Wynand Alkema

Wynand Alkema

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Wynand Alkema

Wynand Alkema

Publications by authors named "Wynand Alkema"

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Magnesium prevents vascular calcification in Klotho deficiency.

Kidney Int 2019 Nov 2. Epub 2019 Nov 2.

Department of Physiology, 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.kint.2019.09.034DOI Listing
November 2019

Biosynthetic homeostasis and resilience of the complement system in health and infectious disease.

EBioMedicine 2019 Jul 29;45:303-313. Epub 2019 Jun 29.

Section Pediatric Infectious Diseases, Laboratory of Medical Immunology, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands; Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1016/j.ebiom.2019.06.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6642076PMC
July 2019

Magnesium deficiency prevents high-fat-diet-induced obesity in mice.

Diabetologia 2018 09 9;61(9):2030-2042. Epub 2018 Jul 9.

Department of Physiology (286), Radboud Institute for Molecular Life Sciences, Radboud university medical center, P. O. Box 9101, 6500 HB, Nijmegen, the Netherlands.

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http://dx.doi.org/10.1007/s00125-018-4680-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6096631PMC
September 2018

Primary cilia-regulated transcriptome in the renal collecting duct.

FASEB J 2018 07 8;32(7):3653-3668. Epub 2018 Feb 8.

Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1096/fj.201701228RDOI Listing
July 2018

High-throughput screening of a large collection of non-conventional yeasts reveals their potential for aroma formation in food fermentation.

Food Microbiol 2016 Dec 25;60:147-59. Epub 2016 Jul 25.

NIZO Food Research B.V., P.O. Box 20, 6710 BA, Ede, The Netherlands.

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http://dx.doi.org/10.1016/j.fm.2016.07.006DOI Listing
December 2016

Application of text mining in the biomedical domain.

Methods 2015 Mar 30;74:97-106. Epub 2015 Jan 30.

Computational Discovery & Design Group CMBI, Radboudumc, Nijmegen, The Netherlands; NIZO Food Research BV, Ede, The Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2015.01.015DOI Listing
March 2015

Clustering analyses in peptidomics revealed that peptide profiles of infant formulae are descriptive.

Food Sci Nutr 2015 Jan 30;3(1):81-90. Epub 2014 Dec 30.

Mead Johnson Pediatric Nutrition Institute Nijmegen, The Netherlands.

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http://dx.doi.org/10.1002/fsn3.196DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4304566PMC
January 2015

Assessing the metabolic effects of prednisolone in healthy volunteers using urine metabolic profiling.

Genome Med 2012 30;4(11):94. Epub 2012 Nov 30.

MSD, Molenstraat 110, 5340 BH Oss, The Netherlands ; NIZO food research BV, Health Division, Ede, The Netherlands.

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http://dx.doi.org/10.1186/gm395DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4064315PMC
August 2014

Prednisolone induces the Wnt signalling pathway in 3T3-L1 adipocytes.

Arch Physiol Biochem 2013 May 19;119(2):52-64. Epub 2013 Mar 19.

CDD, CMBI, NCMLS, Radboud University Medical Centre, Nijmegen, The Netherlands.

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http://dx.doi.org/10.3109/13813455.2013.774022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3665230PMC
May 2013

Identification of new biomarker candidates for glucocorticoid induced insulin resistance using literature mining.

BioData Min 2013 Feb 4;6(1). Epub 2013 Feb 4.

Computational Drug Discovery (CDD), CMBI, NCMLS, Radboud University Nijmegen Medical Centre, P,O, Box 9101, 6500 HB, Nijmegen, The Netherlands.

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http://biodatamining.biomedcentral.com/articles/10.1186/1756
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http://dx.doi.org/10.1186/1756-0381-6-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3577498PMC
February 2013

Prednisolone-induced beta cell dysfunction is associated with impaired endoplasmic reticulum homeostasis in INS-1E cells.

Cell Signal 2011 Nov 13;23(11):1708-15. Epub 2011 Jun 13.

Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands.

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http://dx.doi.org/10.1016/j.cellsig.2011.06.002DOI Listing
November 2011

ss-TEA: Entropy based identification of receptor specific ligand binding residues from a multiple sequence alignment of class A GPCRs.

BMC Bioinformatics 2011 Aug 10;12:332. Epub 2011 Aug 10.

Computational Drug Discovery Group, Radboud University NijmegenMedical Centre, Geert Grooteplein, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1186/1471-2105-12-332DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3162937PMC
August 2011

CoPub update: CoPub 5.0 a text mining system to answer biological questions.

Nucleic Acids Res 2011 Jul 27;39(Web Server issue):W450-4. Epub 2011 May 27.

Computational Drug Discovery, CMBI, NCMLS, Radboud University Nijmegen Medical Centre, 6500 HB Nijmegen, The Netherlands.

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http://dx.doi.org/10.1093/nar/gkr310DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125746PMC
July 2011

Prednisolone-induced changes in gene-expression profiles in healthy volunteers.

Pharmacogenomics 2011 Jul 2;12(7):985-98. Epub 2011 Jun 2.

MSD Research Laboratories, Oss, The Netherlands.

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http://dx.doi.org/10.2217/pgs.11.34DOI Listing
July 2011

Literature mining for the discovery of hidden connections between drugs, genes and diseases.

PLoS Comput Biol 2010 Sep 23;6(9). Epub 2010 Sep 23.

Computational Drug Discovery (CDD), Nijmegen Centre for Molecular Life Sciences (NCMLS), Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1371/journal.pcbi.1000943DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2944780PMC
September 2010

Prednisolone-induced differential gene expression in mouse liver carrying wild type or a dimerization-defective glucocorticoid receptor.

BMC Genomics 2010 Jun 5;11:359. Epub 2010 Jun 5.

Computational Drug Discovery (CDD), Nijmegen Centre for Molecular Life Sciences (NCMLS), Radboud University Nijmegen Medical Centre, Geert Grooteplein Zuid 26-28, Nijmegen, the Netherlands.

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http://dx.doi.org/10.1186/1471-2164-11-359DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2895630PMC
June 2010

PhyloPat: an updated version of the phylogenetic pattern database contains gene neighborhood.

Nucleic Acids Res 2009 Jan 2;37(Database issue):D731-7. Epub 2008 Oct 2.

Computational Drug Discovery, CMBI, NCMLS, Radboud University Nijmegen Medical Centre, PO Box 9101, 6500 HB Nijmegen, The Netherlands.

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http://dx.doi.org/10.1093/nar/gkn645DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686476PMC
January 2009

BioVenn - a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams.

BMC Genomics 2008 Oct 16;9:488. Epub 2008 Oct 16.

Computational Drug Discovery, CMBI, NCMLS, Radboud University Nijmegen Medical Centre, PO Box 9101, 6500 HB Nijmegen, The Netherlands.

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http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2164-9-488DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2584113PMC
October 2008

CoPub: a literature-based keyword enrichment tool for microarray data analysis.

Nucleic Acids Res 2008 Jul 28;36(Web Server issue):W406-10. Epub 2008 Apr 28.

Computational Drug Discovery (CDD),, Nijmegen Centre for Molecular Life Sciences (NCMLS), Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1093/nar/gkn215DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447728PMC
July 2008

Saturation mutagenesis reveals the importance of residues alphaR145 and alphaF146 of penicillin acylase in the synthesis of beta-lactam antibiotics.

J Biotechnol 2008 Jan 30;133(1):18-26. Epub 2007 Aug 30.

Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.

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http://linkinghub.elsevier.com/retrieve/pii/S016816560701533
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http://dx.doi.org/10.1016/j.jbiotec.2007.08.039DOI Listing
January 2008

Literature-based compound profiling: application to toxicogenomics.

Pharmacogenomics 2007 Nov;8(11):1521-34

Radboud University Nijmegen Medical Centre, Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, PO Box 9101, 6500 HB Nijmegen, The Netherlands.

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http://dx.doi.org/10.2217/14622416.8.11.1521DOI Listing
November 2007

Quantifying the accessibility of the metagenome by random expression cloning techniques.

Environ Microbiol 2004 Sep;6(9):879-86

Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands.

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http://doi.wiley.com/10.1111/j.1462-2920.2004.00640.x
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http://dx.doi.org/10.1111/j.1462-2920.2004.00640.xDOI Listing
September 2004

MSCAN: identification of functional clusters of transcription factor binding sites.

Nucleic Acids Res 2004 Jul;32(Web Server issue):W195-8

Center for Genomics and Bioinformatics, Karolinska Institutet, SE-17177 Stockholm, Sweden.

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http://dx.doi.org/10.1093/nar/gkh387DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC441525PMC
July 2004

Structural and kinetic studies on ligand binding in wild-type and active-site mutants of penicillin acylase.

Protein Eng Des Sel 2004 May 14;17(5):473-80. Epub 2004 Jul 14.

Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, The Netherlands.

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https://academic.oup.com/peds/article-lookup/doi/10.1093/pro
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http://dx.doi.org/10.1093/protein/gzh057DOI Listing
May 2004

JASPAR: an open-access database for eukaryotic transcription factor binding profiles.

Nucleic Acids Res 2004 Jan;32(Database issue):D91-4

Center for Genomics and Bioinformatics, Karolinska Institutet, Berzelius väg 35, S-17177 Stockholm, Sweden.

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http://dx.doi.org/10.1093/nar/gkh012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC308747PMC
January 2004

Kinetics of enzyme acylation and deacylation in the penicillin acylase-catalyzed synthesis of beta-lactam antibiotics.

Eur J Biochem 2003 Sep;270(18):3675-83

Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, the Netherlands.

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http://dx.doi.org/10.1046/j.1432-1033.2003.03728.xDOI Listing
September 2003

Understanding the language of gene regulation.

Genome Biol 2003 18;4(7):327. Epub 2003 Jun 18.

Center for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden.

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http://genomebiology.biomedcentral.com/articles/10.1186/gb-2
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http://dx.doi.org/10.1186/gb-2003-4-7-327DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC193626PMC
July 2003

Role of alphaArg145 and betaArg263 in the active site of penicillin acylase of Escherichia coli.

Biochem J 2002 Jul;365(Pt 1):303-9

Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.

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http://dx.doi.org/10.1042/BJ20011468DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1222674PMC
July 2002

The role of hydrophobic active-site residues in substrate specificity and acyl transfer activity of penicillin acylase.

Eur J Biochem 2002 Apr;269(8):2093-100

Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, the Netherlands.

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http://dx.doi.org/10.1046/j.1432-1033.2002.02857.xDOI Listing
April 2002