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Lab publications

    2009

  1. Leplae, R., Lima-Mendez, G. and Toussaint, A. (2009). ACLAME: A CLAssification of Mobile genetic Elements, update 2010. Nucleic Acids Res. Pubmed 19933762

  2. 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.

  3. 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.

  4. 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.

  5. Defrance, M. and Helden, J. V. (2009). Info-gibbs: a motif discovery algorithm that directly optimizes information content during sampling. Bioinformatics. Pubmed 19689955

  6. 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].

  7. Lonez, C., Lensink, M. F., Vandenbranden, M. and Ruysschaert, J.-M. 2009. Cationic Lipids Activate Cellular Cascades. Which Receptors are Involved? Biochim. Biophys. Acta 1790, 425-430. Pubmed 19269309

  8. Lensink, M. F., Lonez, C., Ruysschaert, J.-M. and Vandenbranden, M. 2009. Characterization of the Cationic DiC(14)-Amidine Bilayer by Mixed DMPC/DiC(14)-Amidine Molecular Dynamics Simulations shows an Interdigitated Nonlamellar Bilayer Phase. Langmuir 25, 5230-5238. Pubmed 19231818

  9. Faust, K., Croes, D. and van Helden, J. (2009). Metabolic Pathfinding Using RPAIR Annotation. J Mol Biol. Pubmed 19281817

  10. 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

    11. 2008

  11. Kundrotas, P. J., Lensink, M. F. and Alexov, E. 2008. Homology-based Modeling of 3D Structures of Protein-Protein Complexes using Alignments of Modified Sequence Profiles. Int. J. Biol. Macromol. 43, 198-208. Pubmed 18572239

  12. Lensink, M. F. 2008, Membrane-associated Proteins and Peptides. In Molecular Modeling of Proteins. Methods in Molecular Biology. ISBN 978-1-58829-864-5. Pubmed 18446287

  13. Lensink, M. F. and Méndez, R. (2008). Recognition-induced Conformational Changes in Protein-Protein Docking. Curr. Pharm. Biotechnol. 9, 77-86. Review. Pubmed 18393864

  14. Smeesters, P. R., Mardulyn, P., Vergison, A., Leplae, R. and Van Melderen, L. (2008). Genetic diversity of Group A Streptococcus M protein: implications for typing and vaccine development. Vaccine 26, 5835-42. Pubmed 18789365

  15. Kontos, K., Godard, P., Andre, B., van Helden, J. and Bontempi, G. (2008). Machine learning techniques to identify putative genes involved in nitrogen catabolite repression in the yeast Saccharomyces cerevisiae. BMC Proc 2 Suppl 4, S5. Pubmed 19091052

  16. 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

  17. 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

  18. 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

  19. Brohee, S., Faust, K., Lima-Mendez, G., Vanderstocken, G. and van Helden, J. (2008) Network Analysis Tools: from biological networks to clusters and pathways. Nat Protoc, 3, 1616-1629.Pubmed 18802442

  20. 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

  21. 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

  22. 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

  23. 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. Pubmed 18524799

  24. 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

  25. Thomas-Chollier M., Ledent V. (2008). Comparative phylogenomic analyses of teleost fish Hox gene clusters: lessons from the cichlid fish Astatotilapia burtoni: comment. BMC Genomics, 9:35 Pubmed 18218066

  26. 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 doi:10.1093/molbev/msn023

  27. Lima-Mendez, G., van Helden, J., Toussaint, A. and Leplae, R. (2008) Prophinder: a computational tool for prophage prediction in prokaryotic genomes. Bioinformatics, 24, 863-865. doi:10.1093/bioinformatics/btn043

  28. Janky, R. and van Helden, J. Evaluation of phylogenetic footprint discovery for the prediction of bacterial cis-regulatory elements (2008). BMC Bioinformatics 9:37. Biomed Central Pubmed 18215291

  29. Dessailly, B. H., Lensink, M. F., Orengo, C. A. and Wodak, S. J. LigASite--a database of biologically relevant binding sites in proteins with known apo-structures Nucleic Acids Res 36, D667-73 (2008). Pubmed 17933762.

    30. 2007

  30. Lima-Mendez, G., Toussaint, A. & Leplae, R. (2007). Analysis of the phage sequence space: the benefit of structured information. Virology 365, 241-9. Pubmed 17482656

  31. Toussaint, A., Lima-Mendez, G. & Leplae, R. (2007). PhiGO, a phage ontology associated with the ACLAME database. Res Microbiol 158, 567-71. Pubmed 17614261

  32. 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]

  33. 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]

  34. 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. Pubmed 17994088.

  35. 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.

  36. Lensink, M. F., Mendez, R. and Wodak, S. J. Docking and scoring protein complexes: CAPRI 3rd Edition Proteins 69, 704-18 (2007). Pubmed 17918726

  37. Launay G, Mendez R, Wodak SJ, Simonson T. Recognizing protein-protein interfaces with empirical potentials and reduced amino acid alphabets. BMC Bioinformatics. 2007 Jul 27. Pubmed 17662112

  38. Dessailly, B.H., Lensink, M.F. & Wodak, S.J. (2007). Relating destabilizing regions to known functional sites in proteins. BMC Bioinformatics 8, 141. Pubmed 17470296.

  39. 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. Pubmed 17302974

  40. 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. Pubmed 17308034.

    41. 2006

  41. Leplae R, Lima-Mendez G, Toussaint A. (2006). A first global analysis of plasmid encoded proteins in the ACLAME database. FEMS Microbiol Rev. 2006 Nov;30(6):980-94. Pubmed 17064288.

  42. 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.

  43. 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

  44. Brohée, S. & van Helden, J. (2006). Evaluation of clustering algorithms for protein-protein interaction networks. BMC Bioinformatics 7, 488. Pubmed 17087821

    45. 2005

  45. 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

  46. 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.

  47. 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

  48. 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.

  49. 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. Pubmed 15608217

  50. Roosens NH, Bernard C, Leplae R, Verbruggen N. Adaptative evolution of metallothionein 3 in the Cd/Zn hyperaccumulator Thlaspi caerulescens. Z Naturforsch [C] 2005;60(3-4):224-228.

  51. Mendez R, Leplae R, Lensink MF, Wodak SJ. Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures. Proteins 2005;60(2):150-169.

  52. Roosens NH, Leplae R, Bernard C, Verbruggen N. Variations in plant metallothioneins: the heavy metal hyperaccumulator Thlaspi caerulescens as a study case. Planta 2005:1-14.

  53. Frost LS, Leplae R, Summers AO, Toussaint A. Mobile genetic elements: the agents of open source evolution. Nat Rev Microbiol 2005;3(9):722-732.

  54. Jaramillo A, Wodak SJ. Computational protein design is a challenge for implicit solvation models. Biophys J 2005;88(1):156-171.

    55. 2004

  55. van Helden, J. (2004). Metrics for comparing regulatory sequences on the basis of pattern counts. Bioinformatics 20: 399-406. Pubmed 14764560

  56. Simonis, N., J. Pubmed 15128447

  57. 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. Pubmed 15073004

  58. Roosens NH, Bernard C, Leplae R, Verbruggen N. Evidence for copper homeostasis function of metallothionein (MT3) in the hyperaccumulator Thlaspi caerulescens. FEBS Lett 2004;577(1-2):9-16.

  59. Giraldo J, De Maria L, Wodak SJ. Shift in nucleotide conformational equilibrium contributes to increased rate of catalysis of GpAp versus GpA in barnase. Proteins 2004;56(2):261-276.

  60. Ochagavia ME, Wodak S. Progressive combinatorial algorithm for multiple structural alignments: application to distantly related proteins. Proteins 2004;55(2):436-454.

  61. Wodak SJ, Mendez R. Prediction of protein-protein interactions: the CAPRI experiment, its evaluation and implications. Curr Opin Struct Biol 2004;14(2):242-249.

  62. Leplae R, Hebrant A, Wodak SJ, Toussaint A. ACLAME: a CLAssification of Mobile genetic Elements. Nucleic Acids Res 2004;32(Database issue):D45-49.

  63. Lemer C, Antezana E, Couche F, Fays F, Santolaria X, Janky R, Deville Y, Richelle J, Wodak SJ. The aMAZE LightBench: a web interface to a relational database of cellular processes. Nucleic Acids Res 2004;32 Database issue:D443-448.

    64. 2003

  64. Toussaint A, Merlin C, Monchy S, Benotmane MA, Leplae R, Mergeay M, Springael D. The biphenyl- and 4-chlorobiphenyl-catabolic transposon Tn4371, a member of a new family of genomic islands related to IncP and Ti plasmids. Appl Environ Microbiol 2003;69(8):4837-4845.

  65. Govaerts C, Bondue A, Springael JY, Olivella M, Deupi X, Le Poul E, Wodak SJ, Parmentier M, Pardo L, Blanpain C. Activation of CCR5 by chemokines involves an aromatic cluster between transmembrane helices 2 and 3. J Biol Chem 2003;278(3):1892-1903.

  66. Janin J, Henrick K, Moult J, Eyck LT, Sternberg MJ, Vajda S, Vakser I, Wodak SJ. CAPRI: a Critical Assessment of PRedicted Interactions. Proteins 2003;52(1):2-9.

  67. Ogata K, Jaramillo A, Cohen W, Briand JP, Connan F, Choppin J, Muller S, Wodak SJ. Automatic sequence design of major histocompatibility complex class I binding peptides impairing CD8+ T cell recognition. J Biol Chem 2003;278(2):1281-1290.

  68. Wernisch L, Wodak SJ. Identifying structural domains in proteins. Methods Biochem Anal 2003;44:365-385.

  69. Bon E, Casaregola S, Blandin G, Llorente B, Neuveglise C, Munsterkotter M, Guldener U, Mewes HW, van Helden J, Dujon B, Gaillardin C. Molecular evolution of eukaryotic genomes: hemiascomycetous yeast spliceosomal introns. Nucleic Acids Res 2003;31(4):1121-1135.

  70. Hulzink RJ, Weerdesteyn H, Croes AF, Gerats T, van Herpen MM, van Helden J. In silico identification of putative regulatory sequence elements in the 5'-untranslated region of genes that are expressed during male gametogenesis. Plant Physiol 2003;132(1):75-83.

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

  72. van Helden J. Regulatory sequence analysis tools. Nucleic Acids Res 2003;31(13):3593-3596.

  73. Mendez R, Leplae R, De Maria L, Wodak SJ. Assessment of blind predictions of protein-protein interactions: current status of docking methods. Proteins 2003;52(1):51-67.

  74. Deville Y, Gilbert D, van Helden J, Wodak SJ. An overview of data models for the analysis of biochemical pathways. Brief Bioinform 2003;4(3):246-259.

    75. 2002

  75. Leplae R, Hubbard TJ. MaxBench: evaluation of sequence and structure comparison methods. Bioinformatics 2002;18(3):494-495.

  76. Janin J, Wodak SJ. Protein modules and protein-protein interaction. Introduction. Adv Protein Chem 2002;61:1-8.

  77. Jaramillo A, Wernisch L, Hery S, Wodak SJ. Folding free energy function selects native-like protein sequences in the core but not on the surface. Proc Natl Acad Sci U S A 2002;99(21):13554-13559.

  78. Ochagavia ME, Richelle J, Wodak SJ. Advanced pairwise structure alignments of proteins and analysis of conformational changes. Bioinformatics 2002;18(4):637-640.

  79. Ogata K, Wodak SJ. Conserved water molecules in MHC class-I molecules and their putative structural and functional roles. Protein Eng 2002;15(8):697-705.

  80. Pajon A, Vranken WF, Jimenez MA, Rico M, Wodak SJ. Pescador: the PEptides in Solution ConformAtion Database: Online Resource. J Biomol NMR 2002;23(2):85-102.

  81. Radresa O, Ogata K, Wodak S, Ruysschaert JM, Goormaghtigh E. Modeling the three-dimensional structure of H+-ATPase of Neurospora crassa. Eur J Biochem 2002;269(21):5246-5258.

  82. van Helden J, Wernisch L, Gilbert D, Wodak SJ. Graph-based analysis of metabolic networks. Ernst Schering Res Found Workshop 2002(38):245-274.

  83. Wodak SJ, Janin J. Structural basis of macromolecular recognition. Adv Protein Chem 2002;61:9-73.

  84. Couche F. Recherche de chemins ans les voies métaboliques. Bruxelles: université Libre ed Bruxelles; 2002.

    85. 2001

  85. Tramontano A, Leplae R, Morea V. Analysis and assessment of comparative modeling predictions in CASP4. Proteins 2001;Suppl 5:22-38.

  86. Das U, Chen S, Fuxreiter M, Vaguine AA, Richelle J, Berman HM, Wodak SJ. Checking nucleic acid crystal structures. Acta Crystallogr D Biol Crystallogr 2001;57(Pt 6):813-828.

  87. Govaerts C, Lefort A, Costagliola S, Wodak SJ, Ballesteros JA, Van Sande J, Pardo L, Vassart G. A conserved Asn in transmembrane helix 7 is an on/off switch in the activation of the thyrotropin receptor. J Biol Chem 2001;276(25):22991-22999.

  88. Govaerts C, Blanpain C, Deupi X, Ballet S, Ballesteros JA, Wodak SJ, Vassart G, Pardo L, Parmentier M. The TXP motif in the second transmembrane helix of CCR5. A structural determinant of chemokine-induced activation. J Biol Chem 2001;276(16):13217-13225.

  89. Jaramillo A, Wernisch L, Hery S, Wodak SJ. Automatic procedures for protein design. Comb Chem High Throughput Screen 2001;4(8):643-659.

  90. Martins JC, Enassar M, Willem R, Wieruzeski JM, Lippens G, Wodak SJ. Solution structure of the main alpha-amylase inhibitor from amaranth seeds. Eur J Biochem 2001;268(8):2379-2389.

  91. Nadassy K, Tomas-Oliveira I, Alberts I, Janin J, Wodak SJ. Standard atomic volumes in double-stranded DNA and packing in protein--DNA interfaces. Nucleic Acids Res 2001;29(16):3362-3376.

  92. Schroeder M, Gilbert D, van Helden J, Noy P. Approaches to visualisation in bioinformatics: from dendrograms to Space Explorer. Information Science 2001;139(1):19-57.

  93. van Helden J, Gilbert D, Wernisch L, Schroeder M, Wodak S. Applications of regulatory sequence analysis and metabolic network analysis to the interpretation of gene expression data. In: Gascuel O, Sagot M-F, editors; 2001; Montpellier. Springer-Verlag. p 155-172.

  94. van Helden J, Naim A, Lemer C, Mancuso R, Eldridge M, Wodak SJ. From molecular activities and processes to biological function. Brief Bioinform 2001;2(1):81-93.

  95. 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.

    96. 2000

  96. Van Belle D, De Maria L, Iurcu G, Wodak SJ. Pathways of ligand clearance in acetylcholinesterase by multiple copy sampling. J Mol Biol 2000;298(4):705-726.

  97. Wernisch L, Hery S, Wodak SJ. Automatic protein design with all atom force-fields by exact and heuristic optimization. J Mol Biol 2000;301(3):713-736.

  98. Gilbert DR, Schroeder M, van Helden J. Interactive visualization and exploration of relationships between biological objects. Trends Biotechnol 2000;18(12):487-494.

  99. van Helden J, Naim A, Mancuso R, Eldridge M, Wernisch L, Gilbert D, Wodak SJ. Representing and analysing molecular and cellular function using the computer. Biol Chem 2000;381(9-10):921-935.

  100. van Helden J, Rios AF, Collado-Vides J. Discovering regulatory elements in non-coding sequences by analysis of spaced dyads. Nucleic Acids Res 2000;28(8):1808-1818.

  101. van Helden J, del Olmo M, Perez-Ortin JE. Statistical analysis of yeast genomic downstream sequences reveals putative polyadenylation signals. Nucleic Acids Res 2000;28(4):1000-1010.Pubmed 10648794

  102. van Helden J, Andre B, Collado-Vides J. A web site for the computational analysis of yeast regulatory sequences. Yeast 2000;16(2):177-187.

    103. 1999

  103. Morel N, Bon S, Greenblatt HM, Van Belle D, Wodak SJ, Sussman JL, Massoulie J, Silman I. Effect of mutations within the peripheral anionic site on the stability of acetylcholinesterase. Mol Pharmacol 1999;55(6):982-992.

  104. Nadassy K, Wodak SJ, Janin J. Structural features of protein-nucleic acid recognition sites. Biochemistry 1999;38(7):1999-2017.

  105. Vaguine AA, Richelle J, Wodak SJ. SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model. Acta Crystallogr D Biol Crystallogr 1999;55 (Pt 1):191-205.

  106. Wernisch L, Hunting M, Wodak SJ. Identification of structural domains in proteins by a graph heuristic. Proteins 1999;35(3):338-352.

  107. Salgado H, Santos A, Garza-Ramos U, van Helden J, Diaz E, Collado-Vides J. RegulonDB (version 2.0): a database on transcriptional regulation in Escherichia coli. Nucleic Acids Res 1999;27(1):59-60.

  108. van Helden J, Gilbert DR, Wernisch L, Wodak S. Logical tools for querying and assisting annotation of a metabolic and regulatory pathway database. ISMB 1999.

    109. 1998

  109. Leplae R, Hubbard T, Tramontano A. GLASS: a tool to visualize protein structure prediction data in three dimensions and evaluate their consistency. Proteins 1998;30(4):339-351.

  110. Morea V, Leplae R, Tramontano A. Protein structure prediction and design. Biotechnol Annu Rev 1998;4:177-214.

  111. Giraldo J, Wodak SJ, van Belle D. Conformational analysis of GpA and GpAp in aqueous solution by molecular dynamics and statistical methods. J Mol Biol 1998;283(4):863-882.

  112. Wintjens R, Wodak SJ, Rooman M. Typical interaction patterns in alphabeta and betaalpha turn motifs. Protein Eng 1998;11(7):505-522.

  113. Grillenzoni N, van Helden J, Dambly-Chaudiere C, Ghysen A. The iroquois complex controls the somatotopy of Drosophila notum mechanosensory projections. Development 1998;125(18):3563-3569.

  114. van Helden J, Andre B, Collado-Vides J. Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J Mol Biol 1998;281(5):827-842.Pubmed 9719638

  115. Alberts IL, Nadassy K, Wodak SJ. Analysis of zinc binding sites in protein crystal structures. Protein Sci 1998;7(8):1700-1716.

    116. 1997

  116. Sanchez L, van Helden J, Thieffry D. Establishement of the dorso-ventral pattern during embryonic development of drosophila melanogasater: a logical analysis. J Theor Biol 1997;189(4):377-389.

    117. 1996

  117. Hubbard T, Park J, Lahm A, Leplae R, Tramontano A. Protein structure prediction: playing the fold. Trends Biochem Sci 1996;21(8):279-281.

  118. Gordon-Beresford RM, Van Belle D, Giraldo J, Wodak SJ. Effect of nucleotide substrate binding on the pKa of catalytic residues in barnase. Proteins 1996;25(2):180-194.

  119. Gray PM, Kemp GJ, Rawlings CJ, Brown NP, Sander C, Thornton JM, Orengo CM, Wodak SJ, Richelle J. Macromolecular structure information and databases. The EU BRIDGE Database Project Consortium. Trends Biochem Sci 1996;21(7):251-256.

  120. Kocher JP, Prevost M, Wodak SJ, Lee B. Properties of the protein matrix revealed by the free energy of cavity formation. Structure 1996;4(12):1517-1529.

  121. Pontius J, Richelle J, Wodak SJ. Deviations from standard atomic volumes as a quality measure for protein crystal structures. J Mol Biol 1996;264(1):121-136.

  122. Wintjens RT, Rooman MJ, Wodak SJ. Automatic classification and analysis of alpha alpha-turn motifs in proteins. J Mol Biol 1996;255(1):235-253.

  123. Wodak SJ. Extending molecular systematics to the third dimension. Nat Struct Biol 1996;3(7):575-578.

    124. 1995

  124. De Bolle X, Vinals C, Prozzi D, Paquet JY, Leplae R, Depiereux E, Vandenhaute J, Feytmans E. Identification of residues potentially involved in the interactions between subunits in yeast alcohol dehydrogenases. Eur J Biochem 1995;231(1):214-219.

  125. Leplae R, Tramontano A. PLANET: a phage library analysis expert tool. Physiol Chem Phys Med NMR 1995;27(4):331-338.

  126. Boutonnet NS, Rooman MJ, Wodak SJ. Automatic analysis of protein conformational changes by multiple linkage clustering. J Mol Biol 1995;253(4):633-647.

  127. Boutonnet NS, Rooman MJ, Ochagavia ME, Richelle J, Wodak SJ. Optimal protein structure alignments by multiple linkage clustering: application to distantly related proteins. Protein Eng 1995;8(7):647-662.

  128. Kajava AV, Vassart G, Wodak SJ. Modeling of the three-dimensional structure of proteins with the typical leucine-rich repeats. Structure 1995;3(9):867-877.

  129. Lemer CM, Rooman MJ, Wodak SJ. Protein structure prediction by threading methods: evaluation of current techniques. Proteins 1995;23(3):337-355.

  130. Lippens G, Najib J, Wodak SJ, Tartar A. NMR sequential assignments and solution structure of chlorotoxin, a small scorpion toxin that blocks chloride channels. Biochemistry 1995;34(1):13-21.

  131. Pugliese L, Prevost M, Wodak SJ. Unfolding simulations of the 85-102 beta-hairpin of barnase. J Mol Biol 1995;251(3):432-447.

  132. Rooman MJ, Wodak SJ. Are database-derived potentials valid for scoring both forward and inverted protein folding? Protein Eng 1995;8(9):849-858.

  133. Huang F, van Helden J, Dambly-Chaudiere C, Ghysen A. Contribution of the gene extramachrochaete to the precise positioning of bristles in Drosophila. Roux's Arch Dev Biol 1995;204:336-343.

    134. 1994

  134. Cerf C, Lippens G, Ramakrishnan V, Muyldermans S, Segers A, Wyns L, Wodak SJ, Hallenga K. Homo- and heteronuclear two-dimensional NMR studies of the globular domain of histone H1: full assignment, tertiary structure, and comparison with the globular domain of histone H5. Biochemistry 1994;33(37):11079-11086.

  135. Gustchina A, Sansom C, Prevost M, Richelle J, Wodak SY, Wlodawer A, Weber IT. Energy calculations and analysis of HIV-1 protease-inhibitor crystal structures. Protein Eng 1994;7(3):309-317.

  136. Kocher JP, Rooman MJ, Wodak SJ. Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches. J Mol Biol 1994;235(5):1598-1613.

  137. Pintar A, Chollet A, Bradshaw C, Chaffotte A, Cadieux C, Rooman MJ, Hallenga K, Knowles J, Goldberg M, Wodak SJ. Conformational properties of four peptides corresponding to alpha-helical regions of Rhodospirillum cytochrome c2 and bovine calcium binding protein. Biochemistry 1994;33(37):11158-11173.

    138. 1993

  138. Cerf C, Lippens G, Muyldermans S, Segers A, Ramakrishnan V, Wodak SJ, Hallenga K, Wyns L. Homo- and heteronuclear two-dimensional NMR studies of the globular domain of histone H1: sequential assignment and secondary structure. Biochemistry 1993;32(42):11345-11351.

  139. Janin J, Wodak SJ. The quaternary structure of carbonmonoxy hemoglobin ypsilanti. Proteins 1993;15(1):1-4.

  140. Lippens G, Hallenga K, Van Belle D, Wodak SJ, Nirmala NR, Hill P, Russell KC, Smith DD, Hruby VJ. Transfer nuclear Overhauser effect study of the conformation of oxytocin bound to bovine neurophysin I. Biochemistry 1993;32(36):9423-9434.

    141. 1992

  141. Jenkins J, Janin J, Rey F, Chiadmi M, van Tilbeurgh H, Lasters I, De Maeyer M, Van Belle D, Wodak SJ, Lauwereys M, et al. Protein engineering of xylose (glucose) isomerase from Actinoplanes missouriensis. 1. Crystallography and site-directed mutagenesis of metal binding sites. Biochemistry 1992;31(24):5449-5458.

  142. Lambeir AM, Lauwereys M, Stanssens P, Mrabet NT, Snauwaert J, van Tilbeurgh H, Matthyssens G, Lasters I, De Maeyer M, Wodak SJ, et al. Protein engineering of xylose (glucose) isomerase from Actinoplanes missouriensis. 2. Site-directed mutagenesis of the xylose binding site. Biochemistry 1992;31(24):5459-5466.

  143. Rooman MJ, Kocher JP, Wodak SJ. Extracting information on folding from the amino acid sequence: accurate predictions for protein regions with preferred conformation in the absence of tertiary interactions. Biochemistry 1992;31(42):10226-10238.

  144. Rooman MJ, Wodak SJ. Extracting information on folding from the amino acid sequence: consensus regions with preferred conformation in homologous proteins. Biochemistry 1992;31(42):10239-10249.

  145. Scheerlinck JP, Lasters I, Claessens M, De Maeyer M, Pio F, Delhaise P, Wodak SJ. Recurrent alpha beta loop structures in TIM barrel motifs show a distinct pattern of conserved structural features. Proteins 1992;12(4):299-313.

  146. van Tilbeurgh H, Jenkins J, Chiadmi M, Janin J, Wodak SJ, Mrabet NT, Lambeir AM. Protein engineering of xylose (glucose) isomerase from Actinoplanes missouriensis. 3. Changing metal specificity and the pH profile by site-directed mutagenesis. Biochemistry 1992;31(24):5467-5471.

  147. Schooneveld H, Smidt HM, Ammerlaan W, van Helden J. 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 1992;21:285-298.

    148. 1991

  148. Huysmans M, Richelle J, Wodak SJ. SESAM: a relational database for structure and sequence of macromolecules. Proteins 1991;11(1):59-76.

  149. Karplus M, Prevost M, Tidor B, Wodak S. Simulation analysis of the stability mutants R96H of bacteriophage T4 lysozyme and I96A of barnase. Ciba Found Symp 1991;161:63-74.

  150. Prevost M, Wodak SJ, Tidor B, Karplus M. Contribution of the hydrophobic effect to protein stability: analysis based on simulations of the Ile-96----Ala mutation in barnase. Proc Natl Acad Sci U S A 1991;88(23):10880-10884.

  151. Rooman MJ, Kocher JP, Wodak SJ. Prediction of protein backbone conformation based on seven structure assignments. Influence of local interactions. J Mol Biol 1991;221(3):961-979.

  152. Rooman MJ, Wodak SJ. Weak correlation between predictive power of individual sequence patterns and overall prediction accuracy in proteins. Proteins 1991;9(1):69-78.

  153. van Helden J, Dambly-Chaudiere C, Ghysen A. Axons of sensory bristles do not need achaete, scute or asense to establish the appropriate projection. 1991; St Remy. J. Neurogenet. p 149.

    154. 1990

  154. Lasters I, Wodak SJ, Pio F. The design of idealized alpha/beta-barrels: analysis of beta-sheet closure requirements. Proteins 1990;7(3):249-256.

  155. Moens L, Van Hauwaert ML, De Smet K, Ver Donck K, Van De Peer Y, Van Beeumen J, Wodak S, Alard P, Trotman C. Structural interpretation of the amino acid sequence of a second domain from the Artemia covalent polymer globin. J Biol Chem 1990;265(24):14285-14291.

  156. Rooman MJ, Rodriguez J, Wodak SJ. Relations between protein sequence and structure and their significance. J Mol Biol 1990;213(2):337-350.

  157. Rooman MJ, Rodriguez J, Wodak SJ. Automatic definition of recurrent local structure motifs in proteins. J Mol Biol 1990;213(2):327-336.

  158. Wodak SJ, Lasters I, Pio F, Claessens M. Basic design features of the parallel alpha beta barrel, a ubiquitous protein-folding motif. Biochem Soc Symp 1990;57:99-121.

    159. Before 1990

  159. Claessens M, Van Cutsem E, Lasters I, Wodak S. Modelling the polypeptide backbone with 'spare parts' from known protein structures. Protein Eng 1989;2(5):335-345.

  160. Rooman MJ, Wodak SJ, Thornton JM. Amino acid sequence templates derived from recurrent turn motifs in proteins: critical evaluation of their predictive power. Protein Eng 1989;3(1):23-27.

  161. Lasters I, Wodak SJ, Alard P, van Cutsem E. Structural principles of parallel beta-barrels in proteins. Proc Natl Acad Sci U S A 1988;85(10):3338-3342.

  162. Moens L, Van Hauwaert ML, De Smet K, Geelen D, Verpooten G, Van Beeumen J, Wodak S, Alard P, Trotman C. A structural domain of the covalent polymer globin chains of artemia. Interpretation of amino acid sequence data. J Biol Chem 1988;263(10):4679-4685.

  163. Rey F, Jenkins J, Janin J, Lasters I, Alard P, Claessens M, Matthyssens G, Wodak S. Structural analysis of the 2.8 A model of Xylose isomerase from Actinoplanes missouriensis. Proteins 1988;4(3):165-172.

  164. Rooman MJ, Wodak SJ. Identification of predictive sequence motifs limited by protein structure data base size. Nature 1988;335(6185):45-49.

  165. Van Belle D, Couplet I, Prevost M, Wodak SJ. Calculations of electrostatic properties in proteins. Analysis of contributions from induced protein dipoles. J Mol Biol 1987;198(4):721-735.

  166. Wodak SJ. Computer-aided design in protein engineering. Ann N Y Acad Sci 1987;501:1-13.

  167. Wodak SJ, De Crombrugghe M, Janin J. Computer studies of interactions between macromolecules. Prog Biophys Mol Biol 1987;49(1):29-63.

  168. Wodak SJ, De Coen JL, Edelstein SJ, Demarne H, Beuzard Y. Modification of human hemoglobin by glutathione. III. Perturbations of hemoglobin conformation analyzed by computer modeling. J Biol Chem 1986;261(31):14717-14724.

  169. Janin J, Wodak SJ. Reaction pathway for the quaternary structure change in hemoglobin. Biopolymers 1985;24(3):509-526.

  170. Lesk AM, Janin J, Wodak S, Chothia C. Haemoglobin: the surface buried between the alpha 1 beta 1 and alpha 2 beta 2 dimers in the deoxy and oxy structures. J Mol Biol 1985;183(2):267-270.

  171. Wodak SJ, Alard P, Delhaise P, Renneboog-Squilbin C. Simulation of conformational changes in 2 Zn insulin. J Mol Biol 1985;181(2):317-322.

  172. Janin J, Wodak SJ. Structural domains in proteins and their role in the dynamics of protein function. Prog Biophys Mol Biol 1983;42(1):21-78.

  173. Wodak SJ, Janin J. Location of structural domains in protein. Biochemistry 1981;20(23):6544-6552.

  174. Janin J, Wodak S. Conformation of amino acid side-chains in proteins. J Mol Biol 1978;125(3):357-386.

  175. Wodak SJ, Janin J. Computer analysis of protein-protein interaction. J Mol Biol 1978;124(2):323-342.

  176. Wodak SJ, Janin J. A computer analysis of protein-protein interaction [proceedings]. Arch Int Physiol Biochim 1978;86(2):473-474.

  177. Wodak SY. The structure of cytidilyl(2',5')adenosine when bound to pancreatic ribonuclease S. J Mol Biol 1977;116(4):855-875.

  178. Chothia C, Wodak S, Janin J. Role of subunit interfaces in the allosteric mechanism of hemoglobin. Proc Natl Acad Sci U S A 1976;73(11):3793-3797.

  179. Levinthal C, Wodak SJ, Kahn P, Dadivanian AK. Hemoglobin interaction in sickle cell fibers. I: Theoretical approaches to the molecular contacts. Proc Natl Acad Sci U S A 1975;72(4):1330-1334.