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Indiana University Bloomington

Department of Biology

Faculty & Research

Faculty Profile

Justin (Jeong-Hyeon) Choi

Photo of Justin (Jeong-Hyeon) Choi
Assistant Scientist

IU Affiliations
Center for Genomics & Bioinformatics

Contact Information
By telephone: 812-855-9786
JH 059

Ph.D., Pusan National Universiy, Computer Science, 2004.

Postdoctoral Fellow, Indiana University, School of Informatics, 2004-5.

Research Description

Recent advances in next generation sequencing (NGS) technologies generate high throughput data cost-effectively and enable us to understand biological processes in organisms. In addition NGS technologies are being applied to various fields such as genome sequencing projects, transcriptome analyses, and epigenomics. Another new technology called tiling array technology allows us to measure transcriptional expression at the base level with tiling probes. Yet the development of programs or methodologies to analyze these kinds of high throughput is still slow.

My research focuses on developing computational approaches to analyzing NGS and tiling array data for various biological applications. First, I am participating in genome sequencing projects including Daphnia pulex and magna, identifying the best assembly strategy and studying how to validate and improve draft assemblies. Secondly, NGS technologies are used for transcriptome analysis for non-model organisms such as beetles and snakes. These projects led me to develop a pipeline to analyze full cDNA sequences with available databases and programs. NGS technologies are also used for cancer research such as CpG methylation and histone modification studies that present computational challenges such as mapping short reads to reference sequences and statistically measuring the significance of results. Finally, tiling array experiments provide important insight into the overall transcriptome. It is challenging to combine or improve gene models with tiling array data.

Select Publications
T. Wilkes, A. C. Darby, J. H. Choi, J. K. Colbourne, J. H. Werren, and G. D. D. Hurst. "The draft genome sequence of Arsenophonus nasoniae, son-killer bacterium of Nasonia vitripennis, reveals genes associated with virulence and symbiosis,"  Insect Molecular Biology, 19(s1):59-73, 2010.
The Nasonia Genome Working Group "The genomes of three parasitoid wasp species offer insights into speciation, insect evolution, and parasitoid biology,"  Science, 327(5963):343-348, 2010.
A. C. Darby, J. H. Choi, T. Wilkes, M. A. Hughes, J. H. Werren, G. D. D. Hurst, and J. K. Colbourne "Characteristics of the Arsenophonus nasoniae genome; son-killer bacterium of the wasp Nasonia,"  Insect Molecular Biology, 19(s1):75-89, 2010.
Zuojian Tang, Jeong-Hyeon Choi, Chris Hemmerich, Ankita Sarangi, John K. Colbourne, and Qunfeng Dong. "ESTPiper - A Web-based Analysis Pipeline for Expressed Sequence Tags,"  BMC Genomics, 10:174, April 2009.
Jeong-Hyeon Choi, Sun Kim, Haixu Tang, Justen Andrews, Don G. Gilbert, and John K. Colbourne. "A Machine Learning Approach to Combined Evidence Validation of Genome Assemblies,"  Bioinformatics, 24(6):744-750, March 2008.
Mina Rho, Jeong-Hyeon Choi, Sun Kim, Michael Lynch, and Haixu Tang. "De Novo Identification of LTR Retrotransposons in Eukaryotic Genomes,"  BMC Genomics, 8:90, March 2007.
Bin Song, Jeong-Hyeon Choi, Guangyu Chen, Jacek Szymanski, GQ Zhang, Anthony K.H. Tung, Jaewoo Kang, Sun Kim, and Jiong Yang. "ARCS: An Aggregated Related Column Scoring Scheme for Aligned Sequences,"  Bioinformatics, 22(19):2326-2332, October 2006.
DoHoon Lee, Jeong-Hyeon Choi, Mehmet M. Dalkilic, and Sun Kim. "COMPAM: visualization of combining pairwise alignments for multiple genomes,"  Bioinformatics, 26(2):242-244, January 2006.
Kwangmin Choi, Yu Ma, Jeong-Hyeon Choi, and Sun Kim. "PLATCOM: A Platform for Computational Comparative Genomics,"  Bioinformatics, 21(10):2514-2516, May 2005.
Jeong-Hyeon Choi, Hwan-Gue Cho, and Sun Kim. "GAME: A Simple and Efficient Whole Genome Alignment Method Using Maximal Exact Match Filtering,"  Computational Biology and Chemistry (CBAC), 29(3):244-253, 2005.

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