Publications in international journals 2009
  • Thornton J, Vriend G.
    Annotations for all by all - the BioSapiens network.
    Genome Biology, 10:401., 2009 , PDF

  • Bayjanov J, Wels M, Starrenburg M, van Hylckama Vlieg JET, Siezen RJ, Molenaar D.
    PanCGH: a genotype-calling algorithm for pangenome CGH data.
    Bioinformatics, Feb 1;25(3):309-314., 2009 , PDF

  • van Baarlen P, Troost FJ, van Hemert S, van der Meer C, de Vos WM, de Groot PJ, Hooiveld GJ, Brummer RJ, Kleerebezem M.
    Differential NF-{kappa}B pathways induction by Lactobacillus plantarum in the duodenum of healthy humans correlating with immune tolerance.
    Proc Natl Acad Sci U S A, Feb 17;106(7):2371-2376., 2009 , PDF

  • Teusink B, Wiersma A, Jacobs L, Notebaart RA, Smid EJ.
    Understanding the adaptive growth strategy of Lactobacillus plantarum by in silico optimisation.
    PLoS Comput Biol, Jun;5(6):e1000410., 2009 , PDF

  • Papp B, Teusink B, Notebaart RA.
    A critical view of metabolic network adaptations.
    HFSP J, Feb;3(1):24-35., 2009 , PDF

  • Szklarczyk R, Huynen MA.
    Expansion of the human mitochondrial proteome by intra- and inter-compartmental protein duplication.
    Genome Biol, Nov 24;10(11):R135., 2009 , PDF

  • Siezen RJ, Wilson G.
    Genomics of deep-sea and sub-seafloor microbes.
    Microbial Biotechnology, Feb;2(2):157-163., 2009 , PDF

  • Wels M, Bongers RS, Boekhorst J, Molenaar D, Sturme M, de Vos WM, Siezen RJ, Kleerebezem M.
    Large Intergenic Cruciform-like Supermotifs in the Lactobacillus plantarum Genome.
    J Bacteriology, May;191(10):3420-3423., 2009 , PDF

  • Siezen RJ, Wilson G.
    Bioleaching genomics.
    Microbial Biotechnology, May;2(3):297-303., 2009 , PDF

  • Patel AK, van Oosterwijk N, Singh VK, Rozeboom HJ, Kalk KH, Siezen RJ, Jagannadham MV, Dijkstra BW.
    Crystallization and preliminary X-ray analysis of carnein, a serine protease from Ipomoea carnea.
    Acta Crystallogr Sect F Struct Biol Cryst Commun, Apr 1;65(Pt 4):383-385., 2009 , PDF

  • Parmley JL, Huynen MA.
    Clustering of codons with rare cognate tRNAs in human genes suggests an extra level of expression regulation.
    PLoS Genet, Jul;5(7):e1000548., 2009 , PDF

  • Beekwilder J, Marcozzi D, Vecchi S, de Vos R, Janssen P, Francke C, van Hylckama Vlieg J, Hall RD.
    Characterization of Rhamnosidases from Lactobacillus plantarum and Lactobacillus acidophilus.
    Appl Environ Microbiol, Jun;75(11):3447-3454. , 2009 , PDF

  • Verouden MPH, Notebaart RA, Westerhuis JA, van der Werf MJ, Teusink B, Smilde AK.
    Multi-way analysis of flux distributions across multiple conditions.
    J. Chemometrics, 23(7-8):406-420., 2009 , PDF

  • Kleefstra T, van Zelst-Stams WA, Nillesen WM, Cormier-Daire V, Houge G, Foulds N, van Dooren M, Willemsen MH, Pfundt R, Turner A, Wilson M, McGaughran J, Rauch A, Zenker M, Adam M, Innes M, Davies C, González-Meneses López A, Casalone R, Weber A, Brueton LA, Delicado Navarro A, Palomares Bralo M, Venselaar H, Stegmann SP, Yntema HG, van Bokhoven H, Brunner HG.
    Further clinical and molecular delineation of the 9q Subtelomeric Deletion Syndrome supports a major contribution of EHMT1 haploinsufficiency to the core phenotype.
    J Med Genet, Sep;46(9):598-606., 2009 , PDF

  • van der Woning SP, Venselaar H, van Rotterdam W, Jacobs-Oomen S, van Leeuwen JE, van Zoelen EJ.
    Role of the C-terminal linear region of EGF-like growth factors in ErbB specificity.
    Growth Factors, Jun;27(3):163-172., 2009 , PDF

  • Joosten RP, Womack T, Vriend G, Bricogne G.
    Re-refinement from deposited X-ray data can deliver improved models for most PDB entries.
    Acta Crystallogr D Biol Crystallogr, Feb;65(Pt 2):176-185., 2009 , PDF

  • Joosten RP, Salzemann J, Bloch V, Stockinger H, Berglund A, Blanchet C, Bongcam-Rudloff E, Combet C, Da Costa AL, Deleage G, Diarena M, Fabbretti R, Fettahi G, Flegel V, Gisel A, Kasam V, Kervinen T, Korpelainen E, Mattila K,Pagni M, Reichstadt M,Breton V, Tickle IJ, Vriend G.
    PDB_REDO: automated re-refinement of X-ray structure models in the PDB.
    J. Appl. Cryst, 42:376-384., 2009 , PDF

  • Dutilh BE, Huynen MA, Strous M.
    Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly.
    Bioinformatics, Nov 1;25(21):2878-2881., 2009 , PDF

  • Saada A, Vogel RO, Hoefs SJ, van den Brand MA, Wessels HJ, Willems PH, Venselaar H, Shaag A, Barghuti F, Reish O, Shohat M, Huynen MA, Smeitink JA, van den Heuvel LP, Nijtmans LG.
    Mutations in NDUFAF3 (C3ORF60), encoding an NDUFAF4 (C6ORF66)-interacting complex I assembly protein, cause fatal neonatal mitochondrial disease.
    Am J Hum Genet, Jun;84(6):718-727., 2009 , PDF

  • Kuipers RK, Joosten HJ, Verwiel E, Paans S, Akerboom J, van der Oost J, Leferink NG, van Berkel WJ, Vriend G, Schaap PJ.
    Correlated mutation analyses on super-family alignments reveal functionally important residues.
    Proteins, Aug 15;76(3):608-616., 2009 , PDF

  • Narayanan B, Niu W, Joosten HJ, Li Z, Kuipers RK, Schaap PJ, Dunaway-Mariano D, Herzberg O.
    Structure and function of 2,3-dimethylmalate lyase, a PEP mutase/isocitrate lyase superfamily member.
    J Mol Biol, Feb 20;386(2):486-503., 2009 , PDF

  • Liu M, Siezen RJ, Nauta A.
    In silico prediction of horizontal gene transfer events in Lactobacillus bulgaricus and Streptococcus thermophilus reveals protocooperation in yogurt manufacturing.
    Appl Environ Microbiol, Jun;75(12):4120-4129., 2009 , PDF

  • Thiadens AA, den Hollander AI, Roosing S, Nabuurs SB, Zekveld-Vroon RC, Collin RW, De Baere E, Koenekoop RK, van Schooneveld MJ, Strom TM, van Lith-Verhoeven JJ, Lotery AJ, van Moll-Ramirez N, Leroy BP, van den Born LI, Hoyng CB, Cremers FP, Klaver CC.
    Homozygosity mapping reveals PDE6C mutations in patients with early-onset cone photoreceptor disorders.
    Am J Hum Genet, Aug;85(2):240-247., 2009 , PDF

  • Gorissen M, Bernier NJ, Nabuurs SB, Flik G, Huising MO.
    Two divergent leptin paralogues in zebrafish (Danio rerio) that originate early in teleostean evolution.
    J Endocrinol, Jun;201(3):329-339., 2009 , PDF

  • Pettifer S, Thorne D, McDermott P, Attwood T, Baran J, Bryne JC, Hupponen T, Mowbray D, Vriend G.
    An active registry for bioinformatics web services.
    Bioinformatics, Aug 15;25(16):2090-2091., 2009 , PDF

  • Vaz B, Möcklinghoff S, Folkertsma S, Lusher S, de Vlieg J, Brunsveld L.
    Computational design, synthesis, and evaluation of miniproteins as androgen receptor coactivator mimics.
    Chem Commun (Camb), Sep 28;(36):5377-5379., 2009 , PDF

  • De Pont JJ, Swarts HG, Karawajczyk A, Schaftenaar G, Willems PH, Koenderink JB.
    The non-gastric H,K-ATPase as a tool to study the ouabain-binding site in Na,K-ATPase.
    Pflugers Arch, Jan;457(3):623-634., 2009 , PDF

  • Sanderson K.
    New protein structures replace the old. Dutch software to weed out errors in Protein Data Bank.
    Nature News, 459:1038-1039., 2009 , PDF

  • Doreleijers JF, Vranken WF, Schulte C, Lin J, Wedell JR, Penkett CJ, Vuister GW, Vriend G, Markley JL, Ulrich EL.
    The NMR restraints grid at BMRB for 5,266 protein and nucleic acid PDB entries.
    J Biomol NMR, Dec;45(4):389-396., 2009 , PDF

  • Lee HK, Song MH, Kang M, Lee JT, Kong KA, Choi SJ, Lee KY, Venselaar H, Vriend G, Lee WS, Park HJ, Kwon TK, Bok J, Kim UK.
    Clinical and molecular characterizations of novel POU3F4 mutations reveal that DFN3 is due to null function of POU3F4 protein.
    Physiol Genomics, Nov 6;39(3):195-201., 2009 , PDF

  • Krieger E, Joo K, Lee J, Lee J, Raman S, Thompson J, Tyka M, Baker D, Karplus K.
    Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8.
    Proteins, 12;77(S9):114-122., 2009 , PDF

  • Bagaria A, Baker D, Bardiaux B, Bonvin AM, Cavalli A, Doreleijers JF, Giachetti A, Guerry P, Güntert P, Herrmann T, Huang YJ, Jonker H, Mao B, Malliavin TE, Montelione GT, Nilges M, Raman S, Rosato A, Schot Gvd, Vranken WF, Vuister GW.
    CASD-NMR: critical assessment of automated structure determination by NMR.
    Nat Methods, Sep;6(9):625-626., 2009 , PDF

  • van Baarlen P, Siezen RJ.
    Genomics of plant-associated microbes.
    Microbial Biotechnology, 2(4):406-411., 2009 , PDF

  • Brooijmans RJW, Pastink MI, Siezen RJ.
    Hydrocarbon-degrading bacteria: the oil-spill clean-up crew.
    Microbial Biotechnology, 2(6):587-594., 2009 , PDF

  • Notebaart RA, Kensche PR, Huynen MA, Dutilh BE.
    Asymmetric relationships between proteins shape genome evolution.
    Genome Biol, Feb 12;10(2):R19., 2009 , PDF

  • de Graaf RM, van Alen TA, Dutilh BE, Kuiper JW, van Zoggel HJ, Huynh MB, Görtz HD, Huynen MA, Hackstein JH.
    The mitochondrial genomes of the ciliates Euplotes minuta and Euplotes crassus.
    BMC Genomics, Nov 6;10:514., 2009 , PDF

  • Huynen MA, de Hollander M, Szklarczyk R.
    Mitochondrial proteome evolution and genetic disease.
    Biochim Biophys Acta, Dec;1792(12):1122-1129., 2009 , PDF

  • Jurgelenaite R, Dijkstra TMH, Kocken CHM, Heskes T.
    Gene regulation in the intraerythrocytic cycle of Plasmodium falciparum.
    Bioinformatics, 25(12):1484-1491., 2009 , PDF

  • Doerig C, Baker D, Billker O, Blackman MJ, Chitnis C, Dhar Kumar S, Heussler V, Holder AA, Kocken C, Krishna S, Langsley G, Lasonder E, Menard R, Meissner M, Pradel G, Ranford-Cartwright L, Sharma A, Sharma P, Tardieux T, Tatu U, Alano P.
    Signalling in malaria parasites. The MALSIG consortium.
    Parasite, Sep;16(3):169-182., 2009 , PDF

  • Ferwerda B, Ferwerda G, Plantinga TS, Willment JA, van Spriel AB, Venselaar H, Elbers CC, Johnson MD, Cambi A, Huysamen C, Jacobs L, Jansen T, Verheijen K, Masthoff L, Morré SA, Vriend G, Williams DL, Perfect JR, Joosten LA, Wijmenga C, van der Meer JW, Adema GJ, Kullberg BJ, Brown GD, Netea MG.
    Human dectin-1 deficiency and mucocutaneous fungal infections.
    N Engl J Med, Oct 29;361(18):1760-1767., 2009 , PDF

  • Littink KW, van Genderen MM, Collin RW, Roosing S, de Brouwer AP, Riemslag FC, Venselaar H, Thiadens AA, Hoyng CB, Rohrschneider K, den Hollander AI, Cremers FP, van den Born LI.
    A novel homozygous nonsense mutation in CABP4 causes congenital cone-rod synaptic disorder.
    Invest Ophthalmol Vis Sci, May;50(5):2344-2350., 2009 , PDF

  • Middelbeek J, Clark K, Venselaar H, Huynen MA, Van Leeuwen FN.
    The alpha-kinase family: an exceptional branch on the protein kinase tree.
    Cellular and Molecular Life Sciences, Mar;67(6):875-890., 2009 , PDF

  • Oti M, Huynen MA, Brunner HG.
    The biological coherence of human phenome databases.
    Am J Hum Genet, Dec;85(6):801-808., 2009 , PDF

  • de Graaf RM, Duarte I, van Alen TA, Kuiper JW, Schotanus K, Rosenberg J, Huynen MA, Hackstein JH.
    The hydrogenosomes of Psalteriomonas lanterna.
    BMC Evol Biol, Dec 9;9:287., 2009 , PDF

  • van den Berghe PV, Stapelbroek JM, Krieger E, de Bie P, van de Graaf SF, de Groot RE, van Beurden E, Spijker E, Houwen RH, Berger R, Klomp LW.
    Reduced expression of ATP7B affected by Wilson disease-causing mutations is rescued by pharmacological folding chaperones 4-phenylbutyrate and curcumin.
    Hepatology, Dec;50(6):1783-1795., 2009 , PDF

  • Zachariae U, Giordanetto F, Leach AG.
    Side chain flexibilities in the human ether-a-go-go related gene potassium channel (hERG) together with matched-pair binding studies suggest a new binding mode for channel blockers.
    J Med Chem, Jul 23;52(14):4266-4276., 2009 , PDF

  • Rosato A, Bagaria A, Baker D, Bardiaux B, Cavalli A, Doreleijers JF, Giachetti A, Guerry P, Güntert P, Herrmann T, Huang YJ, Jonker HR, Mao B, Malliavin TE, Montelione GT, Nilges M, Raman S, van der Schot G, Vranken WF, Vuister GW, Bonvin AM.
    CASD-NMR: critical assessment of automated structure determination by NMR.
    Nat Methods, Sep;6(9):625-626., 2009 , PDF