Publications by authors named "Huub C J Hoefsloot"

56Publications

Repeatability and reproducibility of lipoprotein particle profile measurements in plasma samples by ultracentrifugation.

Clin Chem Lab Med 2019 Dec;58(1):103-115

Department of Nutrition, Exercise and Sports, University of Copenhagen, Rolighedsvej 26, DK-1958 Frederiksberg C, Denmark.

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http://dx.doi.org/10.1515/cclm-2019-0729DOI Listing
December 2019

Global testing of shifts in metabolic phenotype.

Metabolomics 2018 10 4;14(10):139. Epub 2018 Oct 4.

Laboratory of Biophysics, Wageningen University, Wageningen, The Netherlands.

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http://dx.doi.org/10.1007/s11306-018-1435-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6208751PMC
October 2018

Proof of concept study of age-dependent DNA methylation markers across different tissues by massive parallel sequencing.

Forensic Sci Int Genet 2018 09 7;36:152-159. Epub 2018 Jul 7.

University of Amsterdam, Swammerdam Institute for Life Sciences, Science Park 904, 1098XH Amsterdam, The Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.fsigen.2018.07.007DOI Listing
September 2018

Training for translation between disciplines: a philosophy for life and data sciences curricula.

Bioinformatics 2018 07;34(13):i4-i12

Department of Computer Science, IBIVU Centre for Integrative Bioinformatics Vrije Universiteit Amsterdam, HV Amsterdam, Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/bty233DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6022589PMC
July 2018

Dynamic elementary mode modelling of non-steady state flux data.

BMC Syst Biol 2018 06 18;12(1):71. Epub 2018 Jun 18.

Grupo de Ingeniería Estadística Multivariante, Departamento de Estadística e IO Aplicadas y Calidad, Universitat Politècnica de València, Valencia, Spain.

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https://bmcsystbiol.biomedcentral.com/articles/10.1186/s1291
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http://dx.doi.org/10.1186/s12918-018-0589-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6006576PMC
June 2018

Stoichiometry, Absolute Abundance, and Localization of Proteins in the Bacillus cereus Spore Coat Insoluble Fraction Determined Using a QconCAT Approach.

J Proteome Res 2018 02 4;17(2):903-917. Epub 2018 Jan 4.

Molecular Biology & Microbial Food Safety, ‡Mass Spectrometry of Biomacromolecules, and §Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam , Science Park 904, 1098 XH Amsterdam, The Netherlands.

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http://dx.doi.org/10.1021/acs.jproteome.7b00732DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5799878PMC
February 2018

Forensic DNA methylation profiling from minimal traces: How low can we go?

Forensic Sci Int Genet 2018 03 13;33:17-23. Epub 2017 Nov 13.

University of Amsterdam, Swammerdam Institute for Life Sciences, Science Park 904, 1098XH Amsterdam, The Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.fsigen.2017.11.004DOI Listing
March 2018

Chronological age prediction based on DNA methylation: Massive parallel sequencing and random forest regression.

Forensic Sci Int Genet 2017 11 1;31:19-28. Epub 2017 Aug 1.

University of Amsterdam, Swammerdam Institute for Life Sciences, Science Park 904, 1098XH Amsterdam, The Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.fsigen.2017.07.015DOI Listing
November 2017

Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize.

Genome Biol 2017 07 21;18(1):137. Epub 2017 Jul 21.

Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1186/s13059-017-1273-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5522596PMC
July 2017

Towards a Hierarchical Strategy to Explore Multi-Scale IP/MS Data for Protein Complexes.

PLoS One 2015 8;10(10):e0139704. Epub 2015 Oct 8.

Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands; Netherlands Institute for Systems Biology, University of Amsterdam, Amsterdam, The Netherlands.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0139704PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4598013PMC
June 2016

Scaling in ANOVA-simultaneous component analysis.

Metabolomics 2015;11(5):1265-1276. Epub 2015 Feb 14.

KU Leuven, Leuven, Belgium.

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http://dx.doi.org/10.1007/s11306-015-0785-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4559107PMC
February 2015

Quantitative proteomics analysis of an ethanol- and a lactate-producing mutant strain of Synechocystis sp. PCC6803.

Biotechnol Biofuels 2015 5;8:111. Epub 2015 Aug 5.

Molecular Microbial Physiology, Swammerdam Institute for Life Sciences, and Netherlands Institute for System Biology, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.

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http://dx.doi.org/10.1186/s13068-015-0294-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4526308PMC
August 2015

Validation and selection of ODE based systems biology models: how to arrive at more reliable decisions.

BMC Syst Biol 2015 Jul 8;9:32. Epub 2015 Jul 8.

Biosystems Data Analysis Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.

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http://www.biomedcentral.com/1752-0509/9/32
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http://dx.doi.org/10.1186/s12918-015-0180-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4493957PMC
July 2015

Time-series analysis of the transcriptome and proteome of Escherichia coli upon glucose repression.

Biochim Biophys Acta 2015 Oct 4;1854(10 Pt A):1269-79. Epub 2015 Jun 4.

Molecular Microbial Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.bbapap.2015.05.017DOI Listing
October 2015

Strategies for individual phenotyping of linoleic and arachidonic acid metabolism using an oral glucose tolerance test.

PLoS One 2015 18;10(3):e0119856. Epub 2015 Mar 18.

Biosystem Data Analysis Group, University of Amsterdam, Amsterdam, The Netherlands; Netherlands Metabolomics Centre, Leiden, The Netherlands.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0119856PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4364740PMC
February 2016

MetDFBA: incorporating time-resolved metabolomics measurements into dynamic flux balance analysis.

Mol Biosyst 2015 Jan 15;11(1):137-45. Epub 2014 Oct 15.

Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academical Medical Centre, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1039/c4mb00510dDOI Listing
January 2015

Capturing Arabidopsis root architecture dynamics with ROOT-FIT reveals diversity in responses to salinity.

Plant Physiol 2014 Nov 30;166(3):1387-402. Epub 2014 Sep 30.

Departments of Plant Physiology (M.M.J., S.M., M.A.H., C.T.) and Biosystems Data Analysis (H.C.J.H.), Swammerdam Institute for Life Sciences, University of Amsterdam, 1090GE Amsterdam, The Netherlands; andENZA Zaden Research and Development B.V., Enkhuizen, The Netherlands (R.F., G.-J.d.B.)

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http://dx.doi.org/10.1104/pp.114.248963DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4226346PMC
November 2014

Correlated measurement error hampers association network inference.

J Chromatogr B Analyt Technol Biomed Life Sci 2014 Sep 2;966:93-9. Epub 2014 May 2.

Analytical BioSciences, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands; Netherlands Metabolomics Centre, Leiden, The Netherlands.

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http://dx.doi.org/10.1016/j.jchromb.2014.04.048DOI Listing
September 2014

How informative is your kinetic model?: using resampling methods for model invalidation.

BMC Syst Biol 2014 May 22;8:61. Epub 2014 May 22.

Biosystems Data Analysis Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1186/1752-0509-8-61DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4046068PMC
May 2014

Network identification of hormonal regulation.

PLoS One 2014 22;9(5):e96284. Epub 2014 May 22.

Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands; Netherlands Metabolomics Centre, Leiden, The Netherlands.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0096284PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4031081PMC
June 2015

Inferring protein-protein interaction complexes from immunoprecipitation data.

BMC Res Notes 2013 Nov 15;6:468. Epub 2013 Nov 15.

Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1186/1756-0500-6-468DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3874675PMC
November 2013

Bioinformatics and systems biology: bridging the gap between heterogeneous student backgrounds.

Brief Bioinform 2013 Sep 19;14(5):589-98. Epub 2013 Apr 19.

Centre for Integrative Bioinformatics VU (IBIVU), VU University Amsterdam, Amsterdam, The Netherlands. Tel.: +31 20 59 87816; Fax: +31 20 59 87653;

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http://dx.doi.org/10.1093/bib/bbt023DOI Listing
September 2013

A critical assessment of feature selection methods for biomarker discovery in clinical proteomics.

Mol Cell Proteomics 2013 Jan 31;12(1):263-76. Epub 2012 Oct 31.

Analytical Biochemistry, Department of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands.

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http://dx.doi.org/10.1074/mcp.M112.022566DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3536906PMC
January 2013

Inferring differences in the distribution of reaction rates across conditions.

Mol Biosyst 2012 Sep 11;8(9):2415-23. Epub 2012 Jul 11.

Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands.

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http://dx.doi.org/10.1039/c2mb25015bDOI Listing
September 2012

Detecting regulatory mechanisms in endocrine time series measurements.

PLoS One 2012 26;7(3):e32985. Epub 2012 Mar 26.

Department of Metabolic Diseases, University Medical Center Utrecht, Utrecht, The Netherlands.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0032985PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3312884PMC
June 2012

Global test for metabolic pathway differences between conditions.

Anal Chim Acta 2012 Mar 4;719:8-15. Epub 2012 Jan 4.

Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.

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http://dx.doi.org/10.1016/j.aca.2011.12.051DOI Listing
March 2012

Generic framework for high-dimensional fixed-effects ANOVA.

Brief Bioinform 2012 Sep 23;13(5):524-35. Epub 2011 Dec 23.

Department of Biosystems Data Analysis, University of Amsterdam, The Netherlands.

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http://dx.doi.org/10.1093/bib/bbr071DOI Listing
September 2012

To aggregate or not to aggregate high-dimensional classifiers.

BMC Bioinformatics 2011 May 13;12:153. Epub 2011 May 13.

Biosystems Data Analysis group, University of Amsterdam, Amsterdam, The Netherlands.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-12-153DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3113942PMC
May 2011

Reverse engineering of metabolic networks, a critical assessment.

Mol Biosyst 2011 Feb 10;7(2):511-20. Epub 2010 Nov 10.

Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands.

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http://dx.doi.org/10.1039/c0mb00083cDOI Listing
February 2011

Computational modeling of the human serum proteome response to colon resection surgery.

Anal Chim Acta 2010 Feb 11;661(1):20-7. Epub 2009 Dec 11.

Biosystems Data Analysis, Swammerdam Institute for Life Science, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands.

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http://dx.doi.org/10.1016/j.aca.2009.12.003DOI Listing
February 2010

Time alignment algorithms based on selected mass traces for complex LC-MS data.

J Proteome Res 2010 Mar;9(3):1483-95

Analytical Biochemistry, Department of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands.

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http://dx.doi.org/10.1021/pr9010124DOI Listing
March 2010

Crossfit analysis: a novel method to characterize the dynamics of induced plant responses.

BMC Bioinformatics 2009 Dec 16;10:425. Epub 2009 Dec 16.

Biosystems Data Analysis, Swammerdam Institute for Life Sciences, Faculty of Sciences, Universiteit van Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands.

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http://dx.doi.org/10.1186/1471-2105-10-425DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3087346PMC
December 2009

The photographer and the greenhouse: how to analyse plant metabolomics data.

Phytochem Anal 2010 Jan-Feb;21(1):48-60

Biosystems Data Analysis, Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands.

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http://dx.doi.org/10.1002/pca.1181DOI Listing
March 2010

Endocrine pulse identification using penalized methods and a minimum set of assumptions.

Am J Physiol Endocrinol Metab 2010 Feb 27;298(2):E146-55. Epub 2009 Oct 27.

BioSystems Data Analysis group, Swammerdam Institute for Life Science, Univ. of Amsterdam, Nieuwe Achtergracht 166, Amsterdam 1018 WV, The Netherlands.

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http://dx.doi.org/10.1152/ajpendo.00048.2009DOI Listing
February 2010

Gaucher disease: a model disorder for biomarker discovery.

Expert Rev Proteomics 2009 Aug;6(4):411-9

Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands.

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http://dx.doi.org/10.1586/epr.09.54DOI Listing
August 2009

Multilevel data analysis of a crossover designed human nutritional intervention study.

J Proteome Res 2008 Oct 28;7(10):4483-91. Epub 2008 Aug 28.

Biosystems Data Analysis, Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands.

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http://dx.doi.org/10.1021/pr800145jDOI Listing
October 2008

Optimized time alignment algorithm for LC-MS data: correlation optimized warping using component detection algorithm-selected mass chromatograms.

Anal Chem 2008 Sep 21;80(18):7012-21. Epub 2008 Aug 21.

Analytical Biochemistry, Department of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands.

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http://pubs.acs.org/doi/abs/10.1021/ac800920h
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http://dx.doi.org/10.1021/ac800920hDOI Listing
September 2008

A classification model for the Leiden proteomics competition.

Stat Appl Genet Mol Biol 2008 19;7(2):Article8. Epub 2008 Feb 19.

University of Amsterdam.

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http://dx.doi.org/10.2202/1544-6115.1351DOI Listing
April 2008

Insights into Sonogashira cross-coupling by high-throughput kinetics and descriptor modeling.

Chemistry 2008 ;14(9):2857-66

Inorganic Chemistry, Zintl-Institute, Darmstadt University of Technology, Petersenstrasse 18, 64287 Darmstadt, Germany.

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http://dx.doi.org/10.1002/chem.200701418DOI Listing
June 2008

Statistical data processing in clinical proteomics.

J Chromatogr B Analyt Technol Biomed Life Sci 2008 Apr 4;866(1-2):77-88. Epub 2007 Nov 4.

Swammerdam Institute for Life Sciences, Universiteit van Amsterdam - Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands.

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http://dx.doi.org/10.1016/j.jchromb.2007.10.042DOI Listing
April 2008

Discovering gene expression patterns in time course microarray experiments by ANOVA-SCA.

Bioinformatics 2007 Jul 22;23(14):1792-800. Epub 2007 May 22.

Departamento de Estadística e Investigación Operativa, Universidad de Alicante, Apartado 03080, Alicante, Spain.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btm251DOI Listing
July 2007

Assessing the statistical validity of proteomics based biomarkers.

Anal Chim Acta 2007 Jun 27;592(2):210-7. Epub 2007 Apr 27.

Swammerdam Institute for Life Sciences, Universiteit van-Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands.

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http://dx.doi.org/10.1016/j.aca.2007.04.043DOI Listing
June 2007

Profiling of liquid crystal displays with Raman spectroscopy: preprocessing of spectra.

Appl Spectrosc 2005 Mar;59(3):267-74

Biosystems Data Analysis Group, Swammerdam Institute for Life Sciences, Faculty of Science, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands.

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http://dx.doi.org/10.1366/0003702053585309DOI Listing
March 2005

ANOVA-simultaneous component analysis (ASCA): a new tool for analyzing designed metabolomics data.

Bioinformatics 2005 Jul 12;21(13):3043-8. Epub 2005 May 12.

Biosystems Data Analysis, Faculty of Sciences, University of Amsterdam Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/bti476DOI Listing
July 2005

Analysis of longitudinal metabolomics data.

Bioinformatics 2004 Oct 15;20(15):2438-46. Epub 2004 Apr 15.

Biosystems Data Analysis, Faculty of Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/bth268DOI Listing
October 2004

How to choose the right process analyzer.

Anal Chem 2002 Jul;74(13):368A-373A

University of Amsterdam, The Netherlands.

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http://dx.doi.org/10.1021/ac022066dDOI Listing
July 2002

Selection of optimal process analyzers for plant-wide monitoring.

Anal Chem 2002 Jul;74(13):3105-11

Process Analysis and Chemometrics, University of Amsterdam, The Netherlands.

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http://dx.doi.org/10.1021/ac020148wDOI Listing
July 2002