With the availability of increasing amounts of genomic sequences, it is becoming clear that genomes experience horizontal transfer and incorporation of genetic information. However, to what extent such horizontal gene transfer (HGT) affects the core genealogical history of organisms remains controversial. Based on initial analyses of complete genomic sequences, HGT has been suggested to be so w...

Genomic imprinting has been thought to play an important role in seed development in flowering plants. Seed in a flowering plant normally contains diploid embryo and triploid endosperm. Empirical studies have shown that some economically important endosperm traits are genetically controlled by imprinted genes. However, the exact number and location of the imprinted genes are largely unknown due...

This thesis deals with statistical questions raised by the analysis of highdimensional genomic data for cancer research. In the first part, we study asymptotic properties of multiple testing procedures that aim at controlling the False Discovery Rate (FDR), that is, the expected False Discovery Proportion (FDP) among rejected hypotheses. We develop a versatile formalism to calculate the asympto...

MOTIVATION As cancer progresses, DNA copy number aberrations accumulate and the genomic entropy (chromosomal disorganization) increases. For this surge to have any oncogenetic effect, it should (to some extent) be reflected at other molecular levels of the cancer cell, in particular that of the transcriptome. Such a coincidence of cancer progression and the propagation of an entropy increase th...

Array-based comparative genomic hybridization (ABCGH) is an emerging high-resolution and high-throughput molecular genetic technique that allows genome-wide screening for chromosome alterations associated with tumorigenesis. Like the cDNA microarrays, ABCGH uses two differentially labeled test and reference DNAs which are cohybridized to cloned genomic fragments immobilized on glass slides. The...

RNA-Seq technologies are quickly revolutionizing genomic studies, and statistical methods for RNA-seq data are under continuous development. Timely review and comparison of the most recently proposed statistical methods will provide a useful guide for choosing among them for data analysis. Particular interest surrounds the ability to detect differential expression (DE) in genes. Here we compare...

BACKGROUND One of the major mechanisms of generating mRNA diversity is alternative splicing, a regulated process that allows for the flexibility of producing functionally different proteins from the same genomic sequences. This process is often altered in cancer cells to produce aberrant proteins that drive the progression of cancer. A better understanding of the misregulation of alternative sp...

Population differentiation (PD) and ecological association (EA) tests have recently emerged as prominent statistical methods to investigate signatures of local adaptation using population genomic data. Based on statistical models, these genomewide testing procedures have attracted considerable attention as tools to identify loci potentially targeted by natural selection. An important issue with...

MOTIVATION False discovery rate (FDR) is defined as the expected percentage of false positives among all the claimed positives. In practice, with the true FDR unknown, an estimated FDR can serve as a criterion to evaluate the performance of various statistical methods under the condition that the estimated FDR approximates the true FDR well, or at least, it does not improperly favor or disfavor...