Emanuele Raineri

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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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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April 2017

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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November 2016

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

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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November 2016

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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January 2017

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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December 2015

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

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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July 2015

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

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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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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December 2014

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

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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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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March 2013

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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September 2012

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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November 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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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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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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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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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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July 2010

Impact of genome reduction on bacterial metabolism and its regulation.

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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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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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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April 2008

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