User profiles for Ionas Erb
Ionas ErbCentre 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 …
platforms exist as compositions for which the abundance of each component (eg gene or …
Multiple sequence alignment modeling: methods and applications
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. …
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 …
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 …
important crop class. Legume genomes have been shaped by extensive large-scale gene …
A field guide for the compositional analysis of any-omics data
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 …
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
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 …
demographic history, reveal patterns of genomic erosion that might limit their viability, and …
SwissRegulon: a database of genome-wide annotations of regulatory sites
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 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
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 …
forming foci that sequester silent information regulators (SIR factors), much as …
Alignathon: a competitive assessment of whole-genome alignment methods
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, …
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
Motivation: Probabilistic approaches for inferring transcription factor binding sites (TFBSs)
and regulatory motifs from DNA sequences have been developed for over two decades. …
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
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 …
multiple sequence alignment (MSA) method suitable for aligning most types of biological …