Publications in international journals 2004
  • Abee T, van Schaik W, Siezen RJ.
    Impact of genomics on microbial food safety.
    Trends in Biotechnol, Dec;22(12):653-660., 2004 , PDF


  • van Bakel H, Huynen M, Wijmenga C.
    Prokaryotic diversity of the Saccharomyces cerevisiae Atx1p-mediated copper pathway.
    Bioinformatics, Nov 1;20(16):2644-2655., 2004 , PDF


  • Boekhorst J, Siezen RJ, Zwahlen MC, Vilanova D, Pridmore RD, Mercenier A, Kleerebezem M, de Vos WM, Brüssow H, Desiere F.
    The complete genomes of Lactobacillus plantarum and Lactobacillus johnsonii reveal extensive differences in chromosome organization and gene content.
    Microbiology, Nov;150(Pt 11):3601-3611., 2004 , PDF


  • Borkent JH.
    Cheminformatics and chemistry teaching.
    Cheminformatics Developments, 1(1):203-217 ., 2004 , PDF


  • Boxma B, Voncken F, Jannink S, van Alen T, Akhmanova A, van Weelden SW, van Hellemond JJ, Ricard G, Huynen M, Tielens AG, Hackstein JH.
    The anaerobic chytridiomycete fungus Piromyces sp. E2 produces ethanol via pyruvate:formate lyase and an alcohol dehydrogenase E.
    Mol Microbiol, Mar;51(5):1389-1399., 2004 , PDF


  • Brunner HG, van Driel MA.
    From syndrome families to functional genomics.
    Nature Reviews Genetics , Jul;5(7):545-551., 2004 , PDF


  • Dutilh BE, Huynen MA, Bruno WJ, Snel B.
    The Consistent Phylogenetic Signal in Genome Trees Revealed by Reducing the Impact of Noise.
    J Mol Evol, May;58(5):527-539., 2004 , PDF


  • Eijsink VG, Bjork A, Gaseidnes S, Sirevag R, Synstad B, van den Burg B, Vriend G.
    Rational engineering of enzyme stability.
    J Biotechnol, Sep 30;113(1-3):105-120., 2004 , PDF


  • Ettema TJ, Makarova KS, Jellema GL, Gierman HJ, Koonin EV, Huynen MA, de Vos WM, van der Oost J.
    Identification and functional verification of archaeal-type phosphoenolpyruvate carboxylase, a missing link in archaeal central carbohydrate metabolism.
    J Bacteriol, Nov;186(22):7754-7762., 2004 , PDF


  • Folkertsma S, van Noort P, Van Durme J, Joosten HJ, Bettler E, Fleuren W, Oliveira L, Horn F, de Vlieg J, Vriend G.
    A family-based approach reveals the function of residues in the nuclear receptor ligand-binding domain.
    J Mol Biol, Aug 6;341(2):321-335., 2004 , PDF


  • Franck E, Madsen O, van Rheede T, Ricard G, Huynen MA, de Jong WW.
    Evolutionary diversity of vertebrate small heat shock proteins.
    J Mol Evol, Dec;59(6):792-805., 2004 , PDF


  • Gabaldón T, Huynen MA.
    Prediction of protein function and pathways in the genome era.
    Cell Mol Life Sci, Apr;61(7-8):930-944., 2004 , PDF


  • Gabaldón T, Huynen MA.
    Shaping the mitochondrial proteome.
    Biochim Biophys Acta, Dec 6;1659(2-3):212-220., 2004 , PDF


  • Huynen MA, Snel B, van Noort V.
    Comparative Genomics for reliable protein-function prediction from genomic data.
    Trends Genet , Aug;20(8):340-344., 2004 , PDF


  • Kerkhoven R, Enckevort FHJ van, Boekhorst J, Molenaar D, Siezen RJ.
    Visualization for genomics: the Microbial Genome Viewer.
    Bioinformatics, Jul 22;20(11):1812-1814., 2004 , PDF


  • Koenderink JB, Swarts HG, Willems PH, Krieger E, De Pont JJ.
    A conformation-specific interhelical salt bridge in the K+ binding site of gastric H,K-ATPase.
    J Biol Chem, Apr 16;279(16):16417-16424., 2004 , PDF


  • Krieger E, Darden T, Nabuurs SB, Finkelstein A, Vriend G.
    Making optimal use of empirical energy functions: Force-field parameterization in crystal space.
    Proteins, Dec 1;57(4):678-683., 2004 , PDF


  • Krieger E, Geretti E, Brandner B, Goger B, Wells TN, Kungl AJ.
    A structural and dynamic model for the interaction of interleukin-8 and glycosaminoglycans: support from isothermal fluorescence titrations.
    Proteins, Mar 1;54(4):768-775., 2004 , PDF


  • Le Guezennec X, Vriend G, Stunnenberg HG.
    Molecular determinants of the interaction of Mad with the PAH2 domain of mSin3.
    J Biol Chem, Jun 11;279(24):25823-25829., 2004 , PDF


  • Lopez-Contreras AM, Gabor K, Martens AA, Renckens BA, Claassen PA, Van der Oost J, De Vos WM.
    Substrate-induced production and secretion of cellulases by Clostridium acetobutylicum.
    Appl Environ Microbiol, Sep;70(9):5238-5243., 2004 , PDF


  • Luijendijk MW, Van Wijk E, Bischoff AM, Krieger E, Huygen PL, Pennings RJ, Brunner HG, Cremers CW, Cremers FP, Kremer H.
    Identification and molecular modelling of a mutation in the motor head domain of myosin VIIA in a family with autosomal dominant hearing impairment.
    Hum Genet, Jul;115(2):149-156., 2004 , PDF


  • Nabuurs SB, Nederveen AJ, Vranken W, Doreleijers JF,Bonvin AMJJ, Vuister GW, Vriend G, Spronk CAEM.
    DRESS: a Database of REfined Solution NMR Structures.
    Proteins, May 15;55(3):483-486., 2004 , PDF


  • Nabuurs SB, Spronk CAEM, Vriend G, Vuister GW.
    Concepts and tools for NMR restraint analysis and validation.
    Concepts in Magnetic Resonance, 22A(2):90-105., 2004 , PDF


  • Van Noort V, Snel B, Huynen MA.
    The yeast coexpression network has a small-world, scale-free architecture and can be explained by a simple model.
    EMBO Rep, Mar;5(3):280-284., 2004 , PDF


  • Oliveira L, Hulsen T, Lutje Hulsik D, Paiva AC, Vriend G.
    Heavier-than-air flying machines are impossible.
    FEBS Lett, Apr 30;564(3):269-273., 2004 , PDF


  • Siezen RJ, Enckevort FHJ, Kleerebezem M, Teusink B.
    Genome data mining of lactic acid bacteria: the impact of bioinformatics.
    Curr Opin Biotechnol, Apr;15(2):105-115., 2004 , PDF


  • Snel B, Huynen MA.
    Quantifying modularity in the evolution of biomolecular systems.
    Genome Res , Mar;14(3):391-397., 2004 , PDF


  • Snel B, van Noort V, Huynen MA.
    Gene co-regulation is highly conserved in the evolution of eukaryotes and prokaryotes.
    Nucleic Acids Res, Sep 7;32(16):4725-4731., 2004 , PDF


  • Spronk CA, Nabuurs SB, Krieger E, Vriend G, Vuister GW.
    Validation of protein structures derived by NMR spectroscopy.
    Progress in NMR spectroscopy, 45:315-337., 2004 , PDF


  • Synstad B, Gaseidnes S, Van Aalten DM, Vriend G, Nielsen JE, Eijsink VG.
    Mutational and computational analysis of the role of conserved residues in the active site of a family 18 chitinase.
    Eur J Biochem, Jan;271(2):253-262., 2004 , PDF


  • Tjaden J, Haferkamp I, Boxma B, Tielens AG, Huynen M, Hackstein JH.
    A divergent ADP/ATP carrier in the hydrogenosomes of Trichomonas gallinae argues for an independent origin of these organelles.
    Mol Microbiol , Mar;51(5):1439-1446., 2004 , PDF


  • Verwer P, Leusen FJJ.
    Cheminformatics and molecular modeling.
    Cheminformatics Developments, 175-202., 2004 , PDF


  • Vriend G.
    Protein design: quo vadis?
    Science, Nov 12;306(5699):1135., 2004 , PDF


  • Walma T, Aelen J, Nabuurs SB, Oostendorp M, van den Berk L, Hendriks W, Vuister GW.
    A closed binding pocket and global destabilization modify the binding properties of an alternatively spliced form of the second PDZ domain of PTP-BL.
    Structure , Jan;12(1):11-20., 2004 , PDF


  • Ott MA.
    Cheminformatics and organic chemistry. Computer-assisted synthetic analysis.
    Cheminformatics Developments, 1(1-2):83-109., 2004 , PDF