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Article
Open AccessCirculating metabolomic markers linking diabetic kidney disease and incident cardiovascular disease in type 2 diabetes: analyses from the Hong Kong Diabetes Biobank
The aim of this study was to describe the metabolome in diabetic kidney disease (DKD) and its association with incident CVD in type 2 diabetes, and identify prognostic biomarkers.
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Article
Open AccessECL 3.0: a sensitive peptide identification tool for cross-linking mass spectrometry data analysis
Cross-linking mass spectrometry (XL-MS) is a powerful technique for detecting protein–protein interactions (PPIs) and modeling protein structures in a high-throughput manner. In XL-MS experiments, proteins are...
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Article
Open AccessHigh-density lipoprotein subclasses and cardiovascular disease and mortality in type 2 diabetes: analysis from the Hong Kong Diabetes Biobank
High-density lipoproteins (HDL) comprise particles of different size, density and composition and their vasoprotective functions may differ. Diabetes modifies the composition and function of HDL. We assessed a...
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Article
Feature-based Quality Assessment of Middle Cerebral Artery Occlusion Using 18F-Fluorodeoxyglucose Positron Emission Tomography
In animal experiments, ischemic stroke is usually induced through middle cerebral artery occlusion (MCAO), and quality assessment of this procedure is crucial. However, an accurate assessment method based on 1...
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Chapter
Cross-Linking Mass Spectrometry Data Analysis
In this chapter, we will review mass spectrometry-based proteomics and focus on the development of data analysis methods in chemical cross-linking combined with mass spectrometry (CL-MS). CL-MS is one remarkab...
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Article
Open AccessDevelopment of genome-wide polygenic risk scores for lipid traits and clinical applications for dyslipidemia, subclinical atherosclerosis, and diabetes cardiovascular complications among East Asians
The clinical utility of personal genomic information in identifying individuals at increased risks for dyslipidemia and cardiovascular diseases remains unclear.
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Article
Open AccessRegion-based interaction detection in genome-wide case-control studies
In genome-wide association study (GWAS), conventional interaction detection methods such as BOOST are mostly based on SNP-SNP interactions. Although single nucleotides are the building blocks of human genome, ...
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Article
Open AccessErratum to: Power estimation and sample size determination for replication studies of genome-wide association studies
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Article
Open AccessECL: an exhaustive search tool for the identification of cross-linked peptides using whole database
Chemical cross-linking combined with mass spectrometry (CX-MS) is a high-throughput approach to studying protein-protein interactions. The number of peptide-peptide combinations grows quadratically with respec...
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Article
Open AccessPower estimation and sample size determination for replication studies of genome-wide association studies
Replication study is a commonly used verification method to filter out false positives in genome-wide association studies (GWAS). If an association can be confirmed in a replication study, it will have a high ...
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Article
Open AccessThe complete compositional epistasis detection in genome-wide association studies
The detection of epistasis among genetic markers is of great interest in genome-wide association studies (GWAS). In recent years, much research has been devoted to find disease-associated epistasis in GWAS. Ho...
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Article
Open AccessUsing MicroPET Imaging in Quantitative Verification of the Acupuncture Effect in Ischemia Stroke Treatment
Acupuncture has been indispensable in Chinese medicine. However, its function still remains elusive. This paper studies the effect of acupuncture in ischemia stroke treatment using the Sprague Dawley rat anima...
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Chapter
Bioinformatic Analysis of Data Generated from MALDI Mass Spectrometry for Biomarker Discovery
In this chapter we first describe the applications of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) in biomarker discovery. After a summary of the general analysis pipeline of MALD...
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Article
Open AccessA hidden two-locus disease association pattern in genome-wide association studies
Recent association analyses in genome-wide association studies (GWAS) mainly focus on single-locus association tests (marginal tests) and two-locus interaction detections. These analysis methods have provided ...
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Article
Open AccessMotif-All: discovering all phosphorylation motifs
Phosphorylation motifs represent common patterns around the phosphorylation site. The discovery of such kinds of motifs reveals the underlying regulation mechanism and facilitates the prediction of unknown pho...
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Article
Open AccessScore regularization for peptide identification
Peptide identification from tandem mass spectrometry (MS/MS) data is one of the most important problems in computational proteomics. This technique relies heavily on the accurate assessment of the quality of p...
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Article
Open AccessThe choice of null distributions for detecting gene-gene interactions in genome-wide association studies
In genome-wide association studies (GWAS), the number of single-nucleotide polymorphisms (SNPs) typically ranges between 500,000 and 1,000,000. Accordingly, detecting gene-gene interactions in GWAS is computat...
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Article
Open AccessIdentifying main effects and epistatic interactions from large-scale SNP data via adaptive group Lasso
Single nucleotide polymorphism (SNP) based association studies aim at identifying SNPs associated with phenotypes, for example, complex diseases. The associated SNPs may influence the disease risk individually...
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Article
Open AccessSemi-supervised protein subcellular localization
Protein subcellular localization is concerned with predicting the location of a protein within a cell using computational method. The location information can indicate key functionalities of proteins. Accurate...
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Article
Open AccessMegaSNPHunter: a learning approach to detect disease predisposition SNPs and high level interactions in genome wide association study
The interactions of multiple single nucleotide polymorphisms (SNPs) are highly hypothesized to affect an individual's susceptibility to complex diseases. Although many works have been done to identify and quan...
