List of works - Yves Moreau

A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes.

scientific article

A Simple Genetic Algorithm for Biomarker Mining

A bioinformatics e-dating story: computational prediction and prioritization of receptor-ligand pairs

A genetic algorithm for the detection of new cis-regulatory modules in sets of coregulated genes

article

A guide to web tools to prioritize candidate genes

scientific article published on 21 March 2010

A human phenome-interactome network of protein complexes implicated in genetic disorders

scientific article (publication date: March 2007)

ACE-inhibition induces a cardioprotective transcriptional response in the metabolic syndrome heart

scientific article published in Scientific Reports

Adaptive quality-based clustering of gene expression profiles.

scientific article published in May 2002

AliBiMotif: Integrating alignment and biclustering to unravel transcription factor binding sites in DNA sequences

scientific article published on January 1, 2012

An expanded evaluation of protein function prediction methods shows an improvement in accuracy ⬇️

scientific article

An experimental loop design for the detection of constitutional chromosomal aberrations by array CGH.

scientific article

An unbiased evaluation of gene prioritization tools

article

Annotate-it: a Swiss-knife approach to annotation, analysis and interpretation of single nucleotide variation in human disease

scientific article (publication date: 2012)

Array comparative genomic hybridization and computational genome annotation in constitutional cytogenetics: suggesting candidate genes for novel submicroscopic chromosomal imbalance syndromes

scientific article published on September 2007

Author Correction: Pan-cancer analysis of homozygous deletions in primary tumours uncovers rare tumour suppressors

scientific article published in Nature Communications

Author Correction: Pan-cancer analysis of homozygous deletions in primary tumours uncovers rare tumour suppressors

scholarly article published in Nature Communications

Autosomal-dominant microtia linked to five tandem copies of a copy-number-variable region at chromosome 4p16

scientific article

BMPR1A is a candidate gene for congenital heart defects associated with the recurrent 10q22q23 deletion syndrome

scientific article published on 20 October 2011

Bayesian applications of belief networks and multilayer perceptrons for ovarian tumor classification with rejection

scientific article published on September 2003

Beegle: from literature mining to disease-gene discovery

scientific article published on 17 September 2015

Biclustering microarray data by Gibbs sampling

scientific article

BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis

scientific article

Bioinformatics: Organisms from Venus, Technology from Jupiter, Algorithms from Mars

Biological knowledge bases using Wikis: combining the flexibility of Wikis with the structure of databases

scientific article published on 30 June 2010

Breakage-fusion-bridge cycles leading to inv dup del occur in human cleavage stage embryos

scientific article published in July 2011

Candidate gene prioritization by network analysis of differential expression using machine learning approaches.

scientific article

Candidate gene prioritization with Endeavour.

scientific article published on 30 April 2016

Chromosome Instability Is Common in Human Cleavage-Stage Embryos

Chromosome instability is common in human cleavage-stage embryos.

scientific article published on 26 April 2009

Chronic lymphocytic leukemia and prolymphocytic leukemia with MYC translocations: a subgroup with an aggressive disease course

scientific article published on 30 December 2011

Collaboratively charting the gene-to-phenotype network of human congenital heart defects

scientific article (publication date: March 2010)

Comparison and meta-analysis of microarray data: from the bench to the computer desk.

scientific article published in October 2003

Comparison of vocabularies, representations and ranking algorithms for gene prioritization by text mining.

scientific article published on August 2008

Comprehensive analysis of the base composition around the transcription start site in Metazoa

scientific article

Computational detection of cis -regulatory modules.

scientific article

Computational tools for prioritizing candidate genes: boosting disease gene discovery ⬇️

scientific article published on 03 July 2012

Concordance of gene expression in human protein complexes reveals tissue specificity and pathology

scientific article published on 05 August 2013

Concurrent whole-genome haplotyping and copy-number profiling of single cells

scientific article published on 14 May 2015

Congenital heart defects in a novel recurrent 22q11.2 deletion harboring the genes CRKL and MAPK1.

scientific article published on 8 February 2012

Current cancer driver variant predictors learn to recognize driver genes instead of functional variants

scientific article published on 13 January 2021

DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources

scientific article

DNA methylation analysis of Homeobox genes implicates HOXB7 hypomethylation as risk factor for neural tube defects

scientific article

Detecting cis-regulatory binding sites for cooperatively binding proteins

scientific article published on 9 April 2008

Detection of novel 3' untranslated region extensions with 3' expression microarrays

scientific article

ENDEAVOUR update: a web resource for gene prioritization in multiple species

scientific article

Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome

scientific article

Finding the targets of a drug by integration of gene expression data with a protein interaction network

scientific article

GENESTAT: an information portal for design and analysis of genetic association studies

scientific article (publication date: April 2009)

GRNBoost2 and Arboreto: efficient and scalable inference of gene regulatory networks

scientific article published on 01 June 2019

GRU-ODE-Bayes: Continuous Modeling of Sporadically-Observed Time Series ⬇️

Galahad: a web server for drug effect analysis from gene expression

scientific article published on 4 May 2015

Gene prioritization and clustering by multi-view text mining

scientific article

Gene prioritization through genomic data fusion

scientific article

Gene prioritization using Bayesian matrix factorization with genomic and phenotypic side information.

scientific article

Gene profiling of hippocampal neuronal culture.

scientific article published in June 2003

Genome-Wide Copy Number Variation Scan Identifies Complement Component C4 as Novel Susceptibility Gene for Crohn's Disease

scientific article published on 20 November 2015

Genome-wide copy number profiling of single cells in S-phase reveals DNA-replication domains

scientific article published on 7 January 2013

Haploinsufficiency of TAB2 causes congenital heart defects in humans

scientific article

Heterozygous missense mutations in SMARCA2 cause Nicolaides-Baraitser syndrome

scientific article

INCLUSive: A web portal and service registry for microarray and regulatory sequence analysis

scientific article

INCLUSive: integrated clustering, upstream sequence retrieval and motif sampling

scientific article published in February 2002

Identification of conserved modes of expression profiles during hippocampal development and neuronal differentiation in vitro.

scientific article

Importing MAGE-ML format microarray data into BioConductor

scientific article

Improved detection of chromosomal abnormalities in chronic lymphocytic leukemia by conventional cytogenetics using CpG oligonucleotide and interleukin-2 stimulation: A Belgian multicentric study.

scientific article published in October 2009

In vitro screening of embryos by whole-genome sequencing: now, in the future or never?

scientific article

Insight into the protein solubility driving forces with neural attention

scientific article published on 30 April 2020

Integrating computational biology and forward genetics in Drosophila

scientific article published on 23 January 2009

Interactogeneous: disease gene prioritization using heterogeneous networks and full topology scores

scientific article

Interphase fluorescence in situ hybridization on selected plasma cells is superior in the detection of cytogenetic aberrations in plasma cell dyscrasia

scientific article published on 01 November 2010

Kernel-based data fusion for gene prioritization

scientific article

L2-norm multiple kernel learning and its application to biomedical data fusion.

scientific article

Large-scale benchmark of Endeavour using MetaCore maps

scientific article published on 10 June 2010

Mapping biomedical concepts onto the human genome by mining literature on chromosomal aberrations

scientific article published in April 2007

Meander: visually exploring the structural variome using space-filling curves

scientific article

Methylome analysis for spina bifida shows SOX18 hypomethylation as a risk factor with evidence for a complex (epi)genetic interplay to affect neural tube development.

scientific article

Microarray analysis of copy number variation in single cells.

scientific article published on 19 January 2012

Microarray screening for target genes of the proto-oncogene PLAG1.

scientific article published on January 2004

ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues?

scientific article published on 07 April 2008

Mutual inhibition among postmitotic neurons regulates robustness of brain wiring in Drosophila

scientific article published on 5 March 2013

NGS-Logistics: data infrastructure for efficient analysis of NGS sequence variants across multiple centers.

scientific article published on 28 January 2015

NGS-Logistics: federated analysis of NGS sequence variants across multiple locations

scientific article

Network analysis of differential expression for the identification of disease-causing genes

scientific article

O12: Text Mining for Constitutional Cytogenetics

Optimized data fusion for K-means Laplacian clustering

scientific article

Optimized data fusion for kernel k-means clustering

scientific article

PINTA: a web server for network-based gene prioritization from expression data

scientific article

Pan-cancer analysis of homozygous deletions in primary tumours uncovers rare tumour suppressors.

scientific article published on 31 October 2017

PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences.

scientific article

Positional gene enrichment analysis of gene sets for high-resolution identification of overrepresented chromosomal regions

scientific article published on 16 March 2008

Predicting receptor-ligand pairs through kernel learning

scientific article

Predicting the prognosis of breast cancer by integrating clinical and microarray data with Bayesian networks.

scientific article

Problems with the nested granularity of feature domains in bioinformatics: the eXtasy case

scientific article

Protein fold recognition using geometric kernel data fusion

scientific article

Query-driven module discovery in microarray data.

scientific article

ReLiance: a machine learning and literature-based prioritization of receptor--ligand pairings

scientific article

Single-cell chromosomal imbalances detection by array CGH

scientific article published on 12 May 2006

Single-cell copy number variation detection.

scientific article published on 29 August 2011

Single-cell paired-end genome sequencing reveals structural variation per cell cycle

scientific article

TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis.

scientific article

TXTGate: profiling gene groups with text-based information

scientific article

The genetic heterogeneity and mutational burden of engineered melanomas in zebrafish models

scientific article published on January 2013

Toucan: deciphering the cis-regulatory logic of coregulated genes.

scientific article

Towards Better Prioritization of Epigenetically Modified DNA Regions

Towards practical privacy-preserving genome-wide association study

scientific article published on 20 December 2018

Unraveling genomic variation from next generation sequencing data

scientific article

Using literature and data to learn Bayesian networks as clinical models of ovarian tumors

scientific article

Using ribosomal protein genes as reference: a tale of caution

scientific article (publication date: 2008)

YTPdb: a wiki database of yeast membrane transporters

scientific article published on 19 June 2010

Yves Moreau and Jaap Heringa, on behalf of the ECCB10 organizing and steering committees ⬇️

scientific article published on September 15, 2010

arrayCGHbase: an analysis platform for comparative genomic hybridization microarrays

scientific article

eXtasy: variant prioritization by genomic data fusion.

scientific article

List of works by Yves Moreau

A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes.

A Simple Genetic Algorithm for Biomarker Mining

A bioinformatics e-dating story: computational prediction and prioritization of receptor-ligand pairs

A genetic algorithm for the detection of new cis-regulatory modules in sets of coregulated genes

A guide to web tools to prioritize candidate genes

A human phenome-interactome network of protein complexes implicated in genetic disorders

ACE-inhibition induces a cardioprotective transcriptional response in the metabolic syndrome heart

Adaptive quality-based clustering of gene expression profiles.

AliBiMotif: Integrating alignment and biclustering to unravel transcription factor binding sites in DNA sequences

An expanded evaluation of protein function prediction methods shows an improvement in accuracy ⬇️

An experimental loop design for the detection of constitutional chromosomal aberrations by array CGH.

An unbiased evaluation of gene prioritization tools

Annotate-it: a Swiss-knife approach to annotation, analysis and interpretation of single nucleotide variation in human disease

Array comparative genomic hybridization and computational genome annotation in constitutional cytogenetics: suggesting candidate genes for novel submicroscopic chromosomal imbalance syndromes

Author Correction: Pan-cancer analysis of homozygous deletions in primary tumours uncovers rare tumour suppressors

Author Correction: Pan-cancer analysis of homozygous deletions in primary tumours uncovers rare tumour suppressors

Autosomal-dominant microtia linked to five tandem copies of a copy-number-variable region at chromosome 4p16

BMPR1A is a candidate gene for congenital heart defects associated with the recurrent 10q22q23 deletion syndrome

Bayesian applications of belief networks and multilayer perceptrons for ovarian tumor classification with rejection

Beegle: from literature mining to disease-gene discovery

Biclustering microarray data by Gibbs sampling

BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis

Bioinformatics: Organisms from Venus, Technology from Jupiter, Algorithms from Mars

Biological knowledge bases using Wikis: combining the flexibility of Wikis with the structure of databases

Breakage-fusion-bridge cycles leading to inv dup del occur in human cleavage stage embryos

Candidate gene prioritization by network analysis of differential expression using machine learning approaches.

Candidate gene prioritization with Endeavour.

Chromosome Instability Is Common in Human Cleavage-Stage Embryos

Chromosome instability is common in human cleavage-stage embryos.

Chronic lymphocytic leukemia and prolymphocytic leukemia with MYC translocations: a subgroup with an aggressive disease course

Collaboratively charting the gene-to-phenotype network of human congenital heart defects

Comparison and meta-analysis of microarray data: from the bench to the computer desk.

Comparison of vocabularies, representations and ranking algorithms for gene prioritization by text mining.

Comprehensive analysis of the base composition around the transcription start site in Metazoa

Computational detection of cis -regulatory modules.

Computational tools for prioritizing candidate genes: boosting disease gene discovery ⬇️

Concordance of gene expression in human protein complexes reveals tissue specificity and pathology

Concurrent whole-genome haplotyping and copy-number profiling of single cells

Congenital heart defects in a novel recurrent 22q11.2 deletion harboring the genes CRKL and MAPK1.

Current cancer driver variant predictors learn to recognize driver genes instead of functional variants

DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources

DNA methylation analysis of Homeobox genes implicates HOXB7 hypomethylation as risk factor for neural tube defects

Detecting cis-regulatory binding sites for cooperatively binding proteins

Detection of novel 3' untranslated region extensions with 3' expression microarrays

ENDEAVOUR update: a web resource for gene prioritization in multiple species

Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome

Finding the targets of a drug by integration of gene expression data with a protein interaction network

GENESTAT: an information portal for design and analysis of genetic association studies

GRNBoost2 and Arboreto: efficient and scalable inference of gene regulatory networks

GRU-ODE-Bayes: Continuous Modeling of Sporadically-Observed Time Series ⬇️

Galahad: a web server for drug effect analysis from gene expression

Gene prioritization and clustering by multi-view text mining

Gene prioritization through genomic data fusion

Gene prioritization using Bayesian matrix factorization with genomic and phenotypic side information.

Gene profiling of hippocampal neuronal culture.

Genome-Wide Copy Number Variation Scan Identifies Complement Component C4 as Novel Susceptibility Gene for Crohn's Disease

Genome-wide copy number profiling of single cells in S-phase reveals DNA-replication domains

Haploinsufficiency of TAB2 causes congenital heart defects in humans

Heterozygous missense mutations in SMARCA2 cause Nicolaides-Baraitser syndrome

INCLUSive: A web portal and service registry for microarray and regulatory sequence analysis

INCLUSive: integrated clustering, upstream sequence retrieval and motif sampling

Identification of conserved modes of expression profiles during hippocampal development and neuronal differentiation in vitro.

Importing MAGE-ML format microarray data into BioConductor

Improved detection of chromosomal abnormalities in chronic lymphocytic leukemia by conventional cytogenetics using CpG oligonucleotide and interleukin-2 stimulation: A Belgian multicentric study.

In vitro screening of embryos by whole-genome sequencing: now, in the future or never?

Insight into the protein solubility driving forces with neural attention

Integrating computational biology and forward genetics in Drosophila

Interactogeneous: disease gene prioritization using heterogeneous networks and full topology scores

Interphase fluorescence in situ hybridization on selected plasma cells is superior in the detection of cytogenetic aberrations in plasma cell dyscrasia

Kernel-based data fusion for gene prioritization

L2-norm multiple kernel learning and its application to biomedical data fusion.

Large-scale benchmark of Endeavour using MetaCore maps

Mapping biomedical concepts onto the human genome by mining literature on chromosomal aberrations

Meander: visually exploring the structural variome using space-filling curves

Methylome analysis for spina bifida shows SOX18 hypomethylation as a risk factor with evidence for a complex (epi)genetic interplay to affect neural tube development.

Microarray analysis of copy number variation in single cells.

Microarray screening for target genes of the proto-oncogene PLAG1.

ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues?

Mutual inhibition among postmitotic neurons regulates robustness of brain wiring in Drosophila