Data structures and algorithms for analysis of alternative splicing with RNA-seq data [Elektronische Ressource] / Marcel H. Schulz

Data Structures and Algorithmsfor Analysis of Alternative Splicingwith RNA-Seq DataMarcel H. SchulzJune 2010Dissertation zur Erlangung des Gradeseines Doktors der Naturwissenschaften (Dr. rer. nat.)am Fachbereich Mathematik und Informatikder Freien Universität BerlinGutachter:Prof. Dr. Martin VingronProf. Dr. Jens Stoye1. Referent: Prof. Dr. Martin Vingron2. Prof. Dr. Jens StoyeTag der Promotion: 26 August 2010PrefaceThe first part of the thesis in Chapter 3 was published in the journal Science, as partof a collaborative study that addressed the first application of RNA-Seq experimentsto two human cell lines in 2008 [147]. The methods for prediction and quantificationof alternative isoforms and their application presented in Chapter 3 and 4 appearedin the journal Nucleic Acids Research in 2010 [129]. The last part about the de novotranscriptome assembly method Oases has not been published yet, but a manuscriptis in preparation. The successful application of Oases to human, fly, and worm RNA-Seq data will be published in the report about the RGASP competition this year.My contributions to these papers was the design of statistical methods and the anal-ysis of alternative splicing with junctions reads for the Science paper. I designed,implemented, and analyzed the CASI and DASI method. I was involved in the con-ception and analysis of the POEM method, analysis of the exon array data, as wellas primer design for the PCR experiments and their evaluation.