Theo A Knijnenburg

Theo A Knijnenburg

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Theo A Knijnenburg

Theo A Knijnenburg

Publications by authors named "Theo A Knijnenburg"

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30Publications

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Increased levels of RECQ5 shift DNA repair from canonical to alternative pathways.

Nucleic Acids Res 2018 10;46(18):9496-9509

Department of Biochemistry, University of Washington, 1959 NE Pacific St., Seattle, WA 98195, USA.

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http://dx.doi.org/10.1093/nar/gky727DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6182128PMC
October 2018

Logic models to predict continuous outputs based on binary inputs with an application to personalized cancer therapy.

Sci Rep 2016 11 23;6:36812. Epub 2016 Nov 23.

Netherlands Cancer Institute, Amsterdam, and The Faculty of EEMCS, Delft University of Technology, Delft, The Netherlands.

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http://dx.doi.org/10.1038/srep36812DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5120272PMC
November 2016

Combining dependent P-values with an empirical adaptation of Brown's method.

Bioinformatics 2016 09;32(17):i430-i436

Institute for Systems Biology, Seattle, WA 98109-5263, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw438DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5013915PMC
September 2016

A multilevel pan-cancer map links gene mutations to cancer hallmarks.

Chin J Cancer 2015 Sep 14;34(10):439-49. Epub 2015 Sep 14.

Institute for Systems Biology, Seattle, WA, 98109, USA.

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http://dx.doi.org/10.1186/s40880-015-0050-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4593384PMC
September 2015

SMARCE1 suppresses EGFR expression and controls responses to MET and ALK inhibitors in lung cancer.

Cell Res 2015 Apr 6;25(4):445-58. Epub 2015 Feb 6.

Department of Biochemistry, The Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, QC H3G 1Y6, Canada.

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http://dx.doi.org/10.1038/cr.2015.16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4387553PMC
April 2015

Deletion of the Saccharomyces cerevisiae ARO8 gene, encoding an aromatic amino acid transaminase, enhances phenylethanol production from glucose.

Yeast 2015 Jan 13;32(1):29-45. Epub 2014 May 13.

Department of Biotechnology, Delft University of Technology, Delft, The Netherlands; Kluyver Centre for Genomics of Industrial Fermentation, Delft, The Netherlands.

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http://dx.doi.org/10.1002/yea.3015DOI Listing
January 2015

A regression model approach to enable cell morphology correction in high-throughput flow cytometry.

Mol Syst Biol 2011 Sep 27;7:531. Epub 2011 Sep 27.

Institute for Systems Biology, 401 Terry Avenue North, 1441 North 34th Street, Seattle, WA 98109-5234, USA.

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http://msb.embopress.org/cgi/doi/10.1038/msb.2011.64
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http://dx.doi.org/10.1038/msb.2011.64DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3202802PMC
September 2011

Fewer permutations, more accurate P-values.

Bioinformatics 2009 Jun;25(12):i161-8

Institute for Systems Biology, Seattle, WA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btp211DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2687965PMC
June 2009

Physiological and transcriptional responses of Saccharomyces cerevisiae to zinc limitation in chemostat cultures.

Appl Environ Microbiol 2007 Dec 12;73(23):7680-92. Epub 2007 Oct 12.

Yeast Research Group, Division of Molecular and Life Sciences, University of Abertay, Dundee DD1 1HG, Scotland.

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http://dx.doi.org/10.1128/AEM.01445-07DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168061PMC
December 2007

Quantitative proteomics and transcriptomics of anaerobic and aerobic yeast cultures reveals post-transcriptional regulation of key cellular processes.

Microbiology 2007 Nov;153(Pt 11):3864-78

Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands.

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http://dx.doi.org/10.1099/mic.0.2007/009969-0DOI Listing
November 2007

Generic and specific transcriptional responses to different weak organic acids in anaerobic chemostat cultures of Saccharomyces cerevisiae.

FEMS Yeast Res 2007 Sep 30;7(6):819-33. Epub 2007 Apr 30.

Department of Biotechnology, Delft University of Technology, Delft, The Netherlands.

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http://dx.doi.org/10.1111/j.1567-1364.2007.00242.xDOI Listing
September 2007

Integration of known transcription factor binding site information and gene expression data to advance from co-expression to co-regulation.

Genomics Proteomics Bioinformatics 2007 May;5(2):86-101

Information and Communication Theory Group, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, 2600 GA Delft, the Netherlands.

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http://linkinghub.elsevier.com/retrieve/pii/S167202290760019
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http://dx.doi.org/10.1016/S1672-0229(07)60019-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5054099PMC
May 2007

Exploiting combinatorial cultivation conditions to infer transcriptional regulation.

BMC Genomics 2007 Jan 22;8:25. Epub 2007 Jan 22.

Information and Communication Theory Group, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Mekelweg 4, 2628 CD Delft, The Netherlands.

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http://dx.doi.org/10.1186/1471-2164-8-25DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1797021PMC
January 2007