Ionas Erb

发表

Amalgams: data-driven amalgamation for the dimensionality reduction of compositional data

Thomas P. Quinn, Ionas Erb, I. Erb, 2020, NAR genomics and bioinformatics.

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

Mikhail Pachkov, Phil Arnold, Erik van Nimwegen, 2012, Bioinform..

Understanding sequencing data as compositions: an outlook and review

Thomas P. Quinn, Mark F. Richardson, Tamsyn M. Crowley, 2017 .

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

Ionas Erb, Jose Espinosa-Carrasco, Toni Hermoso Pulido, 2018, iScience.

Understanding sequencing data as compositions: an outlook and review

Thomas P. Quinn, Mark F. Richardson, Tamsyn M. Crowley, 2017, bioRxiv.

Alignathon: A competitive assessment of whole genome alignment methods

David Haussler, Inna Dubchak, Brian J. Raney, 2014 .

Another look at microbe–metabolite interactions: how scale invariant correlations can outperform a neural network

Thomas P. Quinn, Ionas Erb, I. Erb, 2019, bioRxiv.

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

Ionas Erb, Cedric Notredame, Thomas P Quinn, 2019, GigaScience.

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

Hafid Laayouni, Paolo Di Tommaso, Ionas Erb, 2019, Nature Biotechnology.

How should we measure proportionality on relative gene expression data?

Cédric Notredame, Ionas Erb, C. Notredame, 2016, Theory in Biosciences.

Multiple sequence alignment modeling: methods and applications

Cédric Notredame, Carsten Kemena, Jia-Ming Chang, 2016, Briefings Bioinform..

Editorial: Compositional data analysis and related methods applied to genomics—a first special issue from NAR Genomics and Bioinformatics

Gregory B. Gloor, Thomas P. Quinn, Ionas Erb, 2020, NAR genomics and bioinformatics.

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

Ionas Erb, Thomas P Quinn, T. Quinn, 2020, mSystems.

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

Erik van Nimwegen, Ionas Erb, Nacho Molina, 2006, Nucleic Acids Res..

Aitchison's Compositional Data Analysis 40 Years On: A Reappraisal

Michael Greenacre, Thomas Quinn, Ionas Erb, 2022 .

A Critique of Differential Abundance Analysis, and Advocacy for an Alternative

Ionas Erb, Elliott Gordon-Rodriguez, Thomas P Quinn, 2021, 2104.07266.

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

Thomas P. Quinn, Mark F. Richardson, Tamsyn M. Crowley, 2018, bioRxiv.

Genome-wide expression profiling, in vivo DNA binding analysis, and probabilistic motif prediction reveal novel Abf1 target genes during fermentation, respiration, and sporulation in yeast.

Ulrich Schlecht, Michael Primig, Alain Nicolas, 2008, Molecular biology of the cell.

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

Paolo Di Tommaso, Jia-Ming Chang, Jean-François Taly, 2014, Methods in molecular biology.

Transcription Factor Binding Site Positioning in Yeast: Proximal Promoter Motifs Characterize TATA-Less Promoters

Ionas Erb, Erik van Nimwegen, E. van Nimwegen, 2011, PloS one.

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

Matthias Zytnicki, Andreas Wilm, Philipp Bucher, 2011, Nucleic acids research.

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

Carsten Kemena, Paolo Di Tommaso, Ionas Erb, 2011, Nature Protocols.

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

Enrique Blanco, Ionas Erb, Eduardo Eyras, 2012, Nucleic acids research.

Statistical Features of Yeast ’ s Transcriptional Regulatory Code

Erik van Nimwegen, Ionas Erb, E. Nimwegen, 2006 .

Fast and accurate large multiple sequence alignments using root-to-leave regressive computation

Hafid Laayouni, Fyodor A. Kondrashov, Paolo Di Tommaso, 2018 .

Alignathon: a competitive assessment of whole-genome alignment methods

David Haussler, Inna Dubchak, Ngan Nguyen, 2014, bioRxiv.

Differential proportionality –a normalization-free approach to differential gene expression

Thomas P. Quinn, Ionas Erb, David R. Lovell, 2017, bioRxiv.