Computational methods for the analysis of bacterial gene regulation Brouwer, Rutger Wubbe Willem

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1 University of Groningen Computational methods for the analysis of bacterial gene regulation Brouwer, Rutger Wubbe Willem IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below. Document Version Publisher's PDF, also known as Version of record Publication date: 2014 Link to publication in University of Groningen/UMCG research database Citation for published version (APA): Brouwer, R. W. W. (2014). Computational methods for the analysis of bacterial gene regulation Groningen: s.n. Copyright Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons). Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. Downloaded from the University of Groningen/UMCG research database (Pure): For technical reasons the number of authors shown on this cover page is limited to 10 maximum. Download date:

2 Computational methods for the analysis of bacterial gene regulation Rutger Brouwer

3 ISBN/EAN: The work described in this thesis has been performed in the Molecular Genetics group of the Groningen Biomolecular Sciences and Biotechnology Institute (GBB) at the Faculty of mathematics and natural sciences (FWN) of the University of Groningen (RUG). Financial support was received from the Netherlands Bioinformatics Centre (NBIC) through a grant of the BioRange 1 program. The author gratefully acknowledges the Groningen Biomolecular Sciences and Biotechnology Institute for financially supporting the printing of this thesis. Printed by Ipskamp Drukkers

4 Computational methods for the analysis of bacterial gene regulation Proefschrift ter verkrijging van de graad van doctor aan de Rijksuniversiteit Groningen op gezag van de rector magnificus, prof. dr. E. Sterken en volgens besluit van het College voor Promoties. De openbare verdediging zal plaatsvinden op vrijdag 10 januari 2014 om uur door Rutger Wubbe Willem Brouwer geboren op 13 januari, 1982 te Stadskanaal

5 Promotor: Prof. dr. O.P. Kuipers Copromotor: Dr. S.A.F.T. van Hijum Beoordelingscommissie: Prof. dr. R.J. Siezen Prof. dr. B. Teusink Prof dr. J.B.T.M. Roerdink

6 Contents Introduction... 3 Abstract... 3 Bacteria and model organisms... 4 Gene transcription... 4 Transcriptomics and DNA microarrays... 8 Clustering Gene Ontologies Machine learning Thesis outline The relative value of operon predictions Abstract Introduction Computational operon predictions Reported performance of operon prediction methods Comparing the performance of operon predictions Conclusions Operon prediction: back to basics Abstract Introduction Results Discussion Materials and Methods Supplementary materials MINOMICS: visualizing prokaryote transcriptomics and proteomics data in a genomic context Abstract Introduction Features

7 Implementation Conclusions The chronotranscriptome of Lactococcus lactis reveals extensive reprogramming of gene expression during growth Abstract Introduction Results Discussion Materials and methods Supplementary materials The expressed genetic network of Lactococcus lactis subspecies cremoris MG1363 grown under laboratory conditions Abstract Introduction Results Conclusions and discussion Materials and Methods Supplementary materials General discussion Summary Transcriptional organization in bacteria Concluding remarks and future prospects References Nederlandse samenvatting Dankwoord