People:JE Shim

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People JE Shim EDIT.JPG

Jung Eun Shim

  • Ph.D., Yonsei Univ., Dept of Computer Science (03/2003 - 08/2008).

Dissertation: 2-DE Gel based Proteome Analysis Methods for Identification of Differentially Expressed Proteins

  • M.S., Yonsei Univ., Dept of Computer Science (03/2001 - 02/2003).

Thesis: A landmark extraction method for the protein 2DE images

Current Research Interests

  • Datamining, Bioinformatics, OLAP, Clustering


  • Shim JE, Bang C, Yang S, Lee T, Hwang S, Kim CY, Singh-Blom M, Marcotte E, Lee I, "GWAB: a web server for the network-based boosting of human genome-wide association data", Nucleic Acids Res (2017) 45 (W1): W154-W161
  • Shim JE, Lee T, Lee I, "From sequencing data to gene functions: co-functional network approaches", Animal Cells and Systems 2017 April 15; 20:77-83
  • Kim H, Kim BS, Shim JE, Hwang S, Yang S, Kim E, Iyer-Pascuzzi AS, Lee I, "TomatoNet: A genome-wide co-functional network for unveiling complex traits of tomato, a model crop for fleshy fruits", Molecular Plant. 2017 April 3; 10:652–655
  • Shim JE, Lee I, "Weighted mutual information analysis substantially improves domain-based functional network models", Bioinformatics 2016 Sep 15;32(18):2824-30
  • Cho A*, Shim JE, Kim E, Supek F, Lehner B, Lee I, "MUFFINN: cancer gene discovery via network analysis of somatic mutation data", Genome Biology 2016 June 23;17(1):129
  • Shim JE, Lee I, "Network-assisted approaches for human disease research", Animal Cells and Systems 2015 Aug 28
  • Lee T, Oh T, Yang S, Shin J, Hwang S, Kim CY, Kim H, Shim H, Shim JE, Ronald PC, Lee I, "RiceNet v2: an improved network prioritization server for rice genes", Nucleic Acids Research 2015 July 1
  • Shin J, Yang S, Kim E, Kim CY, Shim H, Cho A, Kim H, Hwang S, Shim JE, Lee I, "FlyNet: a versatile network prioritization server for the Drosophila community", Nucleic Acids Research 2015 July 1
  • Shim JE, Hwang S, Lee I, "Pathway-Dependent Effectiveness of Network Algorithms for Gene Prioritization", PLoS One 2015 Jun 19
  • Han H, Shim H, Shin D, Shim JE, Ko Y, Shin J, Kim H, Cho A, Kim E, Lee T, Kim H, Kim K, Yang S, Bae D, Yun A, Kim S, Kim CY, Cho HJ, Kang B, Shin S, Lee I, "TRRUST: a reference database of human transcriptional regulatory interactions", Scientific Reports 2015 Jun 12
  • Kim H, Jung KW, Maeng S, Chen YL, Shin J, Shim JE, Hwang S, Janbon G, Kim T, Heitman J, Bahn YS, Lee I, "Network-assisted genetic dissection of pathogenicity and drug resistance in the opportunistic human pathogenic fungus Cryptococcus neoformans", Scientific Reports 2015 Mar 5
  • Kim H, Shim JE, Shin J, Lee I, "EcoliNet: a database of cofunctional gene network for Escherichia coli", Database 2015 Feb 2
  • Lee T, Yang S, Kim E, Ko Y, Hwang S, Shin J, Shim JE, Shim H, Kim H, Kim C, Lee I, "AraNet v2: an improved database of co-functional gene networks for the study of Arabidopsis thaliana and 27 other nonmodel plant species", Nucleic Acids Research 2015 Jan
  • Hanhae Kim, Junha Shin, Eiru Kim, Hyojin Kim, Sohyun Hwang, Jung Eun Shim, Insuk Lee, "YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae", Nucleic Acids Research, (2014) 42(D1): D731-D736.
  • Yienah Jin, Jung Eun Shim, Won Suk Lee, "A Probability-based Error Spot Filtering Method in Protein 2-DE Image Spot Pattern matching analysis", Expert Systems with Applications, Expert Systems with Applications, (2011) 38(12): 14960-14968.
  • Insuk Lee, U. Martin Blom, Peggy I. Wang, Jung Eun Shim, Edward M. Marcotte, "Prioritizing candidate disease genes by network-based boosting of genome-wide association data", Genome Research, (2011) 21(6): 1109-1121.
  • Jung Eun Shim, Dan Bi Kim, Won Suk Lee, Sang Yun Cho, Eunsil Yu, “Exception Discovery: A Novel Method for the Identification of Differentially Expressed Proteins”, IEEE transactions on information technology in biomedicine, (2010) 14(2): 473-480.
  • Jung Eun Shim, Won Suk Lee, "On-line Analytical Framework for the 2-DE based Proteome Information", Expert Systems with Applications, (2009) 36: 7528–7534.
  • Jung Eun Shim, Won Suk Lee, "A landmark extraction method for protein 2DE gel images based on multi-dimensional clustering", Artificial Intelligence in Medicine (2005) 35: 157-170.
  • Sang Yun Cho, Kang-Sik Park, Jung Eun Shim, Min-Seok Kwon, Kil Hong Joo, Won Suk Lee, Joon Chang, Hoguen Kim, Hyun Cheol Chung, Hyun Ok Kim, Young-Ki Paik, "An integrated proteome database for two-dimensional electrophoresis data analysis and laboratory information management system", Proteomics, (2002) 2(9): 1104-13.
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