Network Biology Lab - User contributions [en]

Domain2Pathway by Pathway Specificity (PS)

2017-09-22T07:59:18Z

Shimje:

Protein domains are basic functional units of proteins, yet domain-based pathway annotations for proteins are still challenging tasks because many domains are pervasive among diverse pathways.
Nevertheless, some domains may exist in specific pathways.
We therefore developed a network-based scoring scheme to quantify '''specificity of domain-pathway associations (PS)''', and then used it to classify ''''Pathway-Specific Domains (PSDs)'''' and ''''Non-Specific Domains (NSDs)''''.

*[https://netbiolab.org/wiki/images/6/68/Ps.zip Source codes and data files for PS calculation]

'''''Citation''''' : Jung Eun Shim, Ji Hyun Kim, Junha Shin, Ji Eun Lee and Insuk Lee, Network-based identification of pathway-specific protein domains and their implications for human diseases (under review)

'''''Contact Information''''' : Insuk Lee (insuklee[at]yonsei[dot]ac[dot]kr)

Domain-based PPI network by Weighted Mutual Information (WMI)

2017-09-22T07:29:34Z

Shimje:

Functional protein-protein interaction (PPI) networks elucidate molecular pathways underlying complex phenotypes, including those of human diseases.
Protein domain is a functional unit of the protein. Therefore, we may effectively infer functional interactions between proteins based on the co-occurrence of domains.
Here, we present a method for inferring accurate functional PPIs based on the similarity of domain composition between proteins by '''''weighted mutual information (WMI)''''' that assigned different weights to the domains based on their genome-wide frequencies.

*[http://www.netbiolab.org/wiki/images/0/09/WMI_program.zip Source codes for WMI calculation]
*[http://www.netbiolab.org/wiki/images/1/1e/SC_WMI_12K.txt Domain-based yeast PPI network by WMI]
*[http://www.netbiolab.org/wiki/images/4/44/HS_WMI_94K.txt Domain-based human PPI network by WMI]

'''''Citation''''' : Jung Eun Shim and Insuk Lee, Weighted mutual information analysis substantially improves domain-based functional network models. Bioinformatics 2016 Sep 15;32(18):2824-30

'''''Contact Information''''' : Insuk Lee (insuklee[at]yonsei[dot]ac[dot]kr)

Domain2Pathway by Pathway Specificity (PS)

2017-09-22T07:27:39Z

Shimje:

Protein domains are basic functional units of proteins, yet domain-based pathway annotations for proteins are still challenging tasks because many domains are pervasive among diverse pathways.
Nevertheless, some domains may exist in specific pathways.
We therefore developed a network-based scoring scheme to quantify '''specificity of domain-pathway associations (PS)''', and then used it to classify ''''Pathway-Specific Domains (PSDs)'''' and ''''Non-Specific Domains (NSDs)''''.

*[https://netbiolab.org/wiki/images/6/68/Ps.zip Source codes and datafile for PS calculation]

'''''Citation''''' : Jung Eun Shim, Ji Hyun Kim, Junha Shin, Ji Eun Lee and Insuk Lee, Network-based identification of pathway-specific protein domains and their implications for human diseases (under review)

'''''Contact Information''''' : Insuk Lee (insuklee[at]yonsei[dot]ac[dot]kr)

Domain2Pathway by Pathway Specificity (PS)

2017-09-22T07:25:59Z

Shimje:

Protein domains are basic functional units of proteins, yet domain-based pathway annotations for proteins are still challenging tasks because many domains are pervasive among diverse pathways.
Nevertheless, some domains may exist in specific pathways.
We therefore developed a network-based scoring scheme to quantify '''specificity of domain-pathway associations''', and then used it to classify ''''pathway-specific domains (PSDs)'''' and ''''non-specific domains (NSDs)''''.

*[https://netbiolab.org/wiki/images/6/68/Ps.zip Source codes and datafile for PS calculation]

'''''Citation''''' : Jung Eun Shim, Ji Hyun Kim, Junha Shin, Ji Eun Lee and Insuk Lee, Network-based identification of pathway-specific protein domains and their implications for human diseases (under review)

'''''Contact Information''''' : Insuk Lee (insuklee[at]yonsei[dot]ac[dot]kr)

File:Ps.zip

2017-09-22T07:25:05Z

Shimje: PathwaySpecificity - Source code - Datafiles (including both example and real data)

PathwaySpecificity
- Source code
- Datafiles (including both example and real data)

Domain2Pathway by Pathway Specificity (PS)

2017-09-22T07:16:39Z

Shimje:

Protein domains are basic functional units of proteins, yet domain-based pathway annotations for proteins are still challenging tasks because many domains are pervasive among diverse pathways.
Nevertheless, some domains may exist in specific pathways.
We therefore developed a network-based scoring scheme to quantify '''specificity of domain-pathway associations''', and then used it to classify ''''pathway-specific domains (PSDs)'''' and ''''non-specific domains (NSDs)''''.

*[http://www.netbiolab.org/wiki/images/0/09/WMI_program.zip Source codes and datafile for PS calculation]

'''''Citation''''' : Jung Eun Shim, Ji Hyun Kim, Junha Shin, Ji Eun Lee and Insuk Lee, Network-based identification of pathway-specific protein domains and their implications for human diseases (under review)

'''''Contact Information''''' : Insuk Lee (insuklee[at]yonsei[dot]ac[dot]kr)

Domain2Pathway by Pathway Specificity (PS)

2017-09-22T06:56:32Z

Shimje:

Protein domains are basic functional units of proteins, yet domain-based pathway annotations for proteins are still challenging tasks because many domains are pervasive among diverse pathways.
Nevertheless, some domains may exist in specific pathways.
We therefore developed a network-based scoring scheme to quantify '''specificity of domain-pathway associations''', and then used it to classify ''''pathway-specific domains (PSDs)'''' and ''''non-specific domains (NSDs)''''.

*[http://www.netbiolab.org/wiki/images/0/09/WMI_program.zip Source codes for PS calculation]
*[http://www.netbiolab.org/wiki/images/1/1e/SC_WMI_12K.txt Example datafile]

'''''Citation''''' : Jung Eun Shim, Ji Hyun Kim, Junha Shin, Ji Eun Lee and Insuk Lee, Network-based identification of pathway-specific protein domains and their implications for human diseases (under review)

'''''Contact Information''''' : Insuk Lee (insuklee[at]yonsei[dot]ac[dot]kr)

Domain2Pathway by Pathway Specificity (PS)

2017-09-22T06:56:08Z

Shimje:

Protein domains are basic functional units of proteins, yet domain-based pathway annotations for proteins are still challenging tasks because many domains are pervasive among diverse pathways.
Nevertheless, some domains may exist in specific pathways.
We therefore developed a network-based scoring scheme to quantify '''specificity of domain-pathway associations''', and then used it to classify ''''pathway-specific domains (PSDs)'''' and ''''non-specific domains (NSDs)''''.

*[http://www.netbiolab.org/wiki/images/0/09/WMI_program.zip Source codes for PS calculation]
*[http://www.netbiolab.org/wiki/images/1/1e/SC_WMI_12K.txt Example datafile]

'''''Citation''''' : Jung Eun Shim, Ji Hyun Kim, Junha Shin, Ji Eun Lee and Insuk Lee, Network-based identification of pathway-specific protein domains and their implications for human diseases '''(under review)'''

'''''Contact Information''''' : Insuk Lee (insuklee[at]yonsei[dot]ac[dot]kr)

Domain2Pathway by Pathway Specificity (PS)

2017-09-22T06:55:11Z

Shimje: Created page with "Protein domains are basic functional units of proteins, yet domain-based pathway annotations for proteins are still challenging tasks because many domains are pervasive among ..."

Protein domains are basic functional units of proteins, yet domain-based pathway annotations for proteins are still challenging tasks because many domains are pervasive among diverse pathways.
Nevertheless, some domains may exist in specific pathways.
We therefore developed a network-based scoring scheme to quantify '''specificity of domain-pathway associations''', and then used it to classify ''''pathway-specific domains (PSDs)'''' and ''''non-specific domains (NSDs)''''.

*[http://www.netbiolab.org/wiki/images/0/09/WMI_program.zip Source codes for PS calculation]
*[http://www.netbiolab.org/wiki/images/1/1e/SC_WMI_12K.txt Example datafile]

'''''Citation''''' : Jung Eun Shim, Ji Hyun Kim, Junha Shin, Ji Eun Lee and Insuk Lee, Network-based identification of pathway-specific protein domains and their implications for human diseases

'''''Contact Information''''' : Insuk Lee (insuklee[at]yonsei[dot]ac[dot]kr)

PS

2017-09-22T06:55:00Z

Shimje: Redirected page to Domain2Pathway by Pathway Specificity (PS)

#REDIRECT [[Domain2Pathway by Pathway Specificity (PS)]]

PS

2017-09-22T06:46:18Z

Protein domains are basic functional units of proteins, yet domain-based pathway annotations for proteins are still challenging tasks because many domains are pervasive among diverse pathways.
Nevertheless, some domains may exist in specific pathways.
We therefore developed a network-based scoring scheme to quantify '''specificity of domain-pathway associations''', and then used it to classify ''''pathway-specific domains (PSDs)'''' and ''''non-specific domains (NSDs)''''.

*[http://www.netbiolab.org/wiki/images/0/09/WMI_program.zip Source codes for PS calculation]
*[http://www.netbiolab.org/wiki/images/1/1e/SC_WMI_12K.txt Example datafile]

'''''Citation''''' : Jung Eun Shim, Ji Hyun Kim, Junha Shin, Ji Eun Lee and Insuk Lee, Network-based identification of pathway-specific protein domains and their implications for human diseases

'''''Contact Information''''' : Insuk Lee (insuklee[at]yonsei[dot]ac[dot]kr)

Software

2017-09-22T06:35:10Z

Shimje:

__NOTOC__
=='''Co-functional gene networks'''==

==''Human and Laboratory Animals''==
{|border="0" width="500"
|align="center"|[[file:Tools_HumanNetLogo.jpg|150px|link=http://www.functionalnet.org/humannet]]
|align="center"|[[file:MouseNetLogo.png|150px|link=http://www.inetbio.org/mousenet]]
|align="center"|[[file:danionet_logo.png|150px|link=http://www.inetbio.org/danionet]]
|align="center"|[[file:Flynet.png|150px|link=http://www.inetbio.org/flynet]]
|align="center"|[[file:WormNetv3.jpg|150px|link=http://www.inetbio.org/wormnet]]
|-
|align="center"|''Homo sapiens''
|align="center"|''Mus musculus''
|align="center"|''Danio rerio''
|align="center"|''Drosophila melanogaster''
|align="center"|''Caenorhabditis elegans''
|}

==''Plants''==
{|border="0" width="400"
|align="center"|[[File:Aranet_v2.jpg|150px|link=http://www.inetbio.org/aranet]]
|align="center"|[[File:Maizenet_logo_4th.png|150px|link=http://www.inetbio.org/maizenet]]
|align="center"|[[file:RiceNetv2 logo.png|150px|link=http://www.inetbio.org/ricenet]]
|align="center"|[[File:WheatNet_logo.png|150px|link=http://www.inetbio.org/wheatnet]]
|align="center"|[[File:Soynetlogo.png|150px|link=http://www.inetbio.org/soynet]]
|align="center"|[[File:Tomatonet_logo.png|150px|link=http://www.inetbio.org/tomatonet]]
|-
|align="center"|''Arabidopsis thaliana''
|align="center"|''Zea mays''
|align="center"|''Oryza sativa''
|align="center"|''Triticum aestivum''
|align="center"|''Glycine max''
|align="center"|''Solanum lycopersicum''
|}

==''Fungi''==
{|border="0" width="200"
|align="center"|[[File:Tools_YesatNetLogo.jpg|150px|link=http://www.inetbio.org/yeastnet]]
|align="center"|[[file:CryptoNet.png|150px|link=http://www.inetbio.org/cryptonet]]
|-
|align="center"|''Saccharomyces cerevisiae''
|align="center"|''Cryptococcus neoformans''
|}

==''Bacteria''==
{|border="0" width="200"
|align="center"|[[File:Staphnet_logo.JPG|150px|link=http://www.inetbio.org/staphnet]]
|align="center"|[[File:Pseudomonas logo.jpg|150px|link=http://www.inetbio.org/pseudomonasnet]]
|align="center"|[[File:EcoliNet.png|150px|link=http://www.inetbio.org/ecolinet]]
|align="center"|[[File:XooNet_logo.png|150px|link=http://www.inetbio.org/xoonet]]
|-
|align="center"|Methicillin-resistant ''Staphylococcus aureus''
|align="center"|''Pseudomonas aeruginosa''
|align="center"|''Escherichia coli''
|align="center"|''Xanthomonas oryzae pv. oryzae''
|}

==''Build your own co-functional networks''==
[[File:Jiffynetlogo4 small.jpg |150px|link=http://www.jiffynet.org]]
'''JiffyNet''': Instant gene network building server for newly sequenced species

=='''Transcriptional Regulatory Networks'''==
[[File:TRRUST_logo.jpg |150px|link=http://www.grnpedia.org/trrust/]] '''TRRUST''': A reference database of TF-target interactions in human and mouse

=='''Network-based Disease Research Servers'''==
[[File:Coexpedia.png |150px|link=http://www.coexpedia.org]] '''COEXPEDIA''': Exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH)

[[File:GWAB_logo.png |150px|link=http://www.inetbio.org/gwab]] '''GWAB''': A web server for network-based boosting of human genome-wide association data

[[File:Cover title muffinn.png |150px|link=http://www.inetbio.org/muffinn/]] '''MUFFINN''': Cancer gene discovery via network analysis of somatic mutation data

[[File:Logo morphin.png|150px|link=http://www.inetbio.org/morphin/]] '''MORPHIN''': Network-assisted prediction of disease pathways in model organisms

[[File:Cover title riddle.jpg|150px|link=http://www.functionalnet.org/riddle]] '''RIDDLE''': Network-assisted Gene Set Analysis (human only)

=='''Domain-based PPI networks by Weighted Mutual Information (WMI) '''==
[[WMI|<big>'''Project Page'''</big>]]

=='''Domain2Pathway by Pathway Specificity (PS) '''==
[[PS|<big>'''Project Page'''</big>]]

Domain-based PPI network by Weighted Mutual Information (WMI)

2017-09-22T06:07:17Z

Shimje:

Functional protein-protein interaction (PPI) networks elucidate molecular pathways underlying complex phenotypes, including those of human diseases.
Protein domain is a functional unit of the protein. Therefore, we may effectively infer functional interactions between proteins based on the co-occurrence of domains.
Here, we present a method for inferring accurate functional PPIs based on the similarity of domain composition between proteins by '''''weighted mutual information (WMI)''''' that assigned different weights to the domains based on their genome-wide frequencies.

*[http://www.netbiolab.org/wiki/images/0/09/WMI_program.zip Source codes for WMI calculation]
*[http://www.netbiolab.org/wiki/images/1/1e/SC_WMI_12K.txt Domain-based yeast PPI network by WMI]
*[http://www.netbiolab.org/wiki/images/4/44/HS_WMI_94K.txt Domain-based human PPI network by WMI]

'''''Citation''''' : Jung Eun Shim and Insuk Lee, Weighted mutual information analysis substantially improves domain-based functional network models

'''''Contact Information''''' : Insuk Lee (insuklee[at]yonsei[dot]ac[dot]kr)

People:JE Shim

2017-07-11T01:22:06Z

Shimje: /* Publications */

{|
|[[File:People_JE_Shim_EDIT.JPG|150px]]
|
===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

==Publications==
* '''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.

People:JE Shim

2017-06-21T05:59:13Z

Shimje: /* Publications */

{|
|[[File:People_JE_Shim_EDIT.JPG|150px]]
|
===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

==Publications==
* '''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 Research 2017 Apr 26.[Epub ahead of print]
* '''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.

Software

2016-03-18T09:07:16Z

Shimje: /* Domain-based PPI networks by Weighted Mutual Information (WMI) */

__NOTOC__
=='''Co-functional networks: Organism-specific network-assisted hypothesis generation servers'''==

==''Animal''==
{|border="0" width="800"
|align="center"|[[file:MouseNetLogo.png|150px|link=http://www.inetbio.org/mousenet]]
|align="center"|[[file:WormNetv3.jpg|150px|link=http://www.inetbio.org/wormnet]]
|align="center"|[[file:Flynet.png|150px|link=http://www.inetbio.org/flynet]]
|align="center"|[[file:Tools_HumanNetLogo.jpg|150px|link=http://www.functionalnet.org/humannet]]
|-
|align="center"|''Mus musculus''
|align="center"|''Caenorhabditis elegans''
|align="center"|''Drosophila melanogaster''
|align="center"|''Homo sapiens''
|}

==''Plant''==
{|border="0" width="400"
|align="center"|[[File:Aranet_v2.jpg|150px|link=http://www.inetbio.org/aranet]]
|align="center"|[[file:RiceNetv2 logo.png|150px|link=http://www.inetbio.org/ricenet]]
|-
|align="center"|''Arabidopsis thaliana''
|align="center"|''Oryza sativa''
|}
==''Microbe''==
{|border="0" width="600"
|align="center"|[[File:EcoliNet.png|150px|link=http://www.inetbio.org/ecolinet]]
|align="center"|[[File:Tools_YesatNetLogo.jpg|150px|link=http://www.inetbio.org/yeastnet]]
|align="center"|[[file:CryptoNet.png|150px|link=http://www.inetbio.org/cryptonet]]
|-
|align="center"|''Escherichia coli''
|align="center"|''Saccharomyces cerevisiae''
|align="center"|''Cryptococcus neoformans''
|}

=='''RIDDLE: Network-assisted Gene Set Analysis (human only)'''==
[[File:Cover title riddle.jpg|150px|link=http://www.functionalnet.org/riddle]] RIDDLE (Reflective diffusion and local extension) is currently available for only human genes.

=='''MORPHIN: Network-assisted prediction of disease pathways in model organisms'''==
[[File:Logo morphin.png|150px|link=http://www.inetbio.org/morphin/]] Morphin (Model Organisms Projected on a Human Integrated Gene Network) is currently available.

=='''JiffyNet:Instant gene network building server for newly sequenced species'''==
[[File:Jiffynetlogo4 small.jpg |150px|link=http://www.jiffynet.org]] Jiffy (instant) gene network modeler for newly sequenced species

=='''TRRUST: A reference database of human TF-target interactions'''==
[[File:TRRUST_logo.jpg |150px|link=http://www.grnpedia.org/trrust/]] TRRUST (Transcriptional Regulatory relationships Unraveled by Sentence-based Text mining) is currently available for only human genes.

=='''Domain-based PPI networks by Weighted Mutual Information (WMI) '''==
[[WMI|<big>'''Project Page'''</big>]]

Software

2016-03-18T08:40:31Z

Shimje: /* Domain-based PPI networks by Weighted Mutual Information (WMI) */

Software

2016-03-18T08:33:28Z

Shimje: /* Domain-based PPI networks by Weighted Mutual Information (WMI) */

WMI

2016-03-18T07:37:05Z

Shimje: Created page with "Redirect Domain-based PPI network by Weighted Mutual Information (WMI)"

[[Redirect Domain-based PPI network by Weighted Mutual Information (WMI)]]

Domain-based PPI network by Weighted Mutual Information (WMI)

2016-03-18T07:18:12Z

Shimje:

<big>We present a method for inferring accurate functional PPIs based on the similarity of domain compositions between proteins by ''weighted mutual information'' that assigned different weights to domains based on their genome-wide frequencies.
</big>

*[http://www.netbiolab.org/wiki/images/0/09/WMI_program.zip Source codes for calculating WMI]
*[http://www.netbiolab.org/wiki/images/1/1e/SC_WMI_12K.txt Yeast PPI network]
*[http://www.netbiolab.org/wiki/images/4/44/HS_WMI_94K.txt Human PPI network]

Domain-based PPI network by Weighted Mutual Information (WMI)

2016-03-18T07:13:37Z

Shimje: Created page with "*[http://www.netbiolab.org/wiki/images/0/09/WMI_program.zip Source codes for calculating WMI] *[http://www.netbiolab.org/wiki/images/1/1e/SC_WMI_12K.txt Yeast PPI network] *[h..."

*[http://www.netbiolab.org/wiki/images/0/09/WMI_program.zip Source codes for calculating WMI]
*[http://www.netbiolab.org/wiki/images/1/1e/SC_WMI_12K.txt Yeast PPI network]
*[http://www.netbiolab.org/wiki/images/4/44/HS_WMI_94K.txt Human PPI network]

Software

2016-03-18T07:13:27Z

Shimje: /* Domain-based PPI networks by Weighted Mutual Information (WMI) */

Software:WMI

2016-03-18T07:11:08Z

Shimje:

File:HS WMI 94K.txt

2016-03-18T06:55:57Z

Shimje: Human PPI network

Human PPI network

File:SC WMI 12K.txt

2016-03-18T06:55:00Z

Shimje: Yeast PPI network

Yeast PPI network

File:WMI program.zip

2016-03-18T06:40:06Z

Shimje: Domain Profiling - WMI SourceCode (zip)

Domain Profiling - WMI SourceCode (zip)

Software

2016-03-18T06:32:32Z

Shimje: /* Domain-based PPI networks by Weighted Mutual Information (WMI) */

Software:WMI

2016-03-18T06:29:02Z

Shimje: Created page with "*Source codes for calculating WMI *Yeast PPI network *Human PPI network"

*Source codes for calculating WMI
*Yeast PPI network
*Human PPI network

Software

2016-03-18T06:28:55Z

Shimje: /* Domain-based PPI networks by Weighted Mutual Information (WMI) */

Software

2016-03-18T06:28:05Z

Shimje: /* Domain-based PPI networks by Weighted Mutual Information (WMI) */

People:JE Shim

2015-10-05T08:25:17Z

Shimje: /* Publications */

{|
|[[File:People_JE_Shim_EDIT.JPG|150px]]
|
===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

==Publications==
* '''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.

People:JE Shim

2014-07-02T04:08:14Z

Shimje: /* Publications */

People

2014-07-02T04:04:42Z

Shimje: /* Research Fellows */

__NOTOC__
=='''Principal Investigator'''==
{|border="0" width="150"
|align="center"|[[File:People_ISLee_03.jpg|77px|link=people:IS_Lee]]
|
|
|-
|align="center"|[[people:IS_Lee|Insuk Lee]]
|
|
|-
|}

=='''Research Fellows'''==
{|border="0" width="450"
|align="center"|[[File:People_JE_Shim_EDIT.JPG|70px|link=people:JE_Shim]]
|align="center" cell-width="200"|[[File:People_SYHwang.JPG|70px|link=people:SH_Hwang]]
|align="center"|[[File:People_Junha_Shin_cut.gif|70px|link=people:JH_Shin]]
|-
|align="center"|[[people:JE_Shim|Jung Eun Shim]]
|align="center"|[[people:SH_Hwang|SoHyun Hwang]]
|align="center"|[[people:JH_Shin|JunHa Shin]]
|-
|align="center"|[[people:JE_Shim|Research Professor]]
|align="center"|[[people:SH_Hwang|Research Professor]]
|align="center"|[[people:JH_Shin|Postdoc Fellow]]
|}

=='''Graduate Students'''==
{|border="0" width="600"
|align="center"|[[File:People_HHKim_cut.jpg|70px|link=people:HH_Kim]]
|align="center"|[[File:People_ARCho_cut.png|70px|link=people:AR_Cho]]
|align="center" cell-width="200"|[[File:Banmyungham.JPG|70px|link=people:ER_Kim]]
|align="center"|[[File:Tak_sajin3.jpg|70px|link=people:T_Lee]]
|-
|align="center"|[[people:HH_Kim|HanHae Kim]]
|align="center"|[[people:AR_Cho|ARa Cho]]
|align="center"|[[people:ER_Kim|Eiru Kim]]
|align="center"|[[people:T_Lee|Tak Lee]]
|-
|align="center"|[[people:HH_Kim|PhD course]]
|align="center"|[[people:AR_Cho|PhD course]]
|align="center"|[[people:ER_Kim|PhD course]]
|align="center"|[[people:T_Lee|PhD course]]
|-
|align="center"|[[File:People_KSKim.jpg|70px|link=people:KS_Kim]]
|align="center"|[[File:heonjong.jpg|70px|link=people:HJ_Han]]
|align="center"|[[File:Hjkim.jpg|70px|link=People:HJ_Kim]]
|align="center"|[[File:HSshim.jpg|70px|link=people:HS_Shim]]
|-
|align="center"|[[people:KS_Kim|Kyung Soo Kim]]
|align="center"|[[people:HJ_Han|Heon Jong Han]]
|align="center"|[[People:HJ Kim|HyoJin Kim]]
|align="center"|[[people:HS_Shim|HongSeok Shim]]
|-
|align="center"|[[people:HJ_Han|PhD course]]
|align="center"|[[People:HJ Kim|PhD course]]
|align="center"|[[people:HS_Shim|MS course]]
|align="center"|[[people:KS_Kim|MS course]]
|}

=='''Research Staffs'''==
{|border="0" width="300"
|align="center"|[[File:Smyang.jpg|70px|link=people:SM_Yang]]
|align="center"|[[File:SYLee.jpg|80px|link=people:SY_Lee]]
|align="center"|[[File:AYYoon.jpg|80px|link=people:AY_Yoon]]
|-
|align="center"|[[people:SM_Yang|SunMo Yang]]
|align="center"|[[people:SY_Lee|Sangyoung Lee]]
|align="center"|[[people:AY_Yoon|Ayeong Yoon]]
|-
|align="center"|[[people:SM_Yang|System Administrator]]
|align="center"|[[people:SY_Lee|Research Assistant]]
|align="center"|[[people:AY_Yoon|Research Assistant]]
|}

=='''Undergraduate Students'''==
{|border="0" width="450"
|align="center"|[[File:배다솜.jpg|70px|link=People:DS Bae]]
|align="center"|[[File:CY KIM.jpg|70px|link=People:CY_Kim]]
|align="center"|[[File:BHKang.jpg|70px|link=People:BH_Kang]]
|-
|align="center"|[[People:DS Bae|Dasom Bae]]
|align="center"|[[People:CY Kim|ChanYoung Kim]]
|align="center"|[[People:BH_Kang|ByungHee Kang]]
|}

=='''Visiting scientists'''==

=='''Alumni'''==
*Former Post-docs and Staff Scientists
**Taeyun Oh (2009.5-2011.12), current position; US-DOE Postdoc fellow, University of California at Davis (Pam Ronald's Lab)
**Samuel Beck (2011.2-2011.12), current position; Postdoc fellow, University of Texas at Austin (Jonghwan Kim's Lab)
**Jawon Song (2011.1-2012.5), current position; Research Scientist, Texas Advanced Computing Center, Austin, TX, USA
**Yoonhee Ko (2012.8-2014.2), current position; Fellow, Severance Medical center (Yonsei Medical school)
**Jonghoon Lee (2013.10-2014.2), current position; Assistant Professor, CHA Medical school

*Former Graduate Students
**Sungou Ji (2009.9-2011.8), MS, went to a graduate school, Sanger Genome Institute, Cambridge University, UK (Research field: Statistical Genomics)

*Former Visiting Scientists
**Minkyung Shin (2012.3-2012.7), went to a graduate school, University of Southern California, USA

*Former Undergraduate Students
**Ila Shin, went to a medical school (Yonsei Univ.)
**Yoonkyung Ko
**Sangyo Park, went to a law school (Kyounghee Univ.)
**Jayoon Shin, went to a medical school (Pusan National Univ.)
**Dongjoo Sun, went to a dental school (Wongwang Univ.)
**Eulsoo Kim
**Myungwhan Lee, went to a medical school (Yonsei Univ.)
**Moonhee Lee
**Jinhyun Ju, went to a graduate school, Cornell Medical School, NY, USA (Research field: Computational Systems Biology)
**Haeyoung Shin, went to a graduate school, Brown University, USA (Research field: Computational Neuroscience)
**Joonghee Soh, went to a graduate school, KAIST, Korea (Research field: Culture Technology)
**Hee Jung Cho
**TaeHwan Kim
**Joohyung Kim

File:People JE Shim EDIT.JPG

2014-07-02T04:04:06Z

Shimje: Shimje uploaded a new version of "File:People JE Shim EDIT.JPG"

People:Album:ThanksGivingDay 2012

2013-06-03T02:25:18Z

Shimje: Created page with "<gallery> File:2012ThanksGiving.jpg File:ThanksGivingDay_2012-0.jpg </gallery>"

<gallery>
File:2012ThanksGiving.jpg
File:ThanksGivingDay_2012-0.jpg
</gallery>

Album

2013-06-03T02:23:31Z

Shimje: /* Group Photo */

__NOTOC__
=='''Group Photo'''==
{|border="0" width="500"
|
[[File:2013단체1.jpg|thumb|2013]]
|align="center"|
[[File:People_Album_Spring2012_main.jpg|thumb|2012]]
|align="center"|
[[File:People_Album_Spring2011_05.jpg|thumb|2011]]
|align="center" |
[[File:People_Album_Spring2010_01.jpg|thumb|2010]]
|}
----
*[[People:Album:2013 Group photo | 2013 Group photo]]
----
*[[People:Album:Teachers' day 2013| 2013 May, Teachers' day]]
----
*[[People:Album:ThanksGivingDay_2012| 2012 Nov, Thanksgiving Day]]
----
*[[People:Album:MT_2012| 2012 June, Summer MT]]
----
*[[People:Album:GroupPhoto_2012_Spring|2012 April, Group Photo]]
----
*[[People:Album:Keystone_2012| 2012 February, Keystone]]
----
*[[People:Album:MT_2011| 2011 August, Summer MT]]
----
*[[People:Album:ISSCR_2011| 2011 June, ISSCR]]
----
*[[People:Album:RECOMB_2011| 2011 March, RECOMB2011]]
----
*[[People:Album:AYRCOB5th_2011| 2011 August, Ayrcob 5th]]
----
*[[People:Album:Teachers_Day_2011| 2011 May, Teacher's day]]
----
*[[People:Album:GroupPhoto_2011_Spring|2011 March, Group Photo]]
----
*[[People:Album:APBC2011|2011 February, APBC (Incheon)]]
----
*[[People:Album:ISMB2010|2010 June, ISMB(Boston)]]
----
*[[People:Album:Sue2010|2010 June, Sue Rhee visit]]
----
*[[People:Album:Cup_cake_2010| 2010 May, Cup Cake professor]]
----
*[[People:Album:Edward_Marcotte_at_NBL|2010 May, Edward Marcotte and @NBL Reunion]]
----
*[[People:Album:GroupPhoto_2010_Spring|2010 March, Group Photo]]
----
*[[People:Album:KSBSB2009|2009 November, KSBSB (Pusan)]]
----
*[[People:Album:ICSB2009|2009 August, ICSB (Stanford)]]
----
*[[People:Album:winter_MT_2008|2008 December, Winter MT]]

File:2012ThanksGiving.jpg

2013-06-03T02:20:47Z

Shimje: 2012ThanksGiving-00

2012ThanksGiving-00

File:ThanksGivingDay 2012-0.jpg

2013-06-03T02:14:12Z

Shimje: ThanksGivingDay_2012-0

ThanksGivingDay_2012-0

Album

2012-11-26T06:12:24Z

Shimje: /* Group Photo */

__NOTOC__
=='''Group Photo'''==
{|border="0" width="500"
|
[[File:People_Album_Spring2012_main.jpg|thumb|2012]]
|align="center"|
[[File:People_Album_Spring2011_05.jpg|thumb|2011]]
|align="center" |
[[File:People_Album_Spring2010_01.jpg|thumb|2010]]
|}
*[[People:Album:MT_2012| 2012 June, Summer MT]]
----
*[[People:Album:GroupPhoto_2012_Spring|2012 April, Group Photo]]
----
*[[People:Album:Keystone_2012| 2012 February, Keystone]]
----
*[[People:Album:MT_2011| 2011 August, Summer MT]]
----
*[[People:Album:ISSCR_2011| 2011 June, ISSCR]]
----
*[[People:Album:RECOMB_2011| 2011 March, RECOMB2011]]
----
*[[People:Album:AYRCOB5th_2011| 2011 August, Ayrcob 5th]]
----
*[[People:Album:Teachers_Day_2011| 2011 May, Teacher's day]]
----
*[[People:Album:GroupPhoto_2011_Spring|2011 March, Group Photo]]
----
*[[People:Album:APBC2011|2011 February, APBC (Incheon)]]
----
*[[People:Album:ISMB2010|2010 June, ISMB(Boston)]]
----
*[[People:Album:Sue2010|2010 June, Sue Rhee visit]]
----
*[[People:Album:Cup_cake_2010| 2010 May, Cup Cake professor]]
----
*[[People:Album:Edward_Marcotte_at_NBL|2010 May, Edward Marcotte and @NBL Reunion]]
----
*[[People:Album:GroupPhoto_2010_Spring|2010 March, Group Photo]]
----
*[[People:Album:KSBSB2009|2009 November, KSBSB (Pusan)]]
----
*[[People:Album:ICSB2009|2009 August, ICSB (Stanford)]]
----
*[[People:Album:winter_MT_2008|2008 December, Winter MT]]

Album

2012-11-26T06:10:23Z

Shimje: /* Group Photo */

__NOTOC__
=='''Group Photo'''==
{|border="0" width="500"
|
[[File:People_Album_Spring2012_main.jpg|thumb|2012]]
|align="center"|
[[File:People_Album_Spring2011_05.jpg|thumb|2011]]
|align="center" |
[[File:People_Album_Spring2010_01.jpg|thumb|2010]]
|}
*[[People:Album:ThanksGivingDay_2012| 2012 Nov, Thanks Giving Day]]
----
*[[People:Album:MT_2012| 2012 June, Summer MT]]
----
*[[People:Album:GroupPhoto_2012_Spring|2012 April, Group Photo]]
----
*[[People:Album:Keystone_2012| 2012 February, Keystone]]
----
*[[People:Album:MT_2011| 2011 August, Summer MT]]
----
*[[People:Album:ISSCR_2011| 2011 June, ISSCR]]
----
*[[People:Album:RECOMB_2011| 2011 March, RECOMB2011]]
----
*[[People:Album:AYRCOB5th_2011| 2011 August, Ayrcob 5th]]
----
*[[People:Album:Teachers_Day_2011| 2011 May, Teacher's day]]
----
*[[People:Album:GroupPhoto_2011_Spring|2011 March, Group Photo]]
----
*[[People:Album:APBC2011|2011 February, APBC (Incheon)]]
----
*[[People:Album:ISMB2010|2010 June, ISMB(Boston)]]
----
*[[People:Album:Sue2010|2010 June, Sue Rhee visit]]
----
*[[People:Album:Cup_cake_2010| 2010 May, Cup Cake professor]]
----
*[[People:Album:Edward_Marcotte_at_NBL|2010 May, Edward Marcotte and @NBL Reunion]]
----
*[[People:Album:GroupPhoto_2010_Spring|2010 March, Group Photo]]
----
*[[People:Album:KSBSB2009|2009 November, KSBSB (Pusan)]]
----
*[[People:Album:ICSB2009|2009 August, ICSB (Stanford)]]
----
*[[People:Album:winter_MT_2008|2008 December, Winter MT]]

Album

2012-11-26T06:05:19Z

Shimje:

Album

2012-11-26T06:01:41Z

Shimje: /* Group Photo */

__NOTOC__
=='''Group Photo'''==
{|border="0" width="500"
|
[[File:People_Album_Spring2012_main.jpg|thumb|2012]]
|align="center"|
[[File:People_Album_Spring2011_05.jpg|thumb|2011]]
|align="center" |
[[File:People_Album_Spring2010_01.jpg|thumb|2010]]
|}
*[[People:Album:ThanksGivingDay_2012| 2012 Nov, Thanks Giving Day]]
----
*[[People:Album:MT_2012| 2012 June, Summer MT]]
----
*[[People:Album:GroupPhoto_2012_Spring|2012 April, Group Photo]]
----
*[[People:Album:Keystone_2012| 2012 February, Keystone]]
----
*[[People:Album:MT_2011| 2011 August, Summer MT]]
----
*[[People:Album:ISSCR_2011| 2011 June, ISSCR]]
----
*[[People:Album:RECOMB_2011| 2011 March, RECOMB2011]]
----
*[[People:Album:AYRCOB5th_2011| 2011 August, Ayrcob 5th]]
----
*[[People:Album:Teachers_Day_2011| 2011 May, Teacher's day]]
----
*[[People:Album:GroupPhoto_2011_Spring|2011 March, Group Photo]]
----
*[[People:Album:APBC2011|2011 February, APBC (Incheon)]]
----
*[[People:Album:ISMB2010|2010 June, ISMB(Boston)]]
----
*[[People:Album:Sue2010|2010 June, Sue Rhee visit]]
----
*[[People:Album:Cup_cake_2010| 2010 May, Cup Cake professor]]
----
*[[People:Album:Edward_Marcotte_at_NBL|2010 May, Edward Marcotte and @NBL Reunion]]
----
*[[People:Album:GroupPhoto_2010_Spring|2010 March, Group Photo]]
----
*[[People:Album:KSBSB2009|2009 November, KSBSB (Pusan)]]
----
*[[People:Album:ICSB2009|2009 August, ICSB (Stanford)]]
----
*[[People:Album:winter_MT_2008|2008 December, Winter MT]]

People:Album:MT 2011

2011-09-15T08:50:32Z

Shimje:

<gallery>
File:NBL_2011SUMMER_1.JPG
File:NBL_2011SUMMER_2.JPG
File:NBL_2011SUMMER_3.JPG
File:NBL_2011SUMMER_4.JPG
File:NBL_2011SUMMER_5.JPG
File:NBL_2011SUMMER_6.JPG
File:Jarbiless.gif
File:NBL2011_SummerMT_beach1.JPG
File:NBL2011_SummerMT_beach2.JPG
</gallery>

File:NBL2011 SummerMT beach2.JPG

2011-09-15T08:49:43Z

Shimje: NBL2011_SummerMT_beach2

NBL2011_SummerMT_beach2

File:NBL2011 SummerMT beach1.JPG

2011-09-15T08:48:36Z

Shimje: NBL2011_SummerMT_beach1

NBL2011_SummerMT_beach1

People:JE Shim

2011-07-08T07:08:29Z

Shimje: /* Publications */

People

2010-08-02T03:13:02Z

Shimje:

[[file:People_Album.jpg|link=People:Album|Album]]
----
{|border="0" width="600"
|align="center"|[[File:People_ISLee_cut.jpg|77px|link=people:IS_Lee]]
|
|
|-
|align="center"|[[people:IS_Lee|InSuk Lee]]
|
|
|-
|align="center"|[[File:People_TYOh_cut.png|70px|link=people:TY_Oh]]
|align="center"|[[File:People_JE_Shim.JPG|70px|link=people:JE_Shim]]
|align="center"|[[File:People_SYHwang.JPG|70px|link=people:SH_Hwang]]
|align="center"|[[File:People_Junha_Shin_cut.gif|70px|link=people:JH_Shin]]
|-
|align="center"|[[people:TY_Oh|TaeYoon Oh]]
|align="center"|[[people:JE_Shim|Jung Eun Shim]]
|align="center"|[[people:SH_Hwang|SoHyun Hwang]]
|align="center"|[[people:JH_Shin|JunHa Shin]]
|-
|-
|align="center"|[[File:People_HHKim_cut.jpg|70px|link=people:HH_Kim]]
|align="center"|[[File:People_SGJi_cut.jpeg|70px|link=people:SG_Ji]]
|align="center"|[[File:People_ARCho_cut.png|70px|link=people:AR_Cho]]
|-
|-
|align="center"|[[people:HH_Kim|HanHae Kim]]
|align="center"|[[people:SG_Ji|SunGou Ji]]
|align="center"|[[people:AR_Cho|ARa Cho]]
|
|-
|-
|align="center" cell-width="200"|[[File:100528-0000.jpg|70px|link=people:IR_Kim]]
|align="center"|[[File:People_TLee.jpg|70px|link=people:T_Lee]]
|-
|
|-
|align="center"|[[people:IR_Kim|Eiru Kim]]
|align="center"|[[people:T_Lee|Tak Lee]]
|-
|
|}

People:JE Shim

2010-05-19T05:27:01Z

Shimje:

People:JE Shim

2010-05-19T05:26:45Z

Shimje:

People:JE Shim

2010-05-19T05:21:34Z

Shimje: