RSAT - Publications

Regulatory Sequence Analysis

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  1. Contreras-Moreira B, Castro-Mondragon JA, Rioualen C, Cantalapiedra CP, van Helden J. (2016). RSAT::Plants: Motif Discovery Within Clusters of Upstream Sequences in Plant Genomes. Methods Mol Biol. 1482:279-95. doi: 10.1007/978-1-4939-6396-6_18. [PMID 27557774]

  2. Castro-Mondragon JA, Rioualen C, Contreras-Moreira B, van Helden J. (2016). RSAT::Plants: Motif Discovery in ChIP-Seq Peaks of Plant Genomes. Methods Mol Biol. 1482:297-322. doi: 10.1007/978-1-4939-6396-6_19. [PMID 27557775]

  3. 2015

  4. Medina-Rivera A, Defrance M, Sand O, Herrmann C, Castro-Mondragon J, Delerce J, Jaeger S, Blanchet C, Vincens P, Caron C, Staines DM, Contreras-Moreira B, Artufel M, Charbonnier-Khamvongsa L, Hernandez C, Thieffry D, Thomas-Chollier M, van Helden J (2015) RSAT 2015: Regulatory Sequence Analysis Tools . Nucleic Acids Res. 2015 (Web Server issue) in press. [Full text]

  5. 2012

  6. 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. [PMID 22836136]

  7. 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. [PMID 22156162] [Open access]

  8. 2011

  9. Thomas-Chollier, M., Defrance, M., Medina-Rivera, A., Sand, O., Herrmann, C., Thieffry, D. and van Helden, J. (2011). RSAT 2011: Regulatory Sequence Analysis Tools. Nucleic Acids Research, 2011, Vol. 39, W86-W91. Web Server issue doi:10.1093/nar/gkr377. [PMID 21715389] [Open access]
  10. Brohee, S., Janky, R., Abdel-Sater, F., Vanderstocken, G., Andre, B. and van Helden, J. (2011). Unraveling networks of co-regulated genes on the sole basis of genome sequences. Nucleic Acids Res 39, 6340-58. [PMID 21572103] [Open access]
  11. 2010

  12. Medina-Rivera, A., Abreu-Goodger, C., Salgado-Osorio, H., Collado-Vides, J. and van Helden, J. (2010). Empirical and theoretical evaluation of transcription factor binding motifs. Nucleic Acids Res. 2010 Oct 4. [Epub ahead of print] [Pubmed 20923783] [Full text].


  13. Sand, O., Thomas-Chollier, M. and van Helden, J. (2009). Retrieve-ensembl-seq: user-friendly and large-scale retrieval of single or multi-genome sequences from Ensembl. Bioinformatics, 2009. DOI:10.1093/bioinformatics/btp519. Pubmed 19720677.

  14. Defrance, M. and Helden, J. V. (2009). Info-gibbs: a motif discovery algorithm that directly optimizes information content during sampling. Bioinformatics. Pubmed 19689955
  15. Janky, R., Helden, J. V. and Babu, M. M. (2009). Investigating transcriptional regulation: From analysis of complex networks to discovery of cis-regulatory elements. Methods. [Pubmed 19450688] [On line].
  16. Vingron, M., Brazma, A., Coulson, R., van Helden, J., Manke, T., Palin, K., Sand, O. and Ukkonen, E. (2009). Integrating sequence, evolution and functional genomics in regulatory genomics. Genome Biol 10, 202. Pubmed 19226437
  17. 2008

  18. Sand, O., Thomas-Chollier, M., Vervisch, E. and van Helden, J. (2008) Analyzing multiple data sets by interconnecting RSAT programs via SOAP Web services-an example with ChIP-chip data. Nat Protoc, 3, 1604-1615. Pubmed 18802441
  19. Defrance, M., Janky, R., Sand, O. and van Helden, J. (2008) Using RSAT oligo-analysis and dyad-analysis tools to discover regulatory signals in nucleic sequences. Nat Protoc, 3, 1589-1603. Pubmed 18802440
  20. Turatsinze, J.V., Thomas-Chollier, M., Defrance, M. and van Helden, J. (2008) Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules. Nat Protoc, 3, 1578-1588. Pubmed 18802439
  21. Thomas-Chollier, M., Sand, O., Turatsinze, J. V., Janky, R., Defrance, M., Vervisch, E., Brohee, S. & van Helden, J. (2008). RSAT: regulatory sequence analysis tools. Nucleic Acids Res. [Pubmed 18495751] [Full text]
  22. Janky, R. and van Helden, J. Evaluation of phylogenetic footprint discovery for the prediction of bacterial cis-regulatory elements (2008). BMC Bioinformatics 2008, 9:37doi:10.1186/1471-2105-9-37. [Pubmed 18215291] [Full text]
  23. Sand, O., Turatsinze, J. V. and van Helden, J. (2008). Evaluating the prediction of cis-acting regulatory elements in genome sequences. In Frishman, D. and Valencia, A. (eds.), Modern genome annotation: the BioSapiens network. Springer.
  24. Coulson, R., Manke, T., Palin, K., Roider, H., Sand, O., van Helden, J., Ukkonen, E., Vingron, M. and Brazma, A. (2008). From gene expression profiling to gene regulation. In Frishman, D. and Valencia, A. (eds.), Modern genome annotation: the BioSapiens network. Springer.
  25. 2007

  26. Aerts, S., van Helden, J., Sand, O. & Hassan, B. A. (2007). Fine-Tuning Enhancer Models to Predict Transcriptional Targets across Multiple Genomes. PLoS ONE 2, e1115. Pubmed 17973026.
  27. Sand, O. & van Helden, J. (2007). Discovery of motifs in promoters of co-regulated genes. In Comparative genomics. Methods in Molecular Biology. ISBN 978-1-58829-693-1 [publisher site]
  28. Janky, R. & van Helden, J. (2007). Discovery of conserved motifs in promoters of orthologous genes or prokaryotes. In Comparative genomics. Methods in Molecular Biology. ISBN 978-1-58829-693-1 [publisher site]
  29. 2005

  30. Tompa, M., Li, N., Bailey, T. L., Church, G. M., De Moor, B., Eskin, E., Favorov, A. V., Frith, M. C., Fu, Y., Kent, W. J., Makeev, V. J., Mironov, A. A., Noble, W. S., Pavesi, G., Pesole, G., Regnier, M., Simonis, N., Sinha, S., Thijs, G., van Helden, J., Vandenbogaert, M., Weng, Z., Workman, C., Ye, C. & Zhu, Z. (2005). Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol 23, 137-44. Pubmed 15637633

  31. Gonze, D., S. Pinloche, O. Gascuel, and J. van Helden. 2005. Discrimination of yeast genes involved in methionine and phosphate metabolism on the basis of upstream motifs. Bioinformatics. Pubmed 15998664.


  32. van Helden, J. (2004). Metrics for comparing regulatory sequences on the basis of pattern counts. Bioinformatics, 2004 20(3):399-406. [Pubmed 14764560] [Full text via OUP]

  33. Simonis, N., J. Van Helden, G.N. Cohen, and S.J. Wodak. 2004. Transcriptional regulation of protein complexes in yeast. Genome Biol 5: R33. [Pubmed 15128447] [Full text]

  34. Simonis, N., S.J. Wodak, G.N. Cohen, and J. Van Helden. 2004. Combining pattern discovery and discriminant analysis to predict gene co-regulation. Bioinformatics. Pubmed 15073004


  35. van Helden, J. (2003). Prediction of transcriptional regulation by analysis of the non-coding genome. Current Genomics 4(3), 217-224.

  36. van Helden, J. (2003). Regulatory sequence analysis tools. Nucleic Acids Res. 2003 Jul 1;31(13):3593-6. [Pubmed 12824373] [Full text] [pdf]


  37. 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. Lecture Notes in Computer Sciences 2066: 155-172.

    Last Century

  38. van Helden, J., Andr�, B. & Collado-Vides, J. (2000). A web site for the computational analysis of yeast regulatory sequences. Yeast 16(2), 177-187. [Pubmed 10641039]

  39. van Helden, J., Olmo, M. & Perez-Ortin, J. E. (2000). Statistical analysis of yeast genomic downstream sequences reveals putative polyadenylation signals. Nucleic Acids Res 28(4), 1000-1010. [Pubmed 10648794] [Full text]

  40. van Helden, J., Rios, A. F. & Collado-Vides, J. (2000). Discovering regulatory elements in intergenic sequences by analysis of spaced dyads. Nucleic Acids Res. 28(8):1808-18. [Pubmed 10734201] [Full text].

  41. van Helden, J., Andr�, B. & Collado-Vides, J. (1998). Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J Mol Biol 281(5), 827-42. [Pubmed 9719638]

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