ausblenden:
Schlagwörter:
high-throughput sequencing; read counts; statistical modeling; CNV; RNA-Seq; ChIP-Seq
Zusammenfassung:
All of the work presented in this thesis grew out of collaborations with other researchers.
For each chapter, I brie
y summarize my contribution and acknowledge the contributions
of others.
Chapter 2 represents a conceptual framework for modeling read counts using various
distributions. These ideas grew out of conversations with Ho-Ryun Chung at the Max
Planck Institute for Molecular Genetics (MPIMG) in Berlin and Simon Anders at the
European Molecular Biology Laboratories (EMBL) in Heidelberg.
Chapter 3 was published in Statistical Applications in Genetics and Molecular Biology
[1]. The idea for detecting copy number variants in exome-enriched sequencing data was
proposed by Stefan Haas and with Alena van Bommel various methods were tested and
evaluated. My contribution was developing the hidden Markov model, implementing the
software and testing the performance. I wish to acknowledge the X-linked intellectual
disabilities project team at MPIMG including H.-Hilger Ropers, Vera Kalscheuer, Ruping
Sun, Anne-Katrin Emde, Wei Chen, Hao Hu and Tomasz Zemojtel, who provided helpful
discussions.
Chapter 4 resulted from a 5 month visit to the group of Wolfgang Huber at EMBL in
Heidelberg. Simon Anders proposed the idea of incorporating priors for dispersion and
log fold change into the DESeq framework. My contribution was to implement these new
statistical methods as a new package DESeq2, with closer integration with core Bioconductor
packages. I would like to acknowledge all the members of the Huber group for
helpful discussions.
Chapter 5 resulted from a collaboration with the Transcriptional Regulation Group of
Sebastiaan Meijsing at the MPIMG. I would like to thank Stephan Starick who initially
proposed to investigate the interaction between glucocorticoid receptor and the chromatin
landscape. My contribution was the statistical analysis presented in the chapter. Sebastiaan
Meijsing provided valuable feedback during the evolution of the project. I wish to
acknowledge the contributions of Morgane Thomas-Chollier, Katja Borzym, Sam Cooper
and Ho-Ryun Chung.
