11 Result(s)
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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 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 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...
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Article
Open AccessComparison of public peak detection algorithms for MALDI mass spectrometry data analysis
In mass spectrometry (MS) based proteomic data analysis, peak detection is an essential step for subsequent analysis. Recently, there has been significant progress in the development of various peak detection ...
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Chapter and Conference Paper
Optimization-Based Peptide Mass Fingerprinting for Protein Mixture Identification
In current proteome research, the most widely used method for protein mixture identification is probably peptide sequencing. Peptide sequencing is based on tandem Mass Spectrometry (MS/MS) data. The disadvanta...
