Publications in international journals 2010
  • Liu M, Bayjanov JR, Renckens B, Nauta A, Siezen RJ.
    The proteolytic system of lactic acid bacteria revisited: a genomic comparison.
    BMC Genomics, Jan 15;11:36., 2010 , PDF


  • Siezen RJ, Tzeneva VA, Castioni A, Wels M, Phan HT, Rademaker JL, Starrneburg MJ, Kleerebezem M, Molenaar D, van Hylckama Vlieg JE.
    Phenotypic and genomic diversity of Lactobacillus plantarum strains isolated from various environmental niches.
    Environmental Microbiology, Mar;12(3):758-773., 2010 , PDF


  • Szklarczyk R, Huynen MA.
    Mosaic origin of the mitochondrial proteome.
    Proteomics, Nov;10(22):4012-4024., 2010 , PDF


  • Nouws J, Nijtmans L, Houten SM, van den Brand M, Huynen M, Venselaar H, Hoefs S, Gloerich J, Kronick J, Hutchin T, Willems P, Rodenburg R, Wanders R, van den Heuvel L, Smeitink J, Vogel RO.
    Acyl-CoA dehydrogenase 9 is required for the biogenesis of oxidative phosphorylation complex I.
    Cell Metab, Sep 8;12(3):283-294., 2010 , PDF


  • Gross G, Snel J, Boekhorst J, Smits MA, Kleerebezem M.
    Biodiversity of mannose-specific adhesion in Lactobacillus plantarum revisited: strain-specific domain composition of the mannose-adhesin.
    Beneficial Microbes, Mar;1(1):61-66., 2010 , PDF


  • Kleerebezem M, Hols P, Bernard E, Rolain T, Zhou M, Siezen RJ, Bron PA.
    The extracellular biology of the lactobacilli.
    FEMS Microbiol Rev, Mar;34(2):199-230., 2010 , PDF


  • Siezen RJ, Wilson G, Todt T.
    Genomics update: Prokaryotic whole-transcriptome analysis: deep sequencing and tiling arrays.
    Microbial Biotechnology, Mar;3(2):125-130., 2010 , PDF


  • Pettifer S, Ison J, Kalas M, Thorne D, McDermott P, Jonassen I, Liaquat A, Fernández JM, Rodriguez JM, Partners I, Pisano DG, Blanchet C, Uludag M, Rice P, Bartaseviciute E, Rapacki K, Hekkelman M, Sand O, Stockinger H, Clegg AB, Bongcam-Rudloff E, Salzemann J, Breton V, Attwood TK, Cameron G, Vriend G.
    The EMBRACE web service collection.
    Nucleic Acids Res, 38(Web Server issue):W683-688., 2010 , PDF


  • Siezen RJ, van Hijum SA.
    Genome (re-)annotation and open-source annotation pipelines.
    Microbial Biotechnology, 3(4):362-369., 2010 , PDF


  • Schürch AC, Kremer K, Kiers A, Daviena O, Boeree MJ, Siezen RJ, Smith NH, van Soolingen D.
    The tempo and mode of molecular evolution of Mycobacterium tuberculosis at patient-to-patient scale.
    Infect Genet Evol, Jan;10(1):108-114., 2010 , PDF


  • Bosman GJ, Lasonder E, Groenen-Döpp YA, Willekens FL, Werre JM, Novotný VM.
    Comparative proteomics of erythrocyte aging in vivo and in vitro.
    J Proteomics, Jan;73(3):396-402., 2010 , PDF


  • van der Wijst J, Glaudemans B, Venselaar H, Nair AV, Forst AL, Hoenderop JG, Bindels RJ.
    Functional analysis of the Kv1.1 N255D mutation associated with autosomal dominant hypomagnesemia.
    J Biol Chem, Jan 1;285(1):171-178., 2010 , PDF


  • Schuemie MJ, Kang N, Hekkelman ML, Kors JA.
    GeneE: gene and protein query expansion with disambiguation.
    Bioinformatics, Jan 1;26(1):147-148., 2010 , PDF


  • van der Velden LM, Stapelbroek JM, Krieger E, van den Berghe PV, Berger R, Verhulst PM, Holthuis JC, Houwen RH, Klomp LW, van de Graaf SF.
    Folding defects in P-type ATP 8B1 associated with hereditary cholestasis are ameliorated by 4-phenylbutyrate.
    Hepatology, Jan;51(1):286-296., 2010 , PDF


  • Medema MH, Zhou M, van Hijum SA, Gloerich J, Wessels HJ, Siezen RJ, Strous M.
    A predicted physicochemically distinct sub-proteome associated with the intracellular organelle of the anammox bacterium Kuenenia stuttgartiensis.
    BMC Genomics, May 12;11(1):299., 2010 , PDF


  • Siezen RJ, Bayjanov J, Renckens B, Wels M, van Hijum SAFT, Molenaar D, van Hylckama Vlieg JET. 
    Complete genome sequence of Lactococcus lactis subsp. lactis KF147, a plant-associated lactic acid bacterium.
    Journal of Bacteriology, May;192(10):2649-2650., 2010 , PDF


  • Bayjanov JR, Siezen RJ, van Hijum SA.
    PanCGHweb: a web tool for genotype calling in pangenome CGH data.
    Bioinformatics, May 1;26(9):1256-1257., 2010 , PDF


  • Kourist R, Jochens H, Bartsch S, Kuipers R, Padhi SK, Gall M, Böttcher D, Joosten HJ, Bornscheuer UT.
    The α/β-Hydrolase Fold 3DM Database (ABHDB) as a Tool for Protein
    ChemBioChem, 11:1635–1643., 2010 , PDF


  • Mazé A, Boël G, Zúñiga M, Bourand A, Loux V, Yebra MJ, Monedero V, Correia K, Jacques N, Beaufils S, Poncet S, Joyet P, Milohanic E, Casarégola S, Auffray Y, Pérez-Martínez G, Gibrat JF, Zagorec M, Francke C, Hartke A, Deutscher J.
    Complete genome sequence of the probiotic Lactobacillus casei strain BL23.
    J. Bacteriology, May;192(10):2647-2648., 2010 , PDF


  • Schürch AC, Kremer K, Daviena O, Kiers A, Boeree MJ, Siezen RJ, van Soolingen D.
    High-resolution typing by integration of genome sequencing data in a large tuberculosis cluster.
    J Clin Microbiol, Sep;48(9):3403-3406., 2010 , PDF


  • de Vries SP, van Hijum SA, Schueler W, Riesbeck K, Hays JP, Hermans PW, Bootsma HJ.
    Genome analysis of Moraxella catarrhalis strain RH4, a human respiratory tract pathogen.
    J bacteriology, 192(14):3574-3583., 2010 , PDF


  • Buschow SI, Lasonder E, van Deutekom HW, Oud MM, Beltrame L, Huynen MA, de Vries IJ, Figdor CG, Cavalieri D.
    Dominant processes during human dendritic cell maturation revealed by integration of proteome and transcriptome at the pathway level.
    J Proteome Res, Apr 5;9(4):1727-1737., 2010 , PDF


  • van Diepen A, Brand HK, Sama I, Lambooy LH, van den Heuvel LP, van der Well L, Huynen M, Osterhaus AD, Andeweg AC, Hermans PW.
    Quantitative proteome profiling of respiratory virus-infected lung epithelial cells.
    J Proteomics, Aug 5;73(9):1680-1693., 2010 , PDF


  • Ettwig KF, Butler MK, Le Paslier D, Pelletier E, Mangenot S, Kuypers MM, Schreiber F, Dutilh BE, Zedelius J, de Beer D, Gloerich J, Wessels HJ, van Alen T, Luesken F, Wu ML, van de Pas-Schoonen KT, Op den Camp HJ, Janssen-Megens EM, Francoijs KJ, Stunnenberg H, Weissenbach J, Jetten MS, Strous M.
    Nitrite-driven anaerobic methane oxidation by oxygenic bacteria.
    Nature, Mar 25;464(7288):543-548., 2010 , PDF


  • Hekkelman ML, Te Beek TA, Pettifer SR, Thorne D, Attwood TK, Vriend G.
    WIWS: a protein structure bioinformatics Web service collection.
    Nucleic Acids Res, Jul 1;38 Suppl:W719-723., 2010 , PDF


  • Khelashvili G, Dorff K, Shan J, Camacho-Artacho M, Skrabanek L, Vroling B, Bouvier M, Devi LA, George SR, Javitch JA, Lohse MJ, Milligan G, Neubig RR, Palczewski K, Parmentier M, Pin JP, Vriend G, Campagne F, Filizola M.
    GPCR-OKB: the G Protein Coupled Receptor Oligomer Knowledge Base.
    Bioinformatics, Jul 15;26(14):1804-1805., 2010 , PDF


  • Kuipers RK, Joosten HJ, van Berkel WJ, Leferink NG, Rooijen E, Ittmann E, van Zimmeren F, Jochens H, Bornscheuer U, Vriend G, dos Santos VA, Schaap PJ.
    3DM: systematic analysis of heterogeneous superfamily data to discover protein functionalities.
    Proteins, Jul;78(9):2101-2113., 2010 , PDF


  • Huberts DH, Venselaar H, Vriend G, Veenhuis M, der Klei IJ.
    The moonlighting function of pyruvate carboxylase resides in the non-catalytic end of the TIM barrel.
    Biochim Biophys Acta, Sep;1803(9):1038-1042., 2010 , PDF


  • Sun Y, Almomani R, Aten E, Celli J, van der Heijden J, Venselaar H, Robertson SP, Baroncini A, Franco B, Basel-Vanagaite L, Horii E, Drut R, Ariyurek Y, den Dunnen JT, Breuning MH.
    Terminal Osseous Dysplasia Is Caused by a Single Recurrent Mutation in the FLNA Gene.
    Am J Hum Genet, Jul 9;87(1):146-153., 2010 , PDF


  • Nikopoulos K, Venselaar H, Collin RW, Riveiro-Alvarez R, Boonstra FN, Hooymans JM, Mukhopadhyay A, Shears D, van Bers M, de Wijs IJ, van Essen AJ, Sijmons RH, Tilanus MA, van Nouhuys CE, Ayuso C, Hoefsloot LH, Cremers FP.
    Overview of the mutation spectrum in familial exudative vitreoretinopathy and Norrie disease with identification of 21 novel variants in FZD4, LRP5, and NDP.
    Hum Mutat, Jun;31(6):656-666., 2010 , PDF


  • Waanders E, Venselaar H, te Morsche RH, de Koning DB, Kamath PS, Torres VE, Somlo S, Drenth JP.
    Secondary and tertiary structure modeling reveals effects of novel mutations in polycystic liver disease genes PRKCSH and SEC63.
    Clin Genet, Jul;78(1):47-56., 2010 , PDF


  • Venselaar H, Joosten RP, Vroling B, Baakman CA, Hekkelman ML, Krieger E, Vriend G.
    Homology modelling and spectroscopy, a never-ending love story.
    Eur Biophys J, Mar;39(4):551-563., 2010 , PDF


  • Dölker N, Zachariae U, Grubmüller H.
    Hydrophilic linkers and polar contacts affect aggregation of FG repeat peptides.
    Biophys J, Jun 2;98(11):2653-2661., 2010 , PDF


  • Stary A, Wacker SJ, Boukharta L, Zachariae U, Karimi-Nejad Y, Aqvist J, Vriend G, de Groot BL.
    Toward a consensus model of the HERG potassium channel.
    ChemMedChem, Mar 1;5(3):455-467., 2010 , PDF


  • Kuipers R, van den Bergh T, Joosten HJ, Lekanne Dit Deprez RH, Mannens MM, Schaap PJ.
    Novel tools for extraction and validation of disease-related mutations applied to fabry disease.
    Hum Mutat, Sep;31(9):1026-1032., 2010 , PDF


  • Kouwenhoven EN, van Heeringen SJ, Tena JJ, Oti M, Dutilh BE, Alonso ME, de la Calle-Mustienes E, Smeenk L, Rinne T, Parsaulian L, Bolat E, Jurgelenaite R, Huynen MA, Hoischen A, Veltman JA, Brunner HG, Roscioli T, Oates E, Wilson M, Manzanares M, Gómez-Skarmeta JL, Stunnenberg HG, Lohrum M, van Bokhoven H, Zhou H.
    Genome-wide profiling of p63 DNA-binding sites identifies an element that regulates gene expression during limb development in the 7q21 SHFM1 locus.
    PLoSGenetics, 6:e1001065, 2010 , PDF


  • Siezen RJ, Wilson G.
    Probiotics genomics.
    Microbial Biotechnology, 3:1-9., 2010 , PDF


  • Medema MH, Zhou M, van Hijum SA, Gloerich J, Wessels HJ, Siezen RJ, Strous M.
    A predicted physicochemically distinct sub-proteome associated with the intracellular organelle of the anammox bacterium Kuenenia stuttgartiensis.
    BMC Genomics, May 12;11(1):299., 2010 , PDF


  • Kandasamy K, Mohan SS, Raju R, Keerthikumar S, Kumar GS, Venugopal AK, Telikicherla D, Navarro JD, Mathivanan S, Pecquet C, Gollapudi SK, Tattikota SG, Mohan S, Padhukasahasram H, Subbannayya Y, Goel R, Jacob HK, Zhong J, Sekhar R, Nanjappa V, Balakrishnan L, Subbaiah R, Ramachandra YL, Rahiman BA, Prasad TS, Lin JX, Houtman JC, Desiderio S, Renauld JC, Constantinescu SN, Ohara O, Hirano T, Kubo M, Singh S, Khatri P, Draghici S, Bader GD, Sander C, Leonard WJ, Pandey A.
    NetPath: a public resource of curated signal transduction pathways.
    Genome Biol, Jan 12;11(1):R3, 2010 , PDF


  • Middelbeek J, Clark K, Venselaar H, Huynen MA, van Leeuwen FN.
    The alpha-kinase family: an exceptional branch on the protein kinase tree.
    Cellulair and molecular life sciences, 67(6):875-890., 2010 , PDF


  • Hijikata A, Raju R, Keerthikumar S, Ramabadran S, Balakrishnan L, Ramadoss SK, Pandey A, Mohan S, Ohara O.
    Mutation@A Glance: an integrative web application for analysing mutations from human genetic diseases.
    DNA Res, Jun;17(3):197-208., 2010 , PDF


  • Brooijmans R, Siezen RJ.
    Genomis update: Genomics of microalgae, fuel for the future?
    Microbial Biotechnology, 3(5):514-522., 2010 , PDF


  • de Brouwer AP, van Bokhoven H, Nabuurs SB, Arts WF, Christodoulou J, Duley J.
    PRPS1 mutations: four distinct syndromes and potential treatment.
    Am J Hum Genet, Apr 9;86(4):506-518., 2010 , PDF


  • Snelders E, Karawajczyk A, Schaftenaar G, Verweij PE, Melchers WJ.
    Azole Resistance Profile of Amino Acid Changes in Aspergillus fumigatus CYP51A Based on Protein Homology Modeling.
    Antimicrob. Agents Chemother, 54:2425-2430., 2010 , PDF


  • Sama IE, Huynen MA.
    Measuring the physical cohesiveness of proteins using Physical Interaction Enrichment (PIE).
    Bioinformatics, Nov 1;26(21):2737-2743., 2010 , PDF


  • Richter R, Rorbach J, Pajak A, Smith PM, Wessels HJ, Huynen MA, Smeitink JA, Lightowlers RN, Chrzanowska-Lightowlers ZM.
    A functional peptidyl-tRNA hydrolase, ICT1, has been recruited into the human mitochondrial ribosome.
    EMBO J, Mar 17;29(6):1116-1125., 2010 , PDF


  • Frijters R, van Vugt M, Smeets R, van Schaik R, de Vlieg J, Alkema W.
    Literature mining for the discovery of hidden connections between drugs, genes and diseases.
    PLoS Comput Biol, Sep 23;6(9):e1000943., 2010 , PDF


  • Frijters R, Fleuren W, Toonen EJ, Tuckermann JP, Reichardt HM, van der Maaden H, van Elsas A, van Lierop MJ, Dokter W, de Vlieg J, Alkema W.
    Prednisolone-induced differential gene expression in mouse liver carrying wild type or a dimerization-defective glucocorticoid receptor.
    BMC Genomics, Jun 5;11:359., 2010 , PDF


  • Venselaar H, Te Beek TA, Kuipers RK, Hekkelman ML, Vriend G.
    Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces.
    BMC Bioinformatics, Nov 8;11(1):548., 2010 , PDF


  • Silvestrini F, Lasonder E, Olivieri A, Camarda G, van Schaijk B, Sanchez M, Younis Younis S, Sauerwein R, Alano P.
    Protein export marks the early phase of gametocytogenesis of the human malaria parasite Plasmodium falciparum.
    Mol Cell Proteomics, Jul;9(7):1437-1448., 2010 , PDF


  • Mair GR, Lasonder E, Garver LS, Franke-Fayard BM, Carret CK, Wiegant JC, Dirks RW, Dimopoulos G, Janse CJ, Waters AP.
    Universal features of post-transcriptional gene regulation are critical for Plasmodium zygote development.
    PLoS Pathog, Feb 12;6(2):e1000767., 2010 , PDF


  • van der Voort R, Verweij V, de Witte TM, Lasonder E, Adema GJ, Dolstra H.
    An alternatively spliced CXCL16 isoform expressed by dendritic cells is a secreted chemoattractant for CXCR6+ cells.
    J Leukoc Biol, Jun;87(6):1029-1039., 2010 , PDF


  • Kashyap MK, Harsha HC, Renuse S, Pawar H, Sahasrabuddhe NA, Kim MS, Marimuthu A, Keerthikumar S, Muthusamy B, Kandasamy K, Subbannayya Y, Prasad TS, Mahmood R, Chaerkady R, Meltzer SJ, Kumar RV, Rustgi AK, Pandey A.
    SILAC-based quantitative proteomic approach to identify potential biomarkers from the esophageal squamous cell carcinoma secretome.
    Cancer Biol Ther, Oct 15;10(8):796-810., 2010 , PDF


  • Prasad TSK, Keerthikumar S, Chaerkady R, Kandasamy K, Renuse S, Marimuthu A, Venugopal AK, Thomas JK, Jacob HKC, et al.
    Comparative Proteomic Analysis of Candida albicans and Candida glabrata.
    Clinical Proteomics, 6(4):163-173., 2010 , PDF


  • Westenberg MA, Roerdink JB, Kuipers OP, van Hijum SA.
    SpotXplore: a Cytoscape plugin for visual exploration of hotspot expression in gene regulatory networks.
    Bioinformatics, Nov 15;26(22):2922-2923., 2010 , PDF


  • Schuerch AC, Siezen RJ.
    Genomic tracing of epidemics and disease outbreaks.
    Microb Biotechnol, Nov;3(6):628-633., 2010 , PDF


  • Zhou M, Theunissen D, Wels M, Siezen RJ.
    LAB-Secretome: a genome-scale comparative analysis of the predicted extracellular and surface-associated proteins of Lactic Acid Bacteria.
    BMC Genomics, Nov 23;11:651., 2010 , PDF


  • Sieuwerts S, Molenaar D, van Hijum SA, Beerthuyzen M, Stevens MJ, Janssen PW, Ingham CJ, de Bok FA, de Vos WM, van Hylckama Vlieg JE.
    Mixed-culture transcriptome analysis reveals the molecular basis of mixed-culture growth in Streptococcus thermophilus and Lactobacillus bulgaricus.
    Appl Environ Microbiol, Dec;76(23):7775-7784., 2010 , PDF


  • de Been M, Tempelaars MH, van Schaik W, Moezelaar R, Siezen RJ, Abee T.
    A novel hybrid kinase is essential for regulating the sigma(B)-mediated stress response of Bacillus cereus.
    Environ Microbiol, Mar;12(3):730-745., 2010 , PDF


  • Siezen RJ, Tzeneva VA, Castioni A, Wels M, Phan HT, Rademaker JL, Starrenburg MJ, Kleerebezem M, Molenaar D, van Hylckama Vlieg JE.
    Phenotypic and genomic diversity of Lactobacillus plantarum strains isolated from various environmental niches.
    Environ Microbiol, Mar;12(3):758-773., 2010 , PDF


  • Meijerink M, van Hemert S, Taverne N, Wels M, de Vos P, Bron PA, Savelkoul HF, van Bilsen J, Kleerebezem M, Wells JM.
    Identification of genetic loci in Lactobacillus plantarum that modulate the immune response of dendritic cells using comparative genome hybridization.
    PLoS One, May 13;5(5):e10632., 2010 , PDF


  • Touw WG, Vriend G.
    On the complexity of Engh and Huber refinement restraints: the angle as example.
    Acta Cryst, D66, 1341-1350. doi:10.1107/S0907444910040928, 2010 , PDF