Publications in international journals 2006
  • Ettema TJ, Brinkman AB, Lamers PP, Kornet NG, de Vos WM, van der Oost J.
    Molecular characterization of a conserved archaeal copper resistance (cop) gene cluster and its copper-responsive regulator in Sulfolobus solfataricus P2.
    Microbiology , Jul;152(Pt 7):1969-1979., 2006 , PDF

  • Boekhorst J, Helmer Q, Kleerebezem M, Siezen RJ.
    Comparative analysis of proteins with a mucus-binding domain found exclusively in lactic acid bacteria.
    Microbiology, Jan;152(Pt 1):273-280., 2006 , PDF

  • van Driel MA, Bruggeman J, Vriend G, Brunner HG, Leunissen JA.
    A text-mining analysis of the human phenome.
    Eur J Hum Genet, May;14(5):535-542., 2006 , PDF

  • Dutilh BE, Huynen MA, Snel B.
    A global definition of expression context is conserved between orthologs but does not correlate with sequence conservation.
    BMC Genomics, Jan 19;7:10., 2006 , PDF

  • Giese TJ, Gregersen BA, Liu Y, Nam K, Mayaan E, Moser A, Range K, Faza ON, Lopez CS, Lera AR, Schaftenaar G, Lopez X, Lee TS, Karypis G, York DM.
    QCRNA 1.0: A database of quantum calculations for RNA catalysis.
    J Mol Graph Model, Dec;25(4):423-433., 2006 , PDF

  • Harjes E, Harjes S, Wohlgemuth S, Muller KH , Krieger E, Herrmann C, Bayer P.
    GTP-Ras Disrupts the Intramolecular Complex of C1 and RA Domains of Nore1.
    Structure, May;14(5):881-888., 2006 , PDF

  • Huising MO, van Schijndel JE, Kruiswijk CP, Nabuurs SB, Savelkoul HF, Flik G, Verburg-van Kemenade BM.
    The presence of multiple and differentially regulated interleukin-12p40 genes in bony fishes signifies an expansion of the vertebrate heterodimeric cytokine family.
    Mol Immunol, Apr;43(10):1519-1533., 2006 , PDF

  • Hulsen T, Huynen MA, de Vlieg J, Groenen PM.
    Benchmarking ortholog identification methods using functional genomics data.
    Genome Biol, 7(4):R31., 2006 , PDF

  • van Hylckama Vlieg J, Rademaker J, Bachmann H, Molenaar D, Kelly W, Siezen RJ.
    Natural diversity and adaptive responses of Lactococcus lactis.
    Current Opinion in Biotechnology, Apr;17(2):183-190., 2006 , PDF

  • Krieger E, Nielsen JE, Spronk CA, Vriend G.
    Fast empirical pK(a) prediction by Ewald summation.
    J Mol Graph Model, Dec;25(4):481-486., 2006 , PDF

  • Lugtenberg D, Yntema HG, Banning MJ, Oudakker AR, Firth HV, Willatt L, Raynaud M, Kleefstra T, Fryns JP, Ropers HH, Chelly J, Moraine C, Gecz J, Reeuwijk J, Nabuurs SB, de Vries BB, Hamel BC, de Brouwer AP, Bokhoven H.
    ZNF674: A New Kruppel-Associated Box-Containing Zinc-Finger Gene Involved in Nonsyndromic X-Linked Mental Retardation.
    Am J Hum Genet, Feb;78(2):265-278., 2006 , PDF

  • Moita LF, Vriend G, Mahairaki V, Louis C, Kafatos FC.
    Integrins of Anopheles gambiae and a putative role of a new beta integrin, BINT2, in phagocytosis of E-coli.
    Insect Biochem Mol Biol, Apr;36(4):282-290., 2006 , PDF

  • Nabuurs SB, Spronk CA, Vuister GW, Vriend G.
    Traditional biomolecular structure determination by NMR spectroscopy allows for major errors.
    PLoS Comput Biol, Feb;2(2):e9., 2006 , PDF

  • Notebaart RA, van Enckevort FJH, Francke C, Siezen RJ, Teusink B.
    Accelerating the reconstruction of genome-scale metabolic networks.
    BMC Bioinformatics, Jun 13;7:296., 2006 , PDF

  • Oti M, Snel B, Huynen MA, Brunner HG.
    Predicting disease genes using protein-protein interactions.
    J Med Genet, Aug;43(8):691-698., 2006 , PDF

  • Tiffin N, Adie E, Turner F, Brunner HG, van Driel MA, Oti M, Lopez-Bigas N, Ouzounis C, Perez-Iratxeta C, Andrade-Navarro MA, Adeyemo A, Patti ME, Semple CA, Hide W.
    Computational disease gene identification: a concert of methods prioritizes type 2 diabetes and obesity candidate genes.
    Nucleic Acids Res, Jun 6;34(10):3067-3081., 2006 , PDF

  • Ricard G, McEwan NR, Dutilh BE, Jouany J-P, Macheboeuf D, Mitsumori M, McIntosh FM, Michalowski T., Nagamine T, Nelson N, Newbold ChJ, Nsabimana E, Takenaka A, Thomas NA, Ushida K, Hackstein JHP, Huynen MA.
    Horizontal Gene Transfer from Bacteria to rumen Ciliates indicates adaptation to their anaerobic carbohydrates, rich-environment.
    BMC Genomics , Feb 10;7:22., 2006 , PDF

  • Siezen RJ, Boekhorst J, Muscariello L, Molenaar D, Renckens B, Kleerebezem M.
    Lactobacillus plantarum gene clusters encoding putative cell-surface protein complexes for carbohydrate utilization are conserved in specific gram-positive bacteria.
    BMC Genomics, May 24;7:126., 2006 , PDF

  • Strous M, Pelletier E, Mangenot S, Rattei Th, Lehner A, Taylor MW, Horn M, Daims H, Bartol-Mavel D, Wincker P, Barbe V, Fonknechten N, Vallenet D, Segurens B, Schenowitz-Truong C, Médigue C, Collingro A, Snel B, Dutilh BE, Op den Camp HJM, van der Drift Ch, Cirpus I, van de Pas-Schoonen KT, Harhangi HR, van Niftrik L, Schmid M, Keltjens J, van de Vossenberg J, Kartal B, Meier H, Frishman D, Huynen MA, Mewes H-W, Weissenbach J, Jetten MSM, Wagner M, Le Paslier D.
    Deciphering the evolution and metabolism of an anammox bacterium from a community genome.
    Nature, Apr 6;440(7085):790-794., 2006 , PDF

  • Teusink B, Smid E.

    Modelling strategies for the industrial exploitation of lactic acid bacteria.
    Nat. Rev. Microbiol, Jan;4(1):46-56., 2006 , PDF

  • Van Durme J, Horn F, Costagliola S, Vriend G, Vassart G.
    GRIS: Glycoprotein-hormone Receptor Information System.
    Mol Endocrinol, Sep;20(9):2247-2255., 2006 , PDF

  • de Vries MC, Siezen RJ, Wijman JG, Zhao Y, Kleerebezem M, de Vos WM, Vaughan EE.
    Comparative and functional analysis of the rRNA-operons and their tRNA gene complement in different lactic acid bacteria.
    System Appl Microbiology, Jul;29(5):358-367., 2006 , PDF

  • Wels M, Francke C, Kerkhoven R, Kleerebezem M, Siezen RJ.
    Predicting cis-acting elements of Lactobacillus plantarum by comparative genomics with different taxonomic subgroups.
    Nucleic Acids Res, Apr 13;34(7):1947-1958., 2006 , PDF

  • von Mering C, Huynen M, Jaeggi D, Schmidt S, Bork P, Snel B.
    STRING: a database of predicted functional associations between proteins.
    Nucleic Acids Res, Jan 1;31(1):258-261., 2006 , PDF

  • Hulsen T, de Vlieg J, Groenen PM.
    PhyloPat: phylogenetic pattern analysis of eukaryotic genes.
    BMC Bioinformatics, Sep 1;7:398., 2006 , PDF

  • Hulsen T, de Vlieg J, Leunissen JA, Groenen PM.
    Testing statistical significance scores of sequence comparison methods with structure similarity.
    BMC Bioinformatics, Oct 12;7:444., 2006 , PDF

  • Folkertsma S.
    The Nuclear Receptor Ligand-Binding Domain: from Biological Function to Drug Design.
    PhD Thesis, , 2006 , PDF

  • Hackstein JH, Tjaden J, Huynen M.
    Mitochondria, hydrogenosomes and mitosomes: products of evolutionary tinkering!
    Curr Genet., Oct;50(4):225-245., 2006 , PDF

  • Pastore C, Adinolfi S, Huynen MA, Rybin V, Martin S, Mayer M, Bukau B, Pastore A.
    YfhJ, a molecular adaptor in iron-sulfur cluster formation or a frataxin-like protein?
    Structure, May;14(5):857-867., 2006 , PDF

  • Oti M, Snel B, Huynen MA, Brunner HG.
    Predicting disease genes using protein-protein interactions.
    J Med Genet., Aug;43(8):691-698., 2006 , PDF

  • Gabaldon T, Snel B, van Zimmeren F, Hemrika W, Tabak H, Huynen MA.
    Origin and evolution of the peroxisomal proteome.
    Biol Direct, Mar 23;1:8., 2006 , PDF

  • van Noort V, Huynen MA.
    Combinatorial gene regulation in Plasmodium falciparum.
    Trends Genet, Feb;22(2):73-78., 2006 , PDF

  • Kuramae EE, Robert V, Snel B, Boekhout T.
    Conflicting phylogenetic position of Schizosaccharomyces pombe.
    Genomics, Oct;88(4):387-393., 2006 , PDF

  • Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P.
    Toward automatic reconstruction of a highly resolved tree of life.
    Science, Mar 3;311(5765):1283-1287., 2006 , PDF

  • Liu M, Siezen RJ.
    Comparative genomics of flavour-forming pathways in lactic acid bacteria.
    Australian Journal of Dairy Technology, 61(2):61-68., 2006 , PDF

  • de Been M, Francke C, Moezelaar R, Abee T, Siezen RJ.
    Comparative analysis of two-component signal transduction systems of Bacillus cereus, Bacillus thuringiensis and bacillus anthracis.
    Microbiology, Oct;152(Pt 10):3035-3048., 2006 , PDF

  • Boekhorst J, Wels M, Kleerebezem M, Siezen RJ.
    The predicted secretome of Lactobacillus plantarum WCFS1 sheds light om interactions with its environment.
    Microbiology, Nov;152(Pt 11):3175-3183., 2006 , PDF

  • Deutscher J, Francke C, Postma PW.
    How phosphotransferase system-related protein phosphorylation regulates carbohydrate metabolism in bacteria.
    Micriobiol Mol Biol Rev, Dec;70(4):939-1031., 2006 , PDF

  • Teusink B, Wiersma A, Molenaar D, Francke C, de Vos WM, Siezen RJ, Smid EJ.
    Analysis of growth of lacobacillus plantarum WCFS1 on a complex medium using a genome-scale metabolic model.
    J Biol Chem, Dec 29;281(52):40041-40048., 2006 , PDF

  • Tabak HF, Hoepfner D, Zand AV, Geuze HJ, Braakman I, Huynen MA.
    Formation of peroxisomes: Present and past.
    Biochim Biophys Acta, Dec;1763(12):1647-1654., 2006 , PDF

  • Tjalsma H, Scholler-Guinard M, Lasonder E, Ruers TJ, Willems HL, Swinkels DW.
    Profiling the humoral immune response in colon cancer patients: diagnostic antigens from Streptococcus bovis.
    Int J Cancer, Nov 1;119(9):2127-2135., 2006 , PDF

  • Vermeulen M, Walter W, Le Guezennec X, Kim J, Edayathumangalam RS, Lasonder E, Luger K, Roeder RG, Logie C, Berger SL, Stunnenberg HG.
    A feed-forward repression mechanism anchors the Sin3/histone deacetylase and N-CoR/SMRT corepressors on chromatin.
    Mol Cell Biol, Jul;26(14):5226-5236., 2006 , PDF

  • Le Guezennec X, Vermeulen M, Brinkman AB, Hoeijmakers WA, Cohen A, Lasonder E, Stunnenberg HG.
    MBD2/NuRD and MBD3/NuRD, two distinct complexes with different biochemical and functional properties.
    Mol Cell Biol, Feb;26(3):843-851., 2006 , PDF

  • Ott MA, Vriend G.
    Correcting ligands, metabolites, and pathways.
    BMC Bioinformatics, Nov 28;7:517., 2006 , PDF

  • van der Woning SP, van Rotterdam W, Nabuurs SB, Venselaar H, Jacobs-Oomen S, Wingens M, Vriend G, Stortelers C, van Zoelen EJ.
    Negative constraints underlie the ErbB specificity of epidermal growth factor-like ligands.
    Journal of Biological Chemistry, Dec 29;281(52):40033-40040., 2006 , PDF

  • Paiva AC, Oliveira L, Horn F, Bywater RP, Vriend G.
    Modeling GPCRs.
    Ernst Schering Found Symp Proc, (2):23-47, 2006 , PDF

  • Huising MO, Geven EJW, Kruiswijk CP, Nabuurs SB, Stolte EH, Spanings FAT, Verburg-van Kemenade BML, Flik G.
    Increased leptin expression in common Carp (Cyprinus carpio) after food intake but not after fasting or feeding to satiation.
    Endocrinology, Dec;147(12):5786-5797., 2006 , PDF

  • Horn SJ, Sikorski P, Cederkvist JB, Vaaje-Kolstad G, Sørlie M, Synstad B, Vriend G, Vårum KM, Eijsink VG.
    Costs and benefits of processivity in enzymatic degradation of recalcitrant polysaccharides.
    Proc Natl Acad Sci U S A, Nov 28;103(48):18089-18094., 2006 , PDF

  • Smeitink JA, Elpeleg O, Antonicka H, Diepstra H, Saada A, Smits P, Sasarman F, Vriend G, Jacob-Hirsch J, Shaag A, Rechavi G, Welling B, Horst J, Rodenburg RJ, van den Heuvel B, Shoubridge EA.
    Distinct clinical phenotypes associated with a mutation in the mitochondrial translation elongation factor EFTs.
    Am J Hum Genet, Nov;79(5):869-877., 2006 , PDF

  • Smith BJ, Huyton T, Joosten RP, McKimm-Breschkin JL, Zhang JG, Luo CS, Lou MZ, Labrou NE, Garrett TP.
    Structure of a calcium-deficient form of influenza virus neuraminidase: implications for substrate binding.
    Acta Crystallogr D Biol Crystallogr, Sep;62(Pt 9):947-952., 2006 , PDF

  • Wessels E, Notebaart RA, Duijsings D, Lanke K, Vergeer B, Melchers WJ, van Kuppeveld FJ.
    Structure-function analysis of the coxsackievirus protein 3A: identification of residues important for dimerization, viral rna replication, and transport inhibition.
    J Biol Chem, Sep 22;281(38):28232-28243., 2006 , PDF