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12 papers found.
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BSPAT: a fast online tool for DNA methylation co-occurrence pattern analysis based on high-throughput bisulfite sequencing data

Background Bisulfite sequencing is one of the most widely used technologies in analyzing DNA methylation patterns, which are important in understanding and characterizing the mechanism of DNA methylation and its functions in disease development. Efficient and user-friendly tools are critical in carrying out such analysis on high-throughput bisulfite sequencing data. However...

Bellerophon: a hybrid method for detecting interchromo-somal rearrangements at base pair resolution using next-generation sequencing data

Matthew Hayes 0 Jing Li 0 0 Department of Electrical Engineering and Computer Science, Case Western Reserve University , 10900 Euclid Ave., Cleveland, OH , USA Background: Somatically-acquired

A new statistical approach to combining p-values using gamma distribution and its application to genome-wide association study

Background Combining information from different studies is an important and useful practice in bioinformatics, including genome-wide association study, rare variant data analysis and other set-based analyses. Many statistical methods have been proposed to combine p-values from independent studies. However, it is known that there is no uniformly most powerful test under all...

Evaluation and integration of existing methods for computational prediction of allergens

Background Allergy involves a series of complex reactions and factors that contribute to the development of the disease and triggering of the symptoms, including rhinitis, asthma, atopic eczema, skin sensitivity, even acute and fatal anaphylactic shock. Prediction and evaluation of the potential allergenicity is of importance for safety evaluation of foods and other environment...

Accurate HLA type inference using a weighted similarity graph

Background The human leukocyte antigen system (HLA) contains many highly variable genes. HLA genes play an important role in the human immune system, and HLA gene matching is crucial for the success of human organ transplantations. Numerous studies have demonstrated that variation in HLA genes is associated with many autoimmune, inflammatory and infectious diseases. However...

A novel approach for haplotype-based association analysis using family data

Background Haplotype-based approaches have been extensively studied for case-control association mapping in recent years. It has been shown that haplotype methods can provide more consistent results comparing to single-locus based approaches, especially in cases where causal variants are not typed. Improved power has been observed by clustering similar or rare haplotypes into...

Generating samples for association studies based on HapMap data

Background With the completion of the HapMap project, a variety of computational algorithms and tools have been proposed for haplotype inference, tag SNP selection and genome-wide association studies. Simulated data are commonly used in evaluating these new developed approaches. In addition to simulations based on population models, empirical data generated by perturbing real...

Phylogenetic analysis of modularity in protein interaction networks

Background In systems biology, comparative analyses of molecular interactions across diverse species indicate that conservation and divergence of networks can be used to understand functional evolution from a systems perspective. A key characteristic of these networks is their modularity, which contributes significantly to their robustness, as well as adaptability. Consequently...

CASCADE_SCAN: mining signal transduction network from high-throughput data based on steepest descent method

Jing Li 0 Tieqiao Wen 0 0 Laboratory of Molecular Neurobiology, School of Life Sciences and Institute of Systems Biology, Shanghai University , Shanghai 200444 , China 1 Department of Mathematics

Haplotype-based quantitative trait mapping using a clustering algorithm

Background With the availability of large-scale, high-density single-nucleotide polymorphism (SNP) markers, substantial effort has been made in identifying disease-causing genes using linkage disequilibrium (LD) mapping by haplotype analysis of unrelated individuals. In addition to complex diseases, many continuously distributed quantitative traits are of primary clinical and...

Discovery of time-delayed gene regulatory networks based on temporal gene expression profiling

Background It is one of the ultimate goals for modern biological research to fully elucidate the intricate interplays and the regulations of the molecular determinants that propel and characterize the progression of versatile life phenomena, to name a few, cell cycling, developmental biology, aging, and the progressive and recurrent pathogenesis of complex diseases. The vast...