Volume 10 Supplement 1
Edited by Michael Q Zhang, Michael S Waterman and Xuegong Zhang
The Seventh Asia Pacific Bioinformatics Conference (APBC 2009). Go to conference site.
Beijing, China13-16 January 2009
Page 2 of 2
Spectra resulting from Surface-Enhanced Laser Desorption/Ionisation (SELDI) mass spectrometry measurements are constructed by combining sub-spectra, each of which are the result of a single firing of the laser...
Although microarray gene expression analysis has become popular, it remains difficult to interpret the biological changes caused by stimuli or variation of conditions. Clustering of genes and associating each ...
The Janus kinase-signal transducer and activator of transcription (JAK/STAT) pathway is one of the most important targets for myeloproliferative disorder (MPD). Although several efforts toward modeling the pat...
The gene shaving algorithm and many other clustering algorithms identify gene clusters showing high variation across samples. However, gene expression in many signaling pathways show only modest and concordant...
Considerable efforts have been made to extract protein-protein interactions from the biological literature, but little work has been done on the extraction of interaction detection methods. It is crucial to an...
Genes show different sensitivities in expression corresponding to various biological conditions. Systematical study of this concept is required because of its important implications in microarray analysis etc....
Supervised learning and many stochastic methods for predicting protein-protein interactions require both negative and positive interactions in the training data set. Unlike positive interactions, negative inte...
Constraint-based modeling of reconstructed genome-scale metabolic networks has been successfully applied on several microorganisms. In constraint-based modeling, in order to characterize all allowable phenotyp...
In addition to component-based comparative approaches, network alignments provide the means to study conserved network topology such as common pathways and more complex network motifs. Yet, unlike in classical se...
Protein-Protein Interactions (PPIs) play important roles in many biological functions. Protein domains, which are defined as independently folding structural blocks of proteins, physically interact with each o...
The COMPARABILITY EDITING problem appears in the context of hierarchical disease classification based on noisy data. We are given a directed graph G representing hierarchical relationships between patient subgrou...
Genome-scale models of metabolism have only been analyzed with the constraint-based modelling philosophy. Some gene deletion studies on in silico organism models at genome-scale have been made, but most of them w...
The syndrome is the basic pathological unit and the key concept in traditional Chinese medicine (TCM) and the herbal remedy is prescribed according to the syndrome a patient catches. Nevertheless, few studies ...
Classification using aCGH data is an important and insufficiently investigated problem in bioinformatics. In this paper we propose a new classification method of DNA copy number data based on the concept of li...
The key roles of epistatic interactions between multiple genetic variants in the pathogenesis of complex diseases notwithstanding, the detection of such interactions remains a great challenge in genome-wide as...
Several features are known to correlate with the GC-content in the human genome, including recombination rate, gene density and distance to telomere. However, by testing for pairwise correlation only, it is im...
Regions with copy number variations (in germline cells) or copy number alteration (in somatic cells) are of great interest for human disease gene mapping and cancer studies. They represent a new type of mutati...
Genome-wide association studies prove to be a powerful approach to identify the genetic basis of different human diseases. We studied the relationship between seven diseases characterized in a previous genome-...
Automated candidate gene prediction systems allow geneticists to hone in on disease genes more rapidly by identifying the most probable candidate genes linked to the disease phenotypes under investigation. Her...
Gene copy number and gene expression values play important roles in cancer initiation and progression. Both can be measured with high-throughput microarrays and some methodologies to integrate and analyze thes...
Recent studies have shown genetic variation is the basis of the genome-wide disease association research. However, due to the high cost on genotyping large number of single nucleotide polymorphisms (SNPs), it ...
We address the problem of studying recombinational variations in (human) populations. In this paper, our focus is on one computational aspect of the general task: Given two networks G1 and G2, with both mutation ...
Handling genotype data typed at hundreds of thousands of loci is very time-consuming and it is no exception for population structure inference. Therefore, we propose to apply PCA to the genotype data of a popu...
Identifying the genetic components of common diseases has long been an important area of research. Recently, genotyping technology has reached the level where it is cost effective to genotype single nucleotide...
In addition to single-locus (main) effects of disease variants, there is a growing consensus that gene-gene and gene-environment interactions may play important roles in disease etiology. However, for the very...
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