I. Erb

发表

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

J. González, C. Notredame, S. Catuara-Solarz, 2016, eNeuro.

On a Notion of Linear Replicator Equations

N. Ay, I. Erb, 2005 .

Third Report on Chicken Genes and Chromosomes 2015

Bronwen L. Aken, Hans H. Cheng, Andrew J. Oler, 2015, Cytogenetic and Genome Research.

Alignathon: a competitive assessment of whole-genome alignment methods

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

Using balances to engineer features for the classification of health biomarkers: a new approach to balance selection

I. Erb, T. Quinn, Ionas Erb, 2019, bioRxiv.

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

M. Tress, J. Rodriguez, A. Valencia, 2016, Genome Biology.

Multi-Information in the Thermodynamic Limit

N. Ay, I. Erb, 2004 .

Partial correlations in compositional data analysis

I. Erb, Ionas Erb, 2019, Applied Computing and Geosciences.

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

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

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

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

Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes

Juliane C. Dohm, R. Guigó, J. Dohm, 2016, Genome Biology.

Efficient and Interpretable Prediction of Protein Functional Classes by Correspondence Analysis and Compact Set Relations

C. Tang, C. Notredame, W. Hsu, 2013, PloS one.

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

J. Lucas, I. Erb, S. de la Luna, 2018, bioRxiv.

Power Transformations of Relative Count Data as a Shrinkage Problem

I. Erb, 2022, 2205.09215.

Four layer multi-omics reveals molecular responses to aneuploidy in Leishmania

C. Notredame, S. Sundar, I. Erb, 2021, bioRxiv.

Examining microbe–metabolite correlations by linear methods

Thomas P. Quinn, I. Erb, Ionas Erb, 2021, Nature methods.

Protocol for Measuring Compulsive-like Feeding Behavior in Mice.

C. Notredame, Jose Espinosa-Carrasco, I. Erb, 2019, Bio-protocol.

Improving sequence alignments with AlphaFold2 regardless of structural modeling accuracy

C. Notredame, I. Erb, Athanasios Baltzis, 2022, bioRxiv.

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

M. Greenacre, E. Grunsky, J. Bacon-Shone, 2022, 2201.05197.

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

C. Notredame, J. Ponomarenko, Jose Espinosa-Carrasco, 2019, Nucleic Acids Res..

Compositional Covariance Shrinkage and Regularised Partial Correlations

C. Notredame, I. Erb, Suzanne Jin, 2022, 2212.00496.

Highly significant improvement of protein sequence alignments with AlphaFold2

C. Notredame, I. Erb, Athanasios Baltzis, 2022, Bioinform..

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.

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

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

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

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

Power transformations of relative count data as a shrinkage problem

I. Erb, Ionas Erb, 2022, Information Geometry.

Multiple sequence alignment modeling: methods and applications

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

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

E. van Nimwegen, S. Nagai, S. Gasser, 2009, Genome research.

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

C. Notredame, Jose Espinosa-Carrasco, I. Erb, 2018, Addiction biology.

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

J. Lucas, I. Erb, S. de la Luna, 2018, Neurobiology of Disease.

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

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

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..

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

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

Statistical Features of Yeast ’ s Transcriptional Regulatory Code

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

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

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

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.

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

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

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

J. González, C. Notredame, S. Catuara-Solarz, 2015, Front. Behav. Neurosci..

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.

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

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

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.

Understanding sequencing data as compositions: an outlook and review

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

How should we measure proportionality on relative gene expression data?

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

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

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

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

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

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

C. Notredame, F. Kondrashov, I. Erb, 2019, Nature Biotechnology.

Multiple Sequence Alignment Computation Using the T-Coffee Regressive Algorithm Implementation.

C. Notredame, I. Erb, Evan W. Floden, 2021, Methods in molecular biology.

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

C. Notredame, Jose Espinosa-Carrasco, I. Erb, 2018, Addiction biology.

Aitchison’s Compositional Data Analysis 40 Years on: A Reappraisal

M. Greenacre, E. Grunsky, J. Bacon-Shone, 2022, Statistical Science.

The Information-Geometric Perspective of Compositional Data Analysis

N. Ay, I. Erb, 2020, 2005.11510.