Ivo Gut

Ivo Gut

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Ivo Gut

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gemBS: high throughput processing for DNA methylation data from bisulfite sequencing.

Bioinformatics 2019 Mar;35(5):737-742

Centro Nacional de Análisis Genómico (CNAG-CRG), Centre de Regulacio Genómico (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.

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http://dx.doi.org/10.1093/bioinformatics/bty690DOI Listing
March 2019

Mutational Profile of Aggressive, Localised Prostate Cancer from African Caribbean Men Versus European Ancestry Men.

Eur Urol 2019 01 21;75(1):11-15. Epub 2018 Sep 21.

CeRePP, Paris, France; Sorbonne Université, GRC n(∘)5, ONCOTYPE-URO, Paris, France; Assistance Publique Hôpitaux de Paris, Department of Urology, Academic Hospital Paris Est, Paris, France. Electronic address:

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http://dx.doi.org/10.1016/j.eururo.2018.08.026DOI Listing
January 2019

Transcription Factors Drive Tet2-Mediated Enhancer Demethylation to Reprogram Cell Fate.

Cell Stem Cell 2018 11 13;23(5):727-741.e9. Epub 2018 Sep 13.

Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S19345909183040
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http://dx.doi.org/10.1016/j.stem.2018.08.016DOI Listing
November 2018

Quantitative DNA Methylation Analysis at Single-Nucleotide Resolution by Pyrosequencing®.

Methods Mol Biol 2018 ;1708:427-445

Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Bâtiment G2, 2 rue Gaston Crémieux, 91000, Evry, France.

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http://dx.doi.org/10.1007/978-1-4939-7481-8_22DOI Listing
July 2018

bigSCale: an analytical framework for big-scale single-cell data.

Genome Res 2018 06 3;28(6):878-890. Epub 2018 May 3.

CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain.

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http://dx.doi.org/10.1101/gr.230771.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5991513PMC
June 2018

Loss of function mutations in EPHB4 are responsible for vein of Galen aneurysmal malformation.

Brain 2018 04;141(4):979-988

Institut National de la Santé et de la Recherche Médicale (Inserm) UMR-1169 and University Paris Sud, Le Kremlin Bicêtre, 94276, France.

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http://dx.doi.org/10.1093/brain/awy020DOI Listing
April 2018

Biallelic mutation of UNC50, encoding a protein involved in AChR trafficking, is responsible for arthrogryposis.

Hum Mol Genet 2017 10;26(20):3989-3994

Institut National de la Santé et de la Recherche Médicale (Inserm) UMR-1169, Université Paris Sud, 94276 Le Kremlin Bicêtre, France.

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http://dx.doi.org/10.1093/hmg/ddx288DOI Listing
October 2017

Mitochondrial Complex I Is a Global Regulator of Secondary Metabolism, Virulence and Azole Sensitivity in Fungi.

PLoS One 2016 20;11(7):e0158724. Epub 2016 Jul 20.

Manchester Fungal Infection Group, Institute of Inflammation and Repair, Faculty of Medicine and Human Sciences, University of Manchester, 2.24 Core technology Building, Grafton St., Manchester, M13 9NT, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0158724PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4954691PMC
July 2017

Mex3a Marks a Slowly Dividing Subpopulation of Lgr5+ Intestinal Stem Cells.

Cell Stem Cell 2017 06 9;20(6):801-816.e7. Epub 2017 Mar 9.

Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2017.02.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5774992PMC
June 2017

In vivo binding of PRDM9 reveals interactions with noncanonical genomic sites.

Genome Res 2017 04 23;27(4):580-590. Epub 2017 Mar 23.

Institut de Génétique Humaine UMR9002 CNRS-Université de Montpellier, 34396 Montpellier Cedex 05, France.

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http://dx.doi.org/10.1101/gr.217240.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5378176PMC
April 2017

A family-based genome-wide association study reveals an association of spondyloarthritis with MAPK14.

Ann Rheum Dis 2017 Jan 26;76(1):310-314. Epub 2016 Jul 26.

Faculty of Health Sciences Simone Veil, University of Versailles Saint-Quentin-en-Yvelines, Montigny-le-Bretonneux, France.

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http://dx.doi.org/10.1136/annrheumdis-2016-209449DOI Listing
January 2017

From Wet-Lab to Variations: Concordance and Speed of Bioinformatics Pipelines for Whole Genome and Whole Exome Sequencing.

Hum Mutat 2016 12 26;37(12):1263-1271. Epub 2016 Sep 26.

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

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http://dx.doi.org/10.1002/humu.23114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5129537PMC
December 2016

Distinct Trends of DNA Methylation Patterning in the Innate and Adaptive Immune Systems.

Cell Rep 2016 11;17(8):2101-2111

CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona 08028, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2016.10.054DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5889099PMC
November 2016

Chimpanzee genomic diversity reveals ancient admixture with bonobos.

Science 2016 10 27;354(6311):477-481. Epub 2016 Oct 27.

Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain. National Centre for Genomic Analysis-Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08028 Barcelona, Spain. Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia 08010, Spain.

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http://dx.doi.org/10.1126/science.aag2602DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5546212PMC
October 2016

PRKG1 and genetic diagnosis of early-onset thoracic aortic disease.

Eur J Clin Invest 2016 Sep 18;46(9):787-94. Epub 2016 Aug 18.

Xenética de Enfermidades Cardiovasculares e Oftalmolóxicas, Instituto de Investigación Sanitaria de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, A Coruña, Spain.

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http://dx.doi.org/10.1111/eci.12662DOI Listing
September 2016

Somatic Embryonic FGFR2 Mutations in Keratinocytic Epidermal Nevi.

J Invest Dermatol 2016 08 19;136(8):1718-1721. Epub 2016 Apr 19.

Department of Dermatology, Parc de Salut Mar, Hospital del Mar, Barcelona, Spain; Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain. Electronic address:

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http://dx.doi.org/10.1016/j.jid.2016.03.040DOI Listing
August 2016

Whole-genome single nucleotide polymorphism-based linkage analysis in spondyloarthritis multiplex families reveals a new susceptibility locus in 13q13.

Ann Rheum Dis 2016 07 14;75(7):1380-5. Epub 2015 Aug 14.

INSERM U1173, UFR Simone Veil, Versailles-Saint Quentin University, Saint-Quentin en Yvelines, France Université Paris Diderot, Sorbonne Paris Cité, Laboratoire d'Excellence, Paris, France Genetics Division, Ambroise Paré Hospital (AP-HP), Boulogne-Billancourt, France.

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http://dx.doi.org/10.1136/annrheumdis-2015-207720DOI Listing
July 2016

Saturation analysis for whole-genome bisulfite sequencing data.

Nat Biotechnol 2016 07 27;34(7):691-693. Epub 2016 Jun 27.

Medical Genomics, UCL Cancer Institute, University College London, London, UK.

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http://dx.doi.org/10.1038/nbt.3524DOI Listing
July 2016

Evolution of Robustness to Protein Mistranslation by Accelerated Protein Turnover.

PLoS Biol 2015 6;13(11):e1002291. Epub 2015 Nov 6.

Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary.

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http://www.umich.edu/~zhanglab/clubPaper/11_19_2015.pdf
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http://dx.plos.org/10.1371/journal.pbio.1002291
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http://dx.doi.org/10.1371/journal.pbio.1002291DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636289PMC
May 2016

MetaTrans: an open-source pipeline for metatranscriptomics.

Sci Rep 2016 05 23;6:26447. Epub 2016 May 23.

Digestive Research Unit, Vall d'Hebron Research Institute, Barcelona, 08035, Spain.

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http://dx.doi.org/10.1038/srep26447DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4876386PMC
May 2016

RNA sequencing validation of the Complexity INdex in SARComas prognostic signature.

Eur J Cancer 2016 Apr 23;57:104-11. Epub 2016 Feb 23.

Inserm U916, Institut Bergonié, Bordeaux, France; Département de pathologie, Institut Bergonié, Bordeaux, France. Electronic address:

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http://dx.doi.org/10.1016/j.ejca.2015.12.027DOI Listing
April 2016

The Fungus Candida albicans Tolerates Ambiguity at Multiple Codons.

Front Microbiol 2016 31;7:401. Epub 2016 Mar 31.

Health Sciences Program, Department of Medical Sciences, Institute of Biomedicine - iBiMED, University of Aveiro Aveiro, Portugal.

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http://dx.doi.org/10.3389/fmicb.2016.00401DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4814463PMC
April 2016

Colorectal adenomas contain multiple somatic mutations that do not coincide with synchronous adenocarcinoma specimens.

PLoS One 2015 16;10(3):e0119946. Epub 2015 Mar 16.

Cancer Genomics Group, IDIVAL, Instituto de Investigación Marqués de Valdecilla, Santander, Spain; Department of Pathology, Hospital Universitario Marqués de Valdecilla, Santander, Spain.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0119946PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4361059PMC
January 2016

A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing.

Nat Commun 2015 Dec 9;6:10001. Epub 2015 Dec 9.

CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.

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http://dx.doi.org/10.1038/ncomms10001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4682041PMC
December 2015

Runs of homozygosity reveal signatures of positive selection for reproduction traits in breed and non-breed horses.

BMC Genomics 2015 Oct 9;16:764. Epub 2015 Oct 9.

Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Bünteweg 17p, 30559, Hannover, Germany.

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http://dx.doi.org/10.1186/s12864-015-1977-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4600213PMC
October 2015

Genomic characterization of mutant laboratory mouse strains by exome sequencing and annotation lift-over.

BMC Genomics 2015 May 6;16:351. Epub 2015 May 6.

Centro Nacional de Análisis Genómico, Parc Científic de Barcelona - Torre I, Baldiri Reixac, 4, 08028, Barcelona, Spain.

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http://dx.doi.org/10.1186/s12864-015-1548-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4422528PMC
May 2015

Common and rare variant analysis in early-onset bipolar disorder vulnerability.

PLoS One 2014 11;9(8):e104326. Epub 2014 Aug 11.

Institut National de la Santé et de la Recherche Médicale U955, Psychiatrie Génétique, Créteil, France; Université Paris-Est, Faculté de Médecine, Créteil, France; Fondation FondaMental, Créteil, France; Assistance Publique - Hôpitaux de Paris, Hôpital Henri Mondor-Albert Chenevier, Pôle de Psychiatry, Créteil, France.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0104326PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4128749PMC
April 2015

Transcription-dependent generation of a specialized chromatin structure at the TCRβ locus.

J Immunol 2015 Apr 2;194(7):3432-43. Epub 2015 Mar 2.

Centre d'Immunologie de Marseille-Luminy, Aix-Marseille University, UM2, 13288 Marseille, France; INSERM, U1104, 13288 Marseille, France; Centre National de la Recherche Scientifique, UMR7280, F-13009 Marseille, France; INSERM U1090, Technological Advances for Genomics and Clinics, F-13009 Marseille, France; Aix-Marseille University, UMR-S 1090, Technological Advances for Genomics and Clinics, F-13009 Marseille, France;

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http://www.jimmunol.org/lookup/doi/10.4049/jimmunol.1400789
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http://dx.doi.org/10.4049/jimmunol.1400789DOI Listing
April 2015

Early-onset chronic axonal neuropathy, strokes, and hemolysis: inherited CD59 deficiency.

Neurology 2015 Mar 25;84(12):1220-4. Epub 2015 Feb 25.

From the Departments of Pediatric Neurology (G.H., B.S., H.T.), Neurology (C.T.), Pediatric Hematology (B.T., M.C.), and Radiology (K.K.O.), Hacettepe University Ankara, Turkey; Unité Mixte de Recherche (UMR)-986 (J. Maluenda, J. Melki), Inserm and University Paris Sud; Hematology Laboratory (C.A., V.P.), AP-HP, CHU Bicêtre, France; and Centro Nacional de Análisis Genómico (I.G.), Barcelona, Spain.

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http://dx.doi.org/10.1212/WNL.0000000000001391DOI Listing
March 2015

Comprehensive characterization of complex structural variations in cancer by directly comparing genome sequence reads.

Nat Biotechnol 2014 Nov 26;32(11):1106-12. Epub 2014 Oct 26.

1] Joint IRB-BSC Program in Computational Biology, Barcelona Supercomputing Center, Barcelona, Spain. [2] Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.

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http://dx.doi.org/10.1038/nbt.3027DOI Listing
November 2014

A comprehensive DNA methylation profile of epithelial-to-mesenchymal transition.

Cancer Res 2014 Oct 8;74(19):5608-19. Epub 2014 Aug 8.

Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat; Barcelona, Spain. Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Spain. Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.

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http://dx.doi.org/10.1158/0008-5472.CAN-13-3659DOI Listing
October 2014

Variation in genomic landscape of clear cell renal cell carcinoma across Europe.

Nat Commun 2014 Oct 29;5:5135. Epub 2014 Oct 29.

1] Department of Human Genetics, McGill University, 1205 Dr Penfield Avenue, Montreal, Quebec, Canada H3A 1B1 [2] Fondation Jean Dausset - Centre d'Etude du Polymorphisme Humain, 27 rue Juliette Dodu, 75010 Paris, France [3] Centre National de Génotypage, CEA - Institute de Génomique, 2 rue Gaston Crémieux, 91000 Evry, France.

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http://dx.doi.org/10.1038/ncomms6135DOI Listing
October 2014

ERBB2 in cat mammary neoplasias disclosed a positive correlation between RNA and protein low expression levels: a model for erbB-2 negative human breast cancer.

PLoS One 2013 26;8(12):e83673. Epub 2013 Dec 26.

Institute for Biotechnology and Bioengineering, Centre of Genomics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal ; Department of Genetics and Biotechnology, School of Life Sciences and Environment, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0083673PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3873372PMC
September 2014

Gibbon genome and the fast karyotype evolution of small apes.

Nature 2014 Sep;513(7517):195-201

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

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http://dx.doi.org/10.1038/nature13679DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4249732PMC
September 2014

A revisit of high collision energy effects on collision-induced dissociation spectra using matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry (MALDI-LIFT-TOF/TOF): application to the sequencing of RNA/DNA chimeras.

Rapid Commun Mass Spectrom 2014 Jul;28(13):1433-43

CEA/Institut de Génomique/Centre National de Génotypage, Bâtiment G2, 2 rue Gaston Crémieux, 91057, Evry Cedex, France.

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http://dx.doi.org/10.1002/rcm.6913DOI Listing
July 2014

Tyrosine phosphorylation of RNA polymerase II CTD is associated with antisense promoter transcription and active enhancers in mammalian cells.

Elife 2014 May 9;3:e02105. Epub 2014 May 9.

Centre d'Immunologie de Marseille-Luminy, Université Aix-Marseille, Marseille, France Centre National de la Recherche Scientifique (CNRS) UMR6102, Marseille, France Inserm U631, Marseille, France Institut de Génétique Moléculaire de Montpellier (IGMM), CNRS-UMR5535, Montpellier, France

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http://dx.doi.org/10.7554/eLife.02105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4042876PMC
May 2014

Structural studies of the sBBI/trypsin non-covalent complex using covalent modification and mass spectrometry.

Rapid Commun Mass Spectrom 2014 Mar;28(5):413-29

CEA/Institut de Génomique/Centre National de Génotypage, Evry, France; CEA/Institut de Génomique/Centre National de Séquençage, Evry, France.

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http://doi.wiley.com/10.1002/rcm.6797
Publisher Site
http://dx.doi.org/10.1002/rcm.6797DOI Listing
March 2014