Integrating sequence, evolution and functional genomics in regulatory genomics (2009)
Vingron, Martin, Brazma, Alvis, Coulson, Richard, Van Helden, Jacques, Manke, Thomas, Palin, Kimmo, ...
Abstract With genome analysis expanding from the study of genes to the study of gene regulation, 'regulatory genomics' utilizes sequence information, evolution and functional genomics measurements to...
Kontos, Kevin, Godard, Patrice, André, Bruno, Van Helden, Jacques, Bontempi, Gianluca
Abstract Background Nitrogen is an essential nutrient for all life forms. Like most unicellular organisms, the yeast Saccharomyces cerevisiae transports and catabolizes good nitrogen sources in...
Janky, Rekin's, Van Helden, Jacques
Abstract Background The detection of conserved motifs in promoters of orthologous genes (phylogenetic footprints) has become a common strategy to predict cis-acting regulatory elements. Several...
Reticulate Representation of Evolutionary and Functional Relationships between Phage Genomes (2008)
Lima-Mendez, Gipsi, Van Helden, Jacques, Toussaint, Ariane, Leplae, Raphaël
Bacteriophage genomes show pervasive mosaicism, indicating the importance of horizontal gene exchange in their evolution. Phage genomes represent unique combinations of modules, each of them with a...
Prophinder: a computational tool for prophage prediction in prokaryotic genomes (2008)
Lima-Mendez, Gipsi, Van Helden, Jacques, Toussaint, Ariane, Leplae, Raphaël
Summary: Prophinder is a prophage prediction tool coupled with a prediction database, a web server and web service. Predicted prophages will help to fill the gaps in the current sparse phage sequence...
RSAT: regulatory sequence analysis tools (2008)
Thomas-Chollier, Morgane, Sand, Olivier, Turatsinze, Jean-Valéry, Janky, Rekin's, Defrance, Matthieu, Vervisch, Eric, ...
The regulatory sequence analysis tools (RSAT, http://rsat.ulb.ac.be/rsat/) is a software suite that integrates a wide collection of modular tools for the detection of cis-regulatory elements in...
NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways (2008)
Brohée, Sylvain, Faust, Karoline, Lima-Mendez, Gipsi, Sand, Olivier, Janky, Rekin's, Vanderstocken, Gilles, ...
The network analysis tools (NeAT) (http://rsat.ulb.ac.be/neat/) provide a user-friendly web access to a collection of modular tools for the analysis of networks (graphs) and clusters (e.g. microarray...
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures (2007)
Lin, Michael F, Kheradpour, Pouya, Pedersen, Jakob S, Parts, Leopold, Carlson, Joseph W, ...
Sequencing of multiple related species followed by comparative genomics analysis constitutes a powerful approach for the systematic understanding of any genome. Here, we use the genomes of 12...
In silicoidentification of NF-kappaB-regulated genes in pancreatic beta-cells (2007)
Naamane, Najib, Van Helden, Jacques, Eizirik, Decio L
Abstract Background Pancreatic beta-cells are the target of an autoimmune attack in type 1 diabetes mellitus (T1DM). This is mediated in part by cytokines, such as interleukin (IL)-1β and interferon...
Evaluation of clustering algorithms for protein-protein interaction networks (2006)
Brohée, Sylvain, Van Helden, Jacques
Abstract Background Protein interactions are crucial components of all cellular processes. Recently, high-throughput methods have been developed to obtain a global description of the interactome (the...
Metabolic PathFinding: inferring relevant pathways in biochemical networks (2005)
Croes, Didier, Couche, Fabian, Wodak, Shoshana J., Van Helden, Jacques
Our knowledge of metabolism can be represented as a network comprising several thousands of nodes (compounds and reactions). Several groups applied graph theory to analyse the topological properties...
Gonze, Didier, Pinloche, Sylvie, Gascuel, Olivier, Van Helden, Jacques
Motivation: In yeast, methionine and phosphate metabolism are regulated by the complexes Met4p/Met28p/Cbf1p and Pho4p, respectively. The binding sites for these factors share a common core CACGTG. We...
Gonze, Didier, Pinloche, Sylvie, Gascuel, Olivier, Van Helden, Jacques
Motivation: In yeast, methionine and phosphate metabolism are regulated by the complexes Met4p/Met28p/Cbf1p and Pho4p respectively. The binding sites for these factors share a common core CACGTG. We...
Transcriptional regulation of protein complexes in yeast (2004)
Simonis, Nicolas, Van Helden, Jacques, Cohen, George N, Wodak, Shoshana J
Abstract Background Multiprotein complexes play an essential role in many cellular processes. But our knowledge of the mechanism of their formation, regulation and lifetimes is very limited. We...
Metrics for comparing regulatory sequences on the basis of pattern counts (2004)
Motivation: Upstream sequences contain short motifs, which mediate transcriptional regulation by specifically binding different transcription factors. The presence of common motifs in the regulatory...
Metrics for comparing regulatory sequences on the basis of pattern counts (2004)
Motivation: Upstream sequences contain short motifs, which mediate transcriptional regulation by specifically binding different transcription factors. The presence of common motifs in the regulatory...
Metrics for comparing regulatory sequences on the basis of pattern counts (2004)
Motivation: Upstream sequences contain short motifs, which mediate transcriptional regulation by specifically binding different transcription factors. The presence of common motifs in the regulatory...
Regulatory Sequence Analysis Tools (2003)
The web resource Regulatory Sequence Analysis Tools (RSAT) (http://rsat.ulb.ac.be/rsat) offers a collection of software tools dedicated to the prediction of regulatory sites in non-coding DNA...
An overview of data models for the analysis of biochemical pathways (2003)
Deville, Yves, Gilbert, David, Van Helden, Jacques, Wodak, Shoshana J.
Biochemical pathways such as metabolic, regulatory or signal transduction pathways can be viewed as interconnected processes forming an intricate network of functional and physical interactions...
From molecular activities and processes to biological function (2001)
Van Helden, Jacques, Naim, Avi, Lemer, Christian, Mancuso, Renato, Eldridge, Matthew, Wodak, Shoshana J.
This paper describes how biological function can be represented in terms of molecular activities and processes. It presents several key features of a data model that is based on a conceptual...
Hulzink, Raymond Jozef Maurinus, Weerdesteyn, Han, Croes, Anton Felix, Gerats, Tom, Van Helden, Jacques
During pollen development, transcription of a large number of genes results in the appearance of distinct sets of transcripts. Similar mRNA sets are present in pollen of both mono- and dicotyledonous...
Regulatory Sequence Analysis Tools
The web resource Regulatory Sequence Analysis Tools (RSAT) (http://rsat.ulb.ac.be/rsat) offers a collection of software tools dedicated to the prediction of regulatory sites in non-coding DNA...
Transcriptional regulation of protein complexes in yeast
Simonis, Nicolas, Van Helden, Jacques, Cohen, George N, Wodak, Shoshana J
This study shows that only a small fraction of yeast protein complexes are coregulated at the transcriptional level.
Metabolic PathFinding: inferring relevant pathways in biochemical networks
Croes, Didier, Couche, Fabian, Wodak, Shoshana J., Van Helden, Jacques
Our knowledge of metabolism can be represented as a network comprising several thousands of nodes (compounds and reactions). Several groups applied graph theory to analyse the topological properties...
Hulzink, Raymond Jozef Maurinus, Weerdesteyn, Han, Croes, Anton Felix, Gerats, Tom, Van Helden, Jacques
During pollen development, transcription of a large number of genes results in the appearance of distinct sets of transcripts. Similar mRNA sets are present in pollen of both mono- and dicotyledonous...
Regulatory Sequence Analysis Tools
The web resource Regulatory Sequence Analysis Tools (RSAT) (http://rsat.ulb.ac.be/rsat) offers a collection of software tools dedicated to the prediction of regulatory sites in non-coding DNA...
Transcriptional regulation of protein complexes in yeast
Simonis, Nicolas, Van Helden, Jacques, Cohen, George N, Wodak, Shoshana J
This study shows that only a small fraction of yeast protein complexes are coregulated at the transcriptional level.
Metabolic PathFinding: inferring relevant pathways in biochemical networks
Croes, Didier, Couche, Fabian, Wodak, Shoshana J., Van Helden, Jacques
Our knowledge of metabolism can be represented as a network comprising several thousands of nodes (compounds and reactions). Several groups applied graph theory to analyse the topological properties...
Godard, Patrice, Urrestarazu, Antonio, Vissers, Stéphan, Kontos, Kevin, Bontempi, Gianluca, Van Helden, Jacques, ...
We compared the transcriptomes of Saccharomyces cerevisiae cells growing under steady-state conditions on 21 unique sources of nitrogen. We found 506 genes differentially regulated by nitrogen and...
Fine-Tuning Enhancer Models to Predict Transcriptional Targets across Multiple Genomes
Aerts, Stein, Van Helden, Jacques, Sand, Olivier, Hassan, Bassem A.
Networks of regulatory relations between transcription factors (TF) and their target genes (TG)- implemented through TF binding sites (TFBS)- are key features of biology. An idealized approach to...
NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways
Brohée, Sylvain, Faust, Karoline, Lima-Mendez, Gipsi, Sand, Olivier, Janky, Rekin's, Vanderstocken, Gilles, ...
The network analysis tools (NeAT) (http://rsat.ulb.ac.be/neat/) provide a user-friendly web access to a collection of modular tools for the analysis of networks (graphs) and clusters (e.g. microarray...
RSAT: regulatory sequence analysis tools
Thomas-Chollier, Morgane, Sand, Olivier, Turatsinze, Jean-Valéry, Janky, Rekin's, Defrance, Matthieu, Vervisch, Eric, ...
The regulatory sequence analysis tools (RSAT, http://rsat.ulb.ac.be/rsat/) is a software suite that integrates a wide collection of modular tools for the detection of cis-regulatory elements in...
Integrating sequence, evolution and functional genomics in regulatory genomics
Vingron, Martin, Brazma, Alvis, Coulson, Richard, Van Helden, Jacques, Manke, Thomas, Palin, Kimmo, ...
Finding transcription factor binding sites in regulatory regions of the genome