Related papers: Estimating heterozygosity from a low-coverage geno…

Heterogeneity is a hallmark of complex diseases. Regression-based heterogeneity analysis, which is directly concerned with outcome-feature relationships, has led to a deeper understanding of disease biology. Such an analysis identifies the…

The rapidly changing landscape of sequencing technologies brings new opportunities to genomics research. Longer sequence reads and higher sequence throughput coupled with ever-improving base accuracy and decreasing per-base cost is now…

The diversity of virus populations within single infected hosts presents a major difficulty for the natural immune response as well as for vaccine design and antiviral drug therapy. Recently developed pyrophosphate based sequencing…

Complete genome sequences contain valuable information about natural selection, but extracting this information for short, widely scattered noncoding elements remains a challenging problem. Here we introduce a new computational method for…

DNA sequencing has faced a huge demand since it was first introduced as a service to the public. This service is often offloaded to the sequencing companies who will have access to full knowledge of individuals' sequences, a major violation…

Much of the on-going statistical analysis of DNA sequences is focused on the estimation of characteristics of coding and non-coding regions that would possibly allow discrimination of these regions. In the current approach, we concentrate…

Genome-Wide Association Studies (GWAS) explain only a small fraction of heritability for most complex human phenotypes. Genomic heritability estimates the variance explained by the SNPs on the whole genome using mixed models and accounts…

Intercellular heterogeneity serves as both a confounding factor in studying individual clones and an information source in characterizing any heterogeneous tissues, such as blood, tumor systems. Due to inevitable sequencing errors and other…

Genomic datasets generated with massively parallel sequencing methods have the potential to propel systematics in new and exciting directions, but selecting appropriate markers and methods is not straightforward. We applied two approaches…

Having a precise knowledge of the dispersal ability of a population in a heterogeneous environment is of critical importance in agroecology and conservation biology as it can provide management tools to limit the effects of pests or to…

We consider the estimation of densities in multiple subpopulations, where the available sample size in each subpopulation greatly varies. This problem occurs in epidemiology, for example, where different diseases may share similar…

Current techniques in sequencing a genome allow a service provider (e.g. a sequencing company) to have full access to the genome information, and thus the privacy of individuals regarding their lifetime secret is violated. In this paper, we…

Haplotypes, the global patterns of DNA sequence variation, have important implications for identifying complex traits. Recently, blocks of limited haplotype diversity have been discovered in human chromosomes, intensifying the research on…

Sex difference in allele frequency is an emerging topic that is critical to our understanding of ascertainment bias, as well as data quality particularly of the largely overlooked X chromosome. To detect sex difference in allele frequency…

A key challenge in building effective regression models for large and diverse populations is accounting for patient heterogeneity. An example of such heterogeneity is in health system risk modeling efforts where different combinations of…

Selection bias is a serious potential problem for inference about relationships of scientific interest based on samples without well-defined probability sampling mechanisms. Motivated by the potential for selection bias in (a) estimated…

We construct genomic predictors for heritable and extremely complex human quantitative traits (height, heel bone density, and educational attainment) using modern methods in high dimensional statistics (i.e., machine learning). Replication…

Successful sequencing experiments require judicious sample selection. However, this selection must often be performed on the basis of limited preliminary data. Predicting the statistical properties of the final sample based on preliminary…

In biomedical research, to obtain more accurate prediction results from a target study, leveraging information from multiple similar source studies is proved to be useful. However, in many biomedical applications based on real-world data,…

Summary: We present a new tool to correct sequencing errors in Illumina data produced from high-coverage whole-genome shotgun resequencing. It uses a non-greedy algorithm and shows comparable performance and higher accuracy in an evaluation…