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Items: 1 to 50 of 61

1.

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

Stelder SK, Benito de Moya C, Hoefsloot HCJ, de Koning LJ, Brul S, de Koster CG.

J Proteome Res. 2018 Feb 2;17(2):903-917. doi: 10.1021/acs.jproteome.7b00732. Epub 2018 Jan 4.

2.

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

Naue J, Hoefsloot HCJ, Kloosterman AD, Verschure PJ.

Forensic Sci Int Genet. 2018 Mar;33:17-23. doi: 10.1016/j.fsigen.2017.11.004. Epub 2017 Nov 13.

PMID:
29175600
3.

Genetic Components of Root Architecture Remodeling in Response to Salt Stress.

Julkowska MM, Koevoets IT, Mol S, Hoefsloot H, Feron R, Tester MA, Keurentjes JJB, Korte A, Haring MA, de Boer GJ, Testerink C.

Plant Cell. 2017 Dec;29(12):3198-3213. doi: 10.1105/tpc.16.00680. Epub 2017 Nov 7.

4.

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

Naue J, Hoefsloot HCJ, Mook ORF, Rijlaarsdam-Hoekstra L, van der Zwalm MCH, Henneman P, Kloosterman AD, Verschure PJ.

Forensic Sci Int Genet. 2017 Nov;31:19-28. doi: 10.1016/j.fsigen.2017.07.015. Epub 2017 Aug 1.

5.

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

Oka R, Zicola J, Weber B, Anderson SN, Hodgman C, Gent JI, Wesselink JJ, Springer NM, Hoefsloot HCJ, Turck F, Stam M.

Genome Biol. 2017 Jul 21;18(1):137. doi: 10.1186/s13059-017-1273-4.

6.

Toward Reliable Lipoprotein Particle Predictions from NMR Spectra of Human Blood: An Interlaboratory Ring Test.

Monsonis Centelles S, Hoefsloot HCJ, Khakimov B, Ebrahimi P, Lind MV, Kristensen M, de Roo N, Jacobs DM, van Duynhoven J, Cannet C, Fang F, Humpfer E, Schäfer H, Spraul M, Engelsen SB, Smilde AK.

Anal Chem. 2017 Aug 1;89(15):8004-8012. doi: 10.1021/acs.analchem.7b01329. Epub 2017 Jul 20.

7.

Culturing Synechocystis sp. Strain PCC 6803 with N2 and CO2 in a Diel Regime Reveals Multiphase Glycogen Dynamics with Low Maintenance Costs.

Angermayr SA, van Alphen P, Hasdemir D, Kramer G, Iqbal M, van Grondelle W, Hoefsloot HC, Choi YH, Hellingwerf KJ.

Appl Environ Microbiol. 2016 Jun 30;82(14):4180-4189. doi: 10.1128/AEM.00256-16. Print 2016 Jul 15.

8.

Identification of Analytical Factors Affecting Complex Proteomics Profiles Acquired in a Factorial Design Study with Analysis of Variance: Simultaneous Component Analysis.

Mitra V, Govorukhina N, Zwanenburg G, Hoefsloot H, Westra I, Smilde A, Reijmers T, van der Zee AG, Suits F, Bischoff R, Horvatovich P.

Anal Chem. 2016 Apr 19;88(8):4229-38. doi: 10.1021/acs.analchem.5b03483. Epub 2016 Mar 28.

PMID:
26959230
9.

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

Kutzera J, Smilde AK, Wilderjans TF, Hoefsloot HC.

PLoS One. 2015 Oct 8;10(10):e0139704. doi: 10.1371/journal.pone.0139704. eCollection 2015.

10.

Scaling in ANOVA-simultaneous component analysis.

Timmerman ME, Hoefsloot HC, Smilde AK, Ceulemans E.

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

11.

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

Borirak O, de Koning LJ, van der Woude AD, Hoefsloot HC, Dekker HL, Roseboom W, de Koster CG, Hellingwerf KJ.

Biotechnol Biofuels. 2015 Aug 5;8:111. doi: 10.1186/s13068-015-0294-z. eCollection 2015.

12.

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

Hasdemir D, Hoefsloot HC, Smilde AK.

BMC Syst Biol. 2015 Jul 8;9:32. doi: 10.1186/s12918-015-0180-0.

13.

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

Borirak O, Rolfe MD, de Koning LJ, Hoefsloot HC, Bekker M, Dekker HL, Roseboom W, Green J, de Koster CG, Hellingwerf KJ.

Biochim Biophys Acta. 2015 Oct;1854(10 Pt A):1269-79. doi: 10.1016/j.bbapap.2015.05.017. Epub 2015 Jun 4.

14.

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

Saccenti E, van Duynhoven J, Jacobs DM, Smilde AK, Hoefsloot HC.

PLoS One. 2015 Mar 18;10(3):e0119856. doi: 10.1371/journal.pone.0119856. eCollection 2015.

15.

Simulation of the rate of transfer of antibiotic resistance between Escherichia coli strains cultured under well controlled environmental conditions.

Smelt JP, Hoefsloot HC, de Koster CG, Schuurmans JM, ter Kuile BH, Brul S.

Food Microbiol. 2015 Feb;45(Pt B):189-94. doi: 10.1016/j.fm.2014.03.019. Epub 2014 Apr 18.

PMID:
25500384
16.

Inversion of peak elution order prevents uniform time alignment of complex liquid-chromatography coupled to mass spectrometry datasets.

Mitra V, Smilde A, Hoefsloot H, Suits F, Bischoff R, Horvatovich P.

J Chromatogr A. 2014 Dec 19;1373:61-72. doi: 10.1016/j.chroma.2014.10.101. Epub 2014 Nov 13.

PMID:
25482036
17.

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

Willemsen AM, Hendrickx DM, Hoefsloot HC, Hendriks MM, Wahl SA, Teusink B, Smilde AK, van Kampen AH.

Mol Biosyst. 2015 Jan;11(1):137-45. doi: 10.1039/c4mb00510d. Epub 2014 Oct 15.

PMID:
25315283
18.

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

Julkowska MM, Hoefsloot HC, Mol S, Feron R, de Boer GJ, Haring MA, Testerink C.

Plant Physiol. 2014 Nov;166(3):1387-402. doi: 10.1104/pp.114.248963. Epub 2014 Sep 30.

19.

Correlated measurement error hampers association network inference.

Kaduk M, Hoefsloot HC, Vis DJ, Reijmers T, van der Greef J, Smilde AK, Hendriks MM.

J Chromatogr B Analyt Technol Biomed Life Sci. 2014 Sep 1;966:93-9. doi: 10.1016/j.jchromb.2014.04.048. Epub 2014 May 2.

PMID:
24951433
20.

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

Hasdemir D, Hoefsloot HC, Westerhuis JA, Smilde AK.

BMC Syst Biol. 2014 May 22;8:61. doi: 10.1186/1752-0509-8-61.

21.

Network identification of hormonal regulation.

Vis DJ, Westerhuis JA, Hoefsloot HC, Roelfsema F, van der Greef J, Hendriks MM, Smilde AK.

PLoS One. 2014 May 22;9(5):e96284. doi: 10.1371/journal.pone.0096284. eCollection 2014.

22.

Inferring protein-protein interaction complexes from immunoprecipitation data.

Kutzera J, Hoefsloot HC, Malovannaya A, Smit AB, Van Mechelen I, Smilde AK.

BMC Res Notes. 2013 Nov 15;6:468. doi: 10.1186/1756-0500-6-468.

23.

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

Abeln S, Molenaar D, Feenstra KA, Hoefsloot HC, Teusink B, Heringa J.

Brief Bioinform. 2013 Sep;14(5):589-98. doi: 10.1093/bib/bbt023. Epub 2013 Apr 19.

PMID:
23603092
24.

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

Christin C, Hoefsloot HC, Smilde AK, Hoekman B, Suits F, Bischoff R, Horvatovich P.

Mol Cell Proteomics. 2013 Jan;12(1):263-76. doi: 10.1074/mcp.M112.022566. Epub 2012 Oct 31.

25.

A critical assessment of SELDI-TOF-MS for biomarker discovery in serum and tissue of patients with an ovarian mass.

Wegdam W, Moerland PD, Meijer D, de Jong SM, Hoefsloot HC, Kenter GG, Buist MR, Aerts JM.

Proteome Sci. 2012 Jul 23;10(1):45. doi: 10.1186/1477-5956-10-45.

26.

Inferring differences in the distribution of reaction rates across conditions.

Hendrickx DM, Hoefsloot HC, Hendriks MM, Vis DJ, Canelas AB, Teusink B, Smilde AK.

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

PMID:
22782002
27.

Between Metabolite Relationships: an essential aspect of metabolic change.

Jansen JJ, Szymańska E, Hoefsloot HC, Jacobs DM, Strassburg K, Smilde AK.

Metabolomics. 2012 Jun;8(3):422-432. Epub 2011 May 24.

28.

Individual differences in metabolomics: individualised responses and between-metabolite relationships.

Jansen JJ, Szymańska E, Hoefsloot HC, Smilde AK.

Metabolomics. 2012 Jun;8(Suppl 1):94-104. Epub 2012 Mar 15.

29.

Detecting regulatory mechanisms in endocrine time series measurements.

Vis DJ, Westerhuis JA, Hoefsloot HC, Roelfsema F, Hendriks MM, Smilde AK.

PLoS One. 2012;7(3):e32985. doi: 10.1371/journal.pone.0032985. Epub 2012 Mar 26.

30.

Global test for metabolic pathway differences between conditions.

Hendrickx DM, Hoefsloot HC, Hendriks MM, Canelas AB, Smilde AK.

Anal Chim Acta. 2012 Mar 16;719:8-15. doi: 10.1016/j.aca.2011.12.051. Epub 2012 Jan 4.

PMID:
22340525
31.

Generic framework for high-dimensional fixed-effects ANOVA.

Smilde AK, Timmerman ME, Hendriks MM, Jansen JJ, Hoefsloot HC.

Brief Bioinform. 2012 Sep;13(5):524-35. doi: 10.1093/bib/bbr071. Epub 2011 Dec 23. Review.

PMID:
22199378
32.

Genome-wide analysis of yeast stress survival and tolerance acquisition to analyze the central trade-off between growth rate and cellular robustness.

Zakrzewska A, van Eikenhorst G, Burggraaff JE, Vis DJ, Hoefsloot H, Delneri D, Oliver SG, Brul S, Smits GJ.

Mol Biol Cell. 2011 Nov;22(22):4435-46. doi: 10.1091/mbc.E10-08-0721. Epub 2011 Sep 30.

33.

To aggregate or not to aggregate high-dimensional classifiers.

Xu CJ, Hoefsloot HC, Smilde AK.

BMC Bioinformatics. 2011 May 13;12:153. doi: 10.1186/1471-2105-12-153.

34.

Reverse engineering of metabolic networks, a critical assessment.

Hendrickx DM, Hendriks MM, Eilers PH, Smilde AK, Hoefsloot HC.

Mol Biosyst. 2011 Feb;7(2):511-20. doi: 10.1039/c0mb00083c. Epub 2010 Nov 10. Review.

PMID:
21069230
35.

Dynamic metabolomic data analysis: a tutorial review.

Smilde AK, Westerhuis JA, Hoefsloot HC, Bijlsma S, Rubingh CM, Vis DJ, Jellema RH, Pijl H, Roelfsema F, van der Greef J.

Metabolomics. 2010 Mar;6(1):3-17. Epub 2009 Dec 4.

36.

Multivariate paired data analysis: multilevel PLSDA versus OPLSDA.

Westerhuis JA, van Velzen EJ, Hoefsloot HC, Smilde AK.

Metabolomics. 2010 Mar;6(1):119-128. Epub 2009 Oct 28.

37.

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

Xu CJ, Hoefsloot HC, Dijkstra M, Havenga K, Roelofsen H, Vonk RJ, Smilde AK.

Anal Chim Acta. 2010 Feb 19;661(1):20-7. doi: 10.1016/j.aca.2009.12.003. Epub 2009 Dec 11.

PMID:
20113711
38.

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

Christin C, Hoefsloot HC, Smilde AK, Suits F, Bischoff R, Horvatovich PL.

J Proteome Res. 2010 Mar 5;9(3):1483-95. doi: 10.1021/pr9010124.

PMID:
20070124
39.

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

Jansen JJ, van Dam NM, Hoefsloot HC, Smilde AK.

BMC Bioinformatics. 2009 Dec 16;10:425. doi: 10.1186/1471-2105-10-425.

40.

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

Jansen JJ, Smit S, Hoefsloot HC, Smilde AK.

Phytochem Anal. 2010 Jan-Feb;21(1):48-60. doi: 10.1002/pca.1181. Review.

PMID:
19904732
41.

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

Vis DJ, Westerhuis JA, Hoefsloot HC, Pijl H, Roelfsema F, van der Greef J, Smilde AK.

Am J Physiol Endocrinol Metab. 2010 Feb;298(2):E146-55. doi: 10.1152/ajpendo.00048.2009. Epub 2009 Oct 27.

42.

Gaucher disease: a model disorder for biomarker discovery.

Boot RG, van Breemen MJ, Wegdam W, Sprenger RR, de Jong S, Speijer D, Hollak CE, van Dussen L, Hoefsloot HC, Smilde AK, de Koster CG, Vissers JP, Aerts JM.

Expert Rev Proteomics. 2009 Aug;6(4):411-9. doi: 10.1586/epr.09.54. Review.

PMID:
19681676
43.

Improved cholesterol phenotype analysis by a model relating lipoprotein life cycle processes to particle size.

van Schalkwijk DB, de Graaf AA, van Ommen B, van Bochove K, Rensen PC, Havekes LM, van de Pas NC, Hoefsloot HC, van der Greef J, Freidig AP.

J Lipid Res. 2009 Dec;50(12):2398-411. doi: 10.1194/jlr.M800354-JLR200. Epub 2009 Jun 10.

44.

Classification-based comparison of pre-processing methods for interpretation of mass spectrometry generated clinical datasets.

Wegdam W, Moerland PD, Buist MR, van Themaat EVL, Bleijlevens B, Hoefsloot HC, de Koster CG, Aerts JM.

Proteome Sci. 2009 May 14;7:19. doi: 10.1186/1477-5956-7-19.

45.

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

van Velzen EJ, Westerhuis JA, van Duynhoven JP, van Dorsten FA, Hoefsloot HC, Jacobs DM, Smit S, Draijer R, Kroner CI, Smilde AK.

J Proteome Res. 2008 Oct;7(10):4483-91. doi: 10.1021/pr800145j. Epub 2008 Aug 28.

PMID:
18754629
46.

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

Christin C, Smilde AK, Hoefsloot HC, Suits F, Bischoff R, Horvatovich PL.

Anal Chem. 2008 Sep 15;80(18):7012-21. doi: 10.1021/ac800920h. Epub 2008 Aug 21.

PMID:
18715018
47.

Biomarkers for lysosomal storage disorders: identification and application as exemplified by chitotriosidase in Gaucher disease.

Aerts JM, van Breemen MJ, Bussink AP, Ghauharali K, Sprenger R, Boot RG, Groener JE, Hollak CE, Maas M, Smit S, Hoefsloot HC, Smilde AK, Vissers JP, de Jong S, Speijer D, de Koster CG.

Acta Paediatr. 2008 Apr;97(457):7-14. doi: 10.1111/j.1651-2227.2007.00641.x. Review.

PMID:
18339181
48.

A classification model for the Leiden proteomics competition.

Hoefsloot HC, Smit S, Smilde AK.

Stat Appl Genet Mol Biol. 2008;7(2):Article8. doi: 10.2202/1544-6115.1351. Epub 2008 Feb 19.

PMID:
18312222
49.

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

an der Heiden MR, Plenio H, Immel S, Burello E, Rothenberg G, Hoefsloot HC.

Chemistry. 2008;14(9):2857-66. doi: 10.1002/chem.200701418.

PMID:
18288651
50.

Statistical data processing in clinical proteomics.

Smit S, Hoefsloot HC, Smilde AK.

J Chromatogr B Analyt Technol Biomed Life Sci. 2008 Apr 15;866(1-2):77-88. Epub 2007 Nov 4. Review.

PMID:
18033744

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