Emanuele Raineri

Emanuele Raineri

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Emanuele Raineri

Emanuele Raineri

Publications by authors named "Emanuele Raineri"

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24Publications

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Recurrent somatic mutations reveal new insights into consequences of mutagenic processes in cancer.

Authors:
Miranda D Stobbe Gian A Thun Andrea Diéguez-Docampo Meritxell Oliva Justin P Whalley Emanuele Raineri Ivo G Gut

PLoS Comput Biol 2019 Nov 25;15(11):e1007496. Epub 2019 Nov 25.

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

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http://dx.doi.org/10.1371/journal.pcbi.1007496DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6901237PMC
November 2019

Labelled regulatory elements are pervasive features of the macrophage genome and are dynamically utilized by classical and alternative polarization signals.

Authors:
Attila Horvath Bence Daniel Lajos Szeles Ixchelt Cuaranta-Monroy Zsolt Czimmerer Lilla Ozgyin Laszlo Steiner Mate Kiss Zoltan Simandi Szilard Poliska Nikolas Giannakis Emanuele Raineri Ivo G Gut Benedek Nagy Laszlo Nagy

Nucleic Acids Res 2019 04;47(6):2778-2792

Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary.

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http://dx.doi.org/10.1093/nar/gkz118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6451134PMC
April 2019

Epigenetic regulation of gene expression in Chinese Hamster Ovary cells in response to the changing environment of a batch culture.

Authors:
Inmaculada Hernandez Heena Dhiman Gerald Klanert Vaibhav Jadhav Norbert Auer Michael Hanscho Martina Baumann Anna Esteve-Codina Marc Dabad Jessica Gómez Tyler Alioto Angelika Merkel Emanuele Raineri Simon Heath Daniel Rico Nicole Borth

Biotechnol Bioeng 2019 03 4;116(3):677-692. Epub 2019 Jan 4.

Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, Vienna, Austria.

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http://dx.doi.org/10.1002/bit.26891DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6492168PMC
March 2019

The neutral frequency spectrum of linked sites.

Authors:
Luca Ferretti Alexander Klassmann Emanuele Raineri Sebastián E Ramos-Onsins Thomas Wiehe Guillaume Achaz

Theor Popul Biol 2018 09 28;123:70-79. Epub 2018 Jun 28.

Institut de Systématique, Evolution, Biodiversité, UMR 7205, MNHN and Centre Interdisciplinaire de Recherche en Biologie, UMR 7241, Collége de France, Paris, France.

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https://linkinghub.elsevier.com/retrieve/pii/S00405809173013
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http://dx.doi.org/10.1016/j.tpb.2018.06.001DOI Listing
September 2018

Corrigendum: A novel translational control mechanism involving RNA structures within coding sequences.

Authors:
Jennifer Jungfleisch Danny D Nedialkova Ivan Dotu Katherine E Sloan Neus Martinez-Bosch Lukas Brüning Emanuele Raineri Pilar Navarro Markus T Bohnsack Sebastian A Leidel Juana Díez

Genome Res 2017 04;27(4):663

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http://dx.doi.org/10.1101/gr.222133.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5378183PMC
April 2017

A novel translational control mechanism involving RNA structures within coding sequences.

Authors:
Jennifer Jungfleisch Danny D Nedialkova Ivan Dotu Katherine E Sloan Neus Martinez-Bosch Lukas Brüning Emanuele Raineri Pilar Navarro Markus T Bohnsack Sebastian A Leidel Juana Díez

Genome Res 2017 01 7;27(1):95-106. Epub 2016 Nov 7.

Molecular Virology Group, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain.

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http://dx.doi.org/10.1101/gr.209015.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5204348PMC
January 2017

Decoding the DNA Methylome of Mantle Cell Lymphoma in the Light of the Entire B Cell Lineage.

Authors:
Ana C Queirós Renée Beekman Roser Vilarrasa-Blasi Martí Duran-Ferrer Guillem Clot Angelika Merkel Emanuele Raineri Nuria Russiñol Giancarlo Castellano Sílvia Beà Alba Navarro Marta Kulis Núria Verdaguer-Dot Pedro Jares Anna Enjuanes María José Calasanz Anke Bergmann Inga Vater Itziar Salaverría Harmen J G van de Werken Wyndham H Wilson Avik Datta Paul Flicek Romina Royo Joost Martens Eva Giné Armando Lopez-Guillermo Hendrik G Stunnenberg Wolfram Klapper Christiane Pott Simon Heath Ivo G Gut Reiner Siebert Elías Campo José I Martín-Subero

Cancer Cell 2016 Nov;30(5):806-821

Departamento de Fundamentos Clínicos, Universitat de Barcelona, Barcelona 08036, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona 08036, Spain. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2016.09.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5805090PMC
November 2016

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

Authors:
Ronald P Schuyler Angelika Merkel Emanuele Raineri Lucia Altucci Edo Vellenga Joost H A Martens Farzin Pourfarzad Taco W Kuijpers Frances Burden Samantha Farrow Kate Downes Willem H Ouwehand Laura Clarke Avik Datta Ernesto Lowy Paul Flicek Mattia Frontini Hendrik G Stunnenberg José I Martín-Subero Ivo Gut Simon Heath

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

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

Authors:
Tyler S Alioto Ivo Buchhalter Sophia Derdak Barbara Hutter Matthew D Eldridge Eivind Hovig Lawrence E Heisler Timothy A Beck Jared T Simpson Laurie Tonon Anne-Sophie Sertier Ann-Marie Patch Natalie Jäger Philip Ginsbach Ruben Drews Nagarajan Paramasivam Rolf Kabbe Sasithorn Chotewutmontri Nicolle Diessl Christopher Previti Sabine Schmidt Benedikt Brors Lars Feuerbach Michael Heinold Susanne Gröbner Andrey Korshunov Patrick S Tarpey Adam P Butler Jonathan Hinton David Jones Andrew Menzies Keiran Raine Rebecca Shepherd Lucy Stebbings Jon W Teague Paolo Ribeca Francesc Castro Giner Sergi Beltran Emanuele Raineri Marc Dabad Simon C Heath Marta Gut Robert E Denroche Nicholas J Harding Takafumi N Yamaguchi Akihiro Fujimoto Hidewaki Nakagawa Víctor Quesada Rafael Valdés-Mas Sigve Nakken Daniel Vodák Lawrence Bower Andrew G Lynch Charlotte L Anderson Nicola Waddell John V Pearson Sean M Grimmond Myron Peto Paul Spellman Minghui He Cyriac Kandoth Semin Lee John Zhang Louis Létourneau Singer Ma Sahil Seth David Torrents Liu Xi David A Wheeler Carlos López-Otín Elías Campo Peter J Campbell Paul C Boutros Xose S Puente Daniela S Gerhard Stefan M Pfister John D McPherson Thomas J Hudson Matthias Schlesner Peter Lichter Roland Eils David T W Jones Ivo G Gut

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

Whole-genome fingerprint of the DNA methylome during human B cell differentiation.

Authors:
Marta Kulis Angelika Merkel Simon Heath Ana C Queirós Ronald P Schuyler Giancarlo Castellano Renée Beekman Emanuele Raineri Anna Esteve Guillem Clot Néria Verdaguer-Dot Martí Duran-Ferrer Nuria Russiñol Roser Vilarrasa-Blasi Simone Ecker Vera Pancaldi Daniel Rico Lidia Agueda Julie Blanc David Richardson Laura Clarke Avik Datta Marien Pascual Xabier Agirre Felipe Prosper Diego Alignani Bruno Paiva Gersende Caron Thierry Fest Marcus O Muench Marina E Fomin Seung-Tae Lee Joseph L Wiemels Alfonso Valencia Marta Gut Paul Flicek Hendrik G Stunnenberg Reiner Siebert Ralf Küppers Ivo G Gut Elías Campo José I Martín-Subero

Nat Genet 2015 Jul 8;47(7):746-56. Epub 2015 Jun 8.

Institut d'Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), Department of Anatomic Pathology, Pharmacology and Microbiology, University of Barcelona, Barcelona, Spain.

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http://dx.doi.org/10.1038/ng.3291DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5444519PMC
July 2015

Whole-epigenome analysis in multiple myeloma reveals DNA hypermethylation of B cell-specific enhancers.

Authors:
Xabier Agirre Giancarlo Castellano Marien Pascual Simon Heath Marta Kulis Victor Segura Anke Bergmann Anna Esteve Angelika Merkel Emanuele Raineri Lidia Agueda Julie Blanc David Richardson Laura Clarke Avik Datta Nuria Russiñol Ana C Queirós Renée Beekman Juan R Rodríguez-Madoz Edurne San José-Enériz Fang Fang Norma C Gutiérrez José M García-Verdugo Michael I Robson Eric C Schirmer Elisabeth Guruceaga Joost H A Martens Marta Gut Maria J Calasanz Paul Flicek Reiner Siebert Elías Campo Jesús F San Miguel Ari Melnick Hendrik G Stunnenberg Ivo G Gut Felipe Prosper José I Martín-Subero

Genome Res 2015 Apr 2;25(4):478-87. Epub 2015 Feb 2.

Unidad de Hematopatología, Servicio de Anatomía Patológica, Hospital Clínic, Universitat de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain;

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http://dx.doi.org/10.1101/gr.180240.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4381520PMC
April 2015

A note on exact differences between beta distributions in genomic (Methylation) studies.

Authors:
Emanuele Raineri Marc Dabad Simon Heath

PLoS One 2014 13;9(5):e97349. Epub 2014 May 13.

Statistical Genomics, Centro Nacional de Análisis Genómico, Barcelona, Catalonia, Spain.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0097349PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4019606PMC
December 2014

The genome sequencing of an albino Western lowland gorilla reveals inbreeding in the wild.

Authors:
Javier Prado-Martinez Irene Hernando-Herraez Belen Lorente-Galdos Marc Dabad Oscar Ramirez Carlos Baeza-Delgado Carlos Morcillo-Suarez Can Alkan Fereydoun Hormozdiari Emanuele Raineri Jordi Estellé Marcos Fernandez-Callejo Mònica Valles Lars Ritscher Torsten Schöneberg Elisa de la Calle-Mustienes Sònia Casillas Raquel Rubio-Acero Marta Melé Johannes Engelken Mario Caceres Jose Luis Gomez-Skarmeta Marta Gut Jaume Bertranpetit Ivo G Gut Teresa Abello Evan E Eichler Ismael Mingarro Carles Lalueza-Fox Arcadi Navarro Tomas Marques-Bonet

BMC Genomics 2013 May 31;14:363. Epub 2013 May 31.

Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Barcelona 08003, Spain.

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http://dx.doi.org/10.1186/1471-2164-14-363DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3673836PMC
May 2013

Dissecting structural and nucleotide genome-wide variation in inbred Iberian pigs.

Authors:
Anna Esteve-Codina Yogesh Paudel Luca Ferretti Emanuele Raineri Hendrik-Jan Megens Luis Silió María C Rodríguez Martein A M Groenen Sebastian E Ramos-Onsins Miguel Pérez-Enciso

BMC Genomics 2013 Mar 5;14:148. Epub 2013 Mar 5.

Center for Research in Agricultural Genomics (CRAG), Campus UAB, Bellaterra, 08193, Spain.

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http://dx.doi.org/10.1186/1471-2164-14-148DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3601988PMC
March 2013

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

Authors:
Thasso Griebel Benedikt Zacher Paolo Ribeca Emanuele Raineri Vincent Lacroix Roderic Guigó Michael Sammeth

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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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
Publisher Site
http://dx.doi.org/10.1093/nar/gks666DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3488205PMC
November 2012

SNP calling by sequencing pooled samples.

Authors:
Emanuele Raineri Luca Ferretti Anna Esteve-Codina Bruno Nevado Simon Heath Miguel Pérez-Enciso

BMC Bioinformatics 2012 Sep 20;13:239. Epub 2012 Sep 20.

Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, Barcelona, 08028, Spain.

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http://dx.doi.org/10.1186/1471-2105-13-239DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3475117PMC
September 2012

Neutrality tests for sequences with missing data.

Authors:
Luca Ferretti Emanuele Raineri Sebastian Ramos-Onsins

Genetics 2012 Aug 1;191(4):1397-401. Epub 2012 Jun 1.

Centre for Research in Agricultural Genomics, 08193 Bellaterra, Spain.

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http://dx.doi.org/10.1534/genetics.112.139949DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416018PMC
August 2012

Fast computation and applications of genome mappability.

Authors:
Thomas Derrien Jordi Estellé Santiago Marco Sola David G Knowles Emanuele Raineri Roderic Guigó Paolo Ribeca

PLoS One 2012 19;7(1):e30377. Epub 2012 Jan 19.

Institut de Génétique et Développement (IGDR), Université Rennes 1, Rennes, France.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0030377PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3261895PMC
June 2012

BlastR--fast and accurate database searches for non-coding RNAs.

Authors:
Giovanni Bussotti Emanuele Raineri Ionas Erb Matthias Zytnicki Andreas Wilm Emmanuel Beaudoing Philipp Bucher Cedric Notredame

Nucleic Acids Res 2011 Sep 30;39(16):6886-95. Epub 2011 May 30.

Bioinformatics and Genomics program, Center for Genomic Regulation (CRG) and UPF, Barcelona, C/ D. Aiguader, 88, 08003 Barcelona, Spain.

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http://dx.doi.org/10.1093/nar/gkr335DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3167602PMC
September 2011

Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis.

Authors:
Rami A Dalloul Julie A Long Aleksey V Zimin Luqman Aslam Kathryn Beal Le Ann Blomberg Pascal Bouffard David W Burt Oswald Crasta Richard P M A Crooijmans Kristal Cooper Roger A Coulombe Supriyo De Mary E Delany Jerry B Dodgson Jennifer J Dong Clive Evans Karin M Frederickson Paul Flicek Liliana Florea Otto Folkerts Martien A M Groenen Tim T Harkins Javier Herrero Steve Hoffmann Hendrik-Jan Megens Andrew Jiang Pieter de Jong Pete Kaiser Heebal Kim Kyu-Won Kim Sungwon Kim David Langenberger Mi-Kyung Lee Taeheon Lee Shrinivasrao Mane Guillaume Marcais Manja Marz Audrey P McElroy Thero Modise Mikhail Nefedov Cédric Notredame Ian R Paton William S Payne Geo Pertea Dennis Prickett Daniela Puiu Dan Qioa Emanuele Raineri Magali Ruffier Steven L Salzberg Michael C Schatz Chantel Scheuring Carl J Schmidt Steven Schroeder Stephen M J Searle Edward J Smith Jacqueline Smith Tad S Sonstegard Peter F Stadler Hakim Tafer Zhijian Jake Tu Curtis P Van Tassell Albert J Vilella Kelly P Williams James A Yorke Liqing Zhang Hong-Bin Zhang Xiaojun Zhang Yang Zhang Kent M Reed

PLoS Biol 2010 Sep 7;8(9). Epub 2010 Sep 7.

Avian Immunobiology Laboratory, Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, Virginia, United States of America.

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http://dx.doi.org/10.1371/journal.pbio.1000475DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2935454PMC
September 2010

A more precise characterization of chaperonin substrates.

Authors:
Emanuele Raineri Paolo Ribeca Luis Serrano Tobias Maier

Bioinformatics 2010 Jul 2;26(14):1685-9. Epub 2010 Jun 2.

CNAG Centro Nacional de Análisis Genómico, Parc Cientific de Barcelona, Baldiri Reixac 4, E-08028 Barcelona, Spain.

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http://dx.doi.org/10.1093/bioinformatics/btq287DOI Listing
July 2010

Impact of genome reduction on bacterial metabolism and its regulation.

Authors:
Eva Yus Tobias Maier Konstantinos Michalodimitrakis Vera van Noort Takuji Yamada Wei-Hua Chen Judith A H Wodke Marc Güell Sira Martínez Ronan Bourgeois Sebastian Kühner Emanuele Raineri Ivica Letunic Olga V Kalinina Michaela Rode Richard Herrmann Ricardo Gutiérrez-Gallego Robert B Russell Anne-Claude Gavin Peer Bork Luis Serrano

Science 2009 Nov;326(5957):1263-8

Centre for Genomic Regulation (CRG) and Universitat Pompeu Fabra, Avenida Dr. Aiguader 88, 08003 Barcelona, Spain.

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http://dx.doi.org/10.1126/science.1177263DOI Listing
November 2009

Faster exact Markovian probability functions for motif occurrences: a DFA-only approach.

Authors:
Paolo Ribeca Emanuele Raineri

Bioinformatics 2008 Dec 9;24(24):2839-48. Epub 2008 Oct 9.

Bioinformatics and Genomics Unit, Center for Genomic Regulation, C/ Dr.Aiguader 88, E08003 Barcelona, Spain.

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http://dx.doi.org/10.1093/bioinformatics/btn525DOI Listing
December 2008

Evolvability and hierarchy in rewired bacterial gene networks.

Authors:
Mark Isalan Caroline Lemerle Konstantinos Michalodimitrakis Carsten Horn Pedro Beltrao Emanuele Raineri Mireia Garriga-Canut Luis Serrano

Nature 2008 Apr;452(7189):840-5

EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), UPF, 08003 Barcelona, Spain.

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http://dx.doi.org/10.1038/nature06847DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2666274PMC
April 2008