Kyungsook Han

Summary

Affiliation: Inha University
Country: Korea

Publications

  1. pmc A semi-supervised learning approach to predict synthetic genetic interactions by combining functional and topological properties of functional gene network
    Zhu Hong You
    Intelligent Computing Lab, Institute of Intelligent Machine, Chinese Academy of Science, P O Box 1130, Hefei, Anhui 230031, China
    BMC Bioinformatics 11:343. 2010
  2. ncbi request reprint A vector-based method for drawing RNA secondary structure
    K Han
    Department of Automation Engineering, Inha University, Inchon 402 751 and College of Pharmacy, Chung Ang University, Seoul 156 756, South Korea
    Bioinformatics 15:286-97. 1999
  3. ncbi request reprint HPID: the Human Protein Interaction Database
    Kyungsook Han
    School of Computer Science and Engineering, Inha University, Inchon 402 751, Korea
    Bioinformatics 20:2466-70. 2004
  4. ncbi request reprint A fast layout algorithm for protein interaction networks
    Kyungsook Han
    School of Computer Science and Engineering, Inha University, Inchon 402 751, Korea
    Bioinformatics 19:1882-8. 2003
  5. ncbi request reprint Prediction of binding motifs in hepatitis C virus NS5A and human proteins
    Guang Zheng Zhang
    School of Computer Science and Engineering, Inha University, Korea
    Protein Pept Lett 15:494-504. 2008
  6. ncbi request reprint PRI-Modeler: extracting RNA structural elements from PDB files of protein-RNA complexes
    Kyungsook Han
    School of Computer Science and Engineering, Inha University, Inchon 402 751, Republic of Korea
    FEBS Lett 581:1881-90. 2007
  7. ncbi request reprint Three-dimensional visualization of protein interaction networks
    Kyungsook Han
    School of Computer Science and Engineering, Inha University, Inchon 402 751, South Korea
    Comput Biol Med 34:127-39. 2004
  8. pmc PSEUDOVIEWER2: Visualization of RNA pseudoknots of any type
    Kyungsook Han
    School of Computer Science and Engineering, Inha University, Inchon 402 751, Korea
    Nucleic Acids Res 31:3432-40. 2003
  9. ncbi request reprint PseudoViewer: automatic visualization of RNA pseudoknots
    Kyungsook Han
    Department of Computer Science and Engineering, Inha University, Inchon 402 751, South Korea
    Bioinformatics 18:S321-8. 2002
  10. ncbi request reprint A graphical tool for parametric simulation of the RNA structure formation
    K Han
    Department of Automation Engineering, Inha University, Inchon, Korea
    Mol Cells 10:348-55. 2000

Collaborators

Detail Information

Publications41

  1. pmc A semi-supervised learning approach to predict synthetic genetic interactions by combining functional and topological properties of functional gene network
    Zhu Hong You
    Intelligent Computing Lab, Institute of Intelligent Machine, Chinese Academy of Science, P O Box 1130, Hefei, Anhui 230031, China
    BMC Bioinformatics 11:343. 2010
    ..Therefore, an accurate computational approach to predict genetic interaction is highly desirable, and such methods have the potential of alleviating the bottleneck on experiment design...
  2. ncbi request reprint A vector-based method for drawing RNA secondary structure
    K Han
    Department of Automation Engineering, Inha University, Inchon 402 751 and College of Pharmacy, Chung Ang University, Seoul 156 756, South Korea
    Bioinformatics 15:286-97. 1999
    ..To produce a polygonal display of RNA secondary structure with minimal overlap and distortion of structural elements, with minimal search for positioning them, and with minimal user intervention...
  3. ncbi request reprint HPID: the Human Protein Interaction Database
    Kyungsook Han
    School of Computer Science and Engineering, Inha University, Inchon 402 751, Korea
    Bioinformatics 20:2466-70. 2004
    ..We have also developed a set of web-based programs so that users can visualize and analyze protein interaction networks in order to explore the networks further...
  4. ncbi request reprint A fast layout algorithm for protein interaction networks
    Kyungsook Han
    School of Computer Science and Engineering, Inha University, Inchon 402 751, Korea
    Bioinformatics 19:1882-8. 2003
    ..Graph drawing algorithms are often used for visualizing relational information, but a naive implementation of a graph drawing algorithm encounters real difficulties when drawing large-scale graphs such as protein interaction networks...
  5. ncbi request reprint Prediction of binding motifs in hepatitis C virus NS5A and human proteins
    Guang Zheng Zhang
    School of Computer Science and Engineering, Inha University, Korea
    Protein Pept Lett 15:494-504. 2008
    ..The binding motif of human proteins often forms a full helix or an extended strand-loop structure, and is in good agreement with the experimental findings of previous studies...
  6. ncbi request reprint PRI-Modeler: extracting RNA structural elements from PDB files of protein-RNA complexes
    Kyungsook Han
    School of Computer Science and Engineering, Inha University, Inchon 402 751, Republic of Korea
    FEBS Lett 581:1881-90. 2007
    ..PRI-Modeler is accessible at http://wilab.inha.ac.kr/primodeler/, and supplementary materials are available in the analysis results section at http://wilab.inha.ac.kr/primodeler/...
  7. ncbi request reprint Three-dimensional visualization of protein interaction networks
    Kyungsook Han
    School of Computer Science and Engineering, Inha University, Inchon 402 751, South Korea
    Comput Biol Med 34:127-39. 2004
    ..Experimental results show that our algorithm efficiently generates a clear and aesthetically pleasing drawing of large-scale protein interaction networks and that it is an order of magnitude faster than other force-directed layouts...
  8. pmc PSEUDOVIEWER2: Visualization of RNA pseudoknots of any type
    Kyungsook Han
    School of Computer Science and Engineering, Inha University, Inchon 402 751, Korea
    Nucleic Acids Res 31:3432-40. 2003
    ..The PSEUDOVIEWER2 algorithm is the first developed for the automatic drawing of RNA secondary structures, including pseudoknots of any type. PSEUDOVIEWER2 is accessible at http://wilab.inha.ac.kr/pseudoviewer2/...
  9. ncbi request reprint PseudoViewer: automatic visualization of RNA pseudoknots
    Kyungsook Han
    Department of Computer Science and Engineering, Inha University, Inchon 402 751, South Korea
    Bioinformatics 18:S321-8. 2002
    ..The task of visualizing RNA pseudoknots by hand becomes more challenging as the size and complexity of the RNA pseudoknots increase...
  10. ncbi request reprint A graphical tool for parametric simulation of the RNA structure formation
    K Han
    Department of Automation Engineering, Inha University, Inchon, Korea
    Mol Cells 10:348-55. 2000
    ..QFolder allows a user to gain insights into the RNA folding process and can be used as useful aids in designing biochemical experiments to elucidate the RNA folding process more accurately...
  11. pmc WebInterViewer: visualizing and analyzing molecular interaction networks
    Kyungsook Han
    School of Computer Science and Engineering, Inha University, Inchon 402 751, Korea
    Nucleic Acids Res 32:W89-95. 2004
    ..WebInterViewer is accessible at http://interviewer.inha.ac.kr/...
  12. ncbi request reprint Visualization and analysis of protein interactions
    Byong Hyon Ju
    Department of Computer Science and Engineering, Inha University, Inchon, 402 751, South Korea
    Bioinformatics 19:317-8. 2003
    ....
  13. ncbi request reprint Discovering the interaction propensities of amino acids and nucleotides from protein-RNA complexes
    Euna Jeong
    School of Computer Science and Engineering, Inha University, Incheon 402 751, Korea
    Mol Cells 16:161-7. 2003
    ..The interaction patterns discovered from the analysis provide useful information for predicting the structure of RNA that binds proteins, and of proteins that bind RNA...
  14. ncbi request reprint Hepatitis C virus contact map prediction based on binary encoding strategy
    Guang Zheng Zhang
    School of Computer Science and Engineering, Inha University, Incheon 402 751, South Korea
    Comput Biol Chem 31:233-8. 2007
    ..This promising result could provide some useful insights into the nature of HCV protein fold mechanism...
  15. pmc PseudoViewer: web application and web service for visualizing RNA pseudoknots and secondary structures
    Yanga Byun
    School of Computer Science and Engineering, Inha University, Inchon 402 751, Korea
    Nucleic Acids Res 34:W416-22. 2006
    ..The web service and web application are available at http://pseudoviewer.inha.ac.kr/...
  16. ncbi request reprint A general computational model for predicting ribosomal frameshifts in genome sequences
    Yanga Byun
    School of Computer Science and Engineering, Inha University, Inchon 402 751, South Korea
    Comput Biol Med 37:1796-801. 2007
    ..FSFinder2 is available at http://wilab.inha.ac.kr/FSFinder...
  17. ncbi request reprint Predicting RNA-binding sites in proteins using the interaction propensity of amino acid triplets
    Mi Ran Yun
    School of Computer Science and Engineering, Inha University, Incheon 402 751, Korea
    Protein Pept Lett 17:1102-10. 2010
    ..Our SVM classifier can also be used to predict protein-binding nucleotides in RNA sequences...
  18. ncbi request reprint Complexity management in visualizing protein interaction networks
    Byong Hyon Ju
    School of Computer Science and Engineering, Inha University, Inchon 402 751, Korea
    Bioinformatics 19:i177-9. 2003
    ..This severely limits the utility of many graph drawing tools because they become too slow for an interactive analysis of the networks and because they produce cluttered drawings with many edge crossings...
  19. pmc Finding motif pairs in the interactions between heterogeneous proteins via bootstrapping and boosting
    Jisu Kim
    School of Computer Science and Engineering, Inha University, Incheon, South Korea
    BMC Bioinformatics 10:S57. 2009
    ..Random selection from non-positive interactions is unsuitable, since the selected data may not reflect the original distribution of data...
  20. doi request reprint PseudoViewer3: generating planar drawings of large-scale RNA structures with pseudoknots
    Yanga Byun
    Department of Computer Science and Engineering, Inha University, Incheon, South Korea
    Bioinformatics 25:1435-7. 2009
    ..The previous version of PseudoViewer visualizes all the known types of RNA pseudoknots as planar drawings, but visualizes some hypothetical pseudoknots as non-planar drawings...
  21. pmc Predicting genes expressed via -1 and +1 frameshifts
    Sanghoon Moon
    School of Computer Science and Engineering, Inha University, Inchon 402 751, Korea
    Nucleic Acids Res 32:4884-92. 2004
    ..FSFinder is useful for discovering unknown genes that utilize alternative decoding, as well as for analyzing frameshift sites. It is freely accessible at http://wilab.inha.ac.kr/FSFinder/...
  22. ncbi request reprint BSFINDER: finding binding sites of HCV proteins using a support vector machine
    Yu Chen
    School of Computer Science and Engineering, Inha University, Incheon, South Korea
    Protein Pept Lett 16:373-82. 2009
    ..inha.ac.kr/bsfinder. BSFinder will be of considerable help in predicting binding residues and potential interacting partners of a protein...
  23. ncbi request reprint Computational analysis of hydrogen bonds in protein-RNA complexes for interaction patterns
    Hyunwoo Kim
    School of Computer Science and Engineering, Inha University, 402 751 Inchon, South Korea
    FEBS Lett 552:231-9. 2003
    ..The interaction patterns discovered from the analysis will provide us with useful information in predicting the structure of the RNA binding protein and the structure of the protein binding RNA...
  24. pmc An algorithm for finding functional modules and protein complexes in protein-protein interaction networks
    Guangyu Cui
    School of Computer Science and Engineering, Inha University, Incheon 402 751, South Korea
    J Biomed Biotechnol 2008:860270. 2008
    ....
  25. doi request reprint ModuleSearch: finding functional modules in a protein-protein interaction network
    Guangyu Cui
    School of Computer Science and Engineering, Inha University, Incheon, 402 751, South Korea
    Comput Methods Biomech Biomed Engin 15:691-9. 2012
    ..ModuleSearch and sample data are freely available to academics at http://bclab.inha.ac.kr/ModuleSearch...
  26. pmc Prediction of RNA-binding amino acids from protein and RNA sequences
    Sungwook Choi
    School of Computer Science and Engineering, Inha University, Inchon 402 751, South Korea
    BMC Bioinformatics 12:S7. 2011
    ..e., RNA) of a protein when they predict RNA-binding amino acids. Thus, they always predict the same RNA-binding sites for a given protein sequence even if the protein binds to different RNA molecules...
  27. doi request reprint A reliability measure of protein-protein interactions and a reliability measure-based search engine
    Byungkyu Park
    Department of Computer Science and Information Engineering, Inha University, Incheon, South Korea
    Comput Methods Biomech Biomed Engin 13:97-104. 2010
    ..The search engine and the reliability measure of protein interactions should provide useful information for determining proteins to focus on...
  28. ncbi request reprint FSDB: a frameshift signal database
    Sanghoon Moon
    School of Computer Science and Engineering, Inha University, Inchon 402 751, Republic of Korea
    Comput Biol Chem 31:298-302. 2007
    ..inha.ac.kr/fsfinder2). We believe FSDB will be a valuable resource for scientists studying programmed ribosomal frameshifting. FSDB is freely accessible at http://wilab.inha.ac.kr/fsdb/...
  29. doi request reprint PPISearchEngine: gene ontology-based search for protein-protein interactions
    Byungkyu Park
    a Institute for Information and Electronics Research, Inha University, Incheon, 402 751, South Korea
    Comput Methods Biomech Biomed Engin 16:691-8. 2013
    ..PPISearchEngine is freely available to academics at http://search.hpid.org/ . ..
  30. pmc Prediction of protein-protein interactions between viruses and human by an SVM model
    Guangyu Cui
    School of Computer Science and Engineering, Inha University, Incheon, South Korea
    BMC Bioinformatics 13:S5. 2012
    ....
  31. pmc An ontology-based search engine for protein-protein interactions
    Byungkyu Park
    School of Computer Science and Engineering, Inha University, Incheon 402 751, South Korea
    BMC Bioinformatics 11:S23. 2010
    ..Such syntactic search methods often retrieve too few search results or no results despite many potential matches present in the database...
  32. pmc Qualitative reasoning of dynamic gene regulatory interactions from gene expression data
    Yu Chen
    School of Computer Science and Engineering, Inha University, Incheon, Korea
    BMC Genomics 11:S14. 2010
    ..Such static networks cannot represent temporal aspects of gene regulatory interactions such as the order of gene regulations or the pace of gene regulations...
  33. doi request reprint InfarctSizer: computing infarct volume from brain images of a stroke animal model
    Jaetak Lee
    School of Computer Science and Engineering, Inha University, Incheon, South Korea
    Comput Methods Biomech Biomed Engin 14:497-504. 2011
    ..InfarctSizer and sample brain images are available at http://wilab.inha.ac.kr/brainimage...
  34. doi request reprint Classification of diffusion tensor images for the early detection of Alzheimer's disease
    Wook Lee
    School of Computer Science and Engineering, Inha University, Incheon, Republic of Korea
    Comput Biol Med 43:1313-20. 2013
    ..The best performance achieved by the SVM model in a 10-fold cross validation and in independent testing was sensitivity of 100%, specificity of 100% and accuracy of 100%. ..
  35. pmc KGVDB: a population-based genomic map of CNVs tagged by SNPs in Koreans
    Sanghoon Moon
    Division of Structural and Functional Genomics, Division of Bio Medical Informatics, Center for Genome Science, National Institute of Health, Chungcheongbuk Do, Korea
    Bioinformatics 29:1481-3. 2013
    ..This article presents a database that provides CNV regions tagged by single nucleotide polymorphisms in about 4700 Koreans, which were detected under strict quality control, manually curated and experimentally validated...
  36. pmc Modeling the interactions of Alzheimer-related genes from the whole brain microarray data and diffusion tensor images of human brain
    Byungkyu Park
    Institute for Information and Electronics Research, Inha University, Incheon, South Korea
    BMC Bioinformatics 13:S10. 2012
    ..The challenge is to integrate various types of data to investigate the interactions of genes that are associated with specific neurological disorder...
  37. pmc Isolation of specific and high-affinity RNA aptamers against NS3 helicase domain of hepatitis C virus
    Byounghoon Hwang
    Department of Molecular Biology, Institute of Nanosensor and Biotechnology, Dankook University, San8 Hannam Dong, Yongsan gu, Seoul 140 714, Korea
    RNA 10:1277-90. 2004
    ..These results suggest that the RNA aptamers selected in vitro could be useful not only as therapeutic and diagnostic agents of HCV infection but also as a powerful tool for the study of HCV helicase mechanism...
  38. ncbi request reprint Predicting key long-range interaction sites by B-factors
    Peng Chen
    Hefei Institute of Intelligent Machines, Chinese Academy of Sciences, Hefei Anhui, 230031, China
    Protein Pept Lett 15:478-83. 2008
    ..As a result, the key long-range interaction residues can be located based on information of local lowest B-factor sites...
  39. ncbi request reprint PSIbase: a database of Protein Structural Interactome map (PSIMAP)
    Sungsam Gong
    Biomatics Lab, Department of Biosystems, KAIST, Daejeon, Korea
    Bioinformatics 21:2541-3. 2005
    ..Users can retrieve possible interaction partners of their proteins of interests if a significant homology assignment is made with their query sequences. AVAILABILITY: http://psimap.org and http://psibase.kaist.ac.kr/..
  40. ncbi request reprint Prevention of passively transferred experimental autoimmune myasthenia gravis by an in vitro selected RNA aptamer
    Byounghoon Hwang
    Department of Molecular Biology, Dankook University, Seoul, 140 714, South Korea
    FEBS Lett 548:85-9. 2003
    ..These results suggested that RNA aptamers could be applied for antigen-specific treatment for autoimmune diseases including MG...
  41. ncbi request reprint Intracellular expression of the T-cell factor-1 RNA aptamer as an intramer
    Kang Hyun Choi
    Department of Molecular Biology, BK21 Graduate Program for RNA Biology, Institute of Nanosensor and Biotechnology, Dankook University, Hannam dong san 8, Yongsan Ku, Seoul 140 714, Korea
    Mol Cancer Ther 5:2428-34. 2006
    ..In addition, it efficiently reduced the growth rate and tumorigenic potential of HCT116 colon cancer cells. Such RNA intramer could lead to valuable gene therapeutics for TCF/beta-catenin-mediated carcinogenesis...