Publications in international journals 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., 2013 , PDF


  • 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., 2013 , PDF


  • Willems P, Wanschers BF, Esseling J, Szklarczyk R, Kudla U, Duarte I, Forkink M, Nooteboom M, Swarts H, Gloerich J, Nijtmans L, Koopman W, Huynen MA.
    BOLA1 Is an Aerobic Protein That Prevents Mitochondrial Morphology Changes Induced by Glutathione Depletion.
    Antioxid Redox Signal, Jan 10;18(2):129-38. doi: 10.1089/ars.2011.4253., 2013 , PDF


  • van de Vossenberg J, Woebken D, Maalcke WJ, Wessels HJ, Dutilh BE, Kartal B, Janssen-Megens EM, Roeselers G, Yan J, Speth D, Gloerich J, Geerts W, van der Biezen E, Pluk W, Francoijs KJ, Russ L, Lam P, Malfatti SA, Tringe SG, Haaijer SC, Op den Camp HJ, Stunnenberg HG, Amann R, Kuypers MM, Jetten MS.
    The metagenome of the marine anammox bacterium 'Candidatus Scalindua profunda' illustrates the versatility of this globally important nitrogen cycle bacterium.
    Environ Microbiol, May;15(5):1275-1289. doi: 10.1111/j.1462-2920.2012.02774.x., 2013 , PDF


  • Khan M, Ajmal M, Micheal S, Azam M, Hussain A, Shahzad A, Venselaar H, Bokhari H, de Wijs I, Hoefsloot L, Waheed N, Collin R, den Hollander A, Qamar R, Cremers F.
    Homozygosity mapping identifies genetic defects in four consanguineous families with retinal dystrophy from Pakistan.
    Clin Genet, Sep;84(3):290-3. doi: 10.1111/cge.12039., 2013 , PDF


  • 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., 2013 , PDF


  • 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., 2013 , PDF


  • Fleuren WW, Toonen EJ, Verhoeven S, Frijters R, Hulsen T, Rullmann T, van Schaik R, de Vlieg J, Alkema W.
    Identification of new biomarker candidates for glucocorticoid induced insulin resistance using literature mining.
    BioData Min, Feb 4;6(1):2. doi: 10.1186/1756-0381-6-2., 2013 , PDF


  • 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., 2013 , PDF


  • 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., 2013 , PDF


  • 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., 2013 , PDF


  • 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., 2013 , PDF


  • Szklarczyk R, Wanschers BF, Nijtmans LG, Rodenburg RJ, Zschocke J, Dikow N, van den Brand MA, Hendriks-Franssen MG, Gilissen C, Veltman JA, Nooteboom M, Koopman WJ, Willems PH, Smeitink JA, Huynen MA, van den Heuvel LP.
    A mutation in the FAM36A gene, the human ortholog of COX20, impairs cytochrome c oxidase assembly and is associated with ataxia and muscle hypotonia.
    Hum Mol Genet, Feb 15;22(4):656-667. doi: 10.1093/hmg/dds473., 2013 , PDF


  • 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., 2013 , PDF


  • Huynen MA, Duarte I, Szklarczyk R.
    Loss, replacement and gain of proteins at the origin of the mitochondria.
    Biochim Biophys Acta, Feb;1827(2):224-231. doi: 10.1016/j.bbabio.2012.08.001., 2013 , PDF


  • Rossell S, Huynen MA, Notebaart RA.
    Inferring metabolic States in uncharacterized environments using gene-expression measurements.
    PLoS Comput Biol, Mar;9(3):e1002988. doi: 10.1371/journal.pcbi.1002988., 2013 , PDF


  • van Dam TJ, Wheway G, Slaats GG, Huynen MA, Giles RH.
    The SYSCILIA gold standard (SCGSv1) of known ciliary components and its applications within a systems biology consortium.
    Cilia, May 31;2(1):7. doi: 10.1186/2046-2530-2-7., 2013 , PDF


  • van de Ven JP, Nilsson SC, Tan PL, Buitendijk GH, Ristau T, Mohlin FC, Nabuurs SB, Schoenmaker-Koller FE, Smailhodzic D, Campochiaro PA, Zack DJ, Duvvari MR, Bakker B, Paun CC, Boon CJ, Uitterlinden AG, Liakopoulos S, Klevering BJ, Fauser S, Daha MR, Katsanis N, Klaver CC, Blom AM, Hoyng CB, den Hollander AI.
    A functional variant in the CFI gene confers a high risk of age-related macular degeneration.
    Nat Genet, Jul;45(7):813-7. doi: 10.1038/ng.2640., 2013 , PDF


  • Lu X, Kensche PR, Huynen MA, Notebaart RA.
    Genome evolution predicts genetic interactions in protein complexes and reveals cancer drug targets.
    Nat Commun, Jul 11;4:2124. doi: 10.1038/ncomms3124., 2013 , PDF


  • Lounnas V, Ritschel T, Kelder J, McGuire R, Bywater RP, Foloppe N.
    Current progress in Structure-Based Rational Drug Design marks a new mindset in drug discovery.
    Computational and Structural Biotechnology Journal, Feb:5(6), http://dx.doi.org/10.5936/csbj.201302011., 2013 , PDF


  • 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., 2013 , PDF


  • Roosing S, van den Born LI, Hoyng CB, Thiadens AA, de Baere E, Collin RW, Koenekoop RK, Leroy BP, van Moll-Ramirez N, Venselaar H, Riemslag FC, Cremers FP, Klaver CC, den Hollander AI.
    Maternal uniparental isodisomy of chromosome 6 reveals a TULP1 mutation as a novel cause of cone dysfunction.
    Ophthalmology, Jun;120(6):1239-1246. doi: 10.1016/j.ophtha.2012.12.005., 2013 , PDF


  • Fleuren WW, Linssen MM, Toonen EJ, van der Zon GC, Guigas B, de Vlieg J, Dokter WH, Ouwens DM, Alkema W.
    Prednisolone induces the Wnt signalling pathway in 3T3-L1 adipocytes.
    Arch Physiol Biochem, May;119(2):52-64. doi: 10.3109/13813455.2013.774022., 2013 , PDF


  • 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., 2013 , PDF


  • Soysa R, Venselaar H, Poston J, Ullman B, Hasne MP.
    Structural model of a putrescine-cadaverine permease from Trypanosoma cruzi predicts residues vital for transport and ligand binding.
    Biochem J, Jun 15;452(3):423-432. doi: 10.1042/BJ20130350., 2013 , PDF


  • 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., 2013 , PDF


  • Mokili JL, Dutilh BE, Lim YW, Schneider BS, Taylor T, Haynes MR, Metzgar D, Myers CA, Blair PJ, Nosrat B, Wolfe ND, Rohwer F.
    Identification of a novel human papillomavirus by metagenomic analysis of samples from patients with febrile respiratory illness.
    PLoS One, 8(3):e58404. doi: 10.1371/journal.pone.0058404., 2013 , PDF


  • Nielsen FG, Kooyman M, Kensche P, Marks H, Stunnenberg H, Huynen M.
    The PinkThing for analysing ChIP profiling data in their genomic context.
    BMC Res Notes, Apr 4;6:133. doi: 10.1186/1756-0500-6-133., 2013 , PDF


  • 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., 2013 , PDF


  • van Dam TJ, Townsend MJ, Turk M, Schlessinger A, Sali A, Field MC, Huynen MA.
    Evolution of modular intraflagellar transport from a coatomer-like progenitor.
    Proc Natl Acad Sci U S A, Apr 23;110(17):6943-6948. doi: 10.1073/pnas.1221011110., 2013 , PDF


  • van Bon BW, Oortveld MA, Nijtmans LG, Fenckova M, Nijhof B, Besseling J, Vos M, Kramer JM, de Leeuw N, Castells-Nobau A, Asztalos L, Viragh E, Ruiter M, Hofmann F, Eshuis L, Collavin L, Huynen MA, Asztalos Z, Verstreken P, Rodenburg RJ, Smeitink JA, de Vries BB, Schenck A.
    CEP89 is required for mitochondrial metabolism and neuronal function in man and fly.
    Hum Mol Genet, Aug 1;22(15):3138-3151. doi: 10.1093/hmg/ddt170., 2013 , PDF


  • Jonckheere AI, Renkema GH, Bras M, van den Heuvel LP, Hoischen A, Gilissen C, Nabuurs SB, Huynen MA, de Vries MC, Smeitink JA, Rodenburg RJ.
    A complex V ATP5A1 defect causes fatal neonatal mitochondrial encephalopathy.
    Brain, May;136(Pt 5):1544-1554. doi: 10.1093/brain/awt086., 2013 , PDF


  • Aerts D, Verhaeghe T, Joosten HJ, Vriend G, Soetaert W, Desmet T.
    Consensus engineering of sucrose phosphorylase: The outcome reflects the sequence input.
    Biotechnol Bioeng, Oct;110(10):2563-2572. doi: 10.1002/bit.24940., 2013 , PDF


  • 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., 2013 , PDF


  • 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., 2013 , PDF


  • 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., 2013 , PDF


  • Vos M, te Beek TA, van Driel MA, Huynen MA, Eyre-Walker A, van Passel MW.
    ODoSE: a webserver for genome-wide calculation of adaptive divergence in prokaryotes.
    PLoS One, May 6;8(5):e62447. doi: 10.1371/journal.pone.0062447., 2013 , PDF


  • 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., 2013 , PDF


  • 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., 2013 , PDF


  • 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., 2013 , PDF


  • Jimenez RC, Albar JP, Bhak J, Blatter MC, Blicher T, Brazas MD, Brooksbank C, Budd A, De Las Rivas J, Dreyer J, van Driel MA, Dunn MJ, Fernandes PL, van Gelder CW, Hermjakob H, Ioannidis V, Judge DP, Kahlem P, Korpelainen E, Kraus HJ, Loveland J, Mayer C, McDowall J, Moran F, Mulder N, Nyronen T, Rother K, Salazar GA, Schneider R, Via A, Villaveces JM, Yu P, Schneider MV, Attwood TK, Corpas M.
    iAnn: an event sharing platform for the life sciences.
    Bioinformatics, Aug 1;29(15):1919-1921., 2013 , PDF


  • Gregor A, Oti M, Kouwenhoven EN, Hoyer J, Sticht H, Ekici AB, Kjaergaard S, Rauch A, Stunnenberg HG, Uebe S, Vasileiou G, Reis A, Zhou H, Zweier C.
    De Novo Mutations in the Genome Organizer CTCF Cause Intellectual Disability.
    Am J Hum Genet, Jul 11;93(1):124-131. doi: 10.1016/j.ajhg.2013.05.007., 2013 , PDF


  • de Voer RM, Geurts van Kessel A, Weren RD, Ligtenberg MJ, Smeets D, Fu L, Vreede L, Kamping EJ, Verwiel ET, Hahn MM, Ariaans M, Spruijt L, van Essen T, Houge G, Schackert HK, Sheng JQ, Venselaar H, van Ravenswaaij-Arts CM, van Krieken JH, Hoogerbrugge N, Kuiper RP.
    Germline Mutations in the Spindle Assembly Checkpoint Genes BUB1 and BUB3 Are Risk Factors for Colorectal Cancer.
    Gastroenterology, Sep;145(3):544-547. doi: 10.1053/j.gastro.2013.06.001., 2013 , PDF


  • 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., 2013 , PDF


  • Smeulders MJ, Pol A, Venselaar H, Barends TR, Hermans J, Jetten MS, Op den Camp HJ.
    Bacterial CS2 Hydrolases from Acidithiobacillus thiooxidans Strains Are Homologous to the Archaeal Catenane CS2 Hydrolase.
    J Bacteriol, Sep;195(18):4046-4056. doi: 10.1128/JB.00627-13., 2013 , PDF


  • 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., 2013 , PDF


  • 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., 2013 , PDF


  • 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


  • Barandun LJ, Immekus F, Kohler PC, Ritschel T, Heine A, Orlando P, Klebe G, Diederich F.
    High-affinity inhibitors of Zymomonas mobilis tRNA-guanine transglycosylase through convergent optimization.
    Acta Crystallogr D Biol Crystallogr, Sep 1;69(Pt 9):1798-1807. doi: 10.1107/S0907444913014509., 2013 , PDF


  • 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., 2013 , PDF


  • Venselaar H, Camilli F, Gholizadeh S, Snelleman M, Brunner HG, Vriend G.
    Status quo of annotation of human disease variants.
    BMC Bioinformatics, Dec 4;14:352. doi: 10.1186/1471-2105-14-352., 2013 , PDF


  • Silva GG, Dutilh BE, Matthews TD, Elkins K, Schmieder R, Dinsdale EA, Edwards RA.
    Combining de novo and reference-guided assembly with scaffold_builder.
    Source Code Biol Med, Nov 22;8(1):23., 2013 , PDF


  • Kim HJ, Won HH, Park KJ, Hong SH, Ki CS, Cho SS, Venselaar H, Vriend G, Kim JW.
    SNP Linkage Analysis and Whole Exome Sequencing Identify a Novel POU4F3 Mutation in Autosomal Dominant Late-Onset Nonsyndromic Hearing Loss (DFNA15).
    PLoS One, Nov 18;8(11):e79063. doi: 10.1371/journal.pone.0079063., 2013 , PDF


  • 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., 2013 , PDF


  • Oortveld MA, Keerthikumar S, Oti M, Nijhof B, Fernandes AC, Kochinke K, Castells-Nobau A, van Engelen E, Ellenkamp T, Eshuis L, Galy A, van Bokhoven H, Habermann B, Brunner HG, Zweier C, Verstreken P, Huynen MA, Schenck A.
    Human intellectual disability genes form conserved functional modules in Drosophila.
    PLoS Genet, Oct;9(10):e1003911. doi: 10.1371/journal.pgen.1003911., 2013 , PDF


  • Roscioli T, Elakis G, Cox TC, Moon DJ, Venselaar H, Turner AM, Le T, Hackett E, Haan E, Colley A, Mowat D, Worgan L, Kirk EP, Sachdev R, Thompson E, Gabbett M, McGaughran J, Gibson K, Gattas M, Freckmann ML, Dixon J, Hoefsloot L, Field M, Hackett A, Kamien B, Edwards M, Adès LC, Collins FA, Wilson MJ, Savarirayan R, Tan TY, Amor DJ, McGillivray G, White SM, Glass IA, David DJ, Anderson PJ, Gianoutsos M, Buckley MF.
    Genotype and clinical care correlations in craniosynostosis: findings from a cohort of 630 Australian and New Zealand patients.
    Am J Med Genet C Semin Med Genet, Nov;163(4):259-270. doi: 10.1002/ajmg.c.31378., 2013 , PDF


  • Ljosa V, Caie PD, Ter Horst R, Sokolnicki KL, Jenkins EL, Daya S, Roberts ME, Jones TR, Singh S, Genovesio A, Clemons PA, Carragher NO, Carpenter AE.
    Comparison of methods for image-based profiling of cellular morphological responses to small-molecule treatment.
    J Biomol Screen, Dec;18(10):1321-1329. doi: 10.1177/1087057113503553., 2013 , PDF


  • Swarts HG, Weigand KM, Venselaar H, van den Maagdenberg AM, Russel FG, Koenderink JB.
    Familial hemiplegic migraine mutations affect Na,K-ATPase domain interactions.
    Biochim Biophys Acta, Dec;1832(12):2173-2179. doi: 10.1016/j.bbadis.2013.08.003., 2013 , PDF


  • Ballouz S, Liu JY, George RA, Bains N, Liu A, Oti M, Gaeta B, Fatkin D, Wouters MA.
    Gentrepid V2.0: a web server for candidate disease gene prediction.
    BMC Bioinformatics, Aug 16;14:249. doi: 10.1186/1471-2105-14-249., 2013 , PDF


  • 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., 2013 , PDF


  • Ferrè S, de Baaij JH, Ferreira P, Germann R, de Klerk JB, Lavrijsen M, van Zeeland F, Venselaar H, Kluijtmans LA, Hoenderop JG, Bindels RJ.
    Mutations in PCBD1 Cause Hypomagnesemia and Renal Magnesium Wasting.
    J Am Soc Nephrol, Nov 7. [Epub ahead of print], 2013


  • Via A, Blicher T, Bongcam-Rudloff E, Brazas MD, Brooksbank C, Budd A, De Las Rivas J, Dreyer J, Fernandes PL, van Gelder C, Jacob J, Jimenez RC, Loveland J, Moran F, Mulder N, Nyrönen T, Rother K, Schneider MV, Attwood TK.
    Best practices in bioinformatics training for life scientists.
    Brief Bioinform, Sep;14(5):528-537. doi: 10.1093/bib/bbt043., 2013 , PDF


  • 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., 2013 , PDF


  • Tucker EJ, Wanschers BF, Szklarczyk R, Mountford HS, Wijeyeratne XW, van den Brand MA, Leenders AM, Rodenburg RJ, Relji? B, Compton AG, Frazier AE, Bruno DL, Christodoulou J, Endo H, Ryan MT, Nijtmans LG, Huynen MA, Thorburn DR.
    Mutations in the UQCC1-Interacting Protein, UQCC2, Cause Human Complex III Deficiency Associated with Perturbed Cytochrome b Protein Expression.
    PLoS Genet, Dec;9(12):e1004034. doi: 10.1371/journal.pgen.1004034., 2013 , PDF


  • 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., 2013 , PDF