Publications by authors named "Ionas Erb"

27Publications

Interpretable Log Contrasts for the Classification of Health Biomarkers: a New Approach to Balance Selection.

mSystems 2020 Apr 7;5(2). Epub 2020 Apr 7.

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/mSystems.00230-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7141889PMC
April 2020

Large multiple sequence alignments with a root-to-leaf regressive method.

Nat Biotechnol 2019 12 2;37(12):1466-1470. Epub 2019 Dec 2.

Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41587-019-0333-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6894943PMC
December 2019

A field guide for the compositional analysis of any-omics data.

Gigascience 2019 09;8(9)

Poultry Hub Australia, University of New England, Elm Avenue, Armidale New South Wales 2351, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/gigascience/giz107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6755255PMC
September 2019

Pergola-web: a web server for the visualization and analysis of longitudinal behavioral data using repurposed genomics tools and standards.

Nucleic Acids Res 2019 07;47(W1):W600-W604

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkz414DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6602478PMC
July 2019

Impaired development of neocortical circuits contributes to the neurological alterations in DYRK1A haploinsufficiency syndrome.

Neurobiol Dis 2019 07 1;127:210-222. Epub 2019 Mar 1.

Instituto de Biología Molecular de Barcelona (IBMB), CSIC, 08028 Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.nbd.2019.02.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6753933PMC
July 2019

Pergola: Boosting Visualization and Analysis of Longitudinal Data by Unlocking Genomic Analysis Tools.

iScience 2018 Nov 26;9:244-257. Epub 2018 Oct 26.

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.isci.2018.10.023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6231116PMC
November 2018

Understanding sequencing data as compositions: an outlook and review.

Bioinformatics 2018 08;34(16):2870-2878

Bioinformatics Core Research Group, Deakin University, Geelong, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/bty175DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6084572PMC
August 2018

Time-course and dynamics of obesity-related behavioral changes induced by energy-dense foods in mice.

Addict Biol 2018 03 10;23(2):531-543. Epub 2018 Jan 10.

Cellular and Systems Neurobiology, Systems Biology Program, The Barcelona Institute of Science and Technology, Centre for Genomic Regulation (CRG), Spain.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1111/adb.12595DOI Listing
March 2018

Extinction and reinstatement of an operant responding maintained by food in different models of obesity.

Addict Biol 2018 03 28;23(2):544-555. Epub 2017 Dec 28.

Laboratori de Neurofarmacologia. Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1111/adb.12597DOI Listing
March 2018

Combined Treatment With Environmental Enrichment and (-)-Epigallocatechin-3-Gallate Ameliorates Learning Deficits and Hippocampal Alterations in a Mouse Model of Down Syndrome.

eNeuro 2016 Sep-Oct;3(5). Epub 2016 Nov 8.

Cellular and Systems Neurobiology, Systems Biology Program, the Barcelona Institute of Science and Technology, Centre for Genomic Regulation (CRG), 08003, Barcelona, Spain; Human Pharmacology and Clinical Neurosciences Research Group, Neurosciences Research Program, Hospital Del Mar Medical Research Institute (IMIM), Barcelona, 08003, Spain; Centro De Investigación Biomédica En Red De Enfermedades Raras, Madrid, 28029, Spain.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1523/ENEURO.0103-16.2016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5099603PMC
October 2017

How should we measure proportionality on relative gene expression data?

Theory Biosci 2016 Jun 13;135(1-2):21-36. Epub 2016 Jan 13.

Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003, Barcelona, Spain.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s12064-015-0220-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4870310PMC
June 2016

Principal Component Analysis of the Effects of Environmental Enrichment and (-)-epigallocatechin-3-gallate on Age-Associated Learning Deficits in a Mouse Model of Down Syndrome.

Front Behav Neurosci 2015 11;9:330. Epub 2015 Dec 11.

Systems Biology Program, Cellular and Systems Neurobiology, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology Barcelona, Spain ; Centre for Genomic Regulation, Universitat Pompeu Fabra Barcelona, Spain ; Centro de Investigación Biomédica en Red de Enfermedades Raras Barcelona, Spain.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.3389/fnbeh.2015.00330DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4675859PMC
December 2015

Third Report on Chicken Genes and Chromosomes 2015.

Authors:
Michael Schmid Jacqueline Smith David W Burt Bronwen L Aken Parker B Antin Alan L Archibald Chris Ashwell Perry J Blackshear Clarissa Boschiero C Titus Brown Shane C Burgess Hans H Cheng William Chow Derrick J Coble Amanda Cooksey Richard P M A Crooijmans Joana Damas Richard V N Davis Dirk-Jan de Koning Mary E Delany Thomas Derrien Takele T Desta Ian C Dunn Matthew Dunn Hans Ellegren Lél Eöry Ionas Erb Marta Farré Mario Fasold Damarius Fleming Paul Flicek Katie E Fowler Laure Frésard David P Froman Valerie Garceau Paul P Gardner Almas A Gheyas Darren K Griffin Martien A M Groenen Thomas Haaf Olivier Hanotte Alan Hart Julien Häsler S Blair Hedges Jana Hertel Kerstin Howe Allen Hubbard David A Hume Pete Kaiser Darek Kedra Stephen J Kemp Christophe Klopp Kalmia E Kniel Richard Kuo Sandrine Lagarrigue Susan J Lamont Denis M Larkin Raman A Lawal Sarah M Markland Fiona McCarthy Heather A McCormack Marla C McPherson Akira Motegi Stefan A Muljo Andrea Münsterberg Rishi Nag Indrajit Nanda Michael Neuberger Anne Nitsche Cedric Notredame Harry Noyes Rebecca O'Connor Elizabeth A O'Hare Andrew J Oler Sheila C Ommeh Helio Pais Michael Persia Frédérique Pitel Likit Preeyanon Pablo Prieto Barja Elizabeth M Pritchett Douglas D Rhoads Charmaine M Robinson Michael N Romanov Max Rothschild Pierre-François Roux Carl J Schmidt Alisa-Sophia Schneider Matthew G Schwartz Steve M Searle Michael A Skinner Craig A Smith Peter F Stadler Tammy E Steeves Claus Steinlein Liang Sun Minoru Takata Igor Ulitsky Qing Wang Ying Wang Wesley C Warren Jonathan M D Wood David Wragg Huaijun Zhou

Cytogenet Genome Res 2015 14;145(2):78-179. Epub 2015 Jul 14.

Department of Human Genetics, University of Würzburg, Würzburg, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1159/000430927DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5120589PMC
October 2015

Alignathon: a competitive assessment of whole-genome alignment methods.

Genome Res 2014 Dec 1;24(12):2077-89. Epub 2014 Oct 1.

Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA; Biomolecular Engineering Department, University of California Santa Cruz, Santa Cruz, California 95064, USA;

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.174920.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4248324PMC
December 2014

T-Coffee: Tree-based consistency objective function for alignment evaluation.

Methods Mol Biol 2014 ;1079:117-29

Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra, Barcelona, Spain.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/978-1-62703-646-7_7DOI Listing
May 2014

Efficient and interpretable prediction of protein functional classes by correspondence analysis and compact set relations.

PLoS One 2013 11;8(10):e75542. Epub 2013 Oct 11.

Comparative Bioinformatics, Bioinformatics and Genomics, Centre for Genomic Regulation (CRG), Barcelona, Spain ; Universitat Pompeu Fabra (UPF), Barcelona, Spain.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0075542PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3795737PMC
July 2014

MotEvo: integrated Bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences.

Bioinformatics 2012 Feb;28(4):487-94

Biozentrum, University of Basel, Swiss Institute of Bioinformatics, Klingelbergstrasse 50-70, 4056 Basel, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btr695DOI Listing
February 2012

Use of ChIP-Seq data for the design of a multiple promoter-alignment method.

Nucleic Acids Res 2012 Apr 9;40(7):e52. Epub 2012 Jan 9.

Bioinformatics and Genomics program, Centre for Genomic Regulation and UPF, 08003 Barcelona, Spain.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkr1292DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3326335PMC
April 2012

Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures.

Nat Protoc 2011 Nov;6(11):1669-82

Comparative Bioinformatics Group, Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra, Barcelona, Spain.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nprot.2011.393DOI Listing
November 2011

Transcription factor binding site positioning in yeast: proximal promoter motifs characterize TATA-less promoters.

PLoS One 2011 9;6(9):e24279. Epub 2011 Sep 9.

Bioinformatics and Genomics program, Center for Genomic Regulation and Pompeu Fabra University, Barcelona, Spain.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0024279PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3170328PMC
March 2012

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

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.

View Article

Download full-text PDF

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

The functional importance of telomere clustering: global changes in gene expression result from SIR factor dispersion.

Genome Res 2009 Apr 29;19(4):611-25. Epub 2009 Jan 29.

Friedrich Miescher Institute for Biomedical Research and National Center for Competence in Research "Frontiers in Genetics," CH-4058 Basel, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.083881.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2665780PMC
April 2009

SwissRegulon: a database of genome-wide annotations of regulatory sites.

Nucleic Acids Res 2007 Jan 27;35(Database issue):D127-31. Epub 2006 Nov 27.

Biozentrum, The University of Basel, Klingelbergstrasse 50/70, 4056-CH, Basel, Switzerland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkl857DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1716717PMC
January 2007