Publications of the Bacterial genomics group

  • 2017 Mobegi FM, Cremers AJ, de Jonge MI, Bentley SD, van Hijum SA, Zomer A.
    Deciphering the distance to antibiotic resistance for the pneumococcus using genome sequencing data.
    Sci Rep., 2017 Feb 16;7:42808 Details

  • 2017 Tunjungputri RN, Mobegi FM, Cremers AJ, van der Gaast-de Jongh CE, Ferwerda G, Meis JF, Roeleveld N, Bentley SD, Pastura AS, van Hijum SA, van der Ven AJ, de Mast Q, Zomer A, de Jonge MI.
    Phage-Derived Protein Induces Increased Platelet Activation and Is Associated with Mortality in Patients with Invasive Pneumococcal Disease
    MBio., 2017 Jan 17;8(1) Details

  • 2017 Wels M, Backus L, Boekhorst J, Dijkstra A, Beerthuyzen M, Siezen RJ, Bachmann H, van Hijum SA.
    Draft Genome Sequences of 11 Lactococcus lactis subsp. cremoris Strains.
    Genome announcements., 2017 Mar 16;5(11) Details

  • 2017 Zeeuwen PL, Boekhorst J, Ederveen TH, Kleerebezem M, Schalkwijk J, van Hijum SA, Timmerman HM.
    Reply to Meisel et al.
    J Invest Dermatol., 2017 Apr;137(4):961-2 Details

  • 2017 Zeeuwen PL, Ederveen TH, van der Krieken DA, Niehues H, Boekhorst J, Kezic S, Hanssen DA, Otero ME, van Vlijmen-Willems IM, Rodijk-Olthuis D, Falcone D, van den Bogaard EH, Kamsteeg M, de Koning HD, Zeeuwen-Franssen ME, van Steensel MA, Kleerebezem M, Timmerman HM, van Hijum SA, Schalkwijk J.
    Gram-positive anaerobe cocci are underrepresented in the microbiome of filaggrin-deficient human skin
    J Allergy Clin Immunol., 2016 Oct 8. pii: S0091-6749(16)31117-4 Details

  • 2017 Backus L, Wels M, Boekhorst J, Dijkstra AR, Beerthuyzen M, Kelly WJ, Siezen RJ, van Hijum SA, Bachmann H
    Draft Genome Sequences of 24 Lactococcus lactis Strains
    Genome announcements, 2017 Mar 30;5(13) Details

  • 2017 Mobegi FM, Zomer A, de Jonge MI, van Hijum SA
    Advances and perspectives in computational prediction of microbial gene essentiality
    Brief Funct Genomics, 2017 Mar 01;16(2):70-9 Details

  • 2017 Nebenzahl-Guimaraes H, van Laarhoven A, Farhat MR, Koeken V, Mandemakers JJ, Zomer A, van Hijum S, Netea MG, Murray M, van Crevel R, van Soolingen D
    Transmissible Mycobacterium tuberculosis Strains Share Genetic Markers and Immune Phenotypes
    Am J Respir Crit Care Med, 2017 Jun 01;195(11):1519-27 Details

  • 2017 Rogier R, Ederveen THA, Boekhorst J, Wopereis H, Scher JU, Manasson J, Frambach S, Knol J, Garssen J, van der Kraan PM, Koenders MI, van den Berg WB, van Hijum S, Abdollahi-Roodsaz S
    Aberrant intestinal microbiota due to IL-1 receptor antagonist deficiency promotes IL-17- and TLR4-dependent arthritis
    Microbiome, 2017 Jun 23;5(1):63 Details

  • 2016 Alkema W, Boekhorst J, Wels M, van Hijum SA
    Microbial bioinformatics for food safety and production
    Brief Bioinform., 2016 Mar;17(2):283-92 Details

  • 2016 Bron PA, Lee IC, Backus L, van Hijum SA, Wels M, Kleerebezem M
    Draft Genome Sequence of Lactobacillus plantarum SF2A35B
    Genome announcements, 2016;4(1) Details

  • 2016 Warda AK, Siezen RJ, Boekhorst J, Wells-Bennik MH, de Jong A, Kuipers OP, Nierop Groot MN, Abee T
    Linking Bacillus cereus Genotypes and Carbohydrate Utilization Capacity
    PLoS One, 2016;11(6):e0156796 Details

  • 2016 Erkus O, de Jager VC, Geene RT, van Alen-Boerrigter I, Hazelwood L, van Hijum SA, Kleerebezem M, Smid EJ
    Use of propidium monoazide for selective profiling of viable microbial cells during Gouda cheese ripening
    Int J Food Microbiol., 2016 Jul 2;228:1-9 Details

  • 2016 Bosma EF, Koehorst JJ, van Hijum SA, Renckens B, Vriesendorp B, van de Weijer AH, Schaap PJ, de Vos WM, van der Oost J, van Kranenburg R
    Complete genome sequence of thermophilic Bacillus smithii type strain DSM 4216(T)
    Stand Genomic Sci, 2016;11(1):52 Details

  • 2016 Dijkstra AR, Alkema W, Starrenburg MJ, Hugenholtz J, van Hijum SA, Bron PA
    Strain-Dependent Transcriptome Signatures for Robustness in Lactococcus lactis
    PLoS One, 2016;11(12):e0167944 Details

  • 2016 Martino ME, Bayjanov JR, Caffrey BE, Wels M, Joncour P, Hughes S, Gillet B, Kleerebezem M, van Hijum SA, Leulier F
    Nomadic lifestyle of Lactobacillus plantarum revealed by comparative genomics of 54 strains isolated from different habitats
    Environ Microbiol., 2016 Dec;18(12):4974-89 Details

  • 2016 Urshev Z, Hajo K, Lenoci L, Bron PA, Dijkstra A, Alkema W, Wels M, Siezen RJ, Minkova S, van Hijum SA
    Draft Genome Sequence of Lactobacillus delbrueckii subsp. bulgaricus LBB.B5
    Genome announcements, 2016 Oct 06;4(5) Details

  • 2016 van der Krieken DA, Ederveen TH, van Hijum SA, Jansen PA, Melchers WJ, Scheepers PT, Schalkwijk J, Zeeuwen PL
    An In vitro Model for Bacterial Growth on Human Stratum Corneum
    Acta Derm Venereol., 2016 Nov 02;96(7):873-9 Details

  • 2015 Ercan O, Wels M, Smid EJ, Kleerebezem M.
    Molecular and metabolic adaptations of Lactococcus lactis at near-zero growth rates.
    Appl Environ Microbiol., Jan;81(1):320-31. doi: 10.1128/AEM.02484-14. Details

  • 2015 Ercan O, Wels M, Smid EJ, Kleerebezem M.
    Genome-Wide Transcriptional Responses to Carbon Starvation in Nongrowing Lactococcus lactis
    Appl Environ Microbiol, Apr 1;81(7):2554-61. doi: 10.1128/AEM.03748-14. Details

  • 2015 Lamontanara A, Caggianiello G, Orru L, Capozzi V, Michelotti V, Bayjanov JR, Renckens B, van Hijum SA, Cattivelli L, Spano G.
    Draft Genome Sequence of Lactobacillus plantarum Lp90 Isolated from Wine
    Genome Announc, Mar 12;3(2). pii: e00097-15. doi: 10.1128/genomeA.00097-15. Details

  • 2015 Sanders JW, Oomes SJ, Membre JM, Wegkamp A, Wels M.
    Biodiversity of spoilage lactobacilli: phenotypic characterisation
    Food Microbiol, Feb;45(Pt A):34-44. doi: 10.1016/j.fm.2014.03.013 Details

  • 2015 van den Kieboom CH, Ahout IM, Zomer A, Brand KH, de Groot R, Ferwerda G, de Jonge MI.
    Nasopharyngeal gene expression, a novel approach to study the course of respiratory syncytial virus infection.
    Eur Respir J., Mar;45(3):718-25. doi: 10.1183/09031936.00085614. Details

  • 2015 Jaeggi T, Kortman GA, Moretti D, Chassard C, Holding P, Dostal A, Boekhorst J, Timmerman HM, Swinkels DW, Tjalsma H, Njenga J, Mwangi A, Kvalsvig J, Lacroix C, Zimmerman MB.
    Iron fortification adversely affects the gut microbiome, increases pathogen abundance and induces intestinal inflammation in Kenyan infants
    Gut, May;64(5):731-42. doi: 10.1136/gutjnl-2014-307720. Details

  • 2015 Metselaar KI, den Besten HM, Boekhorst J, van Hijum SA, Zwietering MH, Abee T
    Diversity of acid stress resistant variants of Listeria monocytogenes and the potential role of ribosomal protein S21 encoded by rpsU
    Front Microbiol, May 8;6:422. doi: 10.3389/fmicb.2015.00422. Details

  • 2015 Xiao Y, van Hijum SA, Abee T, Wells-Bennik MH.
    Genome-Wide Transcriptional Profiling of Clostridium perfringens SM101 during Sporulation Extends the Core of Putative Sporulation Genes and Genes Determining Spore Properties and Germination Characteristics
    PLoS One, May 15;10(5):e0127036. doi: 10.1371/journal.pone.0127036. Details

  • 2015 Overmars L, Siezen RJ, Francke C.
    A Novel Quality Measure and Correction Procedure for the Annotation of Microbial Translation Initiation Sites.
    PLoS One., Jul 23;10(7):e0133691. doi: 10.1371/journal.pone.0133691 Details

  • 2015 Overmars L, van Hijum SA, Siezen RJ, Francke C.
    CiVi: circular genome visualization with unique features to analyze sequence elements.
    Bioinformatics. , Sep 1;31(17):2867-9. doi: 10.1093/bioinformatics/btv249. Details

  • 2015 Alkema W, Boekhorst J, Wels M, van Hijum SA.
    Microbial bioinformatics for food safety and production.
    Brief Bioinform., 2015 Jun 16. pii: bbv034. Details

  • 2015 Dingemanse C, Belzer C, van Hijum SA, Gunthel M, Salvatori D, den Dunnen JT, Kuijper EJ, Devilee P, de Vos WM, van Ommen GB, Robanus-Maandag EC.
    Akkermansia muciniphila and Helicobacter typhlonius modulate intestinal tumor development in mice.
    Carcinogenesis, Nov;36(11):1388-96. doi: 10.1093/carcin/bgv120. Details

  • 2015 Wels M, Serrano LM, Eibrink BJ, Backus L, Bongers RS, Vriesendorp B, Siezen RJ, van Hijum SA, Meijer WC.
    Draft Genome Sequence of Streptococcus thermophilus C106, a Dairy Isolate from an Artisanal Cheese Produced in the Countryside of Ireland.
    Genome Announc, Nov 25;3(6). pii: e01377-15. Details

  • 2015 Kortman GA, Mulder ML, Richters TJ, Shanmugam NK, Trebicka E, Boekhorst J, Timmerman HM, Roelofs R, Wiegerinck ET, Laarakkers CM, Swinkels DW, Bolhuis A, Cherayil BJ, Tjalsma H.
    Low dietary iron intake restrains the intestinal inflammatory response and pathology of enteric infection by food-borne bacterial pathogens.
    Eur J Immunol., Sep;45(9):2553-67. Details

  • 2015 Martino ME, Bayjanov JR, Joncour P, Hughes S, Gillet B, Kleerebezem M, Siezen R, van Hijum SA, Leulier F.
    Nearly Complete Genome Sequence of Lactobacillus plantarum Strain NIZO2877
    Genome Announc., Nov 25;3(6). pii: e01370-15. Details

  • 2015 Cremers AJ, Mobegi FM, de Jonge MI, van Hijum SA, Meis JF, Hermans PW, Ferwerda G, Bentley SD, Zomer AL.
    The post-vaccine microevolution of invasive Streptococcus pneumoniae.
    Sci Rep., Oct 23;5:14952. Details

  • 2015 Martino ME, Bayjanov JR, Joncour P, Hughes S, Gillet B, Kleerebezem M, Siezen R, van Hijum SA, Leulier F.
    Resequencing of the Lactobacillus plantarum Strain WJL Genome.
    Genome Announc., Nov 25;3(6). pii: e01382-15. Details

  • 2014 Dijkstra AR, Setyawati MC, Bayjanov JR, Alkema W, van Hijum SA, Bron PA, Hugenholtz J.
    Diversity in robustness of Lactococcus lactis strains during heat stress, oxidative stress, and spray drying stress.
    Appl Environ Microbiol, Jan;80(2):603-11. doi: 10.1128/AEM.03434-13. Details

  • 2014 Liu M, Bienfait B, Sacher O, Gasteiger J, Siezen RJ, Nauta A, Geurts JM.
    Combining chemoinformatics with bioinformatics: in silico prediction of bacterial flavor-forming pathways by a chemical systems biology approach "reverse pathway engineering".
    PLoS One, Jan 8;9(1):e84769. doi: 10.1371/journal.pone.0084769. Details

  • 2014 Handtke S, Schroeter R, Jürgen B, Methling K, Schlüter R, Albrecht D, van Hijum SA, Bongaerts J, Maurer KH, Lalk M, Schweder T, Hecker M, Voigt B.
    Bacillus pumilus reveals a remarkably high resistance to hydrogen peroxide provoked oxidative stress.
    PLoS One, Jan 20;9(1):e85625. doi: 10.1371/journal.pone.0085625. Details

  • 2014 Verhagen LM, de Jonge MI, Burghout P, Schraa K, Spagnuolo L, Mennens S, Eleveld MJ, van der Gaast-de Jongh CE, Zomer A, Hermans PW, Bootsma HJ.
    Genome-Wide Identification of Genes Essential for the Survival of Streptococcus pneumoniae in Human Saliva.
    PLoS One, Feb 25;9(2):e89541. doi: 10.1371/journal.pone.0089541. Details

  • 2014 de Gouw D, Hermans PW, Bootsma HJ, Zomer A, Heuvelman K, Diavatopoulos DA, Mooi FR.
    Differentially expressed genes in Bordetella pertussis strains belonging to a lineage which recently spread globally.
    PLoS One, Jan 8;9(1):e84523. doi: 10.1371/journal.pone.0084523. Erratum in: PLoS One. 2014;9(1). doi: 10.1371/annotation/1b2cfe52-aaea-4148-aa72-a74c78550192. Details

  • 2014 Kopit LM, Kim EB, Siezen RJ, Harris LJ, Marco ML.
    Safety of the Surrogate Microorganism Enterococcus faecium NRRL B-2354 for Use in Thermal Process Validation.
    Appl Environ Microbiol, Mar;80(6):1899-909. doi: 10.1128/AEM.03859-13. Details

  • 2014 Ferrando ML, van Baarlen P, Orrù G, Piga R, Bongers RS, Wels M, De Greeff A, Smith HE, Wells JM.
    Carbohydrate Availability Regulates Virulence Gene Expression in Streptococcus suis.
    PLoS One, Mar 18;9(3):e89334. doi: 10.1371/journal.pone.0089334. Details

  • 2014 Bottacini F, O'Connell Motherway M, Kuczynski J, O'Connell KJ, Serafini F, Duranti S, Milani C, Turroni F, Lugli GA, Zomer A, Zhurina D, Riedel C, Ventura M, van Sinderen D.
    Comparative genomics of the Bifidobacterium breve taxon.
    BMC Genomics, Mar 1;15:170. doi: 10.1186/1471-2164-15-170. Details

  • 2014 Schuurmans JM, van Hijum SA, Piet JR, Händel N, Smelt J, Brul S, Ter Kuile BH.
    Effect of growth rate and selection pressure on rates of transfer of an antibiotic resistance plasmid between E. coli strains.
    Plasmid, Mar;72:1-8. doi: 10.1016/j.plasmid.2014.01.002. Details

  • 2014 Fineran PC, Gerritzen MJ, Suárez-Diez M, Künne T, Boekhorst J, van Hijum SA, Staals RH, Brouns SJ.
    Degenerate target sites mediate rapid primed CRISPR adaptation.
    Proc Natl Acad Sci U S A, Apr 22;111(16):E1629-38. doi: 10.1073/pnas.1400071111. Details

  • 2014 de Gouw D, de Jonge MI, Hermans PW, Wessels HJ, Zomer A, Berends A, Pratt C, Berbers GA, Mooi FR, Diavatopoulos DA.
    Proteomics-identified Bvg-activated autotransporters protect against Bordetella pertussis in a mouse model.
    PLoS One, Aug 18;9(8):e105011. doi: 10.1371/journal.pone.0105011. Details

  • 2014 Malik S, Siezen RJ, Renckens B, Vaneechoutte M, Vanderleyden J, Lebeer S.
    Draft Genome Sequence of Lactobacillus plantarum CMPG5300, a Human Vaginal Isolate.
    Genome Announc., Nov 13;2(6). pii: e01149-14. doi: 10.1128/genomeA.01149-14. Details

  • 2014 Mobegi FM, van Hijum SA, Burghout P, Bootsma HJ, de Vries SP, van der Gaast-de Jongh CE, Simonetti E, Langereis JD, Hermans PW, de Jonge MI, Zomer A.
    From microbial gene essentiality to novel antimicrobial drug targets.
    BMC Genomics, Nov 5;15:958. doi: 10.1186/1471-2164-15-958. Details

  • 2014 O'Connell KJ, Motherway MO, Liedtke A, Fitzgerald GF, Paul Ross R, Stanton C, Zomer A, van Sinderen D.
    Transcription of two adjacent carbohydrate utilization gene clusters in Bifidobacterium breve UCC2003 is controlled by LacI- and repressor open reading frame kinase (ROK)-type regulators.
    Appl Environ Microbiol., Jun;80(12):3604-14. Details

  • 2014 Steenenga WT, Mischke M, Lute C, Boekschoten MV, Pruis MG, Lendvai A, Verkade HJ, Boekhorst J, Timmerman HM, Plosch T, Muller M.
    Sexually dimorphic characteristics of the small intestine and colon of prepubescent C57BL/6 mice.
    Biol Sex Differ., Aug 29;5:11. doi: 10.1186/s13293-014-0011-9. Details

  • 2014 Szalowska E, Tesfay HA, van Hijum SA, Kersten S.
    Transcriptomic signatures of peroxisome proliferator-activated receptor α (PPARα) in different mouse liver models identify novel aspects of its biology.
    BMC Genomics, Dec 15;15:1106. doi: 10.1186/1471-2164-15-1106. Details

  • 2014 Wilson CM, Loach D, Lawley B, Bell T, Sims IM, O'Toole PW, Zomer A, Tannock GW.
    Lactobacillus reuteri 100-23 modulates urea hydrolysis in the murine stomach.
    Appl Environ Microbiol., Oct;80(19):6104-13. doi: 10.1128/AEM.01876-14. Details

  • 2014 Short KR, Vissers M, de Kleijn S, Zomer AL, Kedzierska K, Grant E, Reading PC, Hermans PWM, Ferwerda G, Diavatopoulos DA
    Bacterial lypopolysaccharide inhibits influenza virus infiection of human macrophages and the consequent induction of CD8+ T cell immunity
    Journal of Innate Immunity, 6(2), 129-39. doi: 10.1159/000353905 Details

  • 2014 Dijkstra AR, Alkema W, Starrenburg MJ, Hugenholtz J, van Hijum SA, Bron PA.
    Fermentation-induced variation in heat and oxidative stress phenotypes of Lactococcus lactis MG1363 reveals transcriptome signatures for robustness.
    Microb Cell Fact., Nov 4;13:148. doi: 10.1186/s12934-014-0148-6. Details

  • 2014 Zeeuwen PL, Ederveen TH, van der Krieken DA, Niehues H, Boekhorst J, Kezic S, Hanssen DA, Otero ME, van Vlijmen-Willems IM, Rodijk-Olthuis D, Falcone D, van den Bogaard EH, Kamsteeg M, de Koning HD, Zeeuwen-Franssen ME, van Steensel MA, Kleerebezem M, Timmerman HM, van Hijum SA, Schalkwijk J
    Gram-positive anaerobe cocci are underrepresented in the microbiome of filaggrin-deficient human skin
    J Allergy Clin Immunol, 2017 Apr;139(4):1368-71 Details

  • 2013 Touw WG, Bayjanov JR, Overmars L, Backus L, Boekhorst J, Wels M, van Hijum SA.
    Data mining in the Life Sciences with Random Forest: a walk in the park or lost in the jungle?
    Brief Bioinform, May;14(3):315-326. doi: 10.1093/bib/bbs034. Details

  • 2013 Anukam KC, Macklaim JM, Gloor GB, Reid G, Boekhorst J, Renckens B, van Hijum SA, Siezen RJ.
    Genome Sequence of Lactobacillus pentosus KCA1: Vaginal Isolate from a Healthy Premenopausal Woman.
    PLoS One, 8(3):e59239. doi: 10.1371/journal.pone.0059239. Details

  • 2013 Caspers MP, Boekhorst J, Abee T, Siezen RJ, Kort R.
    Complete Genome Sequence of Anoxybacillus flavithermus TNO-09.006, a Thermophilic Sporeformer Associated with a Dairy-Processing Environment.
    Genome Announc, Jan;1(1). pii: e00010-13. doi: 10.1128/genomeA.00010-13. Details

  • 2013 Ainsworth S, Zomer A, de Jager V, Bottacini F, van Hijum SA, Mahony J, van Sinderen D.
    Complete Genome of Lactococcus lactis subsp. cremoris UC509.9, Host for a Model Lactococcal P335 Bacteriophage.
    Genome Announc, Jan;1(1). pii: e00119-12. doi: 10.1128/genomeA.00119-12. Details

  • 2013 Verhagen LM, Zomer A, Maes M, Villalba JA, Del Nogal B, Eleveld M, van Hijum SA, de Waard JH, Hermans PW.
    A predictive signature gene set for discriminating active from latent tuberculosis in Warao Amerindian children.
    BMC Genomics, Feb 1;14:74. doi: 10.1186/1471-2164-14-74. Details

  • 2013 Burghout P, Zomer A, van der Gaast-de Jongh CE, Janssen-Megens EM, Françoijs KJ, Stunnenberg HG, Hermans PW.
    Streptococcus pneumoniae Folate Biosynthesis Responds to Environmental CO2 Levels.
    J Bacteriol, Apr;195(7):1573-1582. doi: 10.1128/JB.01942-12. Details

  • 2013 Short KR, Reading PC, Brown LE, Pedersen J, Gilbertson B, Job ER, Edenborough KM, Habets MN, Zomer A, Hermans PW, Diavatopoulos DA, Wijburg OL.
    Influenza-induced inflammation drives pneumococcal otitis media.
    Infect Immun, Mar;81(3):645-652. doi: 10.1128/IAI.01278-12. Details

  • 2013 de Vries SP, Burghout P, Langereis JD, Zomer A, Hermans PW, Bootsma HJ.
    Genetic requirements for Moraxella catarrhalis growth under iron-limiting conditions.
    Mol Microbiol, Jan;87(1):14-29. doi: 10.1111/mmi.12081. Details

  • 2013 van Hijum SA, Vaughan EE, Vogel RF.
    Application of state-of-art sequencing technologies to indigenous food fermentations.
    Curr Opin Biotechnol, Apr;24(2):178-186. doi: 10.1016/j.copbio.2012.08.004. Details

  • 2013 Gori F, Tringe SG, Folino G, van Hijum SA, Op den Camp HJ, Jetten MS, Marchiori E.
    Differences in sequencing technologies improve the retrieval of anammox bacterial genome from metagenomes.
    BMC Genomics, Jan 16;14:7. doi: 10.1186/1471-2164-14-7. Details

  • 2013 Bayjanov JR, Starrenburg MJ, van der Sijde MR, Siezen RJ, van Hijum SA.
    Genotype-phenotype matching analysis of 38 Lactococcus lactis strains using random forest methods.
    BMC Microbiol, Mar 26;13:68. doi: 10.1186/1471-2180-13-68. Details

  • 2013 Overmars L, Kerkhoven R, Siezen RJ, Francke C.
    MGcV: the microbial genomic context viewer for comparative genome analysis.
    BMC Genomics, Apr 1;14:209. doi: 10.1186/1471-2164-14-209. Details

  • 2013 Langereis JD, Zomer A, Stunnenberg HG, Burghout P, Hermans PW.
    Nontypeable Haemophilus influenzae carbonic anhydrase is important for environmental and intracellular survival.
    J Bacteriol, Jun;195(12):2737-2746. doi: 10.1128/JB.01870-12. Details

  • 2013 van den Bogert B, Erkus O, Boekhorst J, de Goffau M, Smid EJ, Zoetendal EG, Kleerebezem M.
    Diversity of human small intestinal Streptococcus and Veillonella populations.
    FEMS Microbiol Ecol, Aug;85(2):376-388. doi: 10.1111/1574-6941.12127. Details

  • 2013 Dutilh BE, Backus L, Edwards RA, Wels M, Bayjanov JR, van Hijum SA.
    Explaining microbial phenotypes on a genomic scale: GWAS for microbes.
    Brief Funct Genomics, Jul;12(4):366-380. doi: 10.1093/bfgp/elt008. Details

  • 2013 Khayatt BI, Overmars L, Siezen RJ, Francke C.
    Classification of the adenylation and acyl-transferase activity of NRPS and PKS systems using ensembles of substrate specific hidden Markov models.
    PLoS One, Apr 18;8(4):e62136. doi: 10.1371/journal.pone.0062136. Details

  • 2013 Ederveen TH, Overmars L, van Hijum SA.
    Reduce manual curation by combining gene predictions from multiple annotation engines, a case study of start codon prediction.
    PLoS One, May 10;8(5):e63523. doi: 10.1371/journal.pone.0063523. Details

  • 2013 Malik S, Petrova MI, Claes IJ, Verhoeven TL, Busschaert P, Vaneechoutte M, Lievens B, Lambrichts I, Siezen RJ, Balzarini J, Vanderleyden J, Lebeer S.
    The highly autoaggregative and adhesive phenotype of the vaginal Lactobacillus plantarum strain CMPG5300 is sortase dependent.
    Appl Environ Microbiol, Aug;79(15):4576-4585. doi: 10.1128/AEM.00926-13. Details

  • 2013 Ainsworth S, Zomer A, Mahony J, van Sinderen D.
    Lytic Infection of Lactococcus lactis by Bacteriophages Tuc2009 and c2 Triggers Alternative Transcriptional Host Responses.
    Appl Environ Microbiol, Aug;79(16):4786-4798. doi: 10.1128/AEM.01197-13. Details

  • 2013 Dutilh BE, Backus L, van Hijum SA, Tjalsma H.
    Screening metatranscriptomes for toxin genes as functional drivers of human colorectal cancer.
    Best Pract Res Clin Gastroenterol, Feb;27(1):85-99. doi: 10.1016/j.bpg.2013.03.008. Details

  • 2013 Smokvina T, Wels M, Polka J, Chervaux C, Brisse S, Boekhorst J, Vlieg JE, Siezen RJ.
    Lactobacillus paracasei Comparative Genomics: Towards Species Pan-Genome Definition and Exploitation of Diversity.
    PLoS One, Jul 19;8(7):e68731. doi: 10.1371/journal.pone.0068731. Details

  • 2013 Leimena MM, Ramiro-Garcia J, Davids M, van den Bogert B, Smidt H, Smid EJ, Boekhorst J, Zoetendal EG, Schaap PJ, Kleerebezem M.
    A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets.
    BMC Genomics, Aug 2;14:530. doi: 10.1186/1471-2164-14-530. Details

  • 2013 Johnston C, Caymaris S, Zomer A, Bootsma HJ, Prudhomme M, Granadel C, Hermans PW, Polard P, Martin B, Claverys JP.
    Natural Genetic Transformation Generates a Population of Merodiploids in Streptococcus pneumoniae.
    PLoS Genet, Sep;9(9):e1003819.

  • 2013 van Bokhorst-van de Veen H, Smelt MJ, Wels M, van Hijum SA, de Vos P, Kleerebezem M, Bron PA.
    Genotypic adaptations associated with prolonged persistence of Lactobacillus plantarum in the murine digestive tract.
    Biotechnol J, Aug;8(8):895-904.

  • 2013 van den Bogert B, Boekhorst J, Smid EJ, Zoetendal EG, Kleerebezem M.
    Draft Genome Sequence of Veillonella parvula HSIVP1, Isolated from the Human Small Intestine.
    Genome Announc, Dec 5;1(6). pii: e00977-13. doi: 10.1128/genomeA.00977-13. Details

  • 2013 de Stoppelaar SF, Bootsma HJ, Zomer A, Roelofs JJ, Hermans PW, van 't Veer C, van der Poll T.
    Streptococcus pneumoniae Serine Protease HtrA, but Not SFP or PrtA, Is a Major Virulence Factor in Pneumonia.
    PLoS One, Nov 11;8(11):e80062. doi: 10.1371/journal.pone.0080062. Details

  • 2013 Erkus O, de Jager VC, Spus M, van Alen-Boerrigter IJ, van Rijswijck IM, Hazelwood L, Janssen PW, van Hijum SA, Kleerebezem M, Smid EJ.
    Multifactorial diversity sustains microbial community stability.
    ISME J, Nov;7(11):2126-2136. doi: 10.1038/ismej.2013.108. Details

  • 2013 Van den Bogert B, Boekhorst J, Herrmann R, Smid EJ, Zoetendal EG, Kleerebezem M.
    Comparative Genomics Analysis of Streptococcus Isolates from the Human Small Intestine Reveals their Adaptation to a Highly Dynamic Ecosystem.
    PLoS One, Dec 30;8(12):e83418. doi: 10.1371/journal.pone.0083418. Details

  • 2013 van den Bogert B, Boekhorst J, Smid EJ, Zoetendal EG, Kleerebezem M.
    Draft Genome Sequence of Enterococcus sp. Strain HSIEG1, Isolated from the Human Small Intestine.
    Genome Announc, Dec 12;1(6). pii: e01013-13. doi: 10.1128/genomeA.01013-13. Details

  • 2012 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. Details

  • 2012 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. Details

  • 2012 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. Details

  • 2012 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] Details

  • 2012 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. Details

  • 2012 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. Details

  • 2012 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. Details

  • 2012 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. Details

  • 2012 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. Details

  • 2012 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. Details

  • 2012 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. Details

  • 2012 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. Details

  • 2012 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. Details

  • 2012 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. Details

  • 2012 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. Details

  • 2012 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. Details

  • 2012 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. Details

  • 2012 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. Details

  • 2012 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. Details

  • 2012 Rodriguez-Campos S, Schürch AC, Dale J, Lohan AJ, Cunha MV, Botelho A, De Cruz K, Boschiroli ML, Boniotti MB, Pacciarini M, Garcia-Pelayo MC, Romero B, de Juan L, Domínguez L, Gordon SV, van Soolingen D, Loftus B, Berg S, Hewinson RG, Aranaz A, Smith NH.
    European 2--a clonal complex of Mycobacterium bovis dominant in the Iberian Peninsula.
    Infect Genet Evol, Jun;12(4):866-872. Details

  • 2012 Todt TJ, Wels M, Bongers RS, Siezen RS, van Hijum SA, Kleerebezem M.
    Genome-Wide Prediction and Validation of Sigma70 Promoters in Lactobacillus plantarum WCFS1.
    PLoS One, 7(9):e45097. doi: 10.1371/journal.pone.0045097. Details

  • 2012 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. Details

  • 2012 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 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. Details

  • 2012 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. Details

  • 2011 Xiao Y, Francke C, Abee T, Wells-Bennik MH.
    Clostridial spore germination versus bacilli: Genome mining and current insights.
    Food Microbiology, Apr;28(2):266-274. Details

  • 2011 Van Boeijen IK, Francke C, Moezelaar R, Abee T, Zwietering MH.
    Isolation of Highly Heat-Resistant Listeria monocytogenes Variants by Use of a Kinetic Modeling-Based Sampling Scheme.
    Appl Environ Microbiol, Apr;77(8):2617-2624. Details

  • 2011 Wels M, Overmars L, Francke C, Kleerebezem M, Siezen RJ.
    Reconstruction of the regulatory network of Lactobacillus plantarum WCFS1 on basis of correlated gene expression and conserved regulatory motifs.
    Microb Biotechnol, May;4(3):333-344. Details

  • 2011 Kant R, Blom J, Palva A, Siezen RJ, De Vos WM.
    Comparative genomics of Lactobacillus.
    Microb Biotechnol, May;4(3):323-332. Details

  • 2011 Schuerch AC, Kremer K, Kiers A, Boeree MJ, Siezen RJ, Soolingen D.
    Preferential Deletion Events in the Direct Repeat Locus of Mycobacterium tuberculosis.
    J Clin Microbiol, Apr;49(4):1318-1322. Details

  • 2011 Machielsen R, Siezen RJ, van Hijum SA, van Hylckama Vlieg JE.
    Molecular description and industrial potential of Tn6098 conjugative transfer conferring alpha-galactoside metabolism in Lactococcus lactis.
    Appl Environ Microbiol, Jan;77(2):555-563. Details

  • 2011 de Been M, Francke C, Siezen RJ, Abee T.
    Novel sigmaB regulation modules of Gram-positive bacteria involve the use of complex hybrid histidine kinases.
    Microbiology, Jan;157(Pt 1):3-12. Details

  • 2011 Siezen RJ, Bayjanov JR, Felis GE, van der Sijde MR, Starrenburg M, Molenaar D, Wels M, van Hijum SA, van Hylckama Vlieg JE.
    Genome-scale diversity and niche adaptation analysis of Lactococcus lactis by comparative genome hybridization using multi-strain arrays.
    Microb Biotechnol, May;4(3):383-402. Details

  • 2011 Schuerch AC, Kremer K, Warren RM, Hung NV, Zhao Y, Wan K, Boeree MJ, Siezen RJ, Smith NH, van Soolingen D.
    Mutations in the regulatory network underlie the recent clonal expansion of a dominant subclone of the Mycobacterium tuberculosis Beijing genotype.
    Infect Genet Evol, Apr;11(3):587-957. Details

  • 2011 Siezen RJ.
    Microbial sunscreens.
    Microbial Biotechnology, Jan;4(1):1-7. Details

  • 2011 Dutilh BE, Jurgelenaite R, Szklarczyk R, van Hijum SA, Harhangi HR, Schmid M, de Wild B, Françoijs KJ, Stunnenberg HG, Strous M, Jetten MS, Op den Camp HJ, Huynen MA.
    FACIL: Fast and Accurate Genetic Code Inference and Logo.
    Bioinformatics, Jul;27(14):1929-1933 Details

  • 2011 Boekhorst J, Wilson G, Siezen RJ.
    Searching in microbial genomes for encoded small proteins.
    Microb Biotechnol, May;4(3):308-313. Details

  • 2011 Winter T, Winter J, Polak M, Kusch K, Mäder U, Sietmann R, Ehlbeck J, van Hijum S, Weltmann KD, Hecker M, Kusch H.
    Characterization of the global impact of low temperature gas plasma on vegetative microorganisms.
    Proteomics, Sept;11(17):3518-3530. Details

  • 2011 Francke C, Groot Kormelink T, Hagemeijer Y, Overmars L, Sluijter V, Moezelaar R, Siezen RJ.
    Comparative analyses imply that the enigmatic sigma factor 54 is a central controller of the bacterial exterior.
    BMC Genomics, Aug 1;12:385. Details

  • 2011 Siezen RJ, Kleerebezem M.
    The human gut microbiome: are we our enterotypes?
    Microbial Biotechnology, 4(5):550-553. Details

  • 2011 de Jager V, Siezen RJ.
    Single-cell genomics: unravelling the genomes of unculturable microorganisms.
    Microb. Biotechnology, Jul;4(4):431-437. Details

  • 2011 de Souza GA, Arntzen MØ, Fortuin S, Schürch AC, Målen H, McEvoy CR, van Soolingen D, Thiede B, Warren RM, Wiker HG.
    Proteogenomic analysis of polymorphisms and gene annotation divergences in prokaryotes using a clustered mass spectrometry-friendly database.
    Mol Cell Proteomics, Jan;10(1):M110.002527. Details

  • 2011 Medema MH, Blin K, Cimermancic P, de Jager V, Zakrzewski P, Fischbach MA, Weber T, Takano E, Breitling R.
    antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences.
    Nucleic Acids Res, 39(Web Server issue):W339-346. Details

  • 2011 O'Connell Motherway M, Zomer A, Leahy SC, Reunanen J, Bottacini F, Claesson MJ, O'Brien F, Flynn K, Casey PG, Munoz JA, Kearney B, Houston AM, O'Mahony C, Higgins DG, Shanahan F, Palva A, de Vos WM, Fitzgerald GF, Ventura M, O'Toole PW, van Sinderen D.
    Functional genome analysis of Bifidobacterium breve UCC2003 reveals type IVb tight adherence (Tad) pili as an essential and conserved host-colonization factor.
    Proc Natl Acad Sci U S A, 108(27):11217-11222. Details

  • 2011 Pokusaeva K, O'Connell-Motherway M, Zomer A, Macsharry J, Fitzgerald GF, van Sinderen D.
    Cellodextrin utilization by bifidobacterium breve UCC2003.
    Appl Environ Microbiol, Mar;77(5):1681-1690. Details

  • 2011 Zhurina D, Zomer A, Gleinser M, Brancaccio VF, Auchter M, Waidmann MS, Westermann C, van Sinderen D, Riedel CU.
    Complete genome sequence of Bifidobacterium bifidum S17.
    J Bacteriol., 193(1):301-302. Details

  • 2011 Schürch AC, Kremer K, Hendriks AC, Freyee B, McEvoy CR, van Crevel R, Boeree MJ, van Helden P, Warren RM, Siezen RJ, van Soolingen D.
    SNP/RD Typing of Mycobacterium tuberculosis Beijing Strains Reveals Local and Worldwide Disseminated Clonal Complexes.
    PLoS One., 6(12):e28365. Details

  • 2011 Schürch AC, van Soolingen D.
    DNA fingerprinting of Mycobacterium tuberculosis: From phage typing to whole-genome sequencing.
    Infect Genet Evol., [Epub ahead of print] Details

  • 2011 Rodriguez-Campos S, Schürch AC, Dale J, Lohan AJ, Cunha MV, Botelho A, Cruz KD, Boschiroli ML, Boniotti MB, Pacciarini M, Garcia-Pelayo MC, Romero B, de Juan L, Domínguez L, Gordon SV, van Soolingen D, Loftus B, Berg S, Hewinson RG, Aranaz A, Smith NH.
    European 2 - A clonal complex of Mycobacterium bovis dominant in the Iberian Peninsula.
    Infect Genet Evol., [Epub ahead of print] Details

  • 2011 Abee T, Wels M, de Been M, den Besten H.
    From transcriptional landscapes to the identification of biomarkers for robustness.
    Microb Cell Fact, Aug 30;10(Suppl 1):S9. Details

  • 2010 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. Details

  • 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. Details

  • 2010 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. Details

  • 2010 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. Details

  • 2010 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. Details

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

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

  • 2010 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. Details

  • 2010 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. Details

  • 2010 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. Details

  • 2010 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. Details

  • 2010 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. Details

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

  • 2010 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. Details

  • 2010 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. Details

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

  • 2010 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. Details

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

  • 2010 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. Details

  • 2010 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. Details

  • 2010 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. Details

  • 2010 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. Details

  • 2010 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. Details

  • 2009 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. Details

  • 2009 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. Details

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

  • 2009 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. Details

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

  • 2009 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. Details

  • 2009 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. Details

  • 2009 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. Details

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

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

  • 2008 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. Details

  • 2008 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. Details

  • 2008 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. Details

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

  • 2008 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. Details

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

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

  • 2008 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. Details

  • 2008 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. Details

  • 2008 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. Details

  • 2008 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. Details

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

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

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

  • 2008 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. Details

  • 2008 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. Details

  • 2007 Siezen RJ, Renckens B, Boekhorst J.
    Evolution of prokaryotic subtilases: genome-wide analysis reveals novel subfamilies with different catalytic residues.
    Proteins: structure, function and bioinformatics, 67(3):681-694. Details

  • 2007 van Baarlen P, van Belkum A, Thomma BP.
    Disease induction by human microbial pathogens in plant-model systems: potential, problems and prospects.
    Drug Discov Today, Feb;12(3-4):167-173. Details

  • 2007 Siebenga JJ, Vennema H, Renckens B, de Bruin E, van der Veer B, Siezen RJ, Koopmans M.
    Epochal Evolution of GGII 4 Norovirus Capsid Proteins from 1995 to 2006.
    J Virol, Sep;81(18):9932-9941. Details

  • 2007 Serrano LM, Molenaar D, Wels M, Teusink B, Bron PA, de Vos WM, Smid EJ.
    Thioredoxin reductase is a key factor in the oxidative stress response of lactobacillus plantarum WCFS1.
    Microb Cell Fact, Aug 28;6:29. Details

  • 2007 Mols M, de Been M, Zwietering M, Moezelaar R, Abee T.
    Metabolic capacity of Bacillus cereus strains ATCC 14579 and ATCC 10987 interlinked with comparative genomics.
    Environ Microbiol, Dec;9(12):2933-2944. Details

  • 2007 Sturme MH, Francke C, Siezen RJ, de Vos WM, Kleerebezem M.
    Making sense of quorum sensing in lactobacilli: a special focus on Lactobacillus plantarum WCFS1. 
    Microbiology, Dec;153(Pt 12):3939-3947. Details

  • 2007 van der Meer-van Kraaij C, Siezen RJ, Kramer E, Reinders M, Blokzijl H, van der Meer R, Keijer J.
    Dietary modulation and structure prediction of rat mucosal pentraxin (Mptx) protein and loss of function in humans.
    Genes Nutrition, Dec;2(3):275-285. Details

  • 2007 van Baarlen P, van Belkum A, Summerbell RC, Crous PW, Thomma BP.
    Molecular mechanisms of pathogenicity: how do pathogenic microorganisms develop cross-kingdom host jumps?
    FEMS Microbiol Rev, Apr;31(3):239-277. Details

  • 2006 Boekhorst J, Helmer Q, Kleerebezem M, Siezen RJ.
    Comparative analysis of proteins with a mucus-binding domain found exclusively in lactic acid bacteria.
    Microbiology, Jan;152(Pt 1):273-280. Details

  • 2006 van Hylckama Vlieg J, Rademaker J, Bachmann H, Molenaar D, Kelly W, Siezen RJ.
    Natural diversity and adaptive responses of Lactococcus lactis.
    Current Opinion in Biotechnology, Apr;17(2):183-190. Details

  • 2006 Notebaart RA, van Enckevort FJH, Francke C, Siezen RJ, Teusink B.
    Accelerating the reconstruction of genome-scale metabolic networks.
    BMC Bioinformatics, Jun 13;7:296. Details

  • 2006 Siezen RJ, Boekhorst J, Muscariello L, Molenaar D, Renckens B, Kleerebezem M.
    Lactobacillus plantarum gene clusters encoding putative cell-surface protein complexes for carbohydrate utilization are conserved in specific gram-positive bacteria.
    BMC Genomics, May 24;7:126. Details

  • 2006

    Teusink B, Smid E.


    Modelling strategies for the industrial exploitation of lactic acid bacteria.
    Nat. Rev. Microbiol, Jan;4(1):46-56. Details

  • 2006 de Vries MC, Siezen RJ, Wijman JG, Zhao Y, Kleerebezem M, de Vos WM, Vaughan EE.
    Comparative and functional analysis of the rRNA-operons and their tRNA gene complement in different lactic acid bacteria.
    System Appl Microbiology, Jul;29(5):358-367. Details

  • 2006 Wels M, Francke C, Kerkhoven R, Kleerebezem M, Siezen RJ.
    Predicting cis-acting elements of Lactobacillus plantarum by comparative genomics with different taxonomic subgroups.
    Nucleic Acids Res, Apr 13;34(7):1947-1958. Details

  • 2006 Liu M, Siezen RJ.
    Comparative genomics of flavour-forming pathways in lactic acid bacteria.
    Australian Journal of Dairy Technology, 61(2):61-68. Details

  • 2006 de Been M, Francke C, Moezelaar R, Abee T, Siezen RJ.
    Comparative analysis of two-component signal transduction systems of Bacillus cereus, Bacillus thuringiensis and bacillus anthracis.
    Microbiology, Oct;152(Pt 10):3035-3048. Details

  • 2006 Boekhorst J, Wels M, Kleerebezem M, Siezen RJ.
    The predicted secretome of Lactobacillus plantarum WCFS1 sheds light om interactions with its environment.
    Microbiology, Nov;152(Pt 11):3175-3183. Details

  • 2006 Deutscher J, Francke C, Postma PW.
    How phosphotransferase system-related protein phosphorylation regulates carbohydrate metabolism in bacteria.
    Micriobiol Mol Biol Rev, Dec;70(4):939-1031. Details

  • 2006 Teusink B, Wiersma A, Molenaar D, Francke C, de Vos WM, Siezen RJ, Smid EJ.
    Analysis of growth of lacobacillus plantarum WCFS1 on a complex medium using a genome-scale metabolic model.
    J Biol Chem, Dec 29;281(52):40041-40048. Details

  • 2005 Boekhorst J, de Been MW, Kleerebezem M, Siezen RJ.
    Genome-Wide Detection and Analysis of Cell Waal-Bound Proteins with LPxTG-Like Sorting Motifs.
    J. Bacteriol, Jul;187(14):4928-4934. Details

  • 2005 Francke C, Siezen RJ, Teusink B.
    Reconstructing the metabolic network of a bacterium from its genome.
    Trends Microbiol, Nov;13(11):550-558. Details

  • 2005 van Kranenburg R, Golic N, Bongers R, Leer RJ, de Vos WM, Siezen RJ, Kleerebezem M.
    Functional Analysis of Three Plasmids from Lactobacillus plantarum.
    Appl Environ Microbiol, Mar;71(3):1223-1230. Details

  • 2005 Liu M, van Enckevort FH, Siezen RJ.
    Genome update: lactic acid bacteria genome sequencing is booming.
    Microbiology, Dec;151(Pt 12):3811-3814. Details

  • 2005 Molenaar D, Bringel F, Schuren FH, de Vos WM, Siezen RJ, Kleerebezem M.
    Exploring Lactobacillus Plantarum genome diversity by using microarrays.
    J Bacteriol, Sep;187(17):6119-6127. Details

  • 2005 Siezen RJ, Renckens B, van Swam I, Peters S, van Kranenburg R, Kleerebezem M, de Vos WM.
    Complete Sequences of Four Plasmids of Lactococcus lactis subsp. cremoris SK11 Reveal Extensive Adaptation to the Dairy Environment.
    Appl Environ Microbiol, Dec;71(12):8371-8382. Details

  • 2005 Smid EJ, van Enckevort FJ, Wegkamp A, Boekhorst J, Molenaar D, Hugenholtz J, Siezen RJ, Teusink B.
    Metabolic models for rational improvement of lactic acid bacteria as cell factories.
    J Appl Microbiol, 98(6):1326-1331. Details

  • 2005 Smid EJ, Molenaar D, Hugenholtz J, de Vos WM, Teusink B.
    Functional ingredients production: application of global metabolic models.
    Curr Opin Biotechnol, Apr;16(2):190-197. Details

  • 2005 Teusink B, van Enckevort FH, Francke C, Wiersma A, Wegkamp A, Smid EJ, Siezen RJ.
    In silico reconstruction of the metabolic pathways of Lactobacillus plantarum: comparing predictions of nutrient requirements with those from growth experiments.
    Appl Environ Microbiol, Nov;71(11):7253-7262. Details

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

  • 2004 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. Details

  • 2004 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. Details

  • 2004 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. Details

  • 2004 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. Details

  • 2003 Kleerebezem M, Boekhorst J, van Kranenburg R, Molenaar D, Kuipers OP, Leer R, Tarchini R, Peters SA, Sandbrink HM, Fiers MW, Stiekema W, Lankhorst RM, Bron PA, Hoffer SM, Groot MN, Kerkhoven R, de Vries M, Ursing B, de Vos WM, Siezen RJ.
    Complete genome sequence of Lactobacillus plantarum WCFS1.
    Proc Natl Acad Sci USA , Feb 18;100(4):1990-1995. Details

  • 2003 Ventura M, Canchaya C, Kleerebezem M, de Vos WM, Siezen RJ, Brüssow H.
    The prophage sequences of Lactobacillus plantarum strain WCFS1.
    Virology , Nov 25;316(2):245-255. Details

  • 2002 Fernandez M, Kleerebezem M, Kuipers OP, Siezen RJ, van Kranenburg R.
    Regulation of the metC-cysK operon, involved in sulfur metabolism in Lactococcus lactis.
    J Bacteriol , Jan;184(1):82-90. Details

  • 2002 Klaenhammer T, Altermann E, Arigoni F, Bolotin A, Breidt F, Broadbent J, Cano R, Chaillou S, Deutscher J, Gasson M, van de Guchte M, Guzzo J, Hartke A, Hawkins T, Hols P, Hutkins R, Kleerebezem M, Kok J, Kuipers O, Lubbers M, Maguin E, McKay L, Mills D, Nauta A, Overbeek R, Pel H, Pridmore D, Saier M, van Sinderen D, Sorokin A, Steele J, O’Sullivan D, de Vos W, Weimer B, Zagorec M, Siezen R.
    Discovering lactic acid bacteria by genomics.
    Antonie van Leeuwenhoek , Aug;82(1-4):29-58. Details

  • 2002 Kluskens LD, Voorhorst WG, Siezen RJ, Schwerdtfeger RM, Antranikian G, Van Der Oost J, De Vos WM.
    Molecular characterization of fervidolysin, a subtilisin-like serine protease from the thermophilic bacterium Fervidobacterium pennivorans.
    Extremophiles, Jun;6(3):185-194. Details

  • 2002 van Kranenburg R, Kleerebezem M, van Hylckama Vlieg J, Ursing BM, Smit BA, Ayad E, Smit G, Siezen RJ.
    Flavour formation from amino acids by lactic acid bacteria: predictions from genome sequence analysis.
    Int. Dairy Journal , 12(2-3), 111-121. Details

  • 2002 Siezen RJ.
    Genomics versterkt biotechnologie.
    Interview in Zuivelzicht, 94, 16-17.

  • 2001 Gey Van Pittius NC, Gamieldien J, Hide W, Brown GD, Siezen RJ, Beyers AD.
    The ESAT-6 gene cluster of Mycobacterium tuberculosis and other high G+C gram-positive bacteria.
    Genome Biology, 2(10):RESEARCH0044. Details

  • 2001 Ursing BM, van Enckevort FH, Leunissen JA, Siezen RJ.
    EXProt - a database for EXPerimentally verified Protein functions.
    In Silico Biol, (1):1-4. Details

  • 2001 de Vos WM, Voorhorst WG, Dijkgraaf M, Kluskens LD, Van der Oost J, Siezen RJ.
    Purification, characterization, and molecular modelling of pyrolysin and other extracellular thermostable serine proteases from hyperthermophilic microorganisms.
    Methods in Enzymology , 330:383-393. Details

  • 2001 Siezen RJ.
    Bioinformatica voorspelt bacterie potentie voor voedingsindustrie.
    B for You, 16:14-15.

  • 2000 van Enckevort FH, Pepels PP, Leunissen JA, Martens GJ, Wendelaar Bonga SE, Balm PH.
    Oreochromis mossambicus (tilapia) corticotropin-releasing hormone (CRH): cDNA sequence and bioactivity.
    J Neuroendocrinol, Feb;12(2):177-186. Details

  • 2000 Fernandez L, Beerthuyzen MM, Brown J, Siezen RJ, Coolbear T, Holland R, Kuipers OP.
    Cloning, characterization, controlled overexpression, and inactivation of the major tributyrin esterase gene of Lactococcus lactis.
    Appl Environ Microbiol, Apr;66(4):1360-1368. Details

  • 2000 Smit G, Verheul A, van Kranenburg R, Ayad, E, Siezen RJ, Engels WJ.
    Cheese flavour development by enzymatic conversions of peptides and amino acids.
    Food Research International , 33(3-4):153-160. Details

  • 2000 Smit G, Siezen RJ, Verheul A, Engels WJ.
    Control, acceleration and diversification of cheese flavour development by enzymatic conversion of amino acids.
    CREAL 98. Paris:Arilait Recherches, ISBN 2-912384-04-4. pp. 60-67.

  • 1999 Siezen RJ.
    Multi-domain, cell-envelope proteinases of lactic acid bacteria.
    Antonie van Leeuwenhoek , Jul-Nov;76(1-4):139-155. Details

  • 1999 van Kraaij C, de Vos WM, Siezen RJ, Kuipers OP.
    Lantibiotics: biosynthesis, mode of action and applications.
    Natural Products Report, Oct;16(5):575-587. Details