Jacques van Helden - Publications

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Scientific publications / publications scientifiques


  1. Castro-Mondragon JA, Jaeger S, Thieffry D, Thomas-Chollier M, van Helden J. (2017). RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections. Nucleic Acids Res. 2017 Jun 7. doi: 10.1093/nar/gkx314. [PMID 28591841]
  2. Dao LTM, Galindo-Albarrán AO, Castro-Mondragon JA, Andrieu-Soler C, Medina-Rivera A, Souaid C, Charbonnier G, Griffon A, Vanhille L, Stephen T, Alomairi J, Martin D, Torres M, Fernandez N, Soler E, van Helden J, Puthier D, Spicuglia S. (2017). Genome-wide characterization of mammalian promoters with distal enhancer functions. Nat Genet. 2017 Jun 5. doi: 10.1038/ng.3884. [PMID 28581502]
  3. 2016

  4. 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]
  5. 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]
  6. van Helden J. (2016). Confidence intervals are no salvation from the alleged fickleness of the P value. Nat Methods. 13(8):605-6. doi: 10.1038/nmeth.3932. [PMID 27467719]
  7. Amrani A, van Helden J, Bergon A, Aouane A, Ben Hania W, Tamburini C, Loriod B, Imbert J, Ollivier B, Pradel N, Dolla A. (2016). Deciphering the adaptation strategies of Desulfovibrio piezophilus to hydrostatic pressure through metabolic and transcriptional analyses. Environ Microbiol Rep. 8(4):520-6. doi: 10.1111/1758-2229.12427. [PMID 27264199]
  8. 2015

  9. Cayrou,C., Ballester,B., Peiffer,I., Fenouil,R., Coulombe,P., Andrau,J.-C., van Helden,J. and Méchali,M. (2015) The chromatin environment shapes DNA replication origin organization and defines origin classes. Genome Res, 25, 1873–1885. [PMID 26560631]
  10. Medina-Rivera, A., Defrance, M., Sand, O., Herrmann, C., Castro-Mondragon, JA., 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, 43, W50–6. [PMID 25904632]
  11. Griffon, A., Barbier, Q., Dalino, J., van Helden, J., Spicuglia, S. and Ballester, B. (2015) Integrative analysis of public ChIP-seq experiments reveals a complex multi-cell regulatory landscape. Nucleic Acids Res, 10.1093/nar/gku1280.
  12. 2014

  13. 14 entries in the Concise Encyclopaedia of Bioinformatics and Computational Biology
    Eds: Marketa J. Zvelebil and John M. Hancock
    Publisher: Wiley-Blackwell
    ISBN: 978-0-470-97871-9
    On publisher's site
  14. 2013

  15. Darbo, E., Herrmann, C., Lecuit, T., Thieffry, D. & van Helden, J. (2013). Transcriptional and epigenetic signatures of zygotic genome activation during early drosophila embryogenesis. BMC Genomics 14, 226. [PMID 23560912] [Open access]
  16. 2012

  17. 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]
  18. Book edition: Jacques van Helden, Ariane Toussaint and Denis Thieffry (2012). Bacterial Molecular Networks. Methods in Molecular Biology, Volume 804 (28 chapters). [Publisher's site]
  19. 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]
  20. Faust, K. and van Helden, J. (2012). Predicting Metabolic Pathways by Sub-network Extraction. Methods Mol Biol 804, 107-30. [PMID 22144151]
  21. 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]
  22. 2011

  23. Geert A. Martens, Lei Jiang, Karine H. Hellemans, Geert Stangé, Harry Heimberg, Finn C. Nielsen, Olivier Sand, Jacques Van Helden, Frans K. Gorus, Daniel G. Pipeleers (2011). Clusters of Conserved Beta Cell Marker Genes for Assessment of Beta Cell Phenotype. PLoSone September 2011, Volume 6, Issue 9, e24134. [PMID 3166300] [Open Access].
  24. 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]
  25. 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]
  26. 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]
  27. Medina-Rivera, A., Abreu-Goodger, C., Salgado-Osorio, H., Collado-Vides, J. and van Helden, J. (2011). Empirical and theoretical evaluation of transcription factor binding motifs. Nucleic Acids Res. 2010 Oct 4. [PMID 20923783] [Open access]
  28. 2010

  29. 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]] [Open access]
  30. Essaghir, A., Toffalini, F., Knoops, L., Kallin, A., van Helden, J. and Demoulin, J. B. (2010). Transcription factor regulation can be accurately predicted from the presence of target gene signatures in microarray gene expression data. Nucleic Acids 28, e120. Res. [PMID 20215436].
  31. 2009

  32. 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. [PMID 20023717]
  33. 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. [PMID 19776213]
  34. 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. [PMID 19720677]
  35. Defrance, M. and Helden, J. V. (2009). Info-gibbs: a motif discovery algorithm that directly optimizes information content during sampling. Bioinformatics 25(20):2715-22. [PMID 19689955].
  36. 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. [PMID 19450688] [On line].
  37. Faust, K., Croes, D. and van Helden, J. (2009). Metabolic Pathfinding Using RPAIR Annotation. J Mol Biol. [PMID 19281817]
  38. 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. [PMID 19226437]
  39. 2008

  40. 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. ISBN: 978-3-211-75122-0
  41. 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. ISBN: 978-3-211-75122-0
  42. Bourguignon, P. Y., Schachter, V., van Helden, J. and Ouzounis, C. A. (2008). Computational analysis of metabolic networks.In Frishman, D. and Valencia, A. (eds.), Modern genome annotation: the BioSapiens network. Springer. ISBN: 978-3-211-75122-0
  43. Brohée, S., Faust, K., Lima-Mendez, G., Vanderstocken, G. and van Helden, J. (2008) Network Analysis Tools: from biological networks to clusters and pathways. Nature Protocols, 3, 1616-1629. [PMID 18802442].
  44. 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. Nature Protocols, 3, 1604-1615. [PMID 18802441].
  45. 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. Nature Protocols, 3, 1589-1603. [PMID 18802440].
  46. 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. Nature Protocols, 3, 1578-1588. [PMID 18802439].
  47. 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. 36 (Web Server issue): W119-27 [PMID 18495751]. [Open access].
  48. Brohee, 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 Res. 36 (Web Server issue): W444-51 [PMID 18524799]. [Open access].
  49. Lima-Mendez, G., van Helden, J., Toussaint, A. and Leplae, R. (2008). Reticulate representation of evolutionary and functional relationships between phage genomes. Molecular Biology and Evolution 25:762-777; doi:10.1093/molbev/msn023 [Open access].
  50. Lima-Mendez, G., van Helden, J., Toussaint, A. and Leplae, R. (2008) Prophinder: a computational tool for prophage prediction in prokaryotic genomes. Bioinformatics Bioinformatics 24:863-865; doi:10.1093/bioinformatics/btn043. [Open access].
  51. 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. [PMID 18215291]. [Open access].
  52. 2007

  53. 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].
  54. Janky, R. & van Helden, J. (2007). Discovery of conserved motifs in promoters of orthologous genes in prokaryotes. In Comparative genomics. Methods in Molecular Biology. ISBN 978-1-58829-693-1 [publisher site].
  55. Naamane, N., van Helden, J. & Eizirik, D. L. (2007). In silico identification of NF-kappaB-regulated genes in pancreatic beta-cells. BMC Bioinformatics 8, 55. [PMID 17302974].
  56. Godard, P., Urrestarazu, A., Vissers, S., Kontos, K., Bontempi, G., van Helden, J. & Andre, B. (2007). Effect of 21 different nitrogen sources on global gene expression in the yeast Saccharomyces cerevisiae. Mol Cell Biol 27, 3065-86. [PMID 17308034].
  57. 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. [PMID 17973026].
  58. Stark, A., Lin, M. F., Kheradpour, P., Pedersen, J. S., Parts, L., Carlson, J. W., Crosby, M. A., Rasmussen, M. D., Roy, S., Deoras, A. N., Ruby, J. G., Brennecke, J., Curators, H. F., Project, B. D., Hodges, E., Hinrichs, A. S., Caspi, A., Paten, B., Park, S. W., Han, M. V., Maeder, M. L., Polansky, B. J., Robson, B. E., Aerts, S., van Helden, J., Hassan, B., Gilbert, D. G., Eastman, D. A., Rice, M., Weir, M., Hahn, M. W., Park, Y., Dewey, C. N., Pachter, L., Kent, W. J., Haussler, D., Lai, E. C., Bartel, D. P., Hannon, G. J., Kaufman, T. C., Eisen, M. B., Clark, A. G., Smith, D., Celniker, S. E., Gelbart, W. M., Kellis, M., Matthews, B. B., Schroeder, A. J., Sian Gramates, L., St Pierre, S. E., Roark, M., Wiley Jr, K. L., Kulathinal, R. J., Zhang, P., Myrick, K. V., Antone, J. V., Yu, C., Park, S. & Wan, K. H. (2007). Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 450, 219-232. [PMID 17994088].
  59. 2006

  60. Croes, D., F. Couche, S.J. Wodak, J. van Helden (2006). Inferring Meaningful Pathways in Weighted Metabolic Networks. J. Mol. Biol. 356:222-36. [PMID 16337962].
  61. Simonis, N., Gonze, D., Orsi, C., van Helden, J. & Wodak, S. J. (2006). Modularity of the transcriptional response of protein complexes in yeast. J Mol Biol 363, 589-610. 16973176].
  62. Brohée, S. & van Helden, J. (2006). Evaluation of clustering algorithms for protein-protein interaction networks. BMC Bioinformatics 7, 488.[PMID 17087821].
  63. 2005

  64. van Helden, J. 2005. The Analysis of Regulatory Sequences. In Multiple Aspects of DNA and RNA: from Biophysics to Bioinformatics (ed. R. Monasson), 24 pages. Elsevier.
  65. Guldener, U., Munsterkotter, M., Kastenmuller, G., Strack, N., van Helden, J., Lemer, C., Richelles, J., Wodak, S. J., Garcia-Martinez, J., Perez-Ortin, J. E., Michael, H., Kaps, A., Talla, E., Dujon, B., Andre, B., Souciet, J. L., De Montigny, J., Bon, E., Gaillardin, C. & Mewes, H. W. (2005). CYGD: the Comprehensive Yeast Genome Database. Nucleic Acids Res 33 Database Issue, D364-8. [PMID 15608217].
  66. 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. Nature Biotechnol 23, 137-44. [PMID 15637633].
  67. 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 21: 3490-500. [PMID 15998664].
  68. 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.[PMID 15980483].
  69. 2004

  70. van Helden, J. (2004). Metrics for comparing regulatory sequences on the basis of pattern counts. Bioinformatics 20: 399-406. [PMID 14764560].
  71. Simonis, N., J. van Helden, G.N. Cohen, and S.J. Wodak. (2004). Transcriptional regulation of protein complexes in yeast. Genome Biol 5: R33. [PMID 15128447].
  72. 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, 20:2370-2379. [PMID 15073004].
  73. 2003

  74. van Helden, J. (2003). Prediction of transcriptional regulation by analysis of the non-coding genome. Current Genomics 4(3), 217-224.
  75. Bon, E., Casaregola, S., Blandin, G., Llorente, B., Neuveglise, C., Munsterkotter, M., Guldener, U., Mewes, H. W., van Helden, J., Dujon, B. & Gaillardin, C. (2003). Molecular evolution of eukaryotic genomes: hemiascomycetous yeast spliceosomal introns. Nucleic Acids Res 31(4), 1121-35. [PMID 22470229].
  76. Hulzink , R. J. M., Weerdesteyn, H. C. M., van Herpen, M. M. A. & van Helden , J. (2003). In Silico Identification of Putative Regulatory Sequence Elements in the 5'-UTR of Genes that are Expressed during Male Gametogenesis. Plant Physiology. 132:75-83. [PMID 12746513].
  77. van Helden, J. (2003). Regulatory sequence analysis tools. Nucleic Acids Res. 2003 Jul 1;31(13):3593-6. [PMID 12824373].
  78. 2002

  79. Schroeder, M., Gilbert, D., van Helden, J. & Noy, P. (2002). Approaches to visualisation in bioinformatics: from dendrograms to Space Explorer. Information Science 139(1), 19-57.
  80. van Helden, J. Wernisch, L., Gilbert, D., and Wodak, S. (2002). Graph-based analysis of metabolic networks. in Ernst Schering Research Foundation Workshop Volume 38: Bioinformatics and Genome Analysis. Editors: H.-W. Mewes, B. Weiss, H. Seidel Springer-Verlag, Berlin Heidelberg 2002. [PMID 12061005].
  81. 2001

  82. van Helden, J., Naim, A., Lemer, C., Mancuso, R., Eldridge, M. & Wodak, S. (2001). From molecular activities and processes to biological function. Briefings in Bioinformatics 2(1): 81-93.
  83. 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.
  84. Last Century / Siècle dernier

  85. 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. [PMID 10648794].
  86. van Helden, J., Rios, A. F. & Collado-Vides, J. (2000). Discovering regulatory elements in non-coding sequences by analysis of spaced dyads. Nucleic Acids Res. 28(8):1808-18. [PMID 10734201].
  87. van Helden, J., Naim, A., Mancuso, R., Eldridge, M., Wernisch, L., Gilbert, D. & Wodak, S. J. (2000). Representing and analysing molecular and cellular function using the computer. Biol Chem 381(9-10), 921-35. [PMID 11076023].
  88. Gilbert, D., Schroeder, M. & van Helden, J. (2000). Interactive visualization and exploration of relationships between biological objects. Trends in Biotechnology 18(December), 487-495. [PMID 11102659].
  89. van Helden, J., André, B. & Collado-Vides, J. (2000). A web site for the computational analysis of yeast regulatory sequences. Yeast 16(2), 177-187. [PMID 10641039].
  90. Salgado, H., Santos, A., Garza-Ramos, U., van Helden, J., Diaz, E. & Collado-Vides, J. (1999). RegulonDB (version 2.0): a database on transcriptional regulation in Escherichia coli. Nucleic Acids Res 27(1), 59-60. [PMID 9847141].
  91. Grillenzoni, N., van Helden, J., Dambly-Chaudiere, C. & Ghysen, A. (1998). The iroquois complex controls the somatotopy of Drosophila notum mechanosensory projections. Development 125(18), 3563-9. [PMID 9716522].
  92. van Helden, J., André, 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. [PMID 9719638].
  93. Sanchez, L., van Helden, J. & Thieffry, D. (1997). Establishement of the dorso-ventral pattern during embryonic development of Drosophila melanogasater: a logical analysis. J Theor Biol 189(4): 377-89. [PMID 9446747].
  94. Huang, F., van Helden, J., Dambly-Chaudière, C., and Ghysen, A. (1995). Contribution of the gene extramachrochaete to the precise positioning of bristles in Drosophila. Roux's Arch Dev Biol 204: 336-343.
  95. Schooneveld, H., Smidt, H.M., Ammerlaan, W., and van Helden, J. (1992). Colocalized FMRFamide-related neuropeptides in the nervous system of the Colorado potato beetle, Leptinotarsa decemlineata (Say) (Coleoptera : Chrysomelidae) demonstrated immunohistochemically with mono- and polyclonal antibodies. Int. J. Insect Morphol & Embryol. 21: 285-298.

Science and society / Science et société

  1. van Helden, J (2016). Du délit de sale gueule au délit de sale gène - le mythe du criminel-né à l’ère du génome. RéfrActions 37.
  2. van Helden, J. (2009). Faut-il chercher dans nos gènes l'origine des comportements sociaux ? Réfractions 23, 39-52.
  3. van Helden, J. (2009). Ce que nous apprend l'analyse des génomes au sujet de l'évolution. In "Comprendre l'évolution 150 ans après Darwin". Ed. Gérard Cobut. DeBoeck, ISBN : 978-2804104764.[preprint pdf].
  4. van Helden, J. (2008). Qui lira notre avenir dans nos gènes ? Lettre de l'Académie Royale de Belgique. [preprint pdf].
  5. van Helden, J. (2007). La critique de l'évolutionnisme par le mouvement de l'Intelligent Design. Eduquer 59 (juin): 11-14. [pdf]
  6. van Helden, J. (2007). OGM: faut-il enseigner les matières à controverses ? Eduquer 59 (juin): 20-22. [pdf]
  7. van Helden, J. (2004). Le biologiste au carrefour du social, de l'économique et du politique. Réfractions 13: 105. [preprint pdf].
  8. van Helden, J. (2003). OGM : les dangers d'une approche réductionniste des systèmes complexes. Science et pseudo-sciences 259. [preprint pdf] [html].