시스템생물학을 위한 바이오정보학 연구동향

이은정,이도헌 대한의료정보학회 2008 Healthcare Informatics Research Vol.14 No.4

Bioinformatics is the information technology to deal with biological data. Recently emerging systems biology has drawn great interest inspired by world‐wide efforts for modeling and analyzing biological processes with a systems perspective. Bioinformatics, which has analyzed multi‐omics data such as genomics, transcriptomics, and proteomics, and explored novel biological patterns embedded within the data, now has a transition to its application to systems biology, called systems bioinformatics. Systems bioinformatics includes various research areas: system modeling, system structure and dynamics analysis, causality analysis, and multi‐omics data fusion. In this review, we introduce bioinformatics for genomics, transcriptomics, proteomics, and systems biology according to the different aspects of biological processes.

Will solid-state drives accelerate your bioinformatics? In-depth profiling, performance analysis and beyond

Lee, Sungmin,Min, Hyeyoung,Yoon, Sungroh Oxford University Press 2016 Briefings in bioinformatics Vol.17 No.4

<P>A wide variety of large-scale data have been produced in bioinformatics. In response, the need for efficient handling of biomedical big data has been partly met by parallel computing. However, the time demand of many bioinformatics programs still remains high for large-scale practical uses because of factors that hinder acceleration by parallelization. Recently, new generations of storage devices have emerged, such as NAND flash-based solid-state drives (SSDs), and with the renewed interest in near-data processing, they are increasingly becoming acceleration methods that can accompany parallel processing. In certain cases, a simple drop-in replacement of hard disk drives by SSDs results in dramatic speedup. Despite the various advantages and continuous cost reduction of SSDs, there has been little review of SSD-based profiling and performance exploration of important but time-consuming bioinformatics programs. For an informative review, we perform in-depth profiling and analysis of 23 key bioinformatics programs using multiple types of devices. Based on the insight we obtain from this research, we further discuss issues related to design and optimize bioinformatics algorithms and pipelines to fully exploit SSDs. The programs we profile cover traditional and emerging areas of importance, such as alignment, assembly, mapping, expression analysis, variant calling and metagenomics. We explain how acceleration by parallelization can be combined with SSDs for improved performance and also how using SSDs can expedite important bioinformatics pipelines, such as variant calling by the Genome Analysis Toolkit and transcriptome analysis using RNA sequencing. We hope that this review can provide useful directions and tips to accompany future bioinformatics algorithm design procedures that properly consider new generations of powerful storage devices.</P>

XML 기반의 생물정보학시스템

신종환,정무영 한국경영과학회 2002 한국경영과학회 학술대회논문집 Vol.- No.1(1)

Bioinformatics can beexplained as the science of developing algorithms, application tools, and computer databases and so on, for the purpose of supporting and enhancing biological research. Bioinformatic information system(BIS) typically handle large data sets and the amount of the data goes up exponentially. Another impediment to easy extraction and retrieval of genomic data in BIS is the need to access different sites for similar information. Recently, here has been some attempts to integrate bioinformatics data in the World Wide Web (WWW) among the bioinformatics community by the internet computing technology. However, the work to integrate bioinformatics data on a universal platform has some problems because of the lack of standard terminologies, semantics, and ontologies about bioinformatics. In this paper, an XML-based BIS architecture is proposed as an technologies allow the creation of meaningful information tags to exchange data between various databases as a standard format, and to create more simple interfaces. This integrated BIS framework has bioinformatics architectural components which is used in the Corporate Information Factory (CIF) method.

Analyzing the field of bioinformatics with the multi-faceted topic modeling technique

Heo, Go Eun,Kang, Keun Young,Song, Min,Lee, Jeong-Hoon BioMed Central 2017 BMC bioinformatics Vol.18 No.suppl7

<P><B>Background</B></P><P>Bioinformatics is an interdisciplinary field at the intersection of molecular biology and computing technology. To characterize the field as convergent domain, researchers have used bibliometrics, augmented with text-mining techniques for content analysis. In previous studies, Latent Dirichlet Allocation (LDA) was the most representative topic modeling technique for identifying topic structure of subject areas. However, as opposed to revealing the topic structure in relation to metadata such as authors, publication date, and journals, LDA only displays the simple topic structure.</P><P><B>Methods</B></P><P>In this paper, we adopt the Tang et al.’s Author-Conference-Topic (ACT) model to study the field of bioinformatics from the perspective of keyphrases, authors, and journals. The ACT model is capable of incorporating the paper, author, and conference into the topic distribution simultaneously. To obtain more meaningful results, we use journals and keyphrases instead of conferences and bag-of-words.. For analysis, we use PubMed to collected forty-six bioinformatics journals from the MEDLINE database. We conducted time series topic analysis over four periods from 1996 to 2015 to further examine the interdisciplinary nature of bioinformatics.</P><P><B>Results</B></P><P>We analyze the ACT Model results in each period. Additionally, for further integrated analysis, we conduct a time series analysis among the top-ranked keyphrases, journals, and authors according to their frequency. We also examine the patterns in the top journals by simultaneously identifying the topical probability in each period, as well as the top authors and keyphrases. The results indicate that in recent years diversified topics have become more prevalent and convergent topics have become more clearly represented.</P><P><B>Conclusion</B></P><P>The results of our analysis implies that overtime the field of bioinformatics becomes more interdisciplinary where there is a steady increase in peripheral fields such as conceptual, mathematical, and system biology. These results are confirmed by integrated analysis of topic distribution as well as top ranked keyphrases, authors, and journals.</P><P><B>Electronic supplementary material</B></P><P>The online version of this article (doi:10.1186/s12859-017-1640-x) contains supplementary material, which is available to authorized users.</P>

바이오데이터베이스와 도구를 활용한 바이오인포매틱스의 동향

임달혁,전수경,박완규,이영주 한국약제학회 2004 Journal of Pharmaceutical Investigation Vol.34 No.1

The union of information-technology and biology presents great possibilities to both applications of bio-information and development of science and technology. Also, meaningful analysis of bio-information brings about a new innovation in the field of bio-market with the advent and growth of bioinformatics. Hence, bioinformatics is the most important aspect for establishing a science-technology-oriented society in the 21^(st) century. This article provides trends in current state of bioinformatics. Technological development of bioinformatics for the rapid growth of bio-industry means that using bioinformatics, a biologist can process and store enormous amount of data such as current Human Genome Project and future data in the field of biology. We have mainly looked at the trends of bio-information, databases and mining tools that are generally used, and strategies and directions for the future.

A Bioinformatics Approach for In Vivo Imaging of Endogenous MicroRNA Targets During Neurogenesis

( Mi Hee Jo ),( Chang Hyun Lee ),( Bahy A Ali ),( Saud A Alarifi ),( Abdulaziz A Al-khedhairy ),( Soon Hag Kim ) 한국조직공학·재생의학회 2012 조직공학과 재생의학 Vol.9 No.3

MicroRNAs (miRNAs), a class of small non-coding RNAs, have been reported to be functionally involved with cellular metabolism and a variety of diseases. The importance of miRNA expression and functional targeting has recently become a focus of intense research. However, their endogenous molecular targets have not been clearly identified despite multiple attempts in prior studies using bioinformatics. Our bioinformatics strategy and in vitro validation by the PCR, identified 16 out of 337 miR124a-predicted targets and 5 out of 299 miR9*-predicted targets were significantly and directly down-regulated by each of the miRNAs during neurogenesis. In vitro and in vivo bioluminescent imaging system was used and successfully monitored the miR9*-mediated repression of SOX2 during neuronal differentiation of the P19 cells. The results of this study demonstrate that our bioinformatics approach offers a powerful and precise method for the identification of novel miR124a and miR9* endogenous targets during neuronal differentiation. This bioinformatics approach, using microarray data available from public DBs, provides a practical means for identifying the endogenous targets of other miRNAs.

COVID-19를 주제로 한 고등학생 대상 ICT 활용 생물정보학 프로그램 개발 및 적용

최지원(Jiwon Choi), 윤용근(Yonggeun Yun), 허희정(Heejeong Heo), 천재순(Jaesun Chun) 학습자중심교과교육학회 2023 학습자중심교과교육연구 Vol.23 No.9

목적 본 연구는 코로나바이러스감염증-19(COVID-19)를 주제로 한 고등학생 대상 정보통신기술(ICT, Information & Communication Technology) 활용 생물정보학 프로그램을 개발하고 적용하여, 학생들의 지식정보처리역량과 과학 흥미도에 미치는 영향에 대해 분석하고자 한다. 방법 프로그램을 개발하기 위해 적합한 ICT 활용 교수⋅학습 유형을 기반으로 하여 5가지 주제로 구성된 15차시 프로그램을 개발하였다. 완성된 프로그램은 8년 이상의 교육 경력을 가진 현직 과학 교사 7인에게 내적 타당도를 받았다. 개발된 프로그램은 2022년 1월에 G시 G고등학교 겨울방학 특강 수업에서 1학년 학생 6명에게 적용하였다. 프로그램의 효과를 확인하기 위해 지식정보처리역량과 과학 흥미도에 대한 사전-사후 검사와 반구조화 면담을 실시하였다. 사전-사후 검사 결과는 윌콕슨 부호 순위 검정 방법을 사용하여 분석하였고, 면담 내용은 전사하여 지식정보처리역량과 과학 흥미도의 하위요인별로 분류하고 범주화하여 의미를 도출하였다. 결과 프로그램은 코로나 바이러스 수용체 ACE2(angiotensin converting enzyme 2)의 동족체인 ACE(angiotensin I converting enzyme) 유전자 실험, 코로나 백신 및 치료제 카드뉴스 제작, 생물정보학 카드뉴스 제작, NCBI(National Center for Biotechnology Information)를 활용한 ACE와 코로나 바이러스의 유전자 분석, 그리고 COVID-19를 주제로 한 생물정보학 신문 제작의 순서로 구성된다. 지식정보처리역량과 과학 흥미도의 사전-사후 검사를 실시한 결과, 사전-사후 차이가 통계적으로 유의미한 것으로 확인되었다(p<.05). 지식정보처리역량의 하위요인별 사전-사후 검사 결과, 하위요인 ‘자료판단’의 평균이 가장 많이 향상되었다. 또한 과학 흥미도의 하위요인별 사전-사후 검사 결과, 하위요인 ‘과학에 대한 흥미와 즐거움’의 평균이 가장 많이 향상되었다. 면담 결과, 학생들은 COVID-19를 주제로 한 ICT 활용 생물정보학 프로그램을 통해 여러 가지의 산출물을 제작하는 능력과 과학에 대한 내적 흥미도 향상에 긍정적인 효과를 보이는 것으로 확인되었다. 결론 본 연구에서는 일반 고등학교 수준에 적용 가능한 수업으로 구성되어 생물정보학과 관련된 수업에서 다양한 형태의 기초 교수-학습 지도안으로 제공될 수 있을 것이며, 추후 생물정보학 관련 교육 연구에 참고 될 수 있을 것으로 기대한다. 또한 과학 교과에서 디지털 시대에 적합한 ICT 활용 수업의 기초 자료로 활용될 수 있을 것이다. Objectives The purpose of this study is to analyze the effect of the students' knowledge and information processing capabilities and scientific interest by developing and applying ICT (Information & Communication Technology) bioinformatics program for high school students under the theme of COVID-19. Methods The 15th class program consisted of 5 topics was developed based on the appropriate teaching and learning types using ICT. The completed program was received internal validity from seven incumbent science teachers with more than eight years of educational experience. The developed program was applied to six first-year students in a special winter vacation class at G High School in G City in January 2022. In order to confirm the effect of the program, pre-post-test and semi-structural interviews were conducted on knowledge information processing capabilities and scientific interest. The pre-post test results were analyzed using the Wilcoxon signed rank test method. And the interview contents were transcribed and classified by sub-factors of knowledge information processing capacity and scientific interest to derive meaning. Results The program consists of the experiments of ACE(angiotensin I converting enzyme) gene which is the homolog of the coronavirus receptor, ACE2 (angiotensin converting enzyme 2), and COVID-19 vaccine and medicine card news production, bioinformatics card news production, and ACE and coronavirus gene analysis using NCBI (National Center for Biotechnology Information). As a result of conducting a pre-post test of knowledge information processing capability and scientific interest, it was confirmed that the pre-post difference was statistically significant (p<.05). As a result of the pre-post inspection by sub-factor of knowledge information processing capability, the average of the sub-factor ‘information analysis’ is the most improved. In addition, as a result of the pre-post-test for each sub-factor of scientific interest, the average of the sub-factors ‘interest and enjoyment in science’ was improved the most. As a result of the interview, it was confirmed that students showed a positive effect on improving their ability to produce various outputs and internal interest in science through the ICT-based bioinformatics program under the theme of COVID-19. Conclusions This study is consisted of classes applicable to the general high school level and can be provided as various forms of basic teaching-learning guidance in classes related to bioinformatics, and is expected to be referred to in future bioinformatics-related educational research. In addition, it can be used as basic data for ICT utilization classes suitable for the digital age in science subjects.

생물정보학을 위한 XML의 활용

이완선,유미애,조환규 한국생명과학회 2002 생명과학회지 Vol.12 No.4

The difficulties in dealing with the Bioinformatics data come more from its idiosyncrasies than from its quantity Currently researchers need to an easy method for data exchange, manage, update. In order to integrate and manage all kinds of biological data, it is reasonable to adopt XML as standard tool since XML is independent of operating system, programming language and hardware platform. Although XML in Bioinformatics has been used widely as a standard notation abroad, however it is the beginning step in the domestic research. This article reviews a basic concept of XML and how to apply XML modeling in Bioinformatics. In addition we present XML applications for genomic sequences, structures and genetic network modeling.

Bioinformatics : Latest Application and Interdisciplinary Field of Computer Science

김기봉(Kim, Ki-Bong) 한국산학기술학회 2010 한국산학기술학회논문지 Vol.11 No.3

본 바이오데이터들이 홍수처럼 쏟아지면서 컴퓨터를 활용해 해결해야 할 많은 문제들이 야기되고 있다. 생체분자들과 연관된 정보들을 대량으로 분석하는 전산기술 응용분야인 생명정보학은 학제간 학문분야로서 현재 확 고히 자리매김하고 있으며. 구조생물학, 유전체학, 단백질체학, 시스템 생물학, 생물통계학 및 전산학 등 광범위한 학 문영역을 포괄한다. 본 총설에서는 생명정보학에 대한 최근 상황과 전반적인 응용분야에 대해 소개하고자 한다. 일반 적으로 널리 사용되는 생명정보 및 바이오데이터베이스들의 유형을 살펴보고, 전산학 분야와 긴밀한 관계가 있는 몇 가지 생명정보학 응용 분야들을 다루고자 한다. A flood of biological data has caused many challenges in computing. Bioinformatics, the application of computational techniques to analyze the information associated with biomolecules on a large-scale, has now firmly established itself as an interdisciplinary subject in molecular biology, and encompasses a wide range of subject areas from structural biology, genomics, proteomics, systems biology, biostatistics to computer science. In this review, I provide an introduction and overview of the current state of bioinformatics. Looking at the types of biological information and databases that are commonly used, I also deals with some of bioinformatics application domains which are closely related to areas of computer science.

Bioinformatics-Inspired Quantized Hard Combination-Based Abnormality Detection for Cooperative Spectrum Sensing in Cognitive Radio Networks

Shah, Hurmat Ali,Usman, Muhammad,Insoo Koo IEEE 2015 IEEE Sensors Journal Vol. No.

<P>String matching algorithms used in bioinformatics can be applied to scenarios in cognitive radios, where reports of cooperative spectrum sensing nodes need to be compared with each other. Cooperative spectrum sensing is susceptible to security risks, where malicious users who participate in the process falsify the spectrum sensing data, thus affecting cognitive radio network performance. In this paper, an efficient spectrum sensing system is developed where each cognitive radio (CR) user senses the spectrum multiple times within an allocated sensing period. Each CR user quantizes its decision to predefined levels so as to achieve a tradeoff between bandwidth utilization and decision reporting accuracy. The reports for all the CR users are compared at the fusion center using Smith-Waterman algorithm, an optimal algorithm for aligning biological sequences used in bioinformatics, and similarity indices are computed. Robust mean and robust deviation of the similarity indices are calculated and a threshold is determined by these values. The CR users who have similarity indices below the given threshold are declared malicious and their reports are discarded. The local decisions of the remaining CR users are combined using the modified rules of decision combination to take a global decision. Simulation results show that our proposed scheme performs better than conventional schemes with and without malicious users.</P>