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Publications of Author

1. Yves Deville, David Gilbert, Jacques van Helden, Shoshana J. Wodak
   An Overview of Data Models for the Analysis of Biochemical Pathways. [Citation Graph (0, 0)][DBLP]
   CMSB, 2003, pp:174- [Conf]
   
2. Jacques van Helden, David Gilbert, Lorenz Wernisch, Renato Mancuso, Matthew Eldridge, Kirill Degtyarenko, Shoshana J. Wodak
   Logical Tools for Quering and Assisting Annotation of a Biochemical Pathway Database. [Citation Graph (0, 0)][DBLP]
   German Conference on Bioinformatics, 1999, pp:227-229 [Conf]
   
3. Jacques van Helden, David Gilbert, Lorenz Wernisch, Michael Schroeder, Shoshana J. Wodak
   Application of Regulatory Sequence Analysis and Metabolic Network Analysis to the Interpretation of Gene Expression Data. [Citation Graph (0, 0)][DBLP]
   JOBIM, 2000, pp:147-164 [Conf]
   
4. Yves Deville, David Gilbert, Jacques van Helden, Shoshana J. Wodak
   An overview of data models for the analysis of biochemical pathways. [Citation Graph (0, 0)][DBLP]
   Briefings in Bioinformatics, 2003, v:4, n:3, pp:246-259 [Journal]
   
5. Jacques van Helden, Avi Naim, Christian Lemer, Renato Mancuso, Matthew Eldridge, Shoshana J. Wodak
   From Molecular Activities and Processes to Biological Function. [Citation Graph (0, 0)][DBLP]
   Briefings in Bioinformatics, 2001, v:2, n:1, pp:81-107 [Journal]
   
6. Didier Gonze, Sylvie Pinloche, Olivier Gascuel, Jacques van Helden
   Discrimination of yeast genes involved in methionine and phosphate metabolism on the basis of upstream motifs. [Citation Graph (0, 0)][DBLP]
   Bioinformatics, 2005, v:21, n:17, pp:3490-3500 [Journal]
   
7. Jacques van Helden
   Metrics for comparing regulatory sequences on the basis of pattern counts. [Citation Graph (0, 0)][DBLP]
   Bioinformatics, 2004, v:20, n:3, pp:399-406 [Journal]
   
8. N. Simonis, Shoshana J. Wodak, G. N. Cohen, Jacques van Helden
   Combining pattern discovery and discriminant analysis to predict gene co-regulation. [Citation Graph (0, 0)][DBLP]
   Bioinformatics, 2004, v:20, n:15, pp:2370-2379 [Journal]
   
9. Michael Schroeder, David Gilbert, Jacques van Helden, Penny Noy
   Approaches to visualisation in bioinformatics: from dendrograms to Space Explorer. [Citation Graph (0, 0)][DBLP]
   Inf. Sci., 2001, v:139, n:1-2, pp:19-57 [Journal]
   
10. Jacques van Helden
    Regulatory Sequence Analysis Tools. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2003, v:31, n:13, pp:3593-3596 [Journal]
    
11. Heladia Salgado, Alberto Santos-Zavaleta, Ulises Garza-Ramos, Jacques van Helden, Edgar Díaz, Julio Collado-Vides
    RegulonDB (version 2.0): a database on transcriptional regulation in Escherichia coli. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 1999, v:27, n:1, pp:59-60 [Journal]
    
12. Ulrich Güldener, Martin Münsterkötter, Gabi Kastenmüller, Norman Strack, Jacques van Helden, Christian Lemer, J. Richelles, Shoshana J. Wodak, J. García-Martínez, J. E. Pérez-Ortín, Holger Michael, Andreas Kaps, E. Talla, Bernard Dujon, B. André, J. L. Souciet, J. De Montigny, E. Bon, C. Gaillardin, Hans-Werner Mewes
    CYGD: the Comprehensive Yeast Genome Database. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Database-Issue, pp:364-368 [Journal]
    
13. Didier Croes, Fabian Couche, Shoshana J. Wodak, Jacques van Helden
    Metabolic PathFinding: inferring relevant pathways in biochemical networks. [Citation Graph (0, 0)][DBLP]
    Nucleic Acids Research, 2005, v:33, n:Web-Server-Issue, pp:326-330 [Journal]
    
14. 
    Gaussian Graphical Models to Infer Putative Genes Involved in Nitrogen Catabolite Repression in S. cerevisiae. [Citation Graph (, )][DBLP]
    
    
15. 
    Prophinder: a computational tool for prophage prediction in prokaryotic genomes. [Citation Graph (, )][DBLP]
    
    
16. 
    Retrieve-ensembl-seq: user-friendly and large-scale retrieval of single or multi-genome sequences from Ensembl. [Citation Graph (, )][DBLP]
    
    
17. 
    info-gibbs: a motif discovery algorithm that directly optimizes information content during sampling. [Citation Graph (, )][DBLP]
    
    
18. 
    In response to 'Can sugars be produced from fatty acids? A test case for pathway analysis tools'. [Citation Graph (, )][DBLP]
    
    
19. 
    Pathway discovery in metabolic networks by subgraph extraction. [Citation Graph (, )][DBLP]
    
    
20. 
    In silico identification of NF-kappaB-regulated genes in pancreatic beta-cells. [Citation Graph (, )][DBLP]
    
    
21. 
    Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution. [Citation Graph (, )][DBLP]
    
    
22. 
    Evaluation of clustering algorithms for protein-protein interaction networks. [Citation Graph (, )][DBLP]