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Genetic Loci Associated With Fluoride Resistance in Streptococcus mutans.

Liao Y, Yang J, Brandt BW, Li J, Crielaard W, van Loveren C, Deng DM.

Front Microbiol. 2018 Dec 11;9:3093. doi: 10.3389/fmicb.2018.03093. eCollection 2018.


Microcosm biofilms cultured from different oral niches in periodontitis patients.

Cieplik F, Zaura E, Brandt BW, Buijs MJ, Buchalla W, Crielaard W, Laine ML, Deng DM, Exterkate RAM.

J Oral Microbiol. 2018 Nov 27;11(1):1551596. doi: 10.1080/20022727.2018.1551596. eCollection 2019.


The efficacy of whole human genome capture on ancient dental calculus and dentin.

Ziesemer KA, Ramos-Madrigal J, Mann AE, Brandt BW, Sankaranarayanan K, Ozga AT, Hoogland M, Hofman CA, Salazar-García DC, Frohlich B, Milner GR, Stone AC, Aldenderfer M, Lewis CM Jr, Hofman CL, Warinner C, Schroeder H.

Am J Phys Anthropol. 2019 Mar;168(3):496-509. doi: 10.1002/ajpa.23763. Epub 2018 Dec 26.


Limited added value of fungal ITS amplicon sequencing in the study of bovine abortion.

Vidal S, Brandt BW, Dettwiler M, Abril C, Bressan J, Greub G, Frey CF, Perreten V, Rodriguez-Campos S.

Heliyon. 2018 Nov 5;4(11):e00915. doi: 10.1016/j.heliyon.2018.e00915. eCollection 2018 Nov.


Subgingival microbiome of rheumatoid arthritis patients in relation to their disease status and periodontal health.

Beyer K, Zaura E, Brandt BW, Buijs MJ, Brun JG, Crielaard W, Bolstad AI.

PLoS One. 2018 Sep 19;13(9):e0202278. doi: 10.1371/journal.pone.0202278. eCollection 2018.


Subsurface landfill leachate contamination affects microbial metabolic potential and gene expression in the Banisveld aquifer.

Tas N, Brandt BW, Braster M, van Breukelen BM, Röling WFM.

FEMS Microbiol Ecol. 2018 Oct 1;94(10). doi: 10.1093/femsec/fiy156.


Efficacy of probiotics: clinical and microbial parameters of halitosis.

Georgiou AC, Laine ML, Deng DM, Brandt BW, van Loveren C, Dereka X.

J Breath Res. 2018 Aug 21;12(4):046010. doi: 10.1088/1752-7163/aacf49.


Microbiomes associated with bovine periodontitis and oral health.

Borsanelli AC, Lappin DF, Viora L, Bennett D, Dutra IS, Brandt BW, Riggio MP.

Vet Microbiol. 2018 May;218:1-6. doi: 10.1016/j.vetmic.2018.03.016. Epub 2018 Mar 16.


Fungal mitochondrial oxygen consumption induces the growth of strict anaerobic bacteria.

Lambooij JM, Hoogenkamp MA, Brandt BW, Janus MM, Krom BP.

Fungal Genet Biol. 2017 Dec;109:1-6. doi: 10.1016/j.fgb.2017.10.001. Epub 2017 Oct 5.


The Fitness Cost of Fluoride Resistance for Different Streptococcus mutans Strains in Biofilms.

Cai Y, Liao Y, Brandt BW, Wei X, Liu H, Crielaard W, Van Loveren C, Deng DM.

Front Microbiol. 2017 Aug 28;8:1630. doi: 10.3389/fmicb.2017.01630. eCollection 2017.


Fluoride resistance in Streptococcus mutans: a mini review.

Liao Y, Brandt BW, Li J, Crielaard W, Van Loveren C, Deng DM.

J Oral Microbiol. 2017 Jul 6;9(1):1344509. doi: 10.1080/20002297.2017.1344509. eCollection 2017. Review.


Effect of erythritol on microbial ecology of in vitro gingivitis biofilms.

Janus MM, Volgenant CMC, Brandt BW, Buijs MJ, Keijser BJF, Crielaard W, Zaura E, Krom BP.

J Oral Microbiol. 2017 Jun 22;9(1):1337477. doi: 10.1080/20002297.2017.1337477. eCollection 2017.


Candida albicans alters the bacterial microbiome of early in vitro oral biofilms.

Janus MM, Crielaard W, Volgenant CM, van der Veen MH, Brandt BW, Krom BP.

J Oral Microbiol. 2017 Jan 23;9(1):1270613. doi: 10.1080/20002297.2016.1270613. eCollection 2017.


Both Intrinsic Substrate Preference and Network Context Contribute to Substrate Selection of Classical Tyrosine Phosphatases.

Palma A, Tinti M, Paoluzi S, Santonico E, Brandt BW, Hooft van Huijsduijnen R, Masch A, Heringa J, Schutkowski M, Castagnoli L, Cesareni G.

J Biol Chem. 2017 Mar 24;292(12):4942-4952. doi: 10.1074/jbc.M116.757518. Epub 2017 Feb 3.


Red fluorescence of dental plaque in children -A cross-sectional study.

Volgenant CM, Zaura E, Brandt BW, Buijs MJ, Tellez M, Malik G, Ismail AI, Ten Cate JM, van der Veen MH.

J Dent. 2017 Mar;58:40-47. doi: 10.1016/j.jdent.2017.01.007. Epub 2017 Jan 20.


On the ecosystemic network of saliva in healthy young adults.

Zaura E, Brandt BW, Prodan A, Teixeira de Mattos MJ, Imangaliyev S, Kool J, Buijs MJ, Jagers FL, Hennequin-Hoenderdos NL, Slot DE, Nicu EA, Lagerweij MD, Janus MM, Fernandez-Gutierrez MM, Levin E, Krom BP, Brand HS, Veerman EC, Kleerebezem M, Loos BG, van der Weijden GA, Crielaard W, Keijser BJ.

ISME J. 2017 May;11(5):1218-1231. doi: 10.1038/ismej.2016.199. Epub 2017 Jan 10.


The mycobiome of root canal infections is correlated to the bacteriome.

Persoon IF, Buijs MJ, Özok AR, Crielaard W, Krom BP, Zaura E, Brandt BW.

Clin Oral Investig. 2017 Jun;21(5):1871-1881. doi: 10.1007/s00784-016-1980-3. Epub 2016 Oct 22.


Integrating Candida albicans metabolism with biofilm heterogeneity by transcriptome mapping.

Rajendran R, May A, Sherry L, Kean R, Williams C, Jones BL, Burgess KV, Heringa J, Abeln S, Brandt BW, Munro CA, Ramage G.

Sci Rep. 2016 Oct 21;6:35436. doi: 10.1038/srep35436.


A Single Nucleotide Change in the Promoter mutp Enhances Fluoride Resistance of Streptococcus mutans.

Liao Y, Brandt BW, Zhang M, Li J, Crielaard W, van Loveren C, Deng DM.

Antimicrob Agents Chemother. 2016 Nov 21;60(12):7509-7512. Print 2016 Dec.


Changes in the oral ecosystem induced by the use of 8% arginine toothpaste.

Koopman JE, Hoogenkamp MA, Buijs MJ, Brandt BW, Keijser BJ, Crielaard W, Ten Cate JM, Zaura E.

Arch Oral Biol. 2017 Jan;73:79-87. doi: 10.1016/j.archoralbio.2016.09.008. Epub 2016 Sep 26.


A novel compound to maintain a healthy oral plaque ecology in vitro.

Janus MM, Crielaard W, Zaura E, Keijser BJ, Brandt BW, Krom BP.

J Oral Microbiol. 2016 Jul 29;8:32513. doi: 10.3402/jom.v8.32513. eCollection 2016.


Corrigendum: Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification.

Ziesemer KA, Mann AE, Sankaranarayanan K, Schroeder H, Ozga AT, Brandt BW, Zaura E, Waters-Rist A, Hoogland M, Salazar-García DC, Aldenderfer M, Speller C, Hendy J, Weston DA, MacDonald SJ, Thomas GH, Collins MJ, Lewis CM, Hofman C, Warinner C.

Sci Rep. 2016 Jun 2;6:27163. doi: 10.1038/srep27163. No abstract available.


Nitrate and the Origin of Saliva Influence Composition and Short Chain Fatty Acid Production of Oral Microcosms.

Koopman JE, Buijs MJ, Brandt BW, Keijser BJ, Crielaard W, Zaura E.

Microb Ecol. 2016 Aug;72(2):479-92. doi: 10.1007/s00248-016-0775-z. Epub 2016 May 7.


The microbiome associated with equine periodontitis and oral health.

Kennedy R, Lappin DF, Dixon PM, Buijs MJ, Zaura E, Crielaard W, O'Donnell L, Bennett D, Brandt BW, Riggio MP.

Vet Res. 2016 Apr 14;47:49. doi: 10.1186/s13567-016-0333-1.


Microbial profiles at baseline and not the use of antibiotics determine the clinical outcome of the treatment of chronic periodontitis.

Bizzarro S, Laine ML, Buijs MJ, Brandt BW, Crielaard W, Loos BG, Zaura E.

Sci Rep. 2016 Feb 1;6:20205. doi: 10.1038/srep20205.


Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification.

Ziesemer KA, Mann AE, Sankaranarayanan K, Schroeder H, Ozga AT, Brandt BW, Zaura E, Waters-Rist A, Hoogland M, Salazar-García DC, Aldenderfer M, Speller C, Hendy J, Weston DA, MacDonald SJ, Thomas GH, Collins MJ, Lewis CM, Hofman C, Warinner C.

Sci Rep. 2015 Nov 13;5:16498. doi: 10.1038/srep16498. Erratum in: Sci Rep. 2016 Jun 02;6:27163.


Same Exposure but Two Radically Different Responses to Antibiotics: Resilience of the Salivary Microbiome versus Long-Term Microbial Shifts in Feces.

Zaura E, Brandt BW, Teixeira de Mattos MJ, Buijs MJ, Caspers MP, Rashid MU, Weintraub A, Nord CE, Savell A, Hu Y, Coates AR, Hubank M, Spratt DA, Wilson M, Keijser BJ, Crielaard W.

MBio. 2015 Nov 10;6(6):e01693-15. doi: 10.1128/mBio.01693-15.


Proteins and peptides in parotid saliva of irradiated patients compared to that of healthy controls using SELDI-TOF-MS.

Laheij AM, Rasch CN, Brandt BW, de Soet JJ, Schipper RG, Loof A, Silletti E, van Loveren C.

BMC Res Notes. 2015 Nov 3;8:639. doi: 10.1186/s13104-015-1641-7.


The Oral Microbiome of Denture Wearers Is Influenced by Levels of Natural Dentition.

O'Donnell LE, Robertson D, Nile CJ, Cross LJ, Riggio M, Sherriff A, Bradshaw D, Lambert M, Malcolm J, Buijs MJ, Zaura E, Crielaard W, Brandt BW, Ramage G.

PLoS One. 2015 Sep 14;10(9):e0137717. doi: 10.1371/journal.pone.0137717. eCollection 2015.


metaModules identifies key functional subnetworks in microbiome-related disease.

May A, Brandt BW, El-Kebir M, Klau GW, Zaura E, Crielaard W, Heringa J, Abeln S.

Bioinformatics. 2016 Jun 1;32(11):1678-85. doi: 10.1093/bioinformatics/btv526. Epub 2015 Sep 5.


Correction: TreeSeq, a Fast and Intuitive Tool for Analysis of Whole Genome and Metagenomic Sequence Data.

Wintermans BB, Brandt BW, Vandenbroucke-Grauls CM, Budding AE.

PLoS One. 2015 Jun 22;10(6):e0131379. doi: 10.1371/journal.pone.0131379. eCollection 2015. No abstract available.


NGS-eval: NGS Error analysis and novel sequence VAriant detection tooL.

May A, Abeln S, Buijs MJ, Heringa J, Crielaard W, Brandt BW.

Nucleic Acids Res. 2015 Jul 1;43(W1):W301-5. doi: 10.1093/nar/gkv346. Epub 2015 Apr 15.


Identification and functional analysis of genome mutations in a fluoride-resistant Streptococcus mutans strain.

Liao Y, Chen J, Brandt BW, Zhu Y, Li J, van Loveren C, Deng DM.

PLoS One. 2015 Apr 9;10(4):e0122630. doi: 10.1371/journal.pone.0122630. eCollection 2015.


The effect of propidium monoazide treatment on the measured bacterial composition of clinical samples after the use of a mouthwash.

Exterkate RA, Zaura E, Brandt BW, Buijs MJ, Koopman JE, Crielaard W, Ten Cate JM.

Clin Oral Investig. 2015 May;19(4):813-22. doi: 10.1007/s00784-014-1297-z. Epub 2014 Aug 10.


NatalieQ: a web server for protein-protein interaction network querying.

El-Kebir M, Brandt BW, Heringa J, Klau GW.

BMC Syst Biol. 2014 Apr 1;8:40. doi: 10.1186/1752-0509-8-40.


Unraveling the outcome of 16S rDNA-based taxonomy analysis through mock data and simulations.

May A, Abeln S, Crielaard W, Heringa J, Brandt BW.

Bioinformatics. 2014 Jun 1;30(11):1530-8. doi: 10.1093/bioinformatics/btu085. Epub 2014 Feb 10.


Towards a database for genotype-phenotype association research: mining data from encyclopaedia.

Pajić VS, Pavloviç-Lazetić GM, Beljanski MV, Brandt BW, Pajić MB.

Int J Data Min Bioinform. 2013;7(2):196-213.


A protein prioritization approach tailored for the FA/BRCA pathway.

Haitjema A, Brandt BW, Ameziane N, May P, Heringa J, de Winter JP, Joenje H, Dorsman JC.

PLoS One. 2013 Apr 19;8(4):e62017. doi: 10.1371/journal.pone.0062017. Print 2013. Erratum in: PLoS One. 2013;8(10). doi:10.1371/annotation/bd2ee3f6-0f2b-4814-9825-7b90a40fb91f.


Comparing clustering and pre-processing in taxonomy analysis.

Bonder MJ, Abeln S, Zaura E, Brandt BW.

Bioinformatics. 2012 Nov 15;28(22):2891-7. doi: 10.1093/bioinformatics/bts552. Epub 2012 Sep 8.


TaxMan: a server to trim rRNA reference databases and inspect taxonomic coverage.

Brandt BW, Bonder MJ, Huse SM, Zaura E.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W82-7. doi: 10.1093/nar/gks418. Epub 2012 May 22.


ProFASTA: a pipeline web server for fungal protein scanning with integration of cell surface prediction software.

de Groot PW, Brandt BW.

Fungal Genet Biol. 2012 Feb;49(2):173-9. doi: 10.1016/j.fgb.2011.12.009. Epub 2012 Jan 3.


Protein analysis tools and services at IBIVU.

Brandt BW, Heringa J.

J Integr Bioinform. 2011 Sep 8;8(2):168. doi: 10.2390/biecoll-jib-2011-168.


Subcellular metabolic organization in the context of dynamic energy budget and biochemical systems theories.

Vinga S, Neves AR, Santos H, Brandt BW, Kooijman SA.

Philos Trans R Soc Lond B Biol Sci. 2010 Nov 12;365(1557):3429-42. doi: 10.1098/rstb.2010.0156. Review.


Multi-Harmony: detecting functional specificity from sequence alignment.

Brandt BW, Feenstra KA, Heringa J.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W35-40. doi: 10.1093/nar/gkq415. Epub 2010 Jun 4.


Genomics and structure/function studies of Rhabdoviridae proteins involved in replication and transcription.

Assenberg R, Delmas O, Morin B, Graham SC, De Lamballerie X, Laubert C, Coutard B, Grimes JM, Neyts J, Owens RJ, Brandt BW, Gorbalenya A, Tucker P, Stuart DI, Canard B, Bourhy H.

Antiviral Res. 2010 Aug;87(2):149-61. doi: 10.1016/j.antiviral.2010.02.322. Epub 2010 Feb 25. Review.


Comprehensive genomic analysis of cell wall genes in Aspergillus nidulans.

de Groot PW, Brandt BW, Horiuchi H, Ram AF, de Koster CG, Klis FM.

Fungal Genet Biol. 2009 Mar;46 Suppl 1:S72-81.


Hepatitis C virus NS4B carboxy terminal domain is a membrane binding domain.

Liefhebber JM, Brandt BW, Broer R, Spaan WJ, van Leeuwen HC.

Virol J. 2009 May 25;6:62. doi: 10.1186/1743-422X-6-62.


PhyloPars: estimation of missing parameter values using phylogeny.

Bruggeman J, Heringa J, Brandt BW.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W179-84. doi: 10.1093/nar/gkp370. Epub 2009 May 13.


webPRC: the Profile Comparer for alignment-based searching of public domain databases.

Brandt BW, Heringa J.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W48-52. doi: 10.1093/nar/gkp279. Epub 2009 May 6.


The 2008 update of the Aspergillus nidulans genome annotation: a community effort.

Wortman JR, Gilsenan JM, Joardar V, Deegan J, Clutterbuck J, Andersen MR, Archer D, Bencina M, Braus G, Coutinho P, von Döhren H, Doonan J, Driessen AJ, Durek P, Espeso E, Fekete E, Flipphi M, Estrada CG, Geysens S, Goldman G, de Groot PW, Hansen K, Harris SD, Heinekamp T, Helmstaedt K, Henrissat B, Hofmann G, Homan T, Horio T, Horiuchi H, James S, Jones M, Karaffa L, Karányi Z, Kato M, Keller N, Kelly DE, Kiel JA, Kim JM, van der Klei IJ, Klis FM, Kovalchuk A, Krasevec N, Kubicek CP, Liu B, Maccabe A, Meyer V, Mirabito P, Miskei M, Mos M, Mullins J, Nelson DR, Nielsen J, Oakley BR, Osmani SA, Pakula T, Paszewski A, Paulsen I, Pilsyk S, Pócsi I, Punt PJ, Ram AF, Ren Q, Robellet X, Robson G, Seiboth B, van Solingen P, Specht T, Sun J, Taheri-Talesh N, Takeshita N, Ussery D, vanKuyk PA, Visser H, van de Vondervoort PJ, de Vries RP, Walton J, Xiang X, Xiong Y, Zeng AP, Brandt BW, Cornell MJ, van den Hondel CA, Visser J, Oliver SG, Turner G.

Fungal Genet Biol. 2009 Mar;46 Suppl 1:S2-13. doi: 10.1016/j.fgb.2008.12.003. Epub 2008 Dec 25.

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