Publications in international journals 2012
  • Ngu LH, Nijtmans LG, Distelmaier F, Venselaar H, van Emst-de Vries SE, van den Brand MA, Stoltenborg BJ, Wintjes LT, Willems PH, van den Heuvel LP, Smeitink JA, Rodenburg RJ.
    A catalytic defect in mitochondrial respiratory chain complex I due to a mutation in NDUFS2 in a patient with Leigh syndrome.
    Biochim Biophys Acta, Feb;1822(2):168-175., 2012 , PDF


  • Prasad TS, Harsha HC, Keerthikumar S, Sekhar NR, Selvan LD, Kumar P, Pinto SM, Muthusamy B, Subbannayya Y, Renuse S, Chaerkady R, Mathur PP, Ravikumar R, Pandey A.
    Proteogenomic Analysis of Candida glabrata using High Resolution Mass Spectrometry.
    J Proteome Res, Jan 1;11(1):247-260., 2012 , PDF


  • Sanders, M.P.A., McGuire, R., Roumen, L., de Esch, I.J., Vlieg, J. de, Klomp, J.P.G. & de Graaf, C.
    From the protein's perspective: the benefits and challenges of protein structure-based pharmacophore modeling.
    Med. Chem. Commun., 3, 28-38, 2012 , PDF


  • Siezen RJ, Francke C, Renckens B, Boekhorst J, Wels M, Kleerebezem M, van Hijum SA.
    Complete Resequencing and Reannotation of the Lactobacillus plantarum WCFS1 Genome.
    J Bacteriol, Jan;194(1):195-196., 2012 , PDF


  • Lusher SJ, Raaijmakers HC, Vu Pham D, Kazemier B, Bosch R, McGuire R, Azevedo R, Dechering K, Oubrie A, van Duin M, de Vlieg J.
    X-ray structures of the progesterone receptor ligand-binding domain in its agonist state reveal differing mechanisms for the mixed profiles of 11β-substituted steroids.
    J Biol Chem, Jun 8;287(24):20333-20343., 2012 , PDF


  • Suijkerbuijk SJ, van Dam TJ, Karagöz GE, von Castelmur E, Hubner NC, Duarte AM, Vleugel M, Perrakis A, Rüdiger SG, Snel B, Kops GJ.
    The Vertebrate Mitotic Checkpoint Protein BUBR1 Is an Unusual Pseudokinase.
    Dev Cell, Jun 12;22(6):1321-1329., 2012 , PDF


  • Lasonder E, Treeck M, Alam M, Tobin AB.
    Insights into the Plasmodium falciparum schizont phospho-proteome.
    Microbes Infect, Aug;14(10):811-819., 2012 , PDF


  • Doreleijers JF, Sousa da Silva AW, Krieger E, Nabuurs SB, Spronk CA, Stevens TJ, Vranken WF, Vriend G, Vuister GW.
    CING: an integrated residue-based structure validation program suite.
    J Biomol NMR, Nov;54(3):267-83. doi: 10.1007/s10858-012-9669-7., 2012 , PDF


  • van Bokhorst-van de Veen H, van Swam I, Wels M, Bron PA, Kleerebezem M.
    Congruent Strain Specific Intestinal Persistence of Lactobacillus plantarum in an Intestine-Mimicking In Vitro System and in Human Volunteers.
    PLoS One, 7(9):e44588., 2012 , PDF


  • Bron PA, Tomita S, van Swam II, Remus DM, Meijerink M, Wels M, Okada S, Wells JM, Kleerebezem M.
    Lactobacillus plantarum possesses the capability for wall teichoic acid backbone alditol switching.
    Microb Cell Fact, Sep 11;11(1):123., 2012 , PDF


  • van Hijum SA, Vaughan EE, Vogel RF.
    Application of state-of-art sequencing technologies to indigenous food fermentations.
    Curr Opin Biotechnol, Sep 6. [Epub ahead of print], 2012 , PDF


  • Smits SL, van Leeuwen M, Schapendonk CM, Schürch AC, Bodewes R, Haagmans BL, Osterhaus AD.
    Picobirnaviruses in the human respiratory tract.
    Emerg Infect Dis, Sep;18(9):1539-1540. doi: 10.3201/eid1809.120507., 2012 , PDF


  • Balsa E, Marco R, Perales-Clemente E, Szklarczyk R, Calvo E, Landázuri MO, Enríquez JA.
    NDUFA4 Is a Subunit of Complex IV of the Mammalian Electron Transport Chain.
    Cell Metab, Sep 5;16(3):378-386., 2012 , PDF


  • Huynen MA, Duarte I, Szklarczyk R.
    Loss, replacement and gain of proteins at the origin of the mitochondria.
    Biochim Biophys Acta, Aug 10. [Epub ahead of print], 2012 , PDF


  • Zomer A, Burghout P, Bootsma HJ, Hermans PW, van Hijum SA.
    ESSENTIALS: Software for Rapid Analysis of High Throughput Transposon Insertion Sequencing Data.
    PLoS One, 7(8):e43012., 2012 , PDF


  • Dessimoz C, Gabaldón T, Roos DS, Sonnhammer EL, Herrero J; Quest for Orthologs Consortium.
    Toward community standards in the quest for orthologs.
    Bioinformatics, Mar 15;28(6):900-904., 2012 , PDF


  • Azevedo R, van Zeeland M, Raaijmakers H, Kazemier B, de Vlieg J, Oubrie A.
    X-ray structure of p38α bound to TAK-715: comparison with three classic inhibitors.
    Acta Crystallogr D Biol Crystallogr, Aug;68(Pt 8):1041-1050., 2012 , PDF


  • Kensche PR, Duarte I, Huynen MA.
    A three-dimensional topology of complex I inferred from evolutionary correlations.
    BMC Struct Biol, Aug 3;12:19., 2012 , PDF


  • Köpfer DA, Hahn U, Ohmert I, Vriend G, Pongs O, de Groot BL, Zachariae U.
    A molecular switch driving inactivation in the cardiac K+ channel HERG.
    PLoS One, 7(7):e41023., 2012 , PDF


  • Wood DJ, Vlieg Jd, Wagener M, Ritschel T.
    Pharmacophore fingerprint-based approach to binding site subpocket similarity and its application to bioisostere replacement.
    J Chem Inf Model, Aug 27;52(8):2031-2043., 2012 , PDF


  • de Beer RJ, Bögels B, Schaftenaar G, Zarzycka B, Quaedflieg PJ, van Delft FL, Nabuurs SB, Rutjes FP.
    Enzyme-Specific Activation versus Leaving Group Ability.
    Chembiochem, Aug 13;13(12):1785-1790. doi: 10.1002/cbic.201200227., 2012 , PDF


  • Zhao Y, Caspers MP, Abee T, Siezen RJ, Kort R.
    Complete genome sequence of Geobacillus thermoglucosidans TNO-09.020, a thermophilic sporeformer associated with a dairy-processing environment.
    J Bacteriol, Aug;194(15):4118., 2012 , PDF


  • van Bokhorst-van de Veen H, Lee IC, Marco ML, Wels M, Bron PA, Kleerebezem M.
    Modulation of Lactobacillus plantarum gastrointestinal robustness by fermentation conditions enables identification of bacterial robustness markers.
    PLoS One, 7(7):e39053., 2012 , PDF


  • Bron PA, Wels M, Bongers RS, van Bokhorst-van de Veen H, Wiersma A, Overmars L, Marco ML, Kleerebezem M.
    Transcriptomes reveal genetic signatures underlying physiological variations imposed by different fermentation conditions in Lactobacillus plantarum.
    PLoS One, 7(7):e38720., 2012 , PDF


  • Trindade-Silva AE, Rua C, Silva GG, Dutilh BE, Moreira AP, Edwards RA, Hajdu E, Lobo-Hajdu G, Vasconcelos AT, Berlinck RG, Thompson FL.
    Taxonomic and functional microbial signatures of the endemic marine sponge Arenosclera brasiliensis.
    PLoS One, 7(7):e39905., 2012 , PDF


  • Barandun LJ, Immekus F, Kohler PC, Tonazzi S, Wagner B, Wendelspiess S, Ritschel T, Heine A, Kansy M, Klebe G, Diederich F.
    From lin-benzoguanines to lin-benzohypoxanthines as ligands for Zymomonas mobilis tRNA-guanine transglycosylase: replacement of protein-ligand hydrogen bonding by importing water clusters.
    Chemistry, Jul 23;18(30):9246-57. doi: 10.1002/chem.201200809., 2012 , PDF


  • Tjalsma H, Boleij A, Marchesi JR, Dutilh BE.
    A bacterial driver-passenger model for colorectal cancer: beyond the usual suspects.
    Nat Rev Microbiol, Jun 25;10(8):575-582. doi: 10.1038/nrmicro2819., 2012 , PDF


  • Boleij A, Dutilh BE, Kortman GA, Roelofs R, Laarakkers CM, Engelke UF, Tjalsma H.
    Bacterial responses to a simulated colon tumor microenvironment.
    Mol Cell Proteomics, Oct;11(10):851-862., 2012


  • Duarte I, Nabuurs SB, Magno R, Huynen M.
    Evolution and Diversification of the Organellar Release Factor Family.
    Mol Biol Evol, Nov;29(11):3497-512. doi: 10.1093/molbev/mss157., 2012 , PDF


  • de Kleijn S, Kox M, Sama IE, Pillay J, van Diepen A, Huijnen MA, van der Hoeven JG, Ferwerda G, Hermans PW, Pickkers P.
    Transcriptome kinetics of circulating neutrophils during human experimental endotoxemia.
    PLoS One, 7(6):e38255., 2012 , PDF


  • Bosman GJ, Lasonder E, Groenen-Döpp YA, Willekens FL, Werre JM.
    The proteome of erythrocyte-derived microparticles from plasma: new clues for erythrocyte aging and vesiculation.
    J Proteomics, Dec;76 Spec No.:203-10. doi: 10.1016/j.jprot.2012.05.031., 2012 , PDF


  • Ajmal M, Khan MI, Micheal S, Ahmed W, Shah A, Venselaar H, Bokhari H, Azam A, Waheed NK, Collin RW, den Hollander AI, Qamar R, Cremers FP.
    Identification of recurrent and novel mutations in TULP1 in Pakistani families with early-onset retinitis pigmentosa.
    Mol Vis, 18:1226-1237., 2012 , PDF


  • Garza DR, Thompson CC, Loureiro EC, Dutilh BE, Inada DT, Junior EC, Cardoso JF, Nunes MR, de Lima CP, Silvestre RV, Nunes KN, Santos EC, Edwards RA, Vicente AC, de Sá Morais LL.
    Genome-wide study of the defective sucrose fermenter strain of Vibrio cholerae from the Latin American cholera epidemic.
    PLoS One, 7(5):e37283., 2012 , PDF


  • Sanders MP, Barbosa AJ, Zarzycka B, Nicolaes GA, Klomp JP, de Vlieg J, Del Rio A.
    Comparative analysis of pharmacophore screening tools.
    J Chem Inf Model, Jun 25;52(6):1607-1620., 2012 , PDF


  • Greupink R, Nabuurs SB, Zarzycka B, Verweij V, Monshouwer M, Huisman MT, Russel FG.
    In Silico Identification of Potential Cholestasis-Inducing Agents via Modeling of Na+-Dependent Taurocholate Cotransporting Polypeptide Substrate Specificity.
    Toxicol Sci, Sep;129(1):35-48., 2012 , PDF


  • Baede EJ, den Bekker E, Boiten JW, Cronin D, van Gammeren R, de Vlieg J.
    Integrated project views: decision support platform for drug discovery project teams.
    J Chem Inf Model, Jun 25;52(6):1438-1449., 2012 , PDF


  • Ruiz L, Zomer A, O'Connell-Motherway M, van Sinderen D, Margolles A.
    Discovering novel bile protection systems in Bifidobacterium breve UCC2003 through functional genomics.
    Appl Environ Microbiol, Feb;78(4):1123-31. doi: 10.1128/AEM.06060-11., 2012 , PDF


  • de Beer RJ, Zarzycka B, Mariman M, Amatdjais-Groenen HI, Mulders MJ, Quaedflieg PJ, van Delft FL, Nabuurs SB, Rutjes FP.
    Papain-specific activating esters in aqueous dipeptide synthesis.
    Chembiochem, Jun 18;13(9):1319-1326. doi: 10.1002/cbic.201200017., 2012 , PDF


  • Cho HJ, Park HJ, Trexler M, Venselaar H, Lee KY, Robertson NG, Baek JI, Kang BS, Morton CC, Vriend G, Patthy L, Kim UK.
    A novel COCH mutation associated with autosomal dominant nonsyndromic hearing loss disrupts the structural stability of the vWFA2 domain.
    J Mol Med (Berl), Nov;90(11):1321-31. doi: 10.1007/s00109-012-0911-2., 2012 , PDF


  • Harakalova M, van Harssel JJ, Terhal PA, van Lieshout S, Duran K, Renkens I, Amor DJ, Wilson LC, Kirk EP, Turner CL, Shears D, Garcia-Minaur S, Lees MM, Ross A, Venselaar H, Vriend G, Takanari H, Rook MB, van der Heyden MA, Asselbergs FW, Breur HM, Swinkels ME, Scurr IJ, Smithson SF, Knoers NV, van der Smagt JJ, Nijman IJ, Kloosterman WP, van Haelst MM, van Haaften G, Cuppen E.
    Dominant missense mutations in ABCC9 cause Cantú syndrome.
    Nat Genet, May 18;44(7):793-796. doi: 10.1038/ng.2324., 2012 , PDF


  • Groot Kormelink T, Koenders E, Hagemeijer Y, Overmars L, Siezen RJ, de Vos WM, Francke C.
    Comparative genome analysis of central nitrogen metabolism and its control by GlnR in the class Bacilli.
    BMC Genomics, May 18;13:191., 2012 , PDF


  • Hensen U, Meyer T, Haas J, Rex R, Vriend G, Grubmüller H.
    Exploring protein dynamics space: the dynasome as the missing link between protein structure and function.
    PLoS One, 7(5):e33931., 2012 , PDF


  • Farhoud MH, Nijtmans LG, Wanders RJ, Wessels HJ, Lasonder E, Janssen AJ, Rodenburg RR, van den Heuvel LP, Smeitink JA.
    Impaired ubiquitin-proteasome-mediated PGC-1α protein turnover and induced mitochondrial biogenesis secondary to complex-I deficiency.
    Proteomics, May;12(9):1349-1362. doi: 10.1002/pmic.201100326., 2012 , PDF


  • Luckwu de Lucena BT, Silva GG, Manoel Dos Santos B, Dias GM, Amaral GR, Moreira AP, de Morais Júnior MA, Dutilh BE, Edwards RA, Balbino V, Thompson CC, Thompson FL.
    Genome sequences of the ethanol-tolerant Lactobacillus vini strains LMG 23202T and JP7.8.9.
    J Bacteriol, Jun;194(11):3018., 2012 , PDF


  • Huynen MA, Duarte I, Chrzanowska-Lightowlers ZM, Nabuurs SB.
    Structure based hypothesis of a mitochondrial ribosome rescue mechanism.
    Biol Direct, May 8;7:14., 2012 , PDF


  • Sanders MP, Roumen L, van der Horst E, Lane JR, Vischer HF, van Offenbeek J, de Vries H, Verhoeven S, Chow KY, Verkaar F, Beukers MW, McGuire R, Leurs R, Ijzerman AP, de Vlieg J, de Esch IJ, Zaman GJ, Klomp JP, Bender A, de Graaf C.
    A prospective cross-screening study on G-protein-coupled receptors: lessons learned in virtual compound library design.
    J Med Chem, Jun 14;55(11):5311-5325., 2012 , PDF


  • Saeed S, Logie C, Francoijs KJ, Frigè G, Romanenghi M, Nielsen FG, Raats L, Shahhoseini M, Huynen M, Altucci L, Minucci S, Martens JH, Stunnenberg HG.
    Chromatin accessibility, p300, and histone acetylation define PML-RARα and AML1-ETO binding sites in acute myeloid leukemia.
    Blood, Oct 11;120(15):3058-68. doi: 10.1182/blood-2011-10-386086., 2012 , PDF


  • Wagener M, Vlieg JD, Nabuurs SB.
    Flexible protein-ligand docking using the Fleksy protocol.
    J Comput Chem, Feb 28. doi: 10.1002/jcc.22948., 2012 , PDF


  • Bayjanov JR, Molenaar D, Tzeneva V, Siezen RJ, van Hijum SA.
    PhenoLink--a web-tool for linking phenotype to ~omics data for bacteria: application to gene-trait matching for Lactobacillus plantarum strains.
    BMC Genomics, May 4;13:170., 2012 , PDF


  • French VM, van de Laar IM, Wessels MW, Rohe C, Roos-Hesselink JW, Wang G, Frohn-Mulder IM, Severijnen LA, de Graaf BM, Schot R, Breedveld G, Mientjes E, van Tienhoven M, Jadot E, Jiang Z, Verkerk A, Swagemakers S, Venselaar H, Rahimi Z, Najmabadi H, Meijers-Heijboer H, de Graaff E, Helbing WA, Willemsen R, Devriendt K, Belmont JW, Oostra BA, Amack JD, Bertoli-Avella AM.
    NPHP4 variants are associated with pleiotropic heart malformations.
    Circ Res, Jun 8;110(12):1564-1574., 2012 , PDF


  • Wittgen HG, van den Heuvel JJ, Krieger E, Schaftenaar G, Russel FG, Koenderink JB.
    Phenylalanine 368 of multidrug resistance-associated protein 4 (MRP4/ABCC4) plays a crucial role in substrate-specific transport activity.
    Biochem Pharmacol, Aug 1;84(3):366-373., 2012 , PDF


  • Pawar H, Sahasrabuddhe NA, Renuse S, Keerthikumar S, Sharma J, Kumar GS, Venugopal A, Sekhar NR, Kelkar DS, Nemade H, Khobragade SN, Muthusamy B, Kandasamy K, Harsha HC, Chaerkady R, Patole MS, Pandey A.
    A proteogenomic approach to map the proteome of an unsequenced pathogen - Leishmania donovani.
    Proteomics, Mar;12(6):832-844. doi: 10.1002/pmic.201100505., 2012 , PDF


  • Liu M, Prakash C, Nauta A, Siezen RJ, Francke C.
    Computational analysis of cysteine and methionine metabolism and its regulation in dairy starter and related bacteria.
    J Bacteriol, Jul;194(13):3522-3533., 2012 , PDF


  • McEvoy CR, Cloete R, Müller B, Schürch AC, van Helden PD, Gagneux S, Warren RM, Gey van Pittius NC.
    Comparative analysis of Mycobacterium tuberculosis pe and ppe genes reveals high sequence variation and an apparent absence of selective constraints.
    PLoS One, 7(4):e30593., 2012 , PDF


  • Axelsson L, Rud I, Naterstad K, Blom H, Renckens B, Boekhorst J, Kleerebezem M, van Hijum S, Siezen RJ.
    Genome sequence of the naturally plasmid-free Lactobacillus plantarum strain NC8 (CCUG 61730).
    J Bacteriol, May;194(9):2391-2392., 2012 , PDF


  • Leimena MM, Wels M, Bongers RS, Smid EJ, Zoetendal EG, Kleerebezem M.
    Comparative analysis of Lactobacillus plantarum WCFS1 transcriptomes by using DNA microarray and next-generation sequencing technologies.
    Appl Environ Microbiol, Jun;78(12):4141-4148., 2012 , PDF


  • Gerrits L, Venselaar H, Wieringa B, Wansink DG, Hendriks WJ.
    Phosphorylation target site specificity for AGC kinases DMPK E and Lats2.
    J Cell Biochem, Jun;113(6):2126-2135. doi: 10.1002/jcb.24086., 2012 , PDF


  • Peeters MC, Wisse LE, Dinaj A, Vroling B, Vriend G, Ijzerman AP.
    The role of the second and third extracellular loops of the adenosine A1 receptor in activation and allosteric modulation.
    Biochem Pharmacol, Jul 1;84(1):76-87., 2012 , PDF


  • Mokili JL, Rohwer F, Dutilh BE.
    Metagenomics and future perspectives in virus discovery.
    Curr Opin Virol, Feb;2(1):63-77., 2012 , PDF


  • Smeets RL, Fleuren WW, He X, Vink PM, Wijnands F, Gorecka M, Klop H, Bauerschmidt S, Garritsen A, Koenen HJ, Joosten I, Boots AM, Alkema W.
    Molecular pathway profiling of T lymphocyte signal transduction pathways; Th1 and Th2 genomic fingerprints are defined by TCR and CD28-mediated signaling.
    BMC Immunol, Mar 14;13:12., 2012 , PDF


  • de Baaij JH, Stuiver M, Meij IC, Lainez S, Kopplin K, Venselaar H, Müller D, Bindels RJ, Hoenderop JG.
    Membrane topology and intracellular processing of cyclin M2 (CNNM2).
    J Biol Chem, Apr 20;287(17):13644-13655., 2012 , PDF


  • Snelders E, Camps SM, Karawajczyk A, Schaftenaar G, Kema GH, van der Lee HA, Klaassen CH, Melchers WJ, Verweij PE.
    Triazole fungicides can induce cross-resistance to medical triazoles in Aspergillus fumigatus.
    PLoS One, 7(3):e31801., 2012 , PDF


  • Schaftenaar G, de Vlieg J.
    Quantum mechanical polar surface area.
    J Comput Aided Mol Des, Mar;26(3):311-318., 2012 , PDF


  • Szklarczyk R, Wanschers BF, Cuypers TD, Esseling JJ, Riemersma M, van den Brand MA, Gloerich J, Lasonder E, van den Heuvel LP, Nijtmans LG, Huynen MA.
    Iterative orthology prediction uncovers new mitochondrial proteins and identifies C12orf62 as the human ortholog of COX14, a protein involved in the assembly of cytochrome c oxidase.
    Genome Biol, Feb 22;13(2):R12., 2012 , PDF


  • Rosato A, Aramini JM, Arrowsmith C, Bagaria A, Baker D, Cavalli A, Doreleijers JF, Eletsky A, Giachetti A, Guerry P, Gutmanas A, Güntert P, He Y, Herrmann T, Huang YJ, Jaravine V, Jonker HR, Kennedy MA, Lange OF, Liu G, Malliavin TE, Mani R, Mao B, Montelione GT, Nilges M, Rossi P, van der Schot G, Schwalbe H, Szyperski TA, Vendruscolo M, Vernon R, Vranken WF, Vries Sd, Vuister GW, Wu B, Yang Y, Bonvin AM.
    Blind testing of routine, fully automated determination of protein structures from NMR data.
    Structure, Feb 8;20(2):227-236., 2012 , PDF


  • Camps SM, Dutilh BE, Arendrup MC, Rijs AJ, Snelders E, Huynen MA, Verweij PE, Melchers WJ.
    Discovery of a HapE mutation that causes azole resistance in Aspergillus fumigatus through whole genome sequencing and sexual crossing.
    PLoS One, 7(11):e50034. doi: 10.1371/journal.pone.0050034., 2012 , PDF


  • C. Francke
    Mogelijkheden en onmogelijkheden van de bio-informatica: op weg naar een beoordelingsmethodologie voor genen met een onbekende functie.
    COGEM Onderzoeksrapport, CGM 2012-03, 2012


  • Lounnas V, Vriend G.
    AsteriX: a Web server to automatically extract ligand coordinates from figures in PDF articles.
    J Chem Inf Model, Feb 27;52(2):568-576., 2012 , PDF


  • Zeeuwen PL, Boekhorst J, van den Bogaard EH, de Koning HD, van de Kerkhof PM, Saulnier DM, van Swam II, van Hijum SA, Kleerebezem M, Schalkwijk J, Timmerman HM.
    Microbiome dynamics of human epidermis following skin barrier disruption.
    Genome Biol, Nov 15;13(11):R101., 2012 , PDF


  • Zoetendal EG, Raes J, van den Bogert B, Arumugam M, Booijink CC, Troost FJ, Bork P, Wels M, de Vos WM, Kleerebezem M.
    The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates.
    ISME J, Jul;6(7):1415-1426. doi: 10.1038/ismej.2011.212., 2012 , PDF


  • Seddon G, Lounnas V, McGuire R, van den Bergh T, Bywater RP, Oliveira L, Vriend G.
    Drug design for ever, from hype to hope.
    J Comput Aided Mol Des, Jan;26(1):137-150., 2012 , PDF


  • van Lierop MJ, Alkema W, Laskewitz AJ, Dijkema R, van der Maaden HM, Smit MJ, Plate R, Conti PG, Jans CG, Timmers CM, van Boeckel CA, Lusher SJ, McGuire R, van Schaik RC, de Vlieg J, Smeets RL, Hofstra CL, Boots AM, van Duin M, Ingelse BA, Schoonen WG, Grefhorst A, van Dijk TH, Kuipers F, Dokter WH.
    Org 214007-0: a novel non-steroidal selective glucocorticoid receptor modulator with full anti-inflammatory properties and improved therapeutic index.
    PLoS One, 7(11):e48385. doi: 10.1371/journal.pone.0048385., 2012 , PDF


  • Wanschers BF, Szklarczyk R, Pajak A, van den Brand MA, Gloerich J, Rodenburg RJ, Lightowlers RN, Nijtmans LG, Huynen MA.
    C7orf30 specifically associates with the large subunit of the mitochondrial ribosome and is involved in translation.
    Nucleic Acids Res, May;40(9):4040-4051., 2012 , PDF


  • Zomer A, de Vries SP, Riesbeck K, Meinke AL, Hermans PW, Bootsma HJ.
    Genome sequence of Moraxella catarrhalis RH4, an isolate of seroresistant lineage.
    J Bacteriol, Dec;194(24):6969. doi: 10.1128/JB.01833-12., 2012 , PDF


  • Sanecka A, Ansems M, van Hout-Kuijer MA, Looman MW, Prosser AC, Welten S, Gilissen C, Sama IE, Huynen MA, Veltman JA, Jansen BJ, Eleveld-Trancikova D, Adema GJ.
    Analysis of genes regulated by the transcription factor LUMAN identifies ApoA4 as a target gene in dendritic cells.
    Mol Immunol, Feb;50(1-2):66-73., 2012 , PDF


  • Altelaar AF, Navarro D, Boekhorst J, van Breukelen B, Snel B, Mohammed S, Heck AJ.
    Database independent proteomics analysis of the ostrich and human proteome.
    Proc Natl Acad Sci U S A, Jan 10;109(2):407-412., 2012 , PDF


  • Krieger E, Dunbrack RL Jr, Hooft RW, Krieger B.
    Assignment of protonation states in proteins and ligands: combining pKa prediction with hydrogen bonding network optimization.
    Methods Mol Biol, 819:405-421., 2012 , PDF


  • Nannapaneni P, Hertwig F, Depke M, Hecker M, Mäder U, Völker U, Steil L, van Hijum SA.
    Defining the structure of the general stress regulon of Bacillus subtilis using targeted microarray analysis and random forest classification.
    Microbiology, Mar;158(Pt 3):696-707., 2012 , PDF


  • Buschow SI, Lasonder E, Szklarczyk R, Oud MM, de Vries IJ, Figdor CG.
    Unraveling the human dendritic cell phagosome proteome by organellar enrichment ranking.
    J Proteomics, Feb 16;75(5):1547-1562., 2012 , PDF


  • Gorlani A, Hulsik DL, Adams H, Vriend G, Hermans P, Verrips T.
    Antibody engineering reveals the important role of J segments in the production efficiency of llama single-domain antibodies in Saccharomyces cerevisiae.
    Protein Eng Des Sel, Jan;25(1):39-46., 2012 , PDF


  • Doreleijers JF, Vranken WF, Schulte C, Markley JL, Ulrich EL, Vriend G, Vuister GW.
    NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB.
    Nucleic Acids Res, Jan;40(Database issue):D519-524., 2012 , PDF


  • Schneider MV, Walter P, Blatter MC, Watson J, Brazas MD, Rother K, Budd A, Via A, van Gelder CW, Jacob J, Fernandes P, Nyrönen TH, De Las Rivas J, Blicher T, Jimenez RC, Loveland J, McDowall J, Jones P, Vaughan BW, Lopez R, Attwood TK, Brooksbank C.
    Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers.
    Brief Bioinform, May;13(3):383-389., 2012 , PDF


  • Schürch AC, van Soolingen D.
    DNA fingerprinting of Mycobacterium tuberculosis: from phage typing to whole-genome sequencing.
    Infect Genet Evol, Jun;12(4):602-609., 2012 , PDF


  • Vroling B, Thorne D, McDermott P, Joosten HJ, Attwood TK, Pettifer S, Vriend G.
    NucleaRDB: information system for nuclear receptors.
    Nucleic Acids Res, Jan;40(Database issue):D377-380., 2012 , PDF


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