Publications by authors named "Sacha A F T van Hijum"

100Publications

A generic workflow for Single Locus Sequence Typing (SLST) design and subspecies characterization of microbiota.

Sci Rep 2019 12 27;9(1):19834. Epub 2019 Dec 27.

Center for Molecular and Biomolecular Informatics (CMBI), Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center (Radboudumc), Nijmegen, The Netherlands.

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http://dx.doi.org/10.1038/s41598-019-56065-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6934516PMC
December 2019

Targeting the Cutaneous Microbiota in Atopic Dermatitis by Coal Tar via AHR-Dependent Induction of Antimicrobial Peptides.

J Invest Dermatol 2020 02 22;140(2):415-424.e10. Epub 2019 Jul 22.

Department of Dermatology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.jid.2019.06.142DOI Listing
February 2020

Reconstruction and inference of the Lactococcus lactis MG1363 gene co-expression network.

PLoS One 2019 22;14(5):e0214868. Epub 2019 May 22.

Top Institute Food and Nutrition (TIFN), Wageningen, The Netherlands.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0214868PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6530827PMC
January 2020

The bacterial and fungal microbiome of the skin of healthy dogs and dogs with atopic dermatitis and the impact of topical antimicrobial therapy, an exploratory study.

Vet Microbiol 2019 Feb 21;229:90-99. Epub 2018 Dec 21.

Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, 3584 CL, the Netherlands; Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, 0110, South Africa. Electronic address:

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http://dx.doi.org/10.1016/j.vetmic.2018.12.022DOI Listing
February 2019

Haemophilus is overrepresented in the nasopharynx of infants hospitalized with RSV infection and associated with increased viral load and enhanced mucosal CXCL8 responses.

Microbiome 2018 01 11;6(1):10. Epub 2018 Jan 11.

Laboratory of Pediatric Infectious Diseases, Radboud Center for Infectious Diseases, Radboud University Medical Center, Geert Grooteplein-Zuid 10 (Route 412), 6525, GA, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1186/s40168-017-0395-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5765694PMC
January 2018

Gut microbiome in ADHD and its relation to neural reward anticipation.

PLoS One 2017 1;12(9):e0183509. Epub 2017 Sep 1.

Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0183509PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5581161PMC
October 2017

Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis.

Clin Microbiol Rev 2017 10;30(4):1015-1063

Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1128/CMR.00016-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5608882PMC
October 2017

Deciphering the distance to antibiotic resistance for the pneumococcus using genome sequencing data.

Sci Rep 2017 02 16;7:42808. Epub 2017 Feb 16.

Laboratory of Pediatric Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen 6525 GA, The Netherlands.

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http://dx.doi.org/10.1038/srep42808DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5311915PMC
February 2017

Reply to Meisel et al.

J Invest Dermatol 2017 04 22;137(4):961-962. Epub 2016 Nov 22.

NIZO Food Research B.V., Ede, The Netherlands.

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http://dx.doi.org/10.1016/j.jid.2016.11.013DOI Listing
April 2017

Complete genome sequence of thermophilic Bacillus smithii type strain DSM 4216(T).

Stand Genomic Sci 2016 24;11(1):52. Epub 2016 Aug 24.

Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands ; Corbion, Arkelsedijk 46, 4206 AC Gorinchem, The Netherlands.

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http://dx.doi.org/10.1186/s40793-016-0172-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4995803PMC
August 2016

Nomadic lifestyle of Lactobacillus plantarum revealed by comparative genomics of 54 strains isolated from different habitats.

Environ Microbiol 2016 12 4;18(12):4974-4989. Epub 2016 Aug 4.

Institut de Génomique Fonctionnelle de Lyon (IGFL), Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Université Claude Bernard Lyon 1, Lyon, France.

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http://dx.doi.org/10.1111/1462-2920.13455DOI Listing
December 2016

Use of propidium monoazide for selective profiling of viable microbial cells during Gouda cheese ripening.

Int J Food Microbiol 2016 Jul 25;228:1-9. Epub 2016 Mar 25.

Top Institute Food and Nutrition (TIFN), Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 557, 6700 AN, Wageningen, The Netherlands; Wageningen University, Laboratory of Food Microbiology, Bornse Weilanden 9, PO Box 17, 6700 AA Wageningen, The Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.ijfoodmicro.2016.03.027DOI Listing
July 2016

An In vitro Model for Bacterial Growth on Human Stratum Corneum.

Acta Derm Venereol 2016 Nov;96(7):873-879

Department of Dermatology, Radboud university medical center, Nijmegen, The Netherlands.

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http://dx.doi.org/10.2340/00015555-2401DOI Listing
November 2016

Draft Genome Sequence of Lactobacillus plantarum SF2A35B.

Genome Announc 2016 Feb 25;4(1). Epub 2016 Feb 25.

TI Food and Nutrition, Wageningen, The Netherlands NIZO food research, Ede, The Netherlands Host Microbe Interactomics Group, Wageningen University & Research Centre, Wageningen, The Netherlands.

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http://genomea.asm.org/lookup/doi/10.1128/genomeA.01638-15
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http://dx.doi.org/10.1128/genomeA.01638-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4767920PMC
February 2016

Advances and perspectives in computational prediction of microbial gene essentiality.

Brief Funct Genomics 2017 03;16(2):70-79

Radboud Institute for Molecular Life Sciences, Laboratory of Paediatric Infectious Diseases, Radboud University Medical Centre, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1093/bfgp/elv063DOI Listing
March 2017

Resequencing of the Lactobacillus plantarum Strain WJL Genome.

Genome Announc 2015 Nov 25;3(6). Epub 2015 Nov 25.

Institut de Génomique Fonctionnelle de Lyon (IGFL), École Normale Supérieure de Lyon, CNRS UMR 5242, Université Claude Bernard Lyon 1, Lyon France

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http://genomea.asm.org/content/3/6/e01382-15.full.pdf
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http://genomea.asm.org/lookup/doi/10.1128/genomeA.01382-15
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http://dx.doi.org/10.1128/genomeA.01382-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4661311PMC
November 2015

Nearly Complete Genome Sequence of Lactobacillus plantarum Strain NIZO2877.

Genome Announc 2015 Nov 25;3(6). Epub 2015 Nov 25.

Institut de Génomique Fonctionnelle de Lyon (IGFL), École Normale Supérieure de Lyon, CNRS UMR, Université Claude Bernard Lyon 1, Lyon, France

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http://dx.doi.org/10.1128/genomeA.01370-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4661306PMC
November 2015

The post-vaccine microevolution of invasive Streptococcus pneumoniae.

Sci Rep 2015 Oct 23;5:14952. Epub 2015 Oct 23.

Radboud university medical center, Laboratory of Pediatric Infectious Diseases, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1038/srep14952DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4615977PMC
October 2015

Akkermansia muciniphila and Helicobacter typhlonius modulate intestinal tumor development in mice.

Carcinogenesis 2015 Nov 29;36(11):1388-96. Epub 2015 Aug 29.

Laboratory of Microbiology, Wageningen University 6703 HB, Wageningen, The Netherlands, Department of Veterinary Biosciences, University of Helsinki 00014, Helsinki, Finland.

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http://carcin.oxfordjournals.org/content/early/2015/09/09/ca
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http://www.carcin.oxfordjournals.org/lookup/doi/10.1093/carc
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http://dx.doi.org/10.1093/carcin/bgv120DOI Listing
November 2015

Diversity of acid stress resistant variants of Listeria monocytogenes and the potential role of ribosomal protein S21 encoded by rpsU.

Front Microbiol 2015 8;6:422. Epub 2015 May 8.

Top Institute Food and Nutrition Wageningen, Netherlands ; Laboratory of Food Microbiology, Wageningen University Wageningen, Netherlands.

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http://dx.doi.org/10.3389/fmicb.2015.00422DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4424878PMC
May 2015

CiVi: circular genome visualization with unique features to analyze sequence elements.

Bioinformatics 2015 Sep 24;31(17):2867-9. Epub 2015 Apr 24.

CMBI, Radboud University Medical Centre, Nijmegen 6525GA, The Netherlands, Netherlands Bioinformatics Centre, Nijmegen 6500HB, The Netherlands, Hogeschool Arnhem en Nijmegen BioCentre, 6525EM Nijmegen, The Netherlands.

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http://bioinformatics.oxfordjournals.org/content/early/2015/
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http://bioinformatics.oxfordjournals.org/content/31/17/2867.
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http://bioinformatics.oxfordjournals.org/lookup/doi/10.1093/
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http://dx.doi.org/10.1093/bioinformatics/btv249DOI Listing
September 2015

Transcriptomic signatures of peroxisome proliferator-activated receptor α (PPARα) in different mouse liver models identify novel aspects of its biology.

BMC Genomics 2014 Dec 15;15:1106. Epub 2014 Dec 15.

RIKILT - Institute of Food Safety, Wageningen UR, P,O, Box 230, 6700 AE Wageningen, The Netherlands.

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http://dx.doi.org/10.1186/1471-2164-15-1106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4378209PMC
December 2014

From microbial gene essentiality to novel antimicrobial drug targets.

BMC Genomics 2014 Nov 5;15:958. Epub 2014 Nov 5.

Radboud Institute for Molecular Life Sciences, Laboratory of Paediatric Infectious Diseases, Radboud University Medical Centre, Nijmegen 6500 HB, The Netherlands.

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http://dx.doi.org/10.1186/1471-2164-15-958DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4233050PMC
November 2014

Degenerate target sites mediate rapid primed CRISPR adaptation.

Proc Natl Acad Sci U S A 2014 Apr 7;111(16):E1629-38. Epub 2014 Apr 7.

Laboratory of Microbiology and Laboratory of Systems and Synthetic Biology, Wageningen University, 6703 HB Wageningen, The Netherlands.

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http://dx.doi.org/10.1073/pnas.1400071111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4000823PMC
April 2014

Effect of growth rate and selection pressure on rates of transfer of an antibiotic resistance plasmid between E. coli strains.

Plasmid 2014 Mar 10;72:1-8. Epub 2014 Feb 10.

Department of Molecular Biology & Microbial Food Safety, Swammerdam Institute of Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands; Office for Risk Assessment and Research, Netherlands Food and Consumer Product Safety Authority, Catharijnesingel 59, 3511 GG Utrecht, The Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.plasmid.2014.01.002DOI Listing
March 2014

Multifactorial diversity sustains microbial community stability.

ISME J 2013 Nov 4;7(11):2126-36. Epub 2013 Jul 4.

1] Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands [2] NIZO food research BV, Ede, The Netherlands [3] Top Institute Food and Nutrition (TIFN), Kluyver Centre for Genomics of Industrial Fermentation, Wageningen, The Netherlands.

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http://dx.doi.org/10.1038/ismej.2013.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3806261PMC
November 2013

Screening metatranscriptomes for toxin genes as functional drivers of human colorectal cancer.

Best Pract Res Clin Gastroenterol 2013 Feb;27(1):85-99

Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands.

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https://linkinghub.elsevier.com/retrieve/pii/S15216918130006
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http://dx.doi.org/10.1016/j.bpg.2013.03.008DOI Listing
February 2013

Reduce manual curation by combining gene predictions from multiple annotation engines, a case study of start codon prediction.

PLoS One 2013 10;8(5):e63523. Epub 2013 May 10.

Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0063523PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3651085PMC
December 2013

Explaining microbial phenotypes on a genomic scale: GWAS for microbes.

Brief Funct Genomics 2013 Jul 26;12(4):366-80. Epub 2013 Apr 26.

CMBI, NCMLS, Radboud University Medical Centre. Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands.

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http://dx.doi.org/10.1093/bfgp/elt008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3743258PMC
July 2013

Genotype-phenotype matching analysis of 38 Lactococcus lactis strains using random forest methods.

BMC Microbiol 2013 Mar 26;13:68. Epub 2013 Mar 26.

Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, PO Box 9101, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1186/1471-2180-13-68DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3637802PMC
March 2013

Differences in sequencing technologies improve the retrieval of anammox bacterial genome from metagenomes.

BMC Genomics 2013 Jan 16;14. Epub 2013 Jan 16.

Radboud University Nijmegen, Institute for Computing and Information Science, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.

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http://dx.doi.org/10.1186/1471-2164-14-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3618311PMC
January 2013

Genome-wide prediction and validation of sigma70 promoters in Lactobacillus plantarum WCFS1.

PLoS One 2012 20;7(9):e45097. Epub 2012 Sep 20.

Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0045097PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3447810PMC
February 2013

Application of state-of-art sequencing technologies to indigenous food fermentations.

Curr Opin Biotechnol 2013 Apr 6;24(2):178-86. Epub 2012 Sep 6.

NIZO Food Research, Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 20, 6710 BA Ede, The Netherlands.

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http://dx.doi.org/10.1016/j.copbio.2012.08.004DOI Listing
April 2013

ESSENTIALS: software for rapid analysis of high throughput transposon insertion sequencing data.

PLoS One 2012 10;7(8):e43012. Epub 2012 Aug 10.

Laboratory of Pediatric Infectious Diseases, Radboud University Medical Centre, Nijmegen, The Netherlands.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0043012PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416827PMC
March 2013

PhenoLink--a web-tool for linking phenotype to ~omics data for bacteria: application to gene-trait matching for Lactobacillus plantarum strains.

BMC Genomics 2012 May 4;13:170. Epub 2012 May 4.

Centre for Molecular and Biomolecular Informatics, Radboud University Nijmegen Medical Centre, PO Box 9101, Nijmegen, The Netherlands.

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http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2164-13-170DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3366882PMC
May 2012

Defining the structure of the general stress regulon of Bacillus subtilis using targeted microarray analysis and random forest classification.

Microbiology (Reading) 2012 Mar 15;158(Pt 3):696-707. Epub 2011 Dec 15.

NIZO Food Research, PO Box 20, 6710 BA Ede, The Netherlands.

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http://dx.doi.org/10.1099/mic.0.055434-0DOI Listing
March 2012

FACIL: Fast and Accurate Genetic Code Inference and Logo.

Bioinformatics 2011 Jul 8;27(14):1929-33. Epub 2011 Jun 8.

Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Geert Grooteplein 28, 6525 GA, Nijmegen, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btr316DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3129529PMC
July 2011

Genome (re-)annotation and open-source annotation pipelines.

Microb Biotechnol 2010 Jul;3(4):362-9

Kluyver Centre for Genomics of Industrial Fermentation, TI Food and Nutrition, 6700AN Wageningen, The Netherlands.

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http://dx.doi.org/10.1111/j.1751-7915.2010.00191.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3815804PMC
July 2010

SpotXplore: a Cytoscape plugin for visual exploration of hotspot expression in gene regulatory networks.

Bioinformatics 2010 Nov 21;26(22):2922-3. Epub 2010 Sep 21.

Department of Mathematics and Computer Science, Eindhoven University of Technology, Eindhoven, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btq535DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2971575PMC
November 2010

Genome analysis of Moraxella catarrhalis strain BBH18, [corrected] a human respiratory tract pathogen.

J Bacteriol 2010 Jul 7;192(14):3574-83. Epub 2010 May 7.

Laboratory of Pediatric Infectious Diseases, Radboud University Nijmegen Medical Centre, P.O. Box 9101 (Route 224), 6500 HB Nijmegen, The Netherlands.

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http://dx.doi.org/10.1128/JB.00121-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2897349PMC
July 2010

Complete genome sequence of Lactococcus lactis subsp. lactis KF147, a plant-associated lactic acid bacterium.

J Bacteriol 2010 May 26;192(10):2649-50. Epub 2010 Mar 26.

NIZO Food Research, Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 20, 6710 BA Ede, The Netherlands.

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http://jb.asm.org/cgi/doi/10.1128/JB.00276-10
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http://dx.doi.org/10.1128/JB.00276-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2863553PMC
May 2010

PanCGHweb: a web tool for genotype calling in pangenome CGH data.

Bioinformatics 2010 May 10;26(9):1256-7. Epub 2010 Mar 10.

Radboud University Medical Centre, Nijmegen Center for Molecular Life Sciences, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btq103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2859125PMC
May 2010

Mechanisms and evolution of control logic in prokaryotic transcriptional regulation.

Microbiol Mol Biol Rev 2009 Sep;73(3):481-509, Table of Contents

Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands.

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http://dx.doi.org/10.1128/MMBR.00037-08DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2738135PMC
September 2009

MOTIFATOR: detection and characterization of regulatory motifs using prokaryote transcriptome data.

Bioinformatics 2009 Feb 25;25(4):550-1. Epub 2009 Jan 25.

Molecular Genetics, Groningen Biomolecular Sciences, University of Groningen, PO Box 800, 9700 AV Groningen, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btp013DOI Listing
February 2009

DISCLOSE : DISsection of CLusters Obtained by SEries of transcriptome data using functional annotations and putative transcription factor binding sites.

BMC Bioinformatics 2008 Dec 16;9:535. Epub 2008 Dec 16.

Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands.

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http://dx.doi.org/10.1186/1471-2105-9-535DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2661003PMC
December 2008

MINOMICS: visualizing prokaryote transcriptomics and proteomics data in a genomic context.

Bioinformatics 2009 Jan 12;25(1):139-40. Epub 2008 Nov 12.

Department of Molecular Genetics Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN, Haren, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btn588DOI Listing
January 2009

Prosecutor: parameter-free inference of gene function for prokaryotes using DNA microarray data, genomic context and multiple gene annotation sources.

BMC Genomics 2008 Oct 21;9:495. Epub 2008 Oct 21.

Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, the Netherlands.

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http://dx.doi.org/10.1186/1471-2164-9-495DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2585105PMC
October 2008

Transcriptome analysis of the Lactococcus lactis ArgR and AhrC regulons.

Appl Environ Microbiol 2008 Aug 6;74(15):4768-71. Epub 2008 Jun 6.

Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, NL-9751 NN Haren, The Netherlands.

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http://dx.doi.org/10.1128/AEM.00117-08DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2519338PMC
August 2008

The relative value of operon predictions.

Brief Bioinform 2008 Sep 17;9(5):367-75. Epub 2008 Apr 17.

Molecular Genetics Department of University of Groningen.

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http://dx.doi.org/10.1093/bib/bbn019DOI Listing
September 2008

Supervised Lowess normalization of comparative genome hybridization data--application to lactococcal strain comparisons.

BMC Bioinformatics 2008 Feb 11;9:93. Epub 2008 Feb 11.

Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-9-93DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2275246PMC
February 2008

Fractional factorial design for optimization of the SELDI protocol for human adipose tissue culture media.

Biotechnol Prog 2007 Jan-Feb;23(1):217-24

Department of Medical Biomics, University Medical Center Groningen, University of Groningen, Post Office Box 30001, 9700 RR Groningen, The Netherlands.

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http://dx.doi.org/10.1021/bp0602294DOI Listing
June 2008

FIVA: Functional Information Viewer and Analyzer extracting biological knowledge from transcriptome data of prokaryotes.

Bioinformatics 2007 May 19;23(9):1161-3. Epub 2007 Jan 19.

Molecular Genetics, Groningen Biomolecular Sciences, University of Groningen, Groningen, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btl658DOI Listing
May 2007

BAGEL: a web-based bacteriocin genome mining tool.

Nucleic Acids Res 2006 Jul;34(Web Server issue):W273-9

Department of Molecular Genetics, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, PO Box 14, 9750 AA Haren, The Netherlands.

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http://dx.doi.org/10.1093/nar/gkl237DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538908PMC
July 2006

Regulation of glutamine and glutamate metabolism by GlnR and GlnA in Streptococcus pneumoniae.

J Biol Chem 2006 Sep 20;281(35):25097-109. Epub 2006 Jun 20.

Department of Molecular Genetics, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, PO Box 14, 9750 AA Haren, The Netherlands.

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http://dx.doi.org/10.1074/jbc.M601661200DOI Listing
September 2006

Transcriptome analysis reveals mechanisms by which Lactococcus lactis acquires nisin resistance.

Antimicrob Agents Chemother 2006 May;50(5):1753-61

Molecular Genetics Group, Department of Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, P.O. Box 14, 9750 AA Haren, The Netherlands.

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http://aac.asm.org/cgi/doi/10.1128/AAC.50.5.1753-1761.2006
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http://dx.doi.org/10.1128/AAC.50.5.1753-1761.2006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1472215PMC
May 2006

Structure-function relationships of glucansucrase and fructansucrase enzymes from lactic acid bacteria.

Microbiol Mol Biol Rev 2006 Mar;70(1):157-76

Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, P.O. Box 14, 9750 AA Haren, The Netherlands.

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http://dx.doi.org/10.1128/MMBR.70.1.157-176.2006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1393251PMC
March 2006

The Lactococcus lactis CodY regulon: identification of a conserved cis-regulatory element.

J Biol Chem 2005 Oct 21;280(40):34332-42. Epub 2005 Jul 21.

Department of Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, Kerklaan 30, 9751 NN Haren and Friesland Foods Corporate Research, P. O. Box 87, 7400 AB Deventer, The Netherlands.

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http://dx.doi.org/10.1074/jbc.M502349200DOI Listing
October 2005

Projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies.

Nucleic Acids Res 2005 Jul;33(Web Server issue):W560-6

Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, PO Box 14, 9750 AA Haren, The Netherlands.

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http://dx.doi.org/10.1093/nar/gki356DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1160117PMC
July 2005

Comparative and functional genomics of lactococci.

FEMS Microbiol Rev 2005 Aug;29(3):411-33

Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands.

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http://dx.doi.org/10.1016/j.femsre.2005.04.004DOI Listing
August 2005

A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data.

BMC Genomics 2005 May 20;6:77. Epub 2005 May 20.

Department of Molecular Genetics, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, PO Box 14, 9750 AA Haren, The Netherlands.

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http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2164-6-77DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1166551PMC
May 2005

MicroPreP: a cDNA microarray data pre-processing framework.

Appl Bioinformatics 2003 ;2(4):241-4

Molecular Genetics, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, Haren, The Netherlands.

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June 2004

Molecular Genetics Information System (MOLGENIS): alternatives in developing local experimental genomics databases.

Bioinformatics 2004 Sep 1;20(13):2075-83. Epub 2004 Apr 1.

Groningen Bioinformatics Center, Faculty of Medical Sciences and Faculty of Mathematics and Natural Sciences, University of Groningen, Groningen, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/bth206DOI Listing
September 2004

Projector: automatic contig mapping for gap closure purposes.

Nucleic Acids Res 2003 Nov;31(22):e144

Molecular Genetics, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, PO Box 14, 9750 AA Haren, The Netherlands.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC275581PMC
http://dx.doi.org/10.1093/nar/gng144DOI Listing
November 2003

UniFrag and GenomePrimer: selection of primers for genome-wide production of unique amplicons.

Bioinformatics 2003 Aug;19(12):1580-2

Molecular Genetics, University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, PO Box 14, 9750 AA Haren, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btg203DOI Listing
August 2003

Transcriptome analysis and related databases of Lactococcus lactis.

Antonie Van Leeuwenhoek 2002 Aug;82(1-4):113-22

University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, PO Box 14, 9750 AA Haren, The Netherlands.

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August 2002