Richard A Notebaart

Richard A Notebaart

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Richard A Notebaart

Richard A Notebaart

Publications by authors named "Richard A Notebaart"

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CRISPR-Directed Microbiome Manipulation across the Food Supply Chain.

Trends Microbiol 2019 Jun 16;27(6):489-496. Epub 2019 Apr 16.

Food Microbiology, Wageningen University and Research, Wageningen, The Netherlands. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S0966842X193007
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http://dx.doi.org/10.1016/j.tim.2019.03.006DOI Listing
June 2019

Delivery of genome editing tools by bacterial extracellular vesicles.

Microb Biotechnol 2019 01 13;12(1):71-73. Epub 2018 Dec 13.

Food Microbiology, Wageningen University and Research, PO Box 17, 6700 AA, Wageningen, The Netherlands.

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https://onlinelibrary.wiley.com/doi/abs/10.1111/1751-7915.13
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http://dx.doi.org/10.1111/1751-7915.13356DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6302703PMC
January 2019

CRISPR-Cas genome engineering of esterase activity in Saccharomyces cerevisiae steers aroma formation.

BMC Res Notes 2018 Sep 27;11(1):682. Epub 2018 Sep 27.

Food Microbiology, Wageningen University & Research, P.O. Box 17, 6700 AA, Wageningen, The Netherlands.

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http://dx.doi.org/10.1186/s13104-018-3788-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6161353PMC
September 2018

Underground metabolism: network-level perspective and biotechnological potential.

Curr Opin Biotechnol 2018 02 29;49:108-114. Epub 2017 Aug 29.

Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Temesvári krt. 62, H-6726 Szeged, Hungary.

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http://dx.doi.org/10.1016/j.copbio.2017.07.015DOI Listing
February 2018

Rewiring monocyte glucose metabolism via C-type lectin signaling protects against disseminated candidiasis.

PLoS Pathog 2017 Sep 18;13(9):e1006632. Epub 2017 Sep 18.

Department of Internal Medicine and Radboud Center for Infectious diseases (RCI), Radboud University Nijmegen Medical Centre, Geert Grooteplein 8, Nijmegen, the Netherlands.

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http://dx.doi.org/10.1371/journal.ppat.1006632DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5619837PMC
September 2017

Estimating Metabolic Fluxes Using a Maximum Network Flexibility Paradigm.

PLoS One 2015 12;10(10):e0139665. Epub 2015 Oct 12.

Institute for Computing and Information Sciences (ICIS), Radboud University, Nijmegen, the Netherlands; Centre for Systems Biology and Bioenergetics (CSBB), Radboud University Medical Centre, Nijmegen, the Netherlands.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0139665PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4601694PMC
June 2016

Adaptive evolution of complex innovations through stepwise metabolic niche expansion.

Nat Commun 2016 05 20;7:11607. Epub 2016 May 20.

Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Temesvári krt. 62, Szeged H-6726, Hungary.

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http://dx.doi.org/10.1038/ncomms11607DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5411730PMC
May 2016

Predicting human genetic interactions from cancer genome evolution.

PLoS One 2015 1;10(5):e0125795. Epub 2015 May 1.

Department of Bioinformatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands; Centre for Systems Biology and Bioenergetics, Radboud University Medical Centre, Nijmegen, The Netherlands.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0125795PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4416779PMC
January 2016

Synthetic dosage lethality in the human metabolic network is highly predictive of tumor growth and cancer patient survival.

Proc Natl Acad Sci U S A 2015 Sep 14;112(39):12217-22. Epub 2015 Sep 14.

Department of Internal Medicine, Radboud University Medical Center, 6525 GA, Nijmegen, The Netherlands

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http://dx.doi.org/10.1073/pnas.1508573112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4593091PMC
September 2015

Skeletal muscle mitochondria of NDUFS4-/- mice display normal maximal pyruvate oxidation and ATP production.

Biochim Biophys Acta 2015 Jun-Jul;1847(6-7):526-33. Epub 2015 Feb 14.

Department of Biochemistry, RIMLS, Radboud University Medical Center, Nijmegen, The Netherlands; Centre for Systems Biology and Bioenergetics, Radboud University Medical Centre, Nijmegen, The Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.bbabio.2015.02.006DOI Listing
August 2015

Network-level architecture and the evolutionary potential of underground metabolism.

Proc Natl Acad Sci U S A 2014 Aug 28;111(32):11762-7. Epub 2014 Jul 28.

Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, 6726, Szeged, Hungary; and

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http://dx.doi.org/10.1073/pnas.1406102111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4136603PMC
August 2014

Genome evolution predicts genetic interactions in protein complexes and reveals cancer drug targets.

Nat Commun 2013 ;4:2124

Department of Bioinformatics, Centre for Molecular Life Sciences, Radboud University Medical Centre, 6525GA Nijmegen, The Netherlands.

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http://dx.doi.org/10.1038/ncomms3124DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3717498PMC
January 2014

Inferring metabolic states in uncharacterized environments using gene-expression measurements.

PLoS Comput Biol 2013 21;9(3):e1002988. Epub 2013 Mar 21.

Department of Bioinformatics (CMBI), Centre for Molecular Life Sciences, Radboud University Nijmegen, The Netherlands.

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http://dx.doi.org/10.1371/journal.pcbi.1002988DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3605102PMC
November 2013

Use of genome-scale metabolic models in evolutionary systems biology.

Methods Mol Biol 2011 ;759:483-97

Institute of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences, Szeged, Hungary.

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http://dx.doi.org/10.1007/978-1-61779-173-4_27DOI Listing
December 2011

Systems-biology approaches for predicting genomic evolution.

Nat Rev Genet 2011 Aug 2;12(9):591-602. Epub 2011 Aug 2.

Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Center, Temesvári krt. 62, H-6726 Szeged, Hungary.

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http://dx.doi.org/10.1038/nrg3033DOI Listing
August 2011

Understanding the adaptive growth strategy of Lactobacillus plantarum by in silico optimisation.

PLoS Comput Biol 2009 Jun 12;5(6):e1000410. Epub 2009 Jun 12.

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

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http://dx.doi.org/10.1371/journal.pcbi.1000410DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2690837PMC
June 2009

Asymmetric relationships between proteins shape genome evolution.

Genome Biol 2009 Feb 12;10(2):R19. Epub 2009 Feb 12.

Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, Geert Grooteplein 26-28, 6525 GA, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1186/gb-2009-10-2-r19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2688278PMC
February 2009

Co-regulation of metabolic genes is better explained by flux coupling than by network distance.

PLoS Comput Biol 2008 Jan;4(1):e26

Center for Molecular and Biomolecular Informatics (NCMLS), Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands.

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http://dx.plos.org/10.1371/journal.pcbi.0040026
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http://dx.doi.org/10.1371/journal.pcbi.0040026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2211535PMC
January 2008

Structure-function analysis of the coxsackievirus protein 3A: identification of residues important for dimerization, viral rna replication, and transport inhibition.

J Biol Chem 2006 Sep 25;281(38):28232-43. Epub 2006 Jul 25.

Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, Nijmegen Centre for Molecular Life Sciences, 6500 HB Nijmegen, The Netherlands.

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http://dx.doi.org/10.1074/jbc.M601122200DOI Listing
September 2006

Accelerating the reconstruction of genome-scale metabolic networks.

BMC Bioinformatics 2006 Jun 13;7:296. Epub 2006 Jun 13.

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

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http://dx.doi.org/10.1186/1471-2105-7-296DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1550432PMC
June 2006

Correlation between sequence conservation and the genomic context after gene duplication.

Nucleic Acids Res 2005 27;33(19):6164-71. Epub 2005 Oct 27.

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

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http://dx.doi.org/10.1093/nar/gki913DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1275583PMC
November 2005

A proline-rich region in the coxsackievirus 3A protein is required for the protein to inhibit endoplasmic reticulum-to-golgi transport.

J Virol 2005 Apr;79(8):5163-73

Department of Medical Microbiology, Nijmegen Center for Molecular Life Sciences, University Medical Center Nijmegen, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands.

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http://dx.doi.org/10.1128/JVI.79.8.5163-5173.2005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1069528PMC
April 2005