• Journal of Photoscience
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• v.9 no.2
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• pp.373-375
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• 2002

Lhcb genes encoding light-harvesting chlorophyll-a/b binding (LHC) proteins of photosystem (PS) II were comprehensively characterized using the expressed sequence tag (EST) databases in the green alga, Chlamydomonas reinhardtii. The gene family was composed of eight Lhcb genes including four new genes, which were isolated and sequenced. The effects of light intensity on the levels of mRNAs accumulation of multiple Lhcb genes were studied under various conditions. The results indicate that Lhcb genes are coordinately regulated in response to light conditions, and repressed when the input light energy exceeded the requirement for $CO_2$ assimilation. The effects of high light on the expression of the Lhcb genes observed in the presence of an electron transport inhibitor, DCMU, and in mutants deficient in photosynthetic reaction centers suggest the presence of two alternative mechanisms for regulating the genes expression under high-light conditions.

• BMB Reports
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• v.40 no.2
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• pp.286-289
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• 2007

Despite considerable interest in the biologic processes of regeneration and stem cell activation, little is known about the genes involved in these transformative events. In a Hydra littoralis model of regeneration, we employed a rapid shotgun suppression subtractive hybridization strategy to identify genes that are uniquely expressed in regenerating tissue. With an adaptor-PCR based technique, 16 candidate transcripts were identified, 15 were confirmed unique to mRNA isolated from hydra undergoing regeneration. Of these, 6 were undescribed in GenBank and allied expressed sequence tag (EST) databases (GenBank + EMBL + DDBJ + PDB and the Hydra EST database). BLAST analysis of these sequences identified remarkably similar sequences in anonymous ESTs found in a wide variety of animal species.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.383-387
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• 2005

One of the most important issues in post-genome era is identifying functions of genes and understanding the interaction among them. Such interactions from complex biochemical pathways, which are very useful to understand the organism system. We present an integrated biochemical pathway database system with a set of software tools for reconstruction, visualization, and simulation of the pathways from the database. The novel features of the presented system include: (a) automatic integration of the heterogeneous biochemical pathway databases, (b) gene ontology for high quality of database in the integration and query (c) various biochemical simulations on the pathway database, (d) dynamic pathway reconstruction for the gene list or sequence data, (e) graphical tools which enable users to view the reconstructed pathways in a dynamic form, (f) importing/exporting SBML documents, a data exchange standard for systems biology.

• ETRI Journal
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• v.35 no.6
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• pp.1021-1028
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• 2013

Automatic facial expression recognition is a widely studied problem in computer vision and human-robot interaction. There has been a range of studies for representing facial descriptors for facial expression recognition. Some prominent descriptors were presented in the first facial expression recognition and analysis challenge (FERA2011). In that competition, the Local Gabor Binary Pattern Histogram Sequence descriptor showed the most powerful description capability. In this paper, we introduce hybrid facial representations for facial expression recognition, which have more powerful description capability with lower dimensionality. Our descriptors consist of a block-based descriptor and a pixel-based descriptor. The block-based descriptor represents the micro-orientation and micro-geometric structure information. The pixel-based descriptor represents texture information. We validate our descriptors on two public databases, and the results show that our descriptors perform well with a relatively low dimensionality.

• Genomics & Informatics
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• v.11 no.3
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• pp.121-128
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• 2013

The introduction of metagenomics into the field of virology has facilitated the exploration of viral communities in various natural habitats. Understanding the viral ecology of a variety of sample types throughout the biosphere is important per se, but it also has potential applications in clinical and diagnostic virology. However, the procedures used by viral metagenomics may produce technical errors, such as amplification bias, while public viral databases are very limited, which may hamper the determination of the viral diversity in samples. This review considers the current state of viral metagenomics, based on examples from Korean viral metagenomic studies-i.e., rice paddy soil, fermented foods, human gut, seawater, and the near-surface atmosphere. Viral metagenomics has become widespread due to various methodological developments, and much attention has been focused on studies that consider the intrinsic role of viruses that interact with their hosts.

• Genomics & Informatics
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• v.11 no.1
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• pp.38-45
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• 2013

In cancer genome studies, the annotation of newly detected oncogene/tumor suppressor gene candidates is a challenging process. We propose using concept lattice analysis for the annotation and interpretation of genes having candidate somatic mutations in whole-exome sequencing in acute myeloid leukemia (AML). We selected 45 highly mutated genes with whole-exome sequencing in 10 normal matched samples of the AML-M2 subtype. To evaluate these genes, we performed concept lattice analysis and annotated these genes with existing knowledge databases.

• Journal of Genetic Medicine
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• v.10 no.1
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• pp.27-32
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• 2013

Post-transcriptional nucleotide sequence modification of transcripts by RNA editing is an important molecular mechanism in the regulation of protein function and is associated with a variety of human disease phenotypes. Identification of RNA editing sites is the basic step for studying RNA editing. Databases and bioinformatics resources are used to annotate and evaluate as well as identify RNA editing sites. No method is free of limitations. Correctly establishing an analytic pipeline and strategic application of both experimental and bioinformatics methods constitute the first step in investigating RNA editing. This review summarizes modern bioinformatics approaches and related resources for RNA editing research.

• Bioinformatics and Biosystems
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• v.2 no.1
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• pp.7-11
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• 2007

Methods for making scoring matrix based on phylogenetic tree for all possible exchanges of one amino acid with another. PFMT(Phylogenetic focused Mutation Tendency) matrix is different BLOSUM62 and PAM160 which are the most used scoring matrixes. This matrix calculates possibility of substitution from common ancestor to high spices. PFMT matrix scores substitution frequency in COGs databases which contain 152 KOGs's dataset. PFMT matrix usefully is able to compare between query sequence and sequences of more higher species and show detailed substitution relation of 20 amino acids.

• Interdisciplinary Bio Central
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• v.5 no.2
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• pp.5.1-5.3
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• 2013

Introduced were two biological investigations in which information biology played a significant role. In the first case independent findings in cancer research over a long period were united and organized by information biology and led to the outcome that was subject to a Nobel Prize. The outcome has revealed that the cause of human cancer is located in the genome in a dormant condition. The second case shows how to elucidate the function of an unknown DNA sequence or ORF in prokaryotes by a large - scale computer homology search and analyses. For the elucidation the International DNA Databases and a large - scale computer were two key factors.

• Proceedings of the Korean Information Science Society Conference
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• 2002.10d
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• pp.358-360
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• 2002

인터넷의 확산과 첨단기술의 발달로 생물학 정보에 대한 온라인 데이터베이스 집합이 급속히 증가하고 있으나, 데이터의 양이 방대하고 이질적인 형태로 제공되기 때문에 실제 현장의 생물학 연구자들이 쉽게 이용하는데는 여러 가지 어려움이 있다. 이 논문에서는 단백질과 핵산 정보를 제공하는 대표적인 온라인 데이터베이스인 NCBL에, 질의를 하여 얻어진 데이터를 포함한 웹 문서로부터, 정보를 추출하여 사용자의 목적에 적합한 맞춤형 데이터베이스를 구축하는 시스템을 제안한다. 온톨로지를 이용하여 질의 처리를 하며, 웹 문서에 대한 정보추출 기법과 계층구조에 따른 유형별 저장방식을 통해 데이터베이스를 구축한다. 한편, 데이터 추출을 위해 식별 및 분류 작업을 수행한다. 제안한 시스템은 서열정보를 분석하는 생물학자들에게 관심대상 정보를 추출하여 맞춤형 데이터베이스를 구축함으로써, 손쉽게 서열정보 분석을 지원하도록 하는데 목적이 있다.