User profiles for Ionas Erb

Ionas Erb

Centre for Genomic Regulation (CRG), Barcelona
Verified email at crg.eu
Cited by 2644

Understanding sequencing data as compositions: an outlook and review

TP Quinn, I Erb, MF Richardson, TM Crowley - Bioinformatics, 2018 - academic.oup.com
Motivation Although seldom acknowledged explicitly, count data generated by sequencing
platforms exist as compositions for which the abundance of each component (eg gene or …

Multiple sequence alignment modeling: methods and applications

…, JM Chang, C Kemena, G Bussotti, I Erb… - Briefings in …, 2016 - academic.oup.com
This review provides an overview on the development of Multiple sequence alignment (MSA)
methods and their main applications. It is focused on progress made over the past decade. …

[HTML][HTML] Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization …

…, M Hernández-Oñate, AE Minoche, I Erb… - Genome biology, 2016 - Springer
Background Legumes are the third largest family of angiosperms and the second most
important crop class. Legume genomes have been shaped by extensive large-scale gene …

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

TP Quinn, I Erb, G Gloor, C Notredame… - …, 2019 - academic.oup.com
Background Next-generation sequencing (NGS) has made it possible to determine the
sequence and relative abundance of all nucleotides in a biological or environmental sample. A …

[HTML][HTML] Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx

…, JM Rodríguez, F Câmara, E Lowy, L Cozzuto, I Erb… - Genome biology, 2016 - Springer
Background Genomic studies of endangered species provide insights into their evolution and
demographic history, reveal patterns of genomic erosion that might limit their viability, and …

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

M Pachkov, I Erb, N Molina… - Nucleic acids …, 2007 - academic.oup.com
SwissRegulon ( ) is a database containing genome-wide annotations of regulatory sites in
the intergenic regions of genomes. The regulatory site annotations are produced using a …

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

A Taddei, G Van Houwe, S Nagai, I Erb… - Genome …, 2009 - genome.cshlp.org
Budding yeast telomeres and cryptic mating-type loci are enriched at the nuclear envelope,
forming foci that sequester silent information regulators (SIR factors), much as …

Alignathon: a competitive assessment of whole-genome alignment methods

…, J Kim, C Kemena, JM Chang, I Erb… - Genome …, 2014 - genome.cshlp.org
Multiple sequence alignments (MSAs) are a prerequisite for a wide variety of evolutionary
analyses. Published assessments and benchmark data sets for protein and, to a lesser extent, …

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

P Arnold, I Erb, M Pachkov, N Molina… - …, 2012 - academic.oup.com
Motivation: Probabilistic approaches for inferring transcription factor binding sites (TFBSs)
and regulatory motifs from DNA sequences have been developed for over two decades. …

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

…, G Bussotti, JM Chang, P Di Tommaso, I Erb… - Nature protocols, 2011 - nature.com
T-Coffee (Tree-based consistency objective function for alignment evaluation) is a versatile
multiple sequence alignment (MSA) method suitable for aligning most types of biological …