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13 papers found.
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Sparse regression models for unraveling group and individual associations in eQTL mapping

Background As a promising tool for dissecting the genetic basis of common diseases, expression quantitative trait loci (eQTL) study has attracted increasing research interest. Traditional eQTL methods focus on testing the associations between individual single-nucleotide polymorphisms (SNPs) and gene expression traits. A major drawback of this approach is that it cannot model the ...

Identification of single-stranded and double-stranded dna binding proteins based on protein structure

Wei Wang 0 Juan Liu 0 Xionghui Zhou 0 0 School of Computer, Wuhan University , Wuhan, Hubei 430072 , People's Republic of China Background: Protein-DNA interactions are essential for many

Fast and robust group-wise eQTL mapping using sparse graphical models

Background Genome-wide expression quantitative trait loci (eQTL) studies have emerged as a powerful tool to understand the genetic basis of gene expression and complex traits. The traditional eQTL methods focus on testing the associations between individual single-nucleotide polymorphisms (SNPs) and gene expression traits. A major drawback of this approach is that it cannot model ...

Fast automatic quantitative cell replication with fluorescent live cell imaging

Background live cell imaging is a useful tool to monitor cellular activities in living systems. It is often necessary in cancer research or experimental research to quantify the dividing capabilities of cells or the cell proliferation level when investigating manipulations of the cells or their environment. Manual quantification of fluorescence microscopic image is difficult ...

Ensemble classifier based on context specific miRNA regulation modules: a new method for cancer outcome prediction

Background Many calssifiers which are constructed with chosen gene markers have been proposed to forecast the prognosis of patients who suffer from breast cancer. However, few of them has been applied in clinical practice because of the bad generalization, which results from the situation that markers selected by one method are very different from those obtained by anohter mothod, ...

A local average distance descriptor for flexible protein structure comparison

Hsin-Wei Wang 0 Chia-Han Chu Wen-Ching Wang Tun-Wen Pai 0 0 Department of Computer Science and Engineering, National Taiwan Ocean University , Keelung , Taiwan Background: Protein structures are

Protein-ligand binding region prediction (PLB-SAVE) based on geometric features and CUDA acceleration

Background Protein-ligand interactions are key processes in triggering and controlling biological functions within cells. Prediction of protein binding regions on the protein surface assists in understanding the mechanisms and principles of molecular recognition. In silico geometrical shape analysis plays a primary step in analyzing the spatial characteristics of protein binding ...

GBNet: Deciphering regulatory rules in the co-regulated genes using a Gibbs sampler enhanced Bayesian network approach

Li Shen 0 Jie Liu 0 Wei Wang 0 0 Address: Department of Chemistry and Biochemistry, University of California , San Diego, California , USA Background: Combinatorial regulation of transcription

Prediction of regulatory elements in mammalian genomes using chromatin signatures

Background Recent genomic scale survey of epigenetic states in the mammalian genomes has shown that promoters and enhancers are correlated with distinct chromatin signatures, providing a pragmatic way for systematic mapping of these regulatory elements in the genome. With rapid accumulation of chromatin modification profiles in the genome of various organisms and cell types, this ...

On the detection of functionally coherent groups of protein domains with an extension to protein annotation

Background Protein domains coordinate to perform multifaceted cellular functions, and domain combinations serve as the functional building blocks of the cell. The available methods to identify functional domain combinations are limited in their scope, e.g. to the identification of combinations falling within individual proteins or within specific regions in a translated genome. ...

High-throughput identification of interacting protein-protein binding sites

Background With the advent of increasing sequence and structural data, a number of methods have been proposed to locate putative protein binding sites from protein surfaces. Therefore, methods that are able to identify whether these binding sites interact are needed. Results We have developed a new method using a machine learning approach to detect if protein binding sites, once ...

easyExon – A Java-based GUI tool for processing and visualization of Affymetrix exon array data

Background Alternative RNA splicing greatly increases proteome diversity and thereby contribute to species- or tissue-specific functions. The possibility to study alternative splicing (AS) events on a genomic scale using splicing-sensitive microarrays, including the Affymetrix GeneChip Exon 1.0 ST microarray (exon array), has appeared very recently. However, the application of this ...

Signature Evaluation Tool (SET): a Java-based tool to evaluate and visualize the sample discrimination abilities of gene expression signatures

Background The identification of specific gene expression signature for distinguishing sample groups is a dominant field in cancer research. Although a number of tools have been developed to identify optimal gene expression signatures, the number of signature genes obtained is often overly large to be applied clinically. Furthermore, experimental verification is sometimes limited ...