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REFERENCE LINKING PLATFORM OF KOREA S&T JOURNALS
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Genomics & Informatics
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Korea Genome Organization
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Volume 1, Issue 2 - Dec 2003
Volume 1, Issue 1 - Sep 2003
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Challenges and New Approaches in Genomics and Bioinformatics
Park, Jong Hwa ; Han, Kyung Sook ;
Genomics & Informatics, volume 1, issue 1, 2003, Pages 1~6
In conclusion, the seemingly fuzzy and disorganized data of biology with thousands of different layers ranging from molecule to the Internet have refused so far to be mapped precisely and predicted successfully by mathematicians, physicists or computer scientists. Genomics and bioinformatics are the fields that process such complex data. The insights on the nature of biological entities as complex interaction networks are opening a door toward a generalization of the representation of biological entities. The main challenge of genomics and bioinformatics now lies in 1) how to data mine the networks of the domains of bioinformatics, namely, the literature, metabolic pathways, and proteome and structures, in terms of interaction; and 2) how to generalize the networks in order to integrate the information into computable genomic data for computers regardless of the levels of layer. Once bioinformatists succeed to find a general principle on the way components interact each other to form any organic interaction network at genomic scale, true simulation and prediction of life in silico will be possible.
Biological Network Evolution Hypothesis Applied to Protein Structural Interactome
Bolser, Dan M. ; Park, Jong Hwa ;
Genomics & Informatics, volume 1, issue 1, 2003, Pages 7~19
The latest measure of the relative evolutionary age of protein structure families was applied (based on taxonomic diversity) using the protein structural interactome map (PSIMAP). It confirms that, in general, protein domains, which are hubs in this interaction network, are older than protein domains with fewer interaction partners. We apply a hypothesis of 'biological network evolution' to explain the positive correlation between interaction and age. It agrees to the previous suggestions that proteins have acquired an increasing number of interaction partners over time via the stepwise addition of new interactions. This hypothesis is shown to be consistent with the scale-free interaction network topologies proposed by other groups. Closely co-evolved structural interaction and the dynamics of network evolution are used to explain the highly conserved core of protein interaction pathways, which exist across all divisions of life.
Global Optimization of Clusters in Gene Expression Data of DNA Microarrays by Deterministic Annealing
Lee, Kwon Moo ; Chung, Tae Su ; Kim, Ju Han ;
Genomics & Informatics, volume 1, issue 1, 2003, Pages 20~24
The analysis of DNA microarry data is one of the most important things for functional genomics research. The matrix representation of microarray data and its successive 'optimal' incisional hyperplanes is a useful platform for developing optimization algorithms to determine the optimal partitioning of pairwise proximity matrix representing completely connected and weighted graph. We developed Deterministic Annealing (DA) approach to determine the successive optimal binary partitioning. DA algorithm demonstrated good performance with the ability to find the 'globally optimal' binary partitions. In addition, the objects that have not been clustered at small nonzero temperature, are considered to be very sensitive to even small randomness, and can be used to estimate the reliability of the clustering.
A Heuristic Algorithm to Find All Normalized Local Alignments Above Threshold
Kim, Sangtae ; Sim, Jeong Seop ; Park, Heejin ; Park, Kunsoo ; Park, Hyunseok ; Seo, Jeong-Sun ;
Genomics & Informatics, volume 1, issue 1, 2003, Pages 25~31
Local alignment is an important task in molecular biology to see if two sequences contain regions that are similar. The most popular approach to local alignment is the use of dynamic programming due to Smith and Waterman, but the alignment reported by the Smith-Waterman algorithm has some undesirable properties. The recent approach to fix these problems is to use the notion of normalized scores for local alignments by Arslan, Egecioglu and Pevzner. In this paper we consider the problem of finding all local alignments whose normalized scores are above a given threshold, and present a fast heuristic algorithm. Our algorithm is 180-330 times faster than Arslan et al.'s for sequences of length about 120 kbp and about 40-50 times faster for sequences of length about 30 kbp.
Gene Expression Pattern Analysis via Latent Variable Models Coupled with Topographic Clustering
Chang, Jeong-Ho ; Chi, Sung Wook ; Zhang, Byoung Tak ;
Genomics & Informatics, volume 1, issue 1, 2003, Pages 32~39
We present a latent variable model-based approach to the analysis of gene expression patterns, coupled with topographic clustering. Aspect model, a latent variable model for dyadic data, is applied to extract latent patterns underlying complex variations of gene expression levels. Then a topographic clustering is performed to find coherent groups of genes, based on the extracted latent patterns as well as individual gene expression behaviors. Applied to cell cycleregulated genes of the yeast Saccharomyces cerevisiae, the proposed method could discover biologically meaningful patterns related with characteristic expression behavior in particular cell cycle phases. In addition, the display of the variation in the composition of these latent patterns on the cluster map provided more facilitated interpretation of the resulting cluster structure. From this, we argue that latent variable models, coupled with topographic clustering, are a promising tool for explorative analysis of gene expression data.
Computational Analysis of Neighboring Genes on Arabidopsis thaliana Chromosomes 4 and 5: Their Genomic Association as Functional Subunits
Goh, Sung-Ho ; Kim, Tae-Hyung ; Kim, Jee-Hyub ; Nam, DouGu ; Choi, Doil ; Hur, Cheol-Goo ;
Genomics & Informatics, volume 1, issue 1, 2003, Pages 40~49
The genes related to specific events or pathways in bacteria are frequently localized proximate to the genome of their neighbors, as with the structures known as operon, but eukaryotic genes seem to be independent of their neighbors, and are dispersed randomly throughout genomes. Although cases are rare, the findings from structures similar to prokaryotic operons in the nematode genome, and the clustering of housekeeping genes on human genome, lead us to assess the genomic association of genes as functional subunits. We evaluated the genomic association of neighboring genes on chromosomes 4 and 5 of Arabidopsis thaliana with and without respectively consideration of the scaffold/matrixattached regions (S/MAR) loci. The observed number of functionally identical bigrams and trig rams were significantly higher than expected, and these results were verified statistically by calculating p-values for weighted random distributions. The observed frequency of functionally identical big rams and trig rams were much higher in chromosome 4 than in chromosome 5, but the frequencies with, and without, consideration of the S/MAR in each chromosome were similar. In this study, a genomic association among functionally related neighboring genes in Arabidopsis thaliana was suggested.
Genome Mapping of an Extreme Thermophile, Thermus caldophilus GK24
Park, Jong Hoon ; Park, Byung Chul ; Koch, Suk Hoon ; Kim, Joong Soo ; Koh, Jeong Heon ; Yang, Moon Hee ; Kim, Yong Sung ; Kim, Cheorl Ho ; Kim, Myoung Hee ; Kwon, Suk Tae ; Lee, Dae-Sil ;
Genomics & Informatics, volume 1, issue 1, 2003, Pages 50~54
Genome of an extreme thermophile, Thermus caldophilus GK24 has been analyzed to construct the genomic map. The genomic DNAs encapsulated in agarose gel were digested with SspI, EcoRI, SpeI, and HpaI restriction endonucleases, and then the resulting genomic DNA fragments were analyzed by pulsed-field gel electrophoresis. Its restriction map has been constructed by analyzing sizes of the restriction fragments obtained from both complete and partial digestions. The circular form of its genome was composed of about 1.98 Mbp and a megaplasmid. The genomic loci for the genes of xylose isomerase, thioredoxin, tRNA-16S rRNA, 23S rRNA, L5 ribosomal protein, ADP-glucose pyrophosphorylase, DNA-ligase, and Tca DNA polymerase were determined by both Southern hybridization and PCR.
A Small Cryptic Plasmid pZMO1 of Zymomonas mobilis ATCC10988
Kang, Hyung-Lyun ; Kang, Hyen-Sam ;
Genomics & Informatics, volume 1, issue 1, 2003, Pages 55~60
The nucleotide sequence of pZMO1, a small cryptic plasmid of Zymomonas mobilis ATCC10988 was determined. Analysis of 1,680 bp of sequence revealed
identity with Shigella sonnei plasmid, pKYM and
identity with Nostoc sp. ss DNA replicating plasmid. Analysis of a deduced amino acid sequence of an orf of pZMO1 revealed
similarity with the repA gene of Synechocystis sp. plasmid pCA2.4. The upstream region of the repA gene of pZMO1 possesses six directed repeat sequences and two inverted repeat sequences at downstream of the IR consensus sequence of nick region of rolling circle replication (RCR) plasmid. A typical terminator hairpin structure was found at the downstream region of repA gene. Degradation of single-stranded plasmid DNA by S1 nuclease was detected by Southern hybridization. It suggests that pZMO1 replicates by a rolling circle mechanism in Z. mobilis ATCC10988 cells.