Publications by authors named "Abel Gonzalez-Perez"

52Publications

Are carcinogens direct mutagens?

Nat Genet 2020 Nov;52(11):1137-1138

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

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http://dx.doi.org/10.1038/s41588-020-00730-wDOI Listing
November 2020

A compendium of mutational cancer driver genes.

Nat Rev Cancer 2020 Oct 10;20(10):555-572. Epub 2020 Aug 10.

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

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http://dx.doi.org/10.1038/s41568-020-0290-xDOI Listing
October 2020

BnpC: Bayesian non-parametric clustering of single-cell mutation profiles.

Bioinformatics 2020 Jun 27. Epub 2020 Jun 27.

Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland.

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http://dx.doi.org/10.1093/bioinformatics/btaa599DOI Listing
June 2020

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.

Nature 2020 02 5;578(7793):102-111. Epub 2020 Feb 5.

The Broad Institute of MIT and Harvard, Cambridge, MA, USA.

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http://dx.doi.org/10.1038/s41586-020-1965-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7054214PMC
February 2020

The mutational footprints of cancer therapies.

Nat Genet 2019 12 18;51(12):1732-1740. Epub 2019 Nov 18.

Institute for Research in Biomedicine Barcelona, The Barcelona Institute of Science and Technology, Barcelona, Spain.

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http://dx.doi.org/10.1038/s41588-019-0525-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6887544PMC
December 2019

Dynamic clonal remodelling in breast cancer metastases is associated with subtype conversion.

Eur J Cancer 2019 10 4;120:54-64. Epub 2019 Sep 4.

GEICAM (Grupo GEICAM de Investigación en Cáncer de Mama), Madrid, Spain; Centro de Investigación Biomédica en Red de Oncología, CIBERONC-ISCIII, Spain; IMIM Hospital del Mar Medical Research Institute; Barcelona, Spain; Medical Oncology Department Hospital del Mar, Barcelona, Barcelona, Spain; Universitat Pompeu Fabra, Barcelona, Spain. Electronic address:

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http://dx.doi.org/10.1016/j.ejca.2019.07.003DOI Listing
October 2019

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

Bioinformatics 2019 11;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
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6853674PMC
November 2019

Local Determinants of the Mutational Landscape of the Human Genome.

Cell 2019 03;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

Network, Transcriptomic and Genomic Features Differentiate Genes Relevant for Drug Response.

Front Genet 2018 25;9:412. Epub 2018 Sep 25.

Integrative Biomedical Informatics Group, Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain.

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https://www.frontiersin.org/article/10.3389/fgene.2018.00412
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http://dx.doi.org/10.3389/fgene.2018.00412DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6168038PMC
September 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

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

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

Mutational landscape of RNA-binding proteins in human cancers.

RNA Biol 2018 01 14;15(1):115-129. Epub 2017 Nov 14.

a Department of Bio Health Informatics, School of Informatics and Computing , Indiana University Purdue University , Indianapolis , Indiana , USA.

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http://dx.doi.org/10.1080/15476286.2017.1391436DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5786023PMC
January 2018

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

Uncovering disease mechanisms through network biology in the era of Next Generation Sequencing.

Sci Rep 2016 Apr 15;6:24570. Epub 2016 Apr 15.

Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), DCEXS, Pompeu Fabra University (UPF). C/Dr. Aiguader, 88. 08003- Barcelona, Spain.

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http://dx.doi.org/10.1038/srep24570DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4832203PMC
April 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

Circuits of cancer drivers revealed by convergent misregulation of transcription factor targets across tumor types.

Genome Med 2016 Jan 20;8(1). Epub 2016 Jan 20.

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://dx.doi.org/10.1186/s13073-015-0260-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4719577PMC
January 2016

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

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

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

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

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

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

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

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

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

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

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

The ubiquity of the insulin superfamily across the eukaryotes detected using a bioinformatics approach.

OMICS 2011 Jul-Aug;15(7-8):439-47. Epub 2011 Mar 16.

Departamento de Bioquímica, Universidad de la Habana, Cuba.

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http://dx.doi.org/10.1089/omi.2010.0141DOI Listing
November 2011

From sequence to dynamics: the effects of transcription factor and polymerase concentration changes on activated and repressed promoters.

BMC Mol Biol 2009 Sep 22;10:92. Epub 2009 Sep 22.

Centro Nacional de Bioinformática, Industria y San José, Capitolio Nacional, CP 10200, Habana Vieja, Ciudad de la Habana, Cuba.

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http://dx.doi.org/10.1186/1471-2199-10-92DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2761915PMC
September 2009

Prediction of TF target sites based on atomistic models of protein-DNA complexes.

BMC Bioinformatics 2008 Oct 16;9:436. Epub 2008 Oct 16.

Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, España.

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http://dx.doi.org/10.1186/1471-2105-9-436DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2585596PMC
October 2008

Conservation of key members in the course of the evolution of the insulin signaling pathway.

Biosystems 2009 Jan 20;95(1):7-16. Epub 2008 Jun 20.

Departamento de Bioquímica, Universidad de la Habana, Calle 25 # 455, esquina I, CP. 10400, Plaza, Ciudad de la Habana, Cuba.

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http://dx.doi.org/10.1016/j.biosystems.2008.06.003DOI Listing
January 2009

Impact of Transcription Units rearrangement on the evolution of the regulatory network of gamma-proteobacteria.

BMC Genomics 2008 Mar 17;9:128. Epub 2008 Mar 17.

Centro Nacional de Bioinformática. Industria y San José, Capitolio Nacional, CP. 10200, Habana Vieja, Ciudad de la Habana, Cuba.

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http://dx.doi.org/10.1186/1471-2164-9-128DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2329645PMC
March 2008

Complementing computationally predicted regulatory sites in Tractor_DB using a pattern matching approach.

In Silico Biol 2005 ;5(2):209-19

National Bioinformatics Center, Industria y San José, Capitolio Nacional, Habana, Cuba.

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http://cimi.ccg.unam.mx/files/WebFM/Computational_Genomics/I
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October 2005