona, Spain.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2669348PMC
April 2009

Prioritization of candidate cancer genes--an aid to oncogenomic studies.

Nucleic Acids Res 2008 Oct 18;36(18):e115. Epub 2008 Aug 18.

Research Unit on Biomedical Informatics, Experimental and Health Science Department, Universitat Pompeu Fabra, Barcelona 08080, Spain.

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http://dx.doi.org/10.1093/nar/gkn482DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2566894PMC
October 2008

Patterns of evolutionary constraints on genes in humans.

BMC Evol Biol 2008 Oct 7;8:275. Epub 2008 Oct 7.

MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, UK.

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http://dx.doi.org/10.1186/1471-2148-8-275DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2587479PMC
October 2008

Distinct patterns in the regulation and evolution of human cancer genes.

In Silico Biol 2008 ;8(1):33-46

Research Unit on Biomedical Informatics, Experimental and Health Science Department, Universitat Pompeu Fabra, Barcelona, 08080, Spain.

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July 2008

On the association between chromosomal rearrangements and genic evolution in humans and chimpanzees.

Genome Biol 2007 ;8(10):R230

Unitat de Biologia Evolutiva Departament de Ciències Experimentals i de la Salut, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Catalonia, Spain.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2246304PMC
May 2008

Functional protein divergence in the evolution of Homo sapiens.

Genome Biol 2008 15;9(2):R33. Epub 2008 Feb 15.

Research Unit on Biomedical Informatics, Experimental and Health Science Department, Universitat Pompeu Fabra, Barcelona, 08003, Spain.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2374701PMC
May 2008

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

A partially supervised classification approach to dominant and recessive human disease gene prediction.

Comput Methods Programs Biomed 2007 Mar 26;85(3):229-37. Epub 2007 Jan 26.

Intelligent Systems Group, Department of Computer Science and Artificial Intelligence, University of the Basque Country UPV-EHU, Paseo Manuel de Lardizabal 1, E-20018 San Sebastián, Spain.

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March 2007

Differences in the evolutionary history of disease genes affected by dominant or recessive mutations.

BMC Genomics 2006 Jul 3;7:165. Epub 2006 Jul 3.

Genome Bioinformatics Laboratory, Centre for Genomic Regulation, Universitat Pompeu Fabra, Pg, Maritim de la Barceloneta 37-49, E-08003, Barcelona, Spain.

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http://dx.doi.org/10.1186/1471-2164-7-165DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1534034PMC
July 2006

Highly consistent patterns for inherited human diseases at the molecular level.

Bioinformatics 2006 Feb 15;22(3):269-77. Epub 2005 Nov 15.

Genome Bioinformatics Laboratory, Center for Genomic Regulation, Universitat Pompeu Fabra, Pg. Maritim de la Barceloneta 37-49, E-08003, Barcelona, Spain.

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http://dx.doi.org/10.1093/bioinformatics/bti781DOI Listing
February 2006

Structural and functional properties of genes involved in human cancer.

BMC Genomics 2006 Jan 11;7. Epub 2006 Jan 11.

Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1186/1471-2164-7-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1373651PMC
January 2006

CoGenT++: an extensive and extensible data environment for computational genomics.

Bioinformatics 2005 Oct;21(19):3806-10

Computational Genomics Group, The European Bioinformatics Institute EMBL, Cambridge Outstation, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1093/bioinformatics/bti579DOI Listing
October 2005

Are splicing mutations the most frequent cause of hereditary disease?

FEBS Lett 2005 Mar;579(9):1900-3

Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1016/j.febslet.2005.02.047DOI Listing
March 2005

Genome-wide identification of genes likely to be involved in human genetic disease.

Nucleic Acids Res 2004 4;32(10):3108-14. Epub 2004 Jun 4.

Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1093/nar/gkh605DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC434425PMC
June 2004

Expression profiles of the connexin genes, Gjb1 and Gjb3, in the developing mouse cochlea.

Mech Dev 2002 Dec;119 Suppl 1:S111-5

Genes and Disease Program, Centre de Regulació Genòmica, Barcelona, Spain.

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http://dx.doi.org/10.1016/s0925-4773(03)00102-3DOI Listing
December 2002

Expression profiles of the connexin genes, Gjb1 and Gjb3, in the developing mouse cochlea.

Gene Expr Patterns 2002 Nov;2(1-2):113-7

Genes and Disease Program, Centre de Regulació Genòmica, Barcelona, Spain.

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http://dx.doi.org/10.1016/s0925-4773(02)00299-xDOI Listing
November 2002

Connexin mutations in hearing loss, dermatological and neurological disorders.

Trends Mol Med 2002 May;8(5):205-12

Deafness Research Group, Genes and Disease Research Program, Center of Genomic Regulation, Barcelona, Spain.

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http://dx.doi.org/10.1016/s1471-4914(02)02327-4DOI Listing
May 2002

A common frameshift mutation and other variants in GJB4 (connexin 30.3): Analysis of hearing impairment families.

Hum Mutat 2002 Apr;19(4):458

Medical and Molecular Genetics Center-IRO, Hospital Duran i Reynals, L'Hospitalet, Barcelona, Spain.

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http://doi.wiley.com/10.1002/humu.9023
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April 2002