Dongdong Pan

Yunnan University · Department of Statistics

Current genome-wide association studies (GWAS) focusing on relatively common single-nucleotide polymorphisms (SNPs) usually adopt a cost-effective multi-staged design in which a proportion of the total samples are genotyped using a commercial SNP array with a reasonably good coverage of the whole genome at the initial stage, and a list of promising...

The sum of squared score (SSU) and sequence kernel association test (SKAT) are the two good alternative tests for genetic association studies in case–control data. Both SSU and SKAT are derived through assuming a dose-response model between the risk of disease and genotypes. However, in practice, the real genetic mode of inheritance is impossible t...

1. Some wild bees can persist in human-altered habitats in the face of global wild bee decline. To date, however, little is known about why those bees can tolerate human disturbances. Here we hypothesized that wild bees living in human-altered habitats could achieve their nesting resources and floral resources. Moreover, persistent provision of tho...

Background Skewed X chromosome inactivation (XCI), which is a non-random process, is frequently observed in both healthy and affected females. Furthermore, skewed XCI has been reported to be related to many X-linked diseases. However, no statistical method is available in the literature to measure the degree of the skewness of XCI for case-control...

In the past decade, genome-wide association studies have identified thousands of susceptible variants associated with complex human diseases and traits. Conducting follow-up genetic association studies has become a standard approach to validate the findings of genome-wide association studies. One problem of high interest in genetic association stud...

The methods commonly used to test the associations between ordinal phenotypes and genotypes often treat either the ordinal phenotype or the genotype as continuous variables. To address limitations of these approaches, we propose a model where both the ordinal phenotype and the genotype are viewed as manifestations of an underlying multivariate norm...

Landscape composition is assumed to modify spatial foraging patterns of bees in agricultural ecosystems which subsequently influence pollination services provided to crops. However, empirical evidence to support this prediction is scarce. We investigated the influences of semi-natural habitats and nesting resources on concentration effect and wayla...

The genetic models are greatly important in the analysis of genetic epidemiologic studies and many of the studies are conducted using the trend test under the additive model. However, for many complex diseases and traits, the underlying genetic model for a genetic locus is usually uncertain. So a robust test free of genetic model is appropriate. In...

In genome-wide association studies (GWASs) to detect the disease-associated genetic variants, two-stage design has received much attention because of its cost effectiveness and high efficiency. Under the framework of a two-stage design, it has been shown that joint analysis is more powerful than replication-based analysis. Several robust tests have...

Principal component analysis (PCA) is a useful tool to identify important linear combination of correlated variables in multivariate analysis and has been applied to detect association between genetic variants and human complex diseases of interest. How to choose adequate number of principal components (PCs) to represent the original system in an o...

Bee species interactions can benefit plant pollination through synergistic effects and complementary effects, or can be of detriment to plant pollination through competition effects by reducing visitation by effective pollinators. Since specific bee interactions influence the foraging performance of bees on flowers, they also act as drivers to regu...

Characteristics of the full and simplified BRT models a. (DOC)

Four instances of honey bees (one, two, three and four honey bees visiting a single squash flower) in the LN habitats. One honey bee (A), two honey bees (B), three honey bees (C) and four honey bees (D). (TIF)

Pearson correlation coefficients among the percentages of the four instances of honey bees (one, two, three, and four honey bees visiting a single squash flower). *** < 0.001; ** < 0.01; * < 0.05; ns: not significant. (DOC)

This work considers two types of combined test statistics from high dimensional normal distributions (in which each unit is truncated), which often appear in current genetic association studies or micro-array experiments. Some useful theoretical results, specifically, the cumulative distribution functions of the proposed test statistics are obtaine...

Joint models for longitudinal and survival data are often used to investigate the association between longitudinal data and survival data in many studies. A common assumption for joint models is that random effects are distributed as a fully parametric distribution such as multivariate normal distribution. The fully parametric distribution assumpti...

Genomic imprinting is a genetic phenomenon in which certain alleles are differentially expressed in a parent-of-origin-specific manner, and plays an important role in the study of complex traits. For a diallelic marker locus in human, the parentalasymmetry tests Q-PAT(c) with any constant c were developed to detect parent-of-origin effects for quan...

Many studies have investigated the individual effects of sedimentation or inundation on the performance of wetland plants, but few have examined the combined influence of these processes. Wetland plants might show greater morphological plasticity in response to inundation than to sedimentation when these processes occur simultaneously since inundat...

Growth, below/above-ground mass ratio (BG:AG ratio), root morphology, carbohydrate content, and alcohol dehydrogenase (ADH) activity in the low-elevation species Phalaris arundinacea and the high-elevation species Miscanthus sacchariflorus buried under 0, 5, and 10 cm of sediment were investigated one, two, and three months after burial. Biomass ac...

Genome-wide association studies (GWASs) in identifying the disease-associated genetic variants have been proved to be a great pioneering work. Two-stage design and analysis are often adopted in GWASs. Considering the genetic model uncertainty, many robust procedures have been proposed and applied in GWASs. However, the existing approaches mostly fo...

Appendix for the main text. The file (including Appendix A, B, C) is a Microsoft Word document. Appendix A gives a detailed description of the joint distribution of the additive trend test statistic T1A in Stage 1 and the joint additive trend test statistic TJA. Appendix B gives a detailed description of the correlation coefficient between the rece...

The cost efficient two-stage design is often used in genome-wide association studies (GWASs) in searching for genetic loci underlying the susceptibility for complex diseases. Replication-based analysis, which considers data from each stage separately, often suffers from loss of efficiency. Joint test that combines data from both stages has been pro...