Network Analysis Tools (NeAT) - Publications

Network Analysis Tools

| 2012 | 2011 | 2010 | 2009 | 2008 | 2006 | <= 2005 |

    2012

  1. Book: Jacques van Helden, Ariane Toussaint and Denis Thieffry (2012). Bacterial Molecular Networks. Volume in the series Methods in Molecular Biology 804 (28 chapters). [Publisher's site]
  2. 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. [PMID 22144145]
  3. Lima-Mendez, G. (2012). Reticulate Classification of Mosaic Microbial Genomes Using NeAT Website. Methods Mol Biol 804, 81-91. [PMID 22144149]
  4. Faust, K. and van Helden, J. (2012). Predicting Metabolic Pathways by Sub-network Extraction. Methods Mol Biol 804, 107-30. [PMID 22144151]
  5. Brohée, S. (2012). Using the NeAT Toolbox to Compare Networks to Networks, Clusters to Clusters, and Network to Clusters. Methods Mol Biol 804, 327-42. [PMID 22144162]
  6. 2011

  7. Faust, K., Croes, D. and van Helden, J. (2011). Prediction of metabolic pathways from genome-scale metabolic networks. Biosystems 105, 109-21. [PMID 21645586] [doi:10.1016/j.biosystems.2011.05.004]
  8. 2010

  9. Faust, K., Dupont, P., Callut, J. and van Helden, J. (2010). Pathway discovery in metabolic networks by subgraph extraction. Bioinformatics 26:1211-8. [Pubmed 20228128]..
  10. 2009

  11. Lima-Mendez, G. and van Helden, J. (2009). The powerful law of the power law and other myths in network biology. Mol. BioSyst., 2009, 5, 1482 - 1493, DOI: 10.1039/b908681a. Pubmed 20023717.
  12. Faust, K., Croes, D. and van Helden, J. (2009). In response to "Can sugars be produced from fatty acids? A test case for pathway analysis tools". Bioinformatics 2009 Sept 23. Pubmed 19776213.
  13. Faust K., Croes, D., van Helden J. (2009). Metabolic Pathfinding Using RPAIR Annotation. Journal of Molecular Biology 388, 390-414. [Pubmed 19281817]
  14. 2008

  15. Brohée S., Faust K., Lima-Mendez G., Vanderstocken G., van Helden J. (2008). Network Analysis Tools: from biological networks to clusters and pathways. Nature protocols 3 (10), 1616-29. [Pubmed 18802442]
  16. Brohée, S., Faust, K., Lima-Mendez, G., Sand, O., Janky, R., Vanderstocken, G., Deville, Y. & van Helden, J. (2008). NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways. Nucleic Acids Research 36, W444-451. [Pubmed 18524799] [Full text]
  17. 2006

  18. Brohée, S. & van Helden, J. (2006). Evaluation of clustering algorithms for protein-protein interaction networks. BMC Bioinformatics 7, 488. Pubmed 17087821
  19. Croes, D., F. Couche, S.J. Wodak, J. van Helden (2006). Inferring Meaningful Pathways in Weighted Metabolic Networks. J. Mol. Biol. 356:222-36. Pubmed 16337962
  20. <= 2005

  21. Croes, D., F. Couche, S.J. Wodak, and J. van Helden. 2005. Metabolic PathFinding: inferring relevant pathways in biochemical networks. Nucleic Acids Res 33: W326-330. Pubmed 15980483
  22. van Helden, J., Wernisch, L., Gilbert, D. & Wodak, S. J. (2002). Graph-based analysis of metabolic networks. In Ernst Schering Res Found Workshop (al., M. H.-W. e., ed.), pp. 245-74. Springer-Verlag.

  23. van Helden, J., Gilbert, D., Wernisch, L., Schroeder, M. & Wodak, S. (2001). Applications of regulatory sequence analysis and metabolic network analysis to the interpretation of gene expression data. Computational Biology : First International Conference on Biology, Informatics, and Mathematics, JOBIM 2000. LNCS volume 2066, Montpellier.

Regulatory Sequence Analysis Tools