Heterogeneous data analysis for annotation of microRNAs and novel genome assembly
Zhang, Y.
Citation
Zhang, Y. (2011, November 24). Heterogeneous data analysis for annotation of microRNAs and novel genome assembly. Retrieved from https://hdl.handle.net/1887/18145
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Heterogeneous Data Analysis for Annotation of microRNAs and Novel Genome Assembly
Yanju Zhang
This work was part of the BioRange programme of the Netherlands Bioinformatics Centre (NBIC), which is supported by a BSIK grant through the Netherlands Genomics Initiative (NGI).
Printed by Ridderprint, RIDDERKERK
ISBN 978-90-5335-491-9
Heterogeneous Data Analysis for Annotation of microRNAs and Novel Genome Assembly
PROEFSCHRIFT
ter verkrijging van
de graad van Doctor aan de Universiteit Leiden,
op gezag van Rector Magnificus Prof. mr. P.F. van der Heijden, volgens besluit van het College voor Promoties
te verdedigen op donderdag 24 november 2011 klokke 16.15 uur
door
Yanju Zhang
Geboren te Guilin, China, in 1980
Promotiecommissie
Promotor:
Prof. dr. J.N. Kok
Co-promotor:
Dr. Ir. F.J. Verbeek
Overige Leden
Prof. dr H.P. Spaink Leiden University
Prof. dr. A.P.J.M Siebes Utrecht University
Prof. dr. H. Blokkeel Katholieke Universiteit Leuven, Belgium
Dr. E. Vreugdenhil Leiden University
Contents
INTRODUCTION
Chapter 1: Introduction . . . 7
MIRNA ANNOTATION Chapter 2: Screen of MicroRNA Targets in Zebrafish Using Heterogeneous Data Sources: A Case Study for Dre-miR-10 and Dre-miR-196 . . . 25
Chapter 3: miRNA Target Prediction through Mining of miRNA Relationships . . . 45
Chapter 4: Comparison and Integration of Target Prediction Algorithms for microRNA Studies . . . 73
GENE ANNOTATION Chapter 5: Identification of Common Carp Innate Immune Genes with Whole-Genome Sequencing and RNA-Seq Data . . . 93
CONCULUSIONS Chapter 6: Conclusions . . . 115
APPENDICES Summary . . . 123
Samenvatting . . . 129
List of publications . . . 135
Curriculum Vitae . . . 137
Acknowledgements . . . 139
