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public:ulb [2012/09/21 07:55] – [Prof. Jacques van Helden] jvanheldpublic:ulb [2019/02/12 09:04] (current) – external edit 127.0.0.1
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 === Bioinformatics approaches and tools === === Bioinformatics approaches and tools ===
  
-== Regulatory Sequence Analysis Tools (RSAT, http://rsat.ulb.ac.be/rsat/) ==+== Regulatory Sequence Analysis Tools (RSAT) ==
  
 +Web site: [[http://rsat.ulb.ac.be/rsat/|http://rsat.ulb.ac.be/rsat/]]
  
 A software suite dedicated to the analysis of motifs in cis-regulatory sequences. RSAT combines several original algorithms for detecting cis-regulatory motifs in promoters of co-expressed genes (transcriptome data), detection of phylogenetic footprints (conserved elements in promoters of orthologous genes), analysis of high-throughput sequencing data (ChIP-seq) or full genomes. To my best knowledge, RSAT is currently the most complete Web resource worldwide for the analysis of regulatory sequences.  A software suite dedicated to the analysis of motifs in cis-regulatory sequences. RSAT combines several original algorithms for detecting cis-regulatory motifs in promoters of co-expressed genes (transcriptome data), detection of phylogenetic footprints (conserved elements in promoters of orthologous genes), analysis of high-throughput sequencing data (ChIP-seq) or full genomes. To my best knowledge, RSAT is currently the most complete Web resource worldwide for the analysis of regulatory sequences. 
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 Since 1999, I developed bioinformatics approaches applying graph theory methods (path finding, subgraph extraction) to discover metabolic pathways in reaction networks (built by compiling all known reactions, their substrates and products). Typical applications are the analysis of metabolic regulation by inferring pathways from groups of co-expressed enzymes, or the reconstruction of bacterial metabolism by building pathways from operons, regulons or groups of genes co-occurring across genomes (phylogenetic profiles).  Since 1999, I developed bioinformatics approaches applying graph theory methods (path finding, subgraph extraction) to discover metabolic pathways in reaction networks (built by compiling all known reactions, their substrates and products). Typical applications are the analysis of metabolic regulation by inferring pathways from groups of co-expressed enzymes, or the reconstruction of bacterial metabolism by building pathways from operons, regulons or groups of genes co-occurring across genomes (phylogenetic profiles). 
  
-== Network analysis tools (NeAT, http://rsat.ulb.ac.be/neat/) ==+== Network analysis tools (NeAT) ==
  
-Since 2005, the RSAT suite has been complemented by a series of specialized tools for the analysis of biomolecular networks. The « Network Analysis Tools » (NeAT, http://rsat.ulb.ac.be/neat/) (11) enable the analysis of various types of biomolecular networks: protein interactions, gene regulation, horizontal transfer between bacterial genomes, etc. The metabolic pathway discovery tools have also been integrated in the NeAT suite. +Web site: [[http://rsat.ulb.ac.be/neat/|http://rsat.ulb.ac.be/neat/]] 
 + 
 +Since 2005, the RSAT suite has been complemented by a series of specialized tools for the analysis of biomolecular networks. The software suite Network Analysis Tools (NeAT) supoprts the analysis of various types of biomolecular networks: protein interactions, gene regulation, horizontal transfer between bacterial genomes, etc. The metabolic pathway discovery tools have also been integrated in the NeAT suite. 
  
 == Assessment of bioinformatics approaches == == Assessment of bioinformatics approaches ==
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 ==== Publications ==== ==== Publications ====
  
 +=== Recent publications ===
 +
 +  * Thomas-Chollier M, Darbo E, Herrmann C, Defrance M, Thieffry D, van Helden J. (2012). A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs. Nat Protoc 7(8): 1551-1568 [[http://www.ncbi.nlm.nih.gov/pubmed/22836136|PMID
 +22836136]]
 +
 +  * Jacques van Helden, Ariane Toussaint and Denis Thieffry (2012). Bacterial Molecular Networks. Methods in Molecular Biology, Volume 804 (28 chapters) [[http://www.springer.com/life+science/microbiology/book/978-1-61779-360-8|Publisher's site]]
 +
 +  * van Helden, J., Toussaint, A. and Thieffry, D. (2012). Bacterial molecular networks: bridging the gap between functional genomics and dynamical modelling. Methods Mol Biol 804, 1-11 [[http://www.ncbi.nlm.nih.gov/pubmed/22144145|PMID 22144145]]
 +
 +  * Faust, K. and van Helden, J. (2012). Predicting Metabolic Pathways by Sub-network Extraction. Methods Mol Biol 804, 107-30.[[http://www.ncbi.nlm.nih.gov/pubmed/22144151|PMID 22144151]]
 +
 +  * Thomas-Chollier M, Herrmann C, Defrance M, Sand O, Thieffry D, van Helden J. (2012). RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets. Nucleic Acids Res 40(4): e31. [[http://www.ncbi.nlm.nih.gov/pubmed/22156162|PMID 22156162]]  [[http://nar.oxfordjournals.org/content/early/2011/12/08/nar.gkr1104.full?keytype=ref&ijkey=zOvloLjtKzL73F8|Open access]]
  
 +== Full list of publications ==
  
 +[[http://www.bigre.ulb.ac.be/Users/jvanheld/publications_JvH.html|http://www.bigre.ulb.ac.be/Users/jvanheld/publications_JvH.html]]
  
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