About
31
Publications
4,077
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
293
Citations
Citations since 2017
Publications
Publications (31)
Genome-wide association study data analyses often face two significant challenges: (i) high dimensionality of single-nucleotide polymorphism (SNP) genotypes and (ii) imputation of missing values. SNPs are not independent due to physical linkage and natural selection. The correlation of nearby SNPs is known as linkage disequilibrium (LD), which can...
The HapMap (haplotype map) projects have produced valuable genetic resources in life science research communities, allowing researchers to investigate sequence variations and conduct genome-wide association study (GWAS) analyses. A typical HapMap project may require sequencing hundreds, even thousands, of individual lines or accessions within a spe...
Brachypodium distachyon is an annual C3 grass used as a monocot model system for functional genomics research. Insertional mutagenesis is a powerful tool for both forward and reverse genetics studies. In this study, we explored the possibility of using tobacco retrotransposon Tnt1 to create a transposon‐based insertion mutant population in B. dista...
Genome-wide association study (GWAS) is a powerful approach that has revolutionized the field of quantitative genetics. Two-dimensional GWAS that accounts for epistatic genetic effects needs to consider the effects of marker pairs, thus quadratic genetic variants, compared to one-dimensional GWAS that accounts for individual genetic variants. Calcu...
SUMMARY:
We present GWASpro, a high-performance web server for the analyses of large-scale genome-wide association studies (GWAS). GWASpro was developed to provide data analyses for large-scale molecular genetic data, coupled with complex replicated experimental designs such as found in plant science investigations, and to overcome the steep learni...
The interactions among genes and between genes and environment contribute significantly to the phenotypic variation of complex traits and may be possible explanations for missing heritability. However, to our knowledge no existing tool can address the two kinds of interactions. Here we propose a novel linear mixed model that considers not only the...
The term epistasis refers to interactions between multiple genetic loci. Genetic epistasis is important in regulating biological function and is considered to explain part of the ‘missing heritability,’ which involves marginal genetic effects that cannot be accounted for in genome-wide association studies. Thus, the study of epistasis is of great i...
The PEPIS running time for estimating the epistatic effect in PEPIS using the simulated data at various dimensions.
Two scenarios are tested corresponding to A) Fixing the sample size at 1,000 while varying the number of bins from 1000 to 20,000; and B) Fixing the number of bins at 1,000 while varying the sample size from 1,000 to 10,000.
(PDF)
The simulated data at various dimensions with different sample sizes and different numbers of bins.
Eleven sub directories are included, and each contains three '.txt' files corresponding to the additive genotypic Z Matrix, the dominance W matrix, and the phenotypic vector.
(ZIP)
The PEPIS running time for kinship matrix calculation using the simulated data at various dimensions.
Two scenarios are tested corresponding to A) Fixing sample size at 1000 while varying the number of bins from 1,000 to 40,000; and B) Fixing the number of bins at 1,000 while varying the sample size from 1,000 to 40,000.
(PDF)
Liquid chromatography-mass spectrometry (LC/MS) metabolite profiling has been widely used in comparative metabolomics studies; however, LC/MS-based comparative metabolomics currently faces several critical challenges. One of the greatest challenges is how to effectively align metabolites across different LC/MS profiles; a single metabolite can give...
BACKGROUND: Extracted ion chromatogram (EIC) extraction and chromatographic peak detection are two important processing procedures in liquid chromatography/mass spectrometry (LC/MS)-based metabolomics data analysis. Most commonly, the LC/MS technique employs electrospray ionization as the ionization method. The EICs from LC/MS data are often noisy...
In this paper, we present a novel LC/MS data processing and analysis platform, MET-COFEA (METabolite COmpound Feature Extraction and Annotation). MET-COFEA detects and clusters chromatograph peak features for each metabolite compound by first comprehensively evaluating retention time and peak shape criteria and then annotating the associations betw...
Supplementary data
ADAP-GC 2.0 has been developed to deconvolute coeluting metabolites that frequently exist in real biological samples of metabolomics studies. Deconvolution is based on a chromatographic model peak approach that combines five metrics of peak qualities for constructing/selecting model peak features. Prior to deconvolution, ADAP-GC 2.0 takes raw mass...
The NuRD (nucleosome remodeling and deacetylase) complex serves as a crucial epigenetic regulator of cell differentiation, proliferation, and hematopoietic development by coupling the deacetylation and demethylation of histones, nucleosome mobilization, and the recruitment of transcription factors. The core nucleosome remodeling function of the mam...
The algorithms for multi-polarimetric synthetic aperture radar (SAR) intensity image compression are investigated. First, the multi-polarimetric SAR intensity images (HH, HV and VV) are considered as a 3D-matrix unit, and then a 3D-matrix transform is adopted to remove the redundancies, which includes ID discrete cosine transform (DCT) in the polar...
