University of Groningen
Computational Methods for High-Throughput Small RNA Analysis in Plants Monteiro Morgado, Lionel
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: 2018
Link to publication in University of Groningen/UMCG research database
Citation for published version (APA):
Monteiro Morgado, L. (2018). Computational Methods for High-Throughput Small RNA Analysis in Plants. University of Groningen.
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): http://www.rug.nl/research/portal. For technical reasons the number of authors shown on this cover page is limited to 10 maximum.
Lionel Morgado
Computational Methods for
High-Throughput
The research described in this thesis was carried out at the Groningen Bioinformatics Centre (GBiC), Faculty of Sciences and Engineering, University of Groningen, The Netherlands.
This thesis should be cited as:
Morgado, L (2017) Computational Methods for High-Throughput Small RNA Analysis in Plants. PhD Thesis, University of Groningen, Groningen, The Netherlands.
© Lionel Morgado 2017 – All rights reserved
No part of this book may be reproduced, stored in a retrieval system, or transmitted in any form or by any means electronic, mechanical, photocopying, recording or otherwise without the prior permission of the author.
Printing: Ridderprint BV | www.ridderprint.nl ISBN (Print): 978-94-034-0541-4
Computational Methods for
High-Throughput
Small RNA Analysis in Plants
PhD thesis
to obtain the degree of PhD at the University of Groningen
on the authority of the Rector Magnificus Prof. E. Sterken
and in accordance with
the decision by the College of Deans. This thesis will be defended in public on
Monday 26 March 2018 at 09.00 hours by
Lionel Monteiro Morgado
born on 24 January 1984 in Saint-Chamond, France
Supervisor Prof. R. C. Jansen Co-supervisor Prof. F. Johannes Assessment Committee Prof. J. Kok Prof. O. C. M. Sibon Prof. D. de Ridder
CONTENTS
CHAPTER 1 Introduction 7
CHAPTER 2 Computational tools for plant small RNA detection and
categorization
21
CHAPTER 3 Learning sequence patterns of AGO-sRNA affinity from
high-throughput sequencing libraries to improve in silico functional sRNA detection and classification in plants
43
CHAPTER 4 hibeRNAte: a framework for plant small RNA analysis 77
CHAPTER 5 Epigenetic mapping of the Arabidopsis metabolome reveals
mediators of the epigenotype-phenotype map
89
CHAPTER 6 Small RNA reflects grandparental environments in apomictic
dandelion
109
CHAPTER 7 Conclusions and perspectives 121
REFERENCES 131
SUMMARY, SAMENVATTING, SUMÁRIO 155
ACKNOWLEDGEMENTS 163
