• Molecules and Cells
• /
• 제25권2호
• /
• pp.279-288
• /
• 2008

The analysis of microarray data is essential for large amounts of gene expression data. In this review we focus on clustering techniques. The biological rationale for this approach is the fact that many co-expressed genes are co-regulated, and identifying co-expressed genes could aid in functional annotation of novel genes, de novo identification of transcription factor binding sites and elucidation of complex biological pathways. Co-expressed genes are usually identified in microarray experiments by clustering techniques. There are many such methods, and the results obtained even for the same datasets may vary considerably depending on the algorithms and metrics for dissimilarity measures used, as well as on user-selectable parameters such as desired number of clusters and initial values. Therefore, biologists who want to interpret microarray data should be aware of the weakness and strengths of the clustering methods used. In this review, we survey the basic principles of clustering of DNA microarray data from crisp clustering algorithms such as hierarchical clustering, K-means and self-organizing maps, to complex clustering algorithms like fuzzy clustering.

• Applied Science and Convergence Technology
• /
• 제24권6호
• /
• pp.203-214
• /
• 2015

We have been developing a new label-free nanobio imaging platform using non-linear optics such as Coherent Anti-Stokes Raman Spectroscopy (CARS) and ion beam techniques based on sputtering and scattering such as Secondary Ion Mass Spectrometry (SIMS) and Medium Energy Ion Scattering Spectroscopy (MEIS), which have been widely used for atomic and molecular level analysis of semiconductors and nanomaterials. To apply techniques developed for semiconductors and nanomaterials for biomedical applications, the convergence of nano-analysis and biology were tried. Our activities on label-free nanobio imaging during the last decade are summarized in this review about non-linear optical 3D imaging, ellipsometric interface imaging, SIMS imaging, and TOF-MEIS nano analysis for cardiovascular tissues, collagen thin films, peptides on microarray, nanoparticles, and cell adhesion studies and finally the present snapshot of nanobio imaging and the future prospect are described.

• Molecules and Cells
• /
• 제39권12호
• /
• pp.841-846
• /
• 2016

Local protein synthesis mediates precise spatio-temporal regulation of gene expression for neuronal functions such as long-term plasticity, axon guidance and regeneration. To reveal the underlying mechanisms of local translation, it is crucial to understand mRNA transport, localization and translation in live neurons. Among various techniques for mRNA analysis, fluorescence microscopy has been widely used as the most direct method to study localization of mRNA. Live-cell imaging of single RNA molecules is particularly advantageous to dissect the highly heterogeneous and dynamic nature of messenger ribonucleoprotein (mRNP) complexes in neurons. Here, we review recent advances in the study of mRNA localization and translation in live neurons using novel techniques for single-RNA imaging.

• 한국막학회:학술대회논문집
• /
• 한국막학회 1995년도 춘계 총회 및 학술발표회
• /
• pp.16-20
• /
• 1995

The spontaneous self-organization of amphiphilic molecules into complex aggregates was undoubtedly an important factor in the emergence of life on earth. We study the parameters governing the self-organization of a simple amphiphilic model system using electron cryomicroscopy of ice-embedded specimens in combination with extensive data analysis. Different stable helices can be generated reproducibly by changing the parameters controlling the molecular aggregation process. The repeating units of the helical aggregates in the micrographs can be found by multivariate statistical image analysis techniques, and these two-dimensional projection images suffice for calculating the three-dimensional density distribution of the fibers. We present a typical structure consisting of a narrow stack of compartmented bilayers twisted into a left-handed helix. Our new techniques directly elucidate the three-dimensional structure of helical assemblies, and can complement or replace diffraction-based approaches.

• BMB Reports
• /
• 제53권1호
• /
• pp.3-9
• /
• 2020

The mitochondrial genome encodes 13 proteins that are components of the oxidative phosphorylation system (OXPHOS), suggesting that precise regulation of these genes is crucial for maintaining OXPHOS functions, including ATP production, calcium buffering, cell signaling, ROS production, and apoptosis. Furthermore, heteroplasmy or mis-regulation of gene expression in mitochondria frequently is associated with human mitochondrial diseases. Thus, various approaches have been developed to investigate the roles of genes encoded by the mitochondrial genome. In this review, we will discuss a wide range of techniques available for investigating the mitochondrial genome, mitochondrial transcription, and mitochondrial translation, which provide a useful guide to understanding mitochondrial gene expression.

• 한국전기전자재료학회:학술대회논문집
• /
• 한국전기전자재료학회 1997년도 추계학술대회 논문집
• /
• pp.112-115
• /
• 1997

In this paper, we investigated the liquid crystal(LC) alignment and generation of pretilt angle by using photo-alignment techniques on two kinds of polyimide(Pl) surface. It was found that the uniform alignment for nematic(N) LC is obtained in a cell with slanted UV light irradiation on PI surface without side-chain. We successfully observed that the pretilt angle of NLC is generated about 3.3 degrees in a cell with an incidence angle of 70 degrees on PI surface without side chain. It is considered that the pretilt angle generation in NLC is attributed to interaction between the LC molecular and the polymer.

• Environmental Analysis Health and Toxicology
• /
• 제23권4호
• /
• pp.231-245
• /
• 2008

Various methods for detecting changes in response behaviors of indicator specimens are presented for monitoring effects of toxic treatments. The movement patterns of individuals are quantitatively characterized by statistical (i.e., ANOVA, multivariate analysis) and computational (i.e., fractal dimension, Fourier transform) methods. Extraction of information in complex behavioral data is further illustrated by techniques in ecological informatics. Multi-Layer Perceptron and Self-Organizing Map are applied for detection and patterning of response behaviors of indicator specimens. The recent techniques of Wavelet analysis and line detection by Recurrent Self-Organizing Map are additionally discussed as an efficient tool for checking time-series movement data. Behavioral monitoring could be established as new methodology in integrative ecological assessment, tilling the gap between large-scale (e.g., community structure) and small-scale (e.g., molecular response) measurements.

• 한국지능정보시스템학회:학술대회논문집
• /
• 한국지능정보시스템학회 2005년도 공동추계학술대회
• /
• pp.258-263
• /
• 2005

Haplotype-based analysis using high-density SNP markers have gained a great attention in evaluating genes in gene analysis and various clinical situations. However, there has been no research on disease diagnostic modeling based on SNPs analysis to our knowledge. The purpose of this study is to explore how knowledge discovery techniques are applied in medical informatics area and proposes a Case Based Reasoning (CBR) technique for diagnosis of gastric caner using Single Nucleotide Polymorphism(SNP).

• Parasites, Hosts and Diseases
• /
• 제51권1호
• /
• pp.51-54
• /
• 2013

Not only Taenia solium and Taenia saginata, but also Taenia asiatica infects humans. The last species is not included in the evaluation of the specificity of the immunodiagnostic techniques for taeniasis/cysticercosis. There is currently no specific immunodiagnostic method for T. asiatica available. Therefore, due to the fact that molecular techniques (the only tool to distinguish the 3 Taenia species) are normally not employed in routine diagnostic methods, the 2 questions concerning T. asiatica (its definite geographic distribution and its ability to cause human cysticercosis), remain open, turning T. asiatica into the most neglected agent of human taeniasis-cysticercosis.

• Molecules and Cells
• /
• 제46권2호
• /
• pp.86-98
• /
• 2023

The genome is almost identical in all the cells of the body. However, the functions and morphologies of each cell are different, and the factors that determine them are the genes and proteins expressed in the cells. Over the past decades, studies on epigenetic information, such as DNA methylation, histone modifications, chromatin accessibility, and chromatin conformation have shown that these properties play a fundamental role in gene regulation. Furthermore, various diseases such as cancer have been found to be associated with epigenetic mechanisms. In this study, we summarized the biological properties of epigenetics and single-cell epigenomic profiling techniques, and discussed future challenges in the field of epigenetics.