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Publications

Some manuscripts are only for INTERNAL use. DO NOT distribute them!
Year Title Authors Publisher Comment
2005 COMPAM :Visualization of Combining Pairwise alignment for Multiple Genomes DoHoon Lee, Jeong-Hyeon Choi, Mehmet Dalkilic, and Sun Kim Bioinformatics, 2005 Dec 16 Application Note
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 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 Kwangmin Choi, Yu Ma, Jeong-Hyeon Choi, and Sun Kim Bioinformatics 2005: 15;21(10):2514-6 Application Note
2005 A Simple and Efficient Alignment Method for Microbial Whole Genomes Using Maximal Exact Match Filtering Choi, J.-H., Cho, H.-G., and Kim, S. Computational Biology and Chemistry 2005: 29(3), 244-253 Research Paper
2005 A Data Management Architecture for Computational Biology Ma, Y., Bramley, R., and Kim, S. Indiana University Computer Science Technical Report 607 Technocal Report
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
2003 Graph theoretic sequence clustering algorithms and their applications to genome comparison Sun Kim Chapter 4 in Computational Biology and Genome Informatics, World Scientific Book Chapter

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Share your tips

  1. How to draw phylogenetic tree using PHYLIP?

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Interesting papers

  • Weekly seminar .
    Date Presenter Title Publisher Authors
    11/15/2006 Kwangmin Choi (1)Network Biology (Review) (2)PPT Nature Barabasi et al.
    11/8/2006 Youngik Yang
    10/4/2006 Kwangmin Choi (1)Global structure (2)Network connectivity + Centtrality (3)Network decomposition (4)Pajek Bioinformatics Ma et al.
    9/28/2006 Youngik Main topic, CPM method(Nature), Supplementary material, PowerPoint
    8/15/2006 Kwangmin Inferring Functional Relationships of Proteins from Local Sequence and Spatial Surface Patterns Jornal of Molecular Biology, Volume 332, Issue 2 , 12 September 2003, Pages 505-526T. Andrew Binkowski, Larisa Adamian and Jie Liang
    8/8/2006 Jason Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions Bioinformatics. 2006 Jul 1;22(13):1623-30 Chua HN, et al.
    8/1/2006 Kwangmin Supra-domains: Evolutionary Units Larger than Single Protein Domains Journal of Molecular Biology Volume 336, Issue 3 Vogel C, et al.
    5/11/2006 Kwangmin Comparative genome analysis of Bacillus cereus group genomes with Bacillus subtilis FEMS Microbiol Lett. 2005 Sep 15;250(2):175-84 Anderson I, et al.
    1/11/2006 Kwangmin ComPath CGB Round Table Talk 12/1/2005 Kwangmin Choi & Sun Kim
    10/12/2005 Amit Alignment of metabolic pathways. Bioinformatics. 2005 Aug 15;21(16):3401-8. Epub 2005 Jun 28. Pinter RY, Rokhlenko O, Yeger-Lotem E, Ziv-Ukelson M.
    9/30/2005 Jason Improved prediction of protein-protein binding sites using a support vector machines approach. Bioinformatics. 2005 Apr 15;21(8):1487-94. Epub 2004 Dec 21. Bradford JR, Westhead DR.
    9/28/2005 Jason Prediction of protein-protein interactions using distant conservation of sequence patterns and structure relationships Bioinformatics. 2005 Aug 15;21(16):3360-8. Epub 2005 Jun 16. Espadaler J, Romero-Isart O, Jackson RM, Oliva B.
    9/21/2005 Kwangmin Phylogenomic inference of protein molecular function: advances and challenges + Superfamily HMM in functional genomics Bioinformatics. 2004 Jan 22;20(2):170-9 Sjolander K.
    9/15/2005 Jason Significance analysis of microarrays applied to the ionizing radiation response Proc Natl Acad Sci U S A. 2001 Apr 24;98(9):5116-21. Epub 2001 Apr 17. Tusher VG, Tibshirani R, Chu G.
    9/7/2005 JH Recognition of spatial motifs in protein structures. J Mol Biol. 1999 Jan 29;285(4):1887-97. Kleywegt G.J.
    9/7/2005 Sun Kim SPRATT + SAM
    9/1/2005 Kwangmin Definitions of enzyme function for the structural genomics era. Curr Opin Chem Biol. 2003 Apr;7(2):230-7. Babbitt PC
    8/25/2005 Kwangmin Computational assignment of the EC numbers for genomic-scale analysis of enzymatic reactions. J Am Chem Soc. 2004 Dec 22;126(50):16487-98. Kotera M
    4/20/2005 Kwangmin PathBLAST: a tool for alignment of protein interaction network Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W83-8. Kelley BP, Yuan B, Lewitter F, Sharan R, Stockwell BR, Ideker T.

  • System Design & Genome Browsing
    1. CoGenT++: an extensive and extensible data environment for computational genomics. Bioinformatics. 2005 Oct 1;21(19):3806-10.
    2. Genomorama & other genome browsers
  • Motif Discovery
    1. Motif-based protein ranking by network propagation. Bioinformatics. 2005 Oct 1;21(19):3711-8. Epub 2005 Aug 2.
    2. FSSM Software
    3. DATF: a database of Arabidopsis transcription factors Bioinformatics Advance Access published on February 24, 2005 Bioinformatics 2005 21: 2568-2569; doi:10.1093/bioinformatics/bti334 Anyuan Guo, Kun He, Di Liu, Shunong Bai, Xiaocheng Gu, Liping Wei, and Jingchu Luo
  • Protein structure and interaction
    1. Macromolecular Structure Database
    2. Inferring protein domain interactions from databases of interacting proteins
    3. Zn-containing ADH
    4. Fe-containg ADH
  • Phylogeny: Tree Analysis etc.
    1. Animal Proteome Explorer
    2. Nexplorer: Phylogeny-based exploration of sequence family data
    3. Paper collection
    4. Subtree power analysis and species selection for comparative genomics Nat Genet. 2005 Jul;37(7):777-82. Epub 2005 Jun 12.
    5. Concerted and Birth-and-Death Evolution of Multigene Families, Annu Rev Genet. 2005;39:121-52.
  • Synteny, Gene Cluster, Functional Coupling
    1. Birth of a metabolic gene cluster in yeast by adaptive gene relocation.
  • Metabolomics
    1. Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective
    2. Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering
    3. Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniae
    4. Genome-scale microbial in silico models: the constraints-based approach
    5. Genome-Scale Metabolic Model of Helicobacter pylori 26695
    6. Pathway tools for MetaCyc/BioCyc
    7. Systems analyses characterize integrated functions of biochemical networks.
    8. Hierarchical thinking in network biology: the unbiased modularization of biochemical networks.
    9. Comparison of network-based pathway analysis methods
    10. Ming Chen : An algorithm for linear metabolic pathway alignment
    11. Paper Selection : Pathway Evolution
    12. Evolution of Metabolisms: A New Method for the Comparison of Metabolic Pathways Using Genomics Information
    13. Phylogenetic Analysis of Metabolic Pathways
    14. PathBLAST: a tool for alignment of protein interaction networks
    15. Reconstruction of regulatory and metabolic pathways in metal-reducing gamma-proteobacteria
    16. Deriving phylogenetic trees from the similarity analysis of metabolic pathways (Long version)
    17. Deriving phylogenetic trees from the similarity analysis of metabolic pathways (Short version)
    18. Lateral Transfer and Recompartmentalization of Calvin Cycle Enzymes of Plants and Algae
    19. Different patterns of evolution for duplicated DNA repair genes in bacteria of the Xanthomonadales group
    20. Rampant Horizontal Transfer ubacteria and Plastids
    21. TRACTOR_DB
    22. Predicting Gene Regulatory Elements in Silico on a Genomic Scale
    23. Evolution of gene fusions: horizontal transfer versus independent events
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    Links

    1. Test page
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    Developers

    1. Prof. Sun Kim : sunkim@bio.infomatics......
    2. Kwangmin Choi : kwchoi@ind......
    3. Jeong-Hyeon Choi : jeochoi@ind...
    4. Zhiping Wang : zhipwang@ind...
    5. Amit Saple : asaple@ind...
    6. Jason Lee : jhl2@ind....
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    Copyright © 2005, Kwangmin Choi