• Siezen RJ, Starrenburg MJC, Boekhorst J, Renckens B, Molenaar D, van Hylckama Vlieg JET.
    Genome-scale genotype-phenotype matching of two Lactococcus lactis plant isolates identifies adaptation mechanisms to the plant niche.
    Appl Environ Microbiol, 74(2):424-436., 2008 , PDF


  • Notebaart RA, Teusink B, Siezen RJ, Papp B.
    Co-regulation of metabolic genes is better explained by flux coupling than by network distance.
    PLoS Comput Biol, 4(1):e26, 2008 , PDF


  • van Baarlen P, van Esse HP, Siezen RJ, Thomma BP.
    Challenges in plant cellular pathway reconstruction based on gene expression profiling.
    Trends Plant Sci, 13(1):44-50., 2008 , PDF


  • Francke C, Kerkhove R, Wels M, Siezen RJ.
    A generic approach to identify Transcription Factor-specific operator motifs; Inferences for LacI-family mediated regulation in Lactobacillus plantarum WCFS1.
    BMC Genomics, Mar 27;9:145., 2008 , PDF


  • Zhou M, Boekhorst J, Francke C, Siezen RJ.
    LocateP: genome-scale subcellular-location predictor for bacterial proteins.
    BMC Bioinformatics, 9:173., 2008 , PDF


  • Iritani N, Vennema H, Siebenga JJ, Siezen RJ, Renckens B, Seto Y, Kaida A, Koopmans M.
    Genetic analysis of the capsid gene of genotype GII.2 Noroviruses.
    J Virol, 82(15):7336-7345., 2008 , PDF


  • Siezen RJ, Wilson G.
    Unpublished but public microbial genomes with biotechnological relevance.
    Microbial Biotechnology, 1(3), 202-207., 2008 , PDF


  • Siezen RJ.
    Wine genomics.
    Micobial Biotechnology, 1(2):97-103., 2008 , PDF


  • Liu M, Nauta A, Francke C, Siezen RJ.
    Comparative genomics of enzymes in flavor-forming pathways from amino acids in lactic acid bacteria.
    Appl Environ Microbiology, 74(15):4590-4600., 2008 , PDF


  • Zachariae U, Schneider R, Velisetty P, Lange A, Seeliger D, Wacker SJ, Karimi-Nejad Y, Vriend G, Becker S, Pongs O, Baldus M, de Groot BL.
    The molecular mechanism of toxin-induced conformational changes in a potassium channel: Relation to C-type inactivation.
    Structure, May 7;16(5):747-754., 2008 , PDF


  • Collin RWJ, Chellappa R, Pauw RJ, Vriend G, Oostrik J, van Drunen W, Huygen PL, Admiraal R, Hoefsloot LH, Cremers FP, Xiang M, Cremers CW, Kremer H.
    Missense mutations in POU4F3 cause autosomal dominant hearing impairment DFNA15 and affect subcellular localization and DNA binding.
    Human Mutation, Apr;29(4):545-554., 2008 , PDF


  • Ye K, Vriend G, IJzerman AP.
    Tracing evolutionary pressure.
    Bioinformatics, Apr 1;24(7):908-15., 2008 , PDF


  • Collin RWJ, Kalay E, Tariq M, Peters T, van der Zwaag B, Venselaar H, Oostrik J, Lee K, Ahmed ZM, Caylan R, Li Y, Spierenburg HA, Eyupoglu E, Heister A, Riazuddin S, Bahat E, Ansar M, Arslan S, Wollnik B, Brunner HG, Cremers CW, Karaguzel A, Ahmad W, Cremers FP, Vriend G, Friedman TB, Riazuddin S, Leal SM, Kremer H.
    Mutations of ESRRB encoding estrogen-related receptor beta cause autosomal-recessive nonsyndromic hearing impairment DFNB35.
    American Journal of Human Genetics, Jan;82(1):125-138., 2008 , PDF


  • von Grotthuss M, Plewczynski D, Vriend G, Rychlewski L.
    3D-Fun: predicting enzyme function from structure.
    Nucleic Acids Res, Jul 1;36(Web Server issue):W303-307., 2008 , PDF


  • de Been M, Bart MJ, Abee T, Siezen RJ, Francke C.
    The identification of response regulator-specific binding sites reveals new roles of two-component systems in Bacillus cereus and closely related low-GC Gram-positives.
    Environ Microbiol, Oct;10(10):2796-2809., 2008 , PDF


  • Wels M, Groot Kormelink T, Kleerebezem M, Siezen RJ, Francke C.
    An in silico analysis of T-box regulated genes and T-box evolution in prokaryotes, with emphasis on prediction of substrate specificity of transporters.
    BMC Genomics, 9(1):330., 2008 , PDF


  • Lambert JM, Siezen RJ, de Vos WM, Kleerebezem M.
    Improved annotation of conjugated bile acid hydrolase superfamily members in Gram-positive bacteria.
    Microbiology, Aug;154(Pt 8):2492-2500., 2008 , PDF


  • Siezen RJ, Khayatt BI.
    Natural products genomics.
    Microbial Biotechnology, 1(4):275-282., 2008 , PDF


  • Siezen RJ, Galardini M.
    Genomics of biological wastewater treatment.
    Microbial Biotechnology, 1(5):333-340., 2008 , PDF


  • Dutilh BE, Snel B, Ettema TJG, Huynen MA.
    Signature genes as a phylogenomic tool.
    Molecular Biology and Evolution, Aug;25(8):1659-1667., 2008 , PDF


  • Oti M, van Reeuwijk J, Huynen MA, Brunner HG.
    Co-expression for candidate disease gene prioritization.
    BMC Bioinformatics, Apr 23;9:208., 2008 , PDF


  • Dutilh BE,  He Y, Hekkelman ML, Huynen MA.
    Signature, a web server for taxonomic characterization of sequence samples using signature genes.
    Nucleic Acids Research, Jul 1;36(Web Server issue):W470-474., 2008 , PDF


  • Kensche PR, Oti M, Dutilh BE, Huynen MA.
    Conservation of divergent transcription in fungi.
    Trends in Genetics, May;24(5):207-211., 2008 , PDF


  • Ulrich EL, Akutsu H, Doreleijers JF, Harano Y, Ioannidis YE, Lin J, Livny M, Mading S, Maziuk D, Miller Z, Nakatani E, Schulte CF, Tolmie DE, Kent Wenger R, Yao H, Markley JL.
    BioMagResBank.
    Nucleic Acids Res , 36(Database issue):D402-408., 2008 , PDF


  • Henrick K, Feng Z, Bluhm WF, Dimitropoulos D, Doreleijers JF, Dutta S, Flippen-Anderson JL, Ionides J, Kamada C, Krissinel E, Lawson CL, Markley JL, Nakamura H, Newman R, Shimizu Y, Swaminathan J, Velankar S, Ory J, Ulrich EL, Vranken W, Westbrook J, Yamashita R, Yang H, Young J, Yousufuddin M, Berman HM.
    Remediation of the protein data bank archive.
    Nucleic Acids Res , 36(Database issue):D426-433., 2008 , PDF


  • Lütteke, T.
    Web Resources for the Glycoscientist.
    Chembiochem, Sep 1;9(13):2155-2160., 2008 , PDF


  • Stolte EH, Nabuurs SB, Bury NR, Sturm A, Flik G, Savelkoul HF, Lidy Verburg-van Kemenade BM.
    Stress and innate immunity in carp: Corticosteroid receptors and pro-inflammatory cytokines.
    Mol Immunol, Nov;46(1):70-79., 2008 , PDF


  • Boon CJ, Klevering BJ, Hoyng CB, Zonneveld-Vrieling MN, Nabuurs SB, Blokland E, Cremers FP, den Hollander AI.
    Basal laminar drusen caused by compound heterozygous variants in the CFH gene.
    Am J Hum Genet, Feb;82(2):516-523., 2008 , PDF


  • Hulsen T, de Vlieg J, Alkema W.
    BioVenn - a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams.
    BMC Genomics, Oct 16;9(1):488., 2008 , PDF


  • Hulsen T, Groenen PM, de Vlieg J, Alkema W.
    PhyloPat: an updated version of the phylogenetic pattern database contains gene neighborhood.
    Nucleic Acids Res, 37(Database issue):D731-737., 2008 , PDF


  • Franck E, Hulsen T, Huynen MA, de Jong WW, Lubsen NH, Madsen O.
    Evolution of closely linked gene pairs in vertebrate genomes.
    Mol Biol Evol, Sep;25(9):1909-1921., 2008 , PDF


  • Frijters R, Heupers B, van Beek P, Bouwhuis M, van Schaik R, de Vlieg J, Polman J, Alkema W.
    CoPub: a literature-based keyword enrichment tool for microarray data analysis.
    Nucleic Acids Res, 36(Web Server issue):W406-410., 2008 , PDF


  • El-Sheikh AA, van den Heuvel JJ, Krieger E, Russel FG, Koenderink JB.
    Functional Role of Arginine 375 in Transmembrane Helix 6 of Multidrug Resistance Protein 4 (MRP4/ABCC4).
    Mol Pharmacol, Oct;74(4):964-971., 2008 , PDF


  • Siezen RJ, Bachmann H.
    Genomics of dairy fermentations.
    Microbial Biotechnology, 1(6):435-442, 2008 , PDF


  • Hatzis P, van der Flier LG, van Driel MA, Guryev V, Nielsen F, Denissov S, Nijman IJ, Koster J, Santo EE, Welboren W, Versteeg R, Cuppen E, van de Wetering M, Clevers H, Stunnenberg HG.
    Genome-wide pattern of TCF7L2/TCF4 chromatin occupancy in colorectal cancer cells.
    Mol Cell Biol, Apr;28(8):2732-2744., 2008 , PDF


  • Troost FJ, van Baarlen P, Lindsey P, Kodde A, de Vos WM, Kleerebezem M, Brummer RJ.
    Identification of the transcriptional response of human intestinal mucosa to Lacobacillus plantarum WCFS1 in vivo.
    BMC Genomics, 9:374., 2008 , PDF


  • Szklarczyk R, Huynen MA, Snel B.
    Complex fate of paralogs.
    BMC Evol Biol, Dec 18;8:337., 2008 , PDF


  • Ala U, Piro RM, Grassi E, Damasco C, Silengo L, Oti M, Provero P, Di Cunto F.
    Prediction of human disease genes by human-mouse conserved coexpression analysis.
    PLoS Comput Biol, Mar 28;4(3):e1000043., 2008 , PDF


  • Oti M, Huynen MA, Brunner HG.
    Phenome connections.
    Trends Genet, Mar;24(3):103-106., 2008 , PDF


  • Warnecke T, JL Parmley, Hurst LD.
    Finding exonic islands in a sea of non-coding sequence: splicing related constraints on protein composition and evolution are common in intron-rich genomes.
    Genome Biol, 9(2):R29., 2008 , PDF


  • Ricard G, de Graaf RM, Dutilh BE, Duarte I, van Alen TA, van Hoek AH, Boxma B, van der Staay GW, Moon van der Staay SY, Chang WJ, Landweber LF, Hackstein JH, Huynen MA.
    Macronuclear genome structure of the ciliate Nyctotherus ovalis: Single-gene chromosomes and tiny introns.
    BMC Genomics, Dec 5;9:587., 2008 , PDF


  • Kensche, PR, van Noort V, Dutilh BE, Huynen MA.
    Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution.
    J R Soc Interface, Feb 6;5(19):151-170., 2008 , PDF


  • Ahmed ZN, Masmoudi S, Kalay E, Belyantseva IA, Mosrati MA, Collin RWJ, Riazuddin S, Hmani-Aifa E, Venselaar H, Kawar MN, Tlili A, Van der Zwaag B, Khan SY, Ayadi L, Riazuddin SA, Morell RJ, Griffith AJ, Charfedine I, Çaylan R, Oostrik J, Karaguzel A, Ghorbel A ,Riazuddin S, Friedman TB, Ayadi H, Kremer H.
    Mutations of LRTOMT, a fusion gene with alternative reading frames, cause nonsyndromic deafness in humans.
    Nature Genetics, 40:1335-1340, 2008 , PDF


  • Ahmed ZM,Riazuddin S, Aye S, Ali RA, Venselaar H, Anwar S, Belyantseva PP, Qasim M, Riazuddin S , Friedman TB.
    Gene structure and mutant alleles of PCDH15: nonsyndromic deafness DFNB23 and type 1 Usher syndrome.
    Hum Genet, Oct;124(3):215-223., 2008 , PDF


  • Thébault S, Cao G, Venselaar H,  Xi  Q, Bindels RJM, Hoenderop JGJ.
    Role of the alpha-kinase domain in TRPM6 channel and regulation by intracellular ATP.
    J Biol Chem, Jul 18;283(29):19999-20007., 2008 , PDF


  • Bych K, Kerscher S, Netz DJ, Pierik AJ, Zwicker K, Huynen MA, Lill R, Brandt U, Balk J.
    The iron-sulphur protein Ind1 is required for effective complex I assembly.
    EMBO J, 27(12):1736-1746., 2008 , PDF


  • Swinkels DW, Venselaar H, Wiegerinck ET, Bakker E, Joosten I,  Jaspers CAJJ, Vasmel WL, Breuning MA.
    A novel (Leu183Pro-)mutation in the HFE-gene co-inherited with the Cys282Tyr mutation in two unrelated Dutch hemochromatosis patients.
    Blood Cells Mol Dis, May-Jun;40(3):334-338., 2008 , PDF


  • Buchanan G, Maillard J, Nabuurs SB, Richardson DJ, Palmer T, Sargent F.
    Features of a twin-arginine signal peptide required for recognition by a Tat proofreading chaperone.
    FEBS Lett, Dec 10;582(29):3979-3984., 2008 , PDF


  • Lasonder E, Janse CJ, van Gemert GJ, Mair GR, Vermunt AM, Douradinha BG, van Noort V, Huynen MA, Luty AJ, Kroeze H, Khan SM, Sauerwein RW, Waters AP, Mann M, Stunnenberg HG.
    Proteomic profiling of Plasmodium sporozoite maturation identifies new proteins essential for parasite development and infectivity.
    PLoS Pathog, 4(10):e1000195., 2008 , PDF


  • Schoeber JP, Topala CN, Lee KP, Lambers TT, Ricard G, van der Kemp AW, Huynen MA, Hoenderop JG, Bindels RJ.
    Identification of Nipsnap1 as a novel auxiliary protein inhibiting TRPV6 activity.
    Pflugers Arch, 457(1):91-101., 2008 , 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., 2008 , 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., 2008 , PDF


  • Clark K, Middelbeek J, Dorovkov MV, Figdor CG, Ryazanov AG, Lasonder E, van Leeuwen FN.
    The alpha-kinases TRPM6 and TRPM7, but not eEF-2 kinase, phosphorylate the assembly domain of myosin IIA, IIB and IIC.
    FEBS , Lett. 582:2993-29977., 2008 , PDF


  • Clark K, Middelbeek J, Lasonder E, Dulyaninova N, Morrice NA, Ryazanov AG, Bresnick AR, Figdor CG, van Leeuwen FN.
    Trpm7 regulates myosin IIA filament stability and protein localization by heavy chain phosphorylation.
    J Mol Biol , May 9;378(4):790-803., 2008 , PDF


  • Clark K, Middelbeek J, Morrice N. Figdor CG, Lasonder E, van Leeuwen FN.
    Massive Autophosphorylation of the Ser/Thr-Rich Domain Controls Protein Kinase Activity of TRPM6 and TRPM7.
    PLoS ONE 3 , Mar 26;3(3):e1876., 2008 , PDF


  • Bosman GJCGM, Lasonder E, Luten M, Roerdinkholder-Stoelwinder B, Novotny VMJ, Bos H, De Grip WJ.
    The proteome of erythrocyte membranes and vesicles during storage in blood bank conditions.
    Transfusion, May;48(5):827-835., 2008 , PDF


  • Pandithage R, Lilischkis R, Harting K, Wolf A, Jedamzik B, Lüscher_Firzlaff J, Vervoorts J, Lasonder E, Kremmer E, Knöll B, Lüscher B.
    The regulation of SIRT2 function by cyclin-dependent kinases affects cell motility.
    J Cell Biol, Mar 10;180(5):915-929., 2008 , PDF


  • Cao G, Thébault S, van der Wijst J, van der Kemp A, Lasonder E, Bindels RJ, Hoenderop JG.
    RACK1 inhibits TRPM6 Activity via Phosphorylation of the Fused alpha-Kinase Domain.
    Curr Biol, Feb 12;18(3):168-176., 2008 , PDF


  • Vandenbussche M, Janssen A, Zethof J, van Orsouw N, Peters J, van Eijk MJ, Rijpkema AS, Schneiders H, Santhanam P, de Been M, van Tunen A, Gerats T.
    Generation of a 3D indexed Petunia insertion database for reverse genetics.
    Plant J, Jun;54(6):1105-1114., 2008 , PDF