Kwangmin Choi's Research Page

| Contact | Education | Research | Publications | CS Skills | Bioinformatics | Biology | Links |

Contact

  1. Name : Kwangmin Choi, M.A.(Microbiology), M.S.(Bioinformatics)
  2. Phone :+1-812-856-3009 (Office)
  3. E-mail : kwchoi {{@}} indiana.edu
  4. Address : 2200 West Sudbury Drive, Bloomington, IN, 47403, USA
  5. Position : Research Programmer, School of Informatics, Indiana University, Bloomington, IN, USA
  6. Personal Webpage
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Education

  1. Indiana University, Bloomington, Indiana, USA
  2. The University of Texas at Austin, Austin, Texas, USA
  3. Korea Advanced Institute of Science and Technology, Taejon, South Korea
    • Graduate Student, Dept. Biological Sciences, 1999
  4. Yonsei University, Seoul, South Korea
    • B.S. in Biology, Feb 1997
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Research Experiences

  1. Indiana University, Bloomington, Indiana, USA
    • Research Assistant, 2001-2004
    • Research Programmer, 2004-2006
    • Ph.D student in Informatics
    • Project: Development of comparative genomics system (PLATCOM system)
      • Genome pairwise comparison DB development
      • Gene neighborhood visualization
      • Gene fusion event detection
      • Data flow management using genome data type concept
    • Project: Development of Metabolic pathway analysis system (ComPath)
      • Genome-wide nalyses combining sequence, structure, phylogenomic, context information
    • Project: Comparative genome annotation system (CGAS)
  2. The University of Texas at Austin, Austin, Texas, USA
    • Research Assistant, 1999-2001
      • Project 1 : NS1B expression in Human Infulenza Virus
      • Project 2 : Endospore structure of Bacillus Anthracis related to anthrax pathogeneicity
  3. Korea Advanced Institute of Science and Technology, Taejon, South Korea
    • Research Assistant, 1999
      • Project 1 : Signal transduction induced by Stress-Activated Protein(SAP) Kinase
      • Project 2 : Cell-to-cell communication under steress condition
  4. Samsung Medical Center, Seoul, South Korea
    • Researcher (Cancer Center), 1997-1999
      • Project 1 : Human gene therapy using retroviral vector carrying IL-12 gene
      • Project 2 : Immunogenetic research on human/mouse dendritic cells
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Publications

Year Title Authors Publisher Comment
2006 Genome Data Type: a Vehicle to Deliver a Genome Comparison System on the Web Kwangmin choi, Amit Saple, and Sun Kim Submitted to ICDB
2006 ComPath: Comparative Metabolic Pathway Analyzer Kwangmin Choi and Sun Kim Submitted to Nucleic Acids Research Web Server Issue
2006 CGAS: a Comparative Genome Annotation System Kwangmin Choi, Young IK Yang, Sun Kim Methods in Molecular Biology (under revision) Book Chapter
2006 Comparative Genome Annotation Systems Kwangmin Choi and Sun Kim Advanced Data Mining Technologies in Bioinformatics. edited by Hui-Huang Hsu, Idea Group, Inc. Book Chapter
2005 PLATCOM: a Platform for Computational Comparative Genomics on the Web Kwangmin Choi, Jeong-Hyeon Choi, Amit Saple, Zhiping Wang, Jason Lee, Sun Kim CSB Workshops 2005: 27-30 Postition Paper
2005 PLATCOM: Current Status and Plan for the Next Stages Kwangmin Choi, Jeong-Hyeon Choi, Amit Saple, Zhiping Wang, Jason Lee, and Sun Kim Data Integration in the Life Sciences 2005: No. 3615 in Lecture Notes in Bioinformatics, pp 300-304, June, 2005, San Diego Lecture Note
2005 PLATCOM: A Platform for Computational Comparative Genomics Kwangmin Choi, Yu Ma, Jeong-Hyeon Choi, and Sun Kim Bioinformatics 2005: 15;21(10):2514-6 Application Note
2004 Multiple Genome Alignment by Clustering Pairwise Matches Jeong-Hyeon Choi, Kwangmin Choi, Hwan-Gue Cho, and Sun Kim Proceedings of the 2nd RECOMB Comparative Genomics Satellite Workshop, Lecture Notes in Bioinformatics, Bertinoro, Italy, 3388 (2005). Springer-Verlag, Berlin Lecture Note
2004 Dendritic Cell Based Cancer Immunotherapy: in vivo Study with Mouse Renal Cell Carcinoma Model (Korean) Hyunah Lee, Kwang-Min Choi, Soyoung Baek, Hong-Ghi Lee, and Chul-Won Jung Immune Network, 4(1): 44-52, (2004) Journal Paper, Korean
2002 Sugar Blues Jeeyoun Lee and Kwangmin Choi Bookline Korean Translation from English
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CS Skills

  1. OS : Linux, Solaris, Windows XP/NT/ME/98, MAC
  2. Programming Languages : Perl, Java, Python
  3. Web Programming : HTML, CGI/Perl, PHP, JavaScript, JSP
  4. Web Server Management : APACHE, TOMCAT
  5. Statistics Programs : SPSS, R
  6. Databases : MySQL
  7. Windows Applications : MS-Office and Many Others
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Bioinformatics Skills

  1. Experiences in developing genome analysis programs in Perl, Java, Python
  2. Proficiency with using Bioinformatics Packages (e.g. BioPerl, BioJava, Pfam, HMMER)
  3. Proficiency with using Web-based/ UNIX-based Tools (e.g. NCBI tools)
  4. Experiences in using Molecular Modelling Tools (e.g. GAMESS)
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Biology Skills

  1. DNA : Cloning, Sequencing, Labelling, Purification, PCR, Southen Blotting
  2. RNA : Isolation, Northern Blotting
  3. Protein : Expression, Purification, Electrophoresis, Chromatography
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DB, Packages, Tools

  1. BioScience Portals
  2. Bioinformatics, Genomics, & Computational Biology
  3. Hot Topics in Bioinformatics
  4. Journals
  5. Organization & Conferences
  6. Reference Databases
  7. Tools

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Interesting Links

Tips
  1. Reserch Groups
    1. Sonnhammer group
    2. http://www-2.cs.cmu.edu/~blmt/Seminar/SeminarMaterials/InteractionsPredict.html
    3. Enright Group
    4. Koonin Group
    5. Gernstein Lab
    6. Univ. Utrecht Theoretical Biology Group
    7. James Cotton's Supertree Page
  2. Phylogenetic Tree Analysis
    1. Subtree power analysis and species selection for comparative genomics
    2. A simple algorithm to infer gene duplication and speciation events on a gene tree.
    3. RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs
    4. Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis.
    5. Phylogenomic inference of protein molecular function: advances and challenges
  3. Metabolic Pathway etc.
    1. Kotera M. : Computational assignment of the EC numbers for genomic-scale analysis of enzymatic reactions.
    2. From DB to Dynamics
    3. Michal Ziv-Ukelson : MetaPathwayHunter: a New Tool for the Alignment of Metabolic Pathways, To appear in BioInformatics (2005)
    4. Schuster S, Fell DA, Dandekar T. : A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. Nat Biotechnol. 2000 Mar;18(3):326-32.
    5. Schuster S, Pfeiffer T, Moldenhauer F, Koch I, Dandekar T. : Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniae. Bioinformatics. 2002 Feb;18(2):351-61.
    6. Schwarz R, Musch P, von Kamp A, Engels B, Schirmer H, Schuster S, Dandekar T. : YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities. BMC Bioinformatics. 2005 Jun 1;6(1):135 [Epub ahead of print]
    7. Stefan Schuster : Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering (1999)
    8. Thomas Dandekar : Pathway Alighment: application to the comparative analysis of glycolytic enzymes (1999)
    9. Ming Chen : An algorithm for linear metabolic pathway alignment (2003)
    10. Paper Selection : Pathway Evolution
    11. Evolution of Metabolisms: A New Method for the Comparison of Metabolic Pathways Using Genomics Information
    12. Phylogenetic Analysis of Metabolic Pathways
    13. PathBLAST: a tool for alignment of protein interaction networks
    14. Reconstruction of regulatory and metabolic pathways in metal-reducing gamma-proteobacteria
    15. Deriving phylogenetic trees from the similarity analysis of metabolic pathways (Long version)
    16. Deriving phylogenetic trees from the similarity analysis of metabolic pathways (Short version)
    17. Lateral Transfer and Recompartmentalization of Calvin Cycle Enzymes of Plants and Algae
    18. Different patterns of evolution for duplicated DNA repair genes in bacteria of the Xanthomonadales group
    19. Rampant Horizontal Transfer ubacteria and Plastids
    20. TRACTOR_DB
    21. Predicting Gene Regulatory Elements in Silico on a Genomic Scale
    22. Evolution of gene fusions: horizontal transfer versus independent events
    23. Click
  4. Operon Prediction
    1. http://nar.oupjournals.org/cgi/content/full/30/10/2212
  5. Gene Fusion Events
    1. http://nar.oupjournals.org/cgi/content/full/32/suppl_1/D273
    2. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=115226
    3. http://www.sciencemag.org/cgi/content/full/285/5428/751
    4. http://www.cbio.mskcc.org/~enright/papers/proteinmaps.pdf
    5. http://www.cbio.mskcc.org/~enright/papers/tribemcl.pdf
    6. http://www.cbio.mskcc.org/~enright/papers/networks.pdf
    7. http://www.nature.com/cgi-taf/DynaPage.taf?file=/ng/journal/v26/n2/full/ng1000_141.html
    8. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=35447
  6. Protein-Protein Interaction
    1. Modeling interactome: scale-free or geometric?

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Kwangmin Choi @ school of Informatics, Indiana University, Bloomington, Indiana, USA