Biomedical subjects

Jin Hwan Do

Publications and source records attributed to Jin Hwan Do.

3 recordsLinked to original sources

PubMed2006

Normalization of microarray data: single-labeled and dual-labeled arrays.

DNA microarray is a powerful tool for high-throughput analysis of biological systems. Various computational tools have been created to facilitate the analysis of the large volume of data produced in DNA microarray experiments. Normalization is a critical step for obtaining data that are reliable and usable for subsequent analysis such as identification of differentially expressed genes and clustering. A variety of normalization methods have been proposed over the past few years, but no methods are still perfect. Various assumptions are often taken in the process of normalization. Therefore, the knowledge of underlying assumption and principle of normalization would be helpful for the correct analysis of microarray data. We present a review of normalization techniques from single-labeled platforms such as the Affymetrix GeneChip array to dual-labeled platforms like spotted array focusing on their principles and assumptions.

Cluster Analysis↗

PubMed2006

Computational approaches to gene prediction.

The problems associated with gene identification and the prediction of gene structure in DNA sequences have been the focus of increased attention over the past few years with the recent acquisition by large-scale sequencing projects of an immense amount of genome data. A variety of prediction programs have been developed in order to address these problems. This paper presents a review of the computational approaches and gene-finders used commonly for gene prediction in eukaryotic genomes. Two approaches, in general, have been adopted for this purpose: similarity-based and ab initio techniques. The information gleaned from these methods is then combined via a variety of algorithms, including Dynamic Programming (DP) or the Hidden Markov Model (HMM), and then used for gene prediction from the genomic sequences.

Animals↗

PubMed2005

A computational approach to the inference of sphingolipid pathways from the genome of Aspergillus fumigatus.

A growing body of evidence suggests that sphingolipids are important bioactive molecules, in addition to being critical structural components of cellular membranes. These molecules have been implicated in regulating cell growth, differentiation, angiogenesis, apoptosis, and senescence. Many of the enzymes involved in sphingolipid biosynthesis are the targets of fungal toxins, thus underscoring the importance of this pathway. An international consortium has made considerable progress in sequencing the genome of Aspergillus fumigatus, one of the most common mold pathogens of humans; however, most genes have not yet been annotated. Here, we have identified genes involved in the sphingolipid pathway of A. fumigatus by comparative analysis with four other fungal species and the gene prediction program GlimmerM. Our results shows that A. fumigatus has most of the sphingolipid pathway genes found in other fungi, except for the CSG2 and IPT1 genes; the former is involved in the mannosylation of inositol phosphorylceramide (IPC) to mannose-inositol-phosphorylceramide and the latter involved in the synthesis of mannose-(inositol-P)(2)-ceramide from mannose-inositol-phosphorylceramide.

Aspergillus fumigatus↗