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Web-based design and analysis tools for CRISPR base editing
Hwang, Gue-Ho,Park, Jeongbin,Lim, Kayeong,Kim, Sunghyun,Yu, Jihyeon,Yu, Eunchong,Kim, Sang-Tae,Eils, Roland,Kim, Jin-Soo,Bae, Sangsu BioMed Central 2018 BMC bioinformatics Vol.19 No.1
<P><B>Background</B></P><P>As a result of its simplicity and high efficiency, the CRISPR-Cas system has been widely used as a genome editing tool. Recently, CRISPR base editors, which consist of deactivated Cas9 (dCas9) or Cas9 nickase (nCas9) linked with a cytidine or a guanine deaminase, have been developed. Base editing tools will be very useful for gene correction because they can produce highly specific DNA substitutions without the introduction of any donor DNA, but dedicated web-based tools to facilitate the use of such tools have not yet been developed.</P><P><B>Results</B></P><P>We present two web tools for base editors, named BE-Designer and BE-Analyzer. BE-Designer provides all possible base editor target sequences in a given input DNA sequence with useful information including potential off-target sites. BE-Analyzer, a tool for assessing base editing outcomes from next generation sequencing (NGS) data, provides information about mutations in a table and interactive graphs. Furthermore, because the tool runs client-side, large amounts of targeted deep sequencing data (< 1 GB) do not need to be uploaded to a server, substantially reducing running time and increasing data security. BE-Designer and BE-Analyzer can be freely accessed at http://www.rgenome.net/be-designer/ and http://www.rgenome.net/be-analyzer/, respectively.</P><P><B>Conclusion</B></P><P>We develop two useful web tools to design target sequence (BE-Designer) and to analyze NGS data from experimental results (BE-Analyzer) for CRISPR base editors.</P><P><B>Electronic supplementary material</B></P><P>The online version of this article (10.1186/s12859-018-2585-4) contains supplementary material, which is available to authorized users.</P>
cDNA 마이크로어레이 이미지를 위한 그래프 모델과 분석 알고리즘
정호열(Ho-Youl Jung),황미녕(Mi-Nyeong Hwang),유영중(Young-Jung Yu),조환규(Hwan-Gue Cho) 한국정보과학회 2002 정보과학회논문지 : 시스템 및 이론 Vol.29 No.7·8
본 논문에서는 마이크로어레이 처리를 위한 새로운 이미지 분석 알고리즘과 격자 반점들의 위상 정보를 이용하여 격자의 위치를 결정하는 방법을 제시한다. 마이크로어레이는 유전자의 발현량의 측정을 위해서 수만 혹은 수십 만개의 유전자에 대해서 한번에 실험을 할 수 있는 장비이다. 한번의 실험으로 생성되는 데이터 양이 엄청나게 많기 때문에 자동화된 분석이 필요하다. 이 마이크로어레이의 실험 결과는 16-비트 회색조 이미지 파일로 하나의 유전자가 여러 개의 픽셀로 뭉쳐져 있는 반점(spot)이 격자 구조 형태로 나타난다. 본 논문에서 이미지 데이터에서 그래프 구조를 생성하여 이들 반점이 어느 격자에 속하는지 결정하는 알고리즘과 격자 구조의 기울어짐을 측정하여 격자의 정확한 위치와 모양을 결정하는 방법을 제시하고 실제 이미지 데이터를 통한 많은 실험 결과를 보여 준다. In this paper we propose a new image analysis algorithm for microarray processing and a method to locate the position of the grid cell using the topology of the grid spots. Microarray is a device which enables a parallel experiment of 10 to 100 thousands of test genes in order to measure the gene expression. Because of the huge data obtained by a experiment automated image analysis is needed. The final output of this microarray experiment is a set of 16-bit gray level image files which consist of grid-structured spots. In this paper we propose one algorithm which locates the address of spots (spot indices) using graph structure from image data and a method which determines the precise location and shape of each spot by measuring the inclination of grid structure. Several experiments are given from real data sets.
Kamchybek,Gue-Dae Cho,Hwang-Ho Shin,Soo-Gon Woo 한국국제농업개발학회 2016 韓國國際農業開發學會誌 Vol.28 No.2
The purpose of this study is to obtain a clear understanding of the current Kyrgyz agriculture conditions. As it is known to all, Kyrgyzstan has made significant progress in transformation from a central command economy to a market economy. During these two and a half decades, the old state and collective farms have been reorganized and converted into numerous individual private farms. Progress has been inconsistent, though, as farmers and institutions require additional adaptations to cope with a market economy. A number of challenges and strategies provide ways to overcome the constraints faced by farmers, agriculture related organizations as well as foreign investors. From 2015, Kyrgyzstan has been a member of the Eurasian Customs Union. Thus, Kyrgyzstan’s small individual producers are forced to compete on a much larger scale in vast markets. Prosperity in this new environment requires additional development. Adaptation to these big new markets demands trained and efficient farmers. Alongside, recent global climate change has led to increasing natural disasters, including floods, due to massive snow melting, severe winters and drought. Such factors affect agriculture in a number of ways: low agricultural productivity and poor food consumption. As a result, food insecurity, affecting the rural population leading to poverty, are increasing.
한국 농업경영주 고령화에 따른 영농형태별 고용인력 수요분석
신황호 ( Hwang Ho Shin ),조규대 ( Gue Dae Cho ),우수곤 ( Soo Gon Wo ) 한국국제농업개발학회 2015 韓國國際農業開發學會誌 Vol.27 No.2
This study utilizes the Census of Agriculture, Forestry, and Fisheries (year 2010) and is a microscopic approach for the analysis of the aging of the agricultural managers and manpower employment demand, which considered the feature of the dependent variable to utilize the recursive bivariate probit form to analyze based on agricultural forms. The elderly farmhouse had a lower probability of employment in most agricultural forms compared to a non-elderly farmhouse but it was analyzed that the effect will be large on special crops and mushrooms in the case for short term employments, and inn middle to long-term employments the effect was large for animal husbandry. The possession of agricultural machine can be thought to be related in the replacement relationship of manpower employment but it was analyzed that in most of agricultural forms, it was only related with high employment probability, and if it is related to manpower that can operate the agricultural machine, it can be analyzed that it is possibly a mutually complementary relationship (+).
농업부문 경영주 고령화와 고용인력수요: 2010년 농림어업총조사자료 분석
신황호 ( Hwang Ho Shin ),조규대 ( Gue Dae Cho ),서종석 ( Jong Seok Seo ),김인석 ( In Seck Kim ) 한국농업경제학회 2013 農業經濟硏究 Vol.54 No.4
Recently, an increasing trend of aging farmers has been major concern because it can affect many areas such as the structure of farming form, polarization of agricultural income in the future, Among the many relative lssues, this paper examines the characteristic of hired farm labor con-nected to aging of farmers and investigates the relationship between aging of farmers and hired farm labor using the 2010 census of agriculture, forestry and fisheries data. This study found that increasing of aging farmers will decrease the possibility of labor hiring compared to relatively young rarmers in general.
Current trends in gene recovery mediated by the CRISPR-Cas system
김장현,Song Beomjong,Hwang Gue-Ho,배상수 생화학분자생물학회 2020 Experimental and molecular medicine Vol.52 No.-
The CRISPR-Cas system has undoubtedly revolutionized the genome editing field, enabling targeted gene disruption, regulation, and recovery in a guide RNA-specific manner. In this review, we focus on currently available gene recovery strategies that use CRISPR nucleases, particularly for the treatment of genetic disorders. Through the action of DNA repair mechanisms, CRISPR-mediated DNA cleavage at a genomic target can shift the reading frame to correct abnormal frameshifts, whereas DNA cleavage at two sites, which can induce large deletions or inversions, can correct structural abnormalities in DNA. Homology-mediated or homology-independent gene recovery strategies that require donor DNAs have been developed and widely applied to precisely correct mutated sequences in genes of interest. In contrast to the DNA cleavage-mediated gene correction methods listed above, base-editing tools enable base conversion in the absence of donor DNAs. In addition, CRISPR-associated transposases have been harnessed to generate a targeted knockin, and prime editors have been developed to edit tens of nucleotides in cells. Here, we introduce currently developed gene recovery strategies and discuss the pros and cons of each.