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ArticlesPeer ReviewedFull Text
A systematic assessment of current genome-scale metabolic reconstruction tools
Author / Creator:Mendoza, Sebastián N. ; Olivier, Brett G. ; Molenaar, Douwe ; Teusink, Bas
Publisher:England: BioMed Central Ltd
Journal title:Genome Biology, 2019-08, Vol.20 (1), p.158-158, Article 158
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Shifts in growth strategies reflect tradeoffs in cellular economics
Author / Creator:Molenaar, Douwe ; van Berlo, Rogier ; de Ridder, Dick ; Teusink, Bas
Publisher:London: Nature Publishing Group UK
Journal title:Molecular systems biology, 2009, Vol.5 (1), p.323-n/a
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Macrophage ATP citrate lyase deficiency stabilizes atherosclerotic plaques
Author / Creator:Baardman, Jeroen ; Verberk, Sanne G. S. ; van der Velden, Saskia ; Gijbels, Marion J. J. ; van Roomen, Cindy P. P. A. ; Sluimer, Judith C. ; Broos, Jelle Y. ; Griffith, Guillermo R. ; Prange, Koen H. M. ; van Weeghel, Michel ; Lakbir, Soufyan ; Molenaar, Douwe ; Meinster, Elisa ; Neele, Annette E. ; Kooij, Gijs ; de Vries, Helga E. ; Lutgens, Esther ; Wellen, Kathryn E. ; de Winther, Menno P. J. ; Van den Bossche, Jan
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2020-12, Vol.11 (1), p.6296-6296, Article 6296
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Availability of public goods shapes the evolution of competing metabolic strategies
Author / Creator:Bachmann, Herwig ; Fischlechner, Martin ; Rabbers, Iraes ; Barfa, Nakul ; dos Santos, Filipe Branco ; Molenaar, Douwe ; Teusink, Bas
Publisher:United States: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2013-08, Vol.110 (35), p.14302-14307
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Proteome constraints reveal targets for improving microbial fitness in nutrient‐rich environments
Author / Creator:Chen, Yu ; van Pelt‐KleinJan, Eunice ; van Olst, Berdien ; Douwenga, Sieze ; Boeren, Sjef ; Bachmann, Herwig ; Molenaar, Douwe ; Nielsen, Jens ; Teusink, Bas
Publisher:London: Nature Publishing Group UK
Journal title:Molecular systems biology, 2021-04, Vol.17 (4), p.e10093-n/a
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A benzene-degrading nitrate-reducing microbial consortium displays aerobic and anaerobic benzene degradation pathways
Author / Creator:Atashgahi, Siavash ; Hornung, Bastian ; van der Waals, Marcelle J. ; da Rocha, Ulisses Nunes ; Hugenholtz, Floor ; Nijsse, Bart ; Molenaar, Douwe ; van Spanning, Rob ; Stams, Alfons Johannes Maria ; Gerritse, Jan ; Smidt, Hauke
Publisher:London: Nature Research
Journal title:Scientific reports, 2018-03, Vol.8 (1), p.4490-12, Article 4490
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Steering microbiomes by organic amendments towards climate-smart agricultural soils
Author / Creator:Brenzinger, Kristof ; Costa, Ohana Y. A. ; Ho, Adrian ; Koorneef, Guusje ; Robroek, Bjorn ; Molenaar, Douwe ; Korthals, Gerard ; Bodelier, Paul L. E.
Publisher:Berlin/Heidelberg: Springer Berlin Heidelberg
Journal title:Biology and fertility of soils, 2021-11, Vol.57 (8), p.1053-1074
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Exploring Metabolic Pathway Reconstruction and Genome-Wide Expression Profiling in Lactobacillus reuteri to Define Functional Probiotic Features
Author / Creator:Saulnier, Delphine M. ; Santos, Filipe ; Roos, Stefan ; Mistretta, Toni-Ann ; Spinler, Jennifer K. ; Molenaar, Douwe ; Teusink, Bas ; Versalovic, James
Publisher:United States: Public Library of Science
Journal title:PloS one, 2011-04, Vol.6 (4), p.e18783-e18783
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Comparative genomics of human Lactobacillus crispatus isolates reveals genes for glycosylation and glycogen degradation: implications for in vivo dominance of the vaginal microbiota
Author / Creator:van der Veer, Charlotte ; Hertzberger, Rosanne Y. ; Bruisten, Sylvia M. ; Tytgat, Hanne L. P. ; Swanenburg, Jorne ; de Kat Angelino-Bart, Alie ; Schuren, Frank ; Molenaar, Douwe ; Reid, Gregor ; de Vries, Henry ; Kort, Remco
Publisher:England: BioMed Central Ltd
Journal title:Microbiome, 2019-03, Vol.7 (1), p.49-49, Article 49
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Identification of Lactobacillus plantarum genes modulating the cytokine response of human peripheral blood mononuclear cells
Author / Creator:van Hemert, Saskia ; Meijerink, Marjolein ; Molenaar, Douwe ; Bron, Peter A ; de Vos, Paul ; Kleerebezem, Michiel ; Wells, Jerry M ; Marco, Maria L
Publisher:England: BioMed Central Ltd
Journal title:BMC microbiology, 2010-11, Vol.10 (1), p.293-293, Article 293
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ArticlesPeer ReviewedFull Text
micro-Petri dish, a million-well growth chip for the culture and high-throughput screening of microorganisms
Author / Creator:Ingham, Colin J ; Sprenkels, Ad ; Bomer, Johan ; Molenaar, Douwe ; van den Berg, Albert ; van Hylckama Vlieg, Johan E.T ; de Vos, Willem M
Publisher:United States: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2007-11, Vol.104 (46), p.18217-18222
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Metabolic shifts: a fitness perspective for microbial cell factories
Author / Creator:Goel, Anisha ; Wortel, Meike Tessa ; Molenaar, Douwe ; Teusink, Bas
Publisher:Dordrecht: Springer-Verlag
Journal title:Biotechnology letters, 2012-12, Vol.34 (12), p.2147-2160
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Adaption to glucose limitation is modulated by the pleotropic regulator CcpA, independent of selection pressure strength
Author / Creator:Price, Claire E. ; Branco dos Santos, Filipe ; Hesseling, Anne ; Uusitalo, Jaakko J. ; Bachmann, Herwig ; Benavente, Vera ; Goel, Anisha ; Berkhout, Jan ; Bruggeman, Frank J. ; Marrink, Siewert-Jan ; Montalban-Lopez, Manolo ; de Jong, Anne ; Kok, Jan ; Molenaar, Douwe ; Poolman, Bert ; Teusink, Bas ; Kuipers, Oscar P.
Publisher:England: BioMed Central Ltd
Journal title:BMC ecology and evolution, 2019-01, Vol.19 (1), p.15-15, Article 15
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Molecular assessment of bacterial vaginosis by Lactobacillus abundance and species diversity
Author / Creator:Dols, Joke A M ; Molenaar, Douwe ; van der Helm, Jannie J ; Caspers, Martien P M ; de Kat Angelino-Bart, Alie ; Schuren, Frank H J ; Speksnijder, Adrianus G C L ; Westerhoff, Hans V ; Richardus, Jan Hendrik ; Boon, Mathilde E ; Reid, Gregor ; de Vries, Henry J C ; Kort, Remco
Publisher:England: BioMed Central Ltd
Journal title:BMC infectious diseases, 2016-04, Vol.16 (175), p.180-180
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Vanishing white matter: deregulated integrated stress response as therapy target
Author / Creator:Abbink, Truus E. M. ; Wisse, Lisanne E. ; Jaku, Ermelinda ; Thiecke, Michiel J. ; Voltolini‐González, Daniel ; Fritsen, Hein ; Bobeldijk, Sander ; Braak, Timo J. ; Polder, Emiel ; Postma, Nienke L. ; Bugiani, Marianna ; Struijs, Eduard A. ; Verheijen, Mark ; Straat, Nina ; Sluis, Sophie ; Thomas, Adri A. M. ; Molenaar, Douwe ; Knaap, Marjo S.
Publisher:United States: John Wiley & Sons, Inc
Journal title:Annals of clinical and translational neurology, 2019-08, Vol.6 (8), p.1407-1422
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ArticlesPeer ReviewedFull Text
Complete Genome Sequence of Lactobacillus plantarum WCFS1
Author / Creator:Kleerebezem, Michiel ; Boekhorst, Jos ; van Kranenburg, Richard ; Molenaar, Douwe ; Kuipers, Oscar P. ; Leer, Rob ; Tarchini, Renato ; Peters, Sander A. ; Sandbrink, Hans M. ; Mark W. E. J. Fiers ; Stiekema, Willem ; René M. Klein Lankhorst ; Bron, Peter A. ; Hoffer, Sally M. ; Masja N. Nierop Groot ; Kerkhoven, Robert ; de Vries, Maaike ; Ursing, Björn ; de Vos, Willem M. ; Siezen, Roland J.
Publisher:United States: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2003-02, Vol.100 (4), p.1990-1995
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Regional vulnerability of brain white matter in vanishing white matter
Author / Creator:Man, Jodie H.K. ; van Gelder, Charlotte A.G.H. ; Breur, Marjolein ; Molenaar, Douwe ; Abbink, Truus ; Altelaar, Maarten ; Bugiani, Marianna ; van der Knaap, Marjo S.
Publisher:England: BioMed Central Ltd
Journal title:Acta neuropathologica communications, 2023-06, Vol.11 (1), p.103-103, Article 103
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High biodiversity in a benzene-degrading nitrate-reducing culture is sustained by a few primary consumers
Author / Creator:Melkonian, Chrats ; Fillinger, Lucas ; Atashgahi, Siavash ; da Rocha, Ulisses Nunes ; Kuiper, Esther ; Olivier, Brett ; Braster, Martin ; Gottstein, Willi ; Helmus, Rick ; Parsons, John R. ; Smidt, Hauke ; van der Waals, Marcelle ; Gerritse, Jan ; Brandt, Bernd W. ; Röling, Wilfred F. M. ; Molenaar, Douwe ; van Spanning, Rob J. M.
Publisher:London: Nature Publishing Group UK
Journal title:Communications biology, 2021-05, Vol.4 (1), p.530-12, Article 530
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Convergence in probiotic Lactobacillus gut-adaptive responses in humans and mice
Author / Creator:Marco, Maria L ; de Vries, Maaike C ; Wels, Michiel ; Molenaar, Douwe ; Mangell, Peter ; Ahrne, Siv ; de Vos, Willem M ; Vaughan, Elaine E ; Kleerebezem, Michiel
Publisher:London: Nature Publishing Group UK
Journal title:The ISME Journal, 2010-11, Vol.4 (11), p.1481-1484
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PhenoLink - a web-tool for linking phenotype to ~omics data for bacteria: application to gene-trait matching for Lactobacillus plantarum strains
Author / Creator:Bayjanov, Jumamurat R ; Molenaar, Douwe ; Tzeneva, Vesela ; Siezen, Roland J ; van Hijum, Sacha A F T
Publisher:England: BioMed Central Ltd
Journal title:BMC genomics, 2012-05, Vol.13 (1), p.170-170, Article 170
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A systematic assessment of current genome-scale metabolic reconstruction tools

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Shifts in growth strategies reflect tradeoffs in cellular economics

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Macrophage ATP citrate lyase deficiency stabilizes atherosclerotic plaques

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Availability of public goods shapes the evolution of competing metabolic strategies

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Proteome constraints reveal targets for improving microbial fitness in nutrient‐rich environments

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A benzene-degrading nitrate-reducing microbial consortium displays aerobic and anaerobic benzene degradation pathways

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Steering microbiomes by organic amendments towards climate-smart agricultural soils

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Exploring Metabolic Pathway Reconstruction and Genome-Wide Expression Profiling in Lactobacillus reuteri to Define Functional Probiotic Features

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Comparative genomics of human Lactobacillus crispatus isolates reveals genes for glycosylation and glycogen degradation: implications for in vivo dominance of the vaginal microbiota

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Identification of Lactobacillus plantarum genes modulating the cytokine response of human peripheral blood mononuclear cells

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micro-Petri dish, a million-well growth chip for the culture and high-throughput screening of microorganisms

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Metabolic shifts: a fitness perspective for microbial cell factories

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Adaption to glucose limitation is modulated by the pleotropic regulator CcpA, independent of selection pressure strength

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Molecular assessment of bacterial vaginosis by Lactobacillus abundance and species diversity

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Vanishing white matter: deregulated integrated stress response as therapy target

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Complete Genome Sequence of Lactobacillus plantarum WCFS1

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Regional vulnerability of brain white matter in vanishing white matter

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High biodiversity in a benzene-degrading nitrate-reducing culture is sustained by a few primary consumers

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Convergence in probiotic Lactobacillus gut-adaptive responses in humans and mice

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

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