Network Biology Lab - User contributions [en]

Finding Interpro annotation without BioMart

2013-04-18T16:41:00Z

Winnie:

[http://www.ebi.ac.uk/interpro/ Interpro] annotation could be retrieved by [http://www.biomart.org/ BioMart]. But sometimes, in some species like Pseudomonas aeruginosa, BioMart didn't provide Interpro annotation data. If then, follow the below three steps.

1. Download interpro annotation file (protein2ipr.dat.gz) regardless of species from [http://www.ebi.ac.uk/interpro/download.html Interpro download site]

2. Find out Uniprot protein IDs of the species that you want

In case of Pseudomonas aeruginosa, the protein IDs of Pseudomonas Genome Database were different of their Uniprot proteins. Therefore, I downloaded Uniprot protein IDs of Pseudomonas aeruginosa at [http://www.uniprot.org/uniprot/ Uniprot homepage]. If you click [http://www.uniprot.org/uniprot/?query=organism%3a208964+keyword%3a1185&format=* this URL], you can see my search result of Pseudomonas aeruginosa.

3. From 'protein2ipr.dat.gz' file, extract only data with uniprot protein IDs of the species that you want to get. If you can use simple script languages, it is an easy job.

Finding Interpro annotation without BioMart

2013-04-18T16:38:49Z

Winnie: Created page with "[http://www.ebi.ac.uk/interpro/ Interpro] annotation could be retrieved by [http://www.biomart.org/ BioMart]. But sometimes, in some species like Pseudomonas aeruginosa, BioMa..."

[http://www.ebi.ac.uk/interpro/ Interpro] annotation could be retrieved by [http://www.biomart.org/ BioMart]. But sometimes, in some species like Pseudomonas aeruginosa, BioMart didn't provide Interpro annotation data. If then, follow the below three steps.

1. Download interpro annotation file (protein2ipr.dat.gz) regardless of species from [http://www.ebi.ac.uk/interpro/download.html Interpro download site]

2. Find out Uniprot protein IDs of the species
In case of Pseudomonas aeruginosa, the protein IDs of Pseudomonas Genome Database were different of their Uniprot proteins. Therefore, I downloaded Uniprot protein IDs of Pseudomonas aeruginosa at [http://www.uniprot.org/uniprot/ Uniprot homepage]. If you click [http://www.uniprot.org/uniprot/?query=organism%3a208964+keyword%3a1185&format=* this URL], you can see my search result of Pseudomonas aeruginosa.

3. From 'protein2ipr.dat.gz' file, extract only data with uniprot protein IDs of the species that you want to get. If you can use simple script languages, it is an easy job.

Protocols

2013-04-18T16:22:44Z

Winnie:

[[media:EMMA_protocol.txt‎|EMMA protocol]]

[[media:REAusingGSEA.txt|Regulon Enrichment Analysis(using GSEA)]]

[[Finding Interpro annotation without BioMart]]

People:SH Hwang

2013-02-14T19:13:49Z

Winnie: /* Publications */

{|
|[[File:People_SYHwang.JPG|150px]]
|
===Sohyun Hwang===
*'''Ph.D.''', ''KAIST'', Dept of Bio and Brain Engineering(09/2004 - 02/2010). 
Dissertation: System level identification of interactions between cell signaling pathways. 
*'''M.S.''', ''KAIST'', Dept of Biology (03/2000 - 02/2002). 
Thesis: Regulation of apoptosis by 2,3,7,8-tetrachlorodibenzo-p-dioxin in MCF-7 cells.
*'''B.S''', ''KAIST'', Dept of Biology (03/1996 - 02/2000).
*''Hansung Science High School'' (03/1994 - 02/1996).
|}

==Current Research Interests==
*Biological data mining, integration, interpretation, hypothesis generation
*Genotype-phenotype mapping by various biological data and modeling algorithms

==Publications==
* Peggy I Wang, '''Sohyun Hwang (co-first)''', Rodney P Kincaid, Christopher S Sullivan, Insuk Lee, and Edward M Marcotte. RIDDLE: Reflective diffusion and local extension reveal functional associations for unannotated gene sets via proximity in a gene network. '''''Genome Biology''''', 13:R125, 2012. [http://www.ncbi.nlm.nih.gov/pubmed/23268829 pubmed]
* '''Sohyun Hwang''', Seung Y. Rhee, Edwawrd M. Marcotte, and Insuk Lee. "Systematic prediction of candidate gene function associated to phenotype traits using the probabilistic functional gene network of Arabidopsis thaliana", '''''Nature Protocols''''', 6:1429-1442, 2011. [http://www.ncbi.nlm.nih.gov/pubmed/21886106 pubmed][[media:2011.08.25.online.nprot.2011.372.pdf|pdf]]
* Insuk Lee, Young-Su Seo, Dusical Coltrane, '''Sohyun Hwang''', Taeyun Oh, Edward M. Marcotte, Pamela C Ronald, "Genetic dissection of the biotic stress response using a genome-scale gene network for rice", '''''PNAS''''' 108(45):18548-53, 2011.
* Young-Su Seo, Mawsheng Chen, Laura E Bartley, Muho Han, Ki-Hong Jung, Inusk Lee, Harkamal Walia, Xia Xu, Peijian Cao, Wei Bai, Rajeshwari Ramanan, Fawn Amonpant, Loganathan Arul, Patrick E Canlas, Randy Ruan, Chang-Jin Park, Xuewei Chen, '''Sohyun Hwang''', Jong-Seong, Jeon, Pamela C Ronald, “Towards Establishment of a Rice Stress Response Interactome” '''''PLoS Genetics''''', 7(4):e1002020, 2011.
* '''Sohyun Hwang''', Sangwoo Kim, Heesung Shim, Doheon Lee, “Context-dependent transcriptional regulations between signal transduction pathways”, '''''BMC Bioinformatics''''', 12:19, 2011.
* '''Sohyun Hwang''', Seung-Woo Son, Sang Cheol Kim, Young Joo Kim, Hawoong Jeong and Doheon Lee, “A protein interaction network associated with asthma”, '''''J. of Theor. Biol.''''', Vol 252, Issue 4, pp 722-731, 2008. ''(Yonhap news reported “Asthma candidate genes have been identified by bioinformatics” as a creditable achievement in June 2008.)''
* Jin Ok Yang, '''Sohyun Hwang (Co-first)''', Jeongsu Oh, Jong Bhak and Tae-Kwon Sohn, “An integrated database-pipeline system for studying single nucleotide polymorphisms and disease”, '''''BMC Bioinformatics''''', vol 9, Suppl 12: S19, 2008.
* Jung Kyoon Choi, '''Sohyun Hwang''', Young-Joon Kim, “Stochastic and regulatory role of chromatin silencing in genomic response to environmental changes”, '''''PLoS ONE''''', Vol 3, No. 8: e3002. 2008.
* Jungsun Park, '''Sohyun Hwang (Co-first)''', Yong Seok Lee, Sang-Cheol Kim and Doheon Lee, “SNP@Ethnos: a database of ethnically variant single-nucleotide polymorphisms”, '''''Nucleic Acids Res.''''' Vol. 35, Database issue D711-D715, 2006.
* Hyojin Kang, Taehui Hong, Won-Hyung Chung, Younguk Kim, Jinhee Jung, '''Sohyun Hwang''', Areum Han and Young Joo Kim, “D2GSNP: a web server for the selection of single nucleotide polymorphisms within human disease genes”, '''''Genomics & Informatics''''', Vol. 4, No. 1, pp 45-47, 2006.
* Seong-Bae Park, '''Sohyun Hwang''', and Byoung-Tak Zhang, “Classification of Human Papillomavirus (HPV) Risk Type via Text Mining”, '''''Genomics & Informatics''''', Vol. 1, No. 2, pp. 80-86, 2003.
* '''Sohyun Hwang''', Jaehong Suh and Cheol O. Joe, “Estrogen inhibits Bcl-2 expression and stimulate apoptosis mediated by 2,3,7,8-Tetrachlorodibenzo-p-dioxin.” '''''J. Toxicol. Pub. Health''''' vol. 19 No. 4, pp 325-330, 2003.

People:SH Hwang

2013-01-22T04:49:37Z

Winnie: /* Publications */

{|
|[[File:People_SYHwang.JPG|150px]]
|
===Sohyun Hwang===
*'''Ph.D.''', ''KAIST'', Dept of Bio and Brain Engineering(09/2004 - 02/2010). 
Dissertation: System level identification of interactions between cell signaling pathways. 
*'''M.S.''', ''KAIST'', Dept of Biology (03/2000 - 02/2002). 
Thesis: Regulation of apoptosis by 2,3,7,8-tetrachlorodibenzo-p-dioxin in MCF-7 cells.
*'''B.S''', ''KAIST'', Dept of Biology (03/1996 - 02/2000).
*''Hansung Science High School'' (03/1994 - 02/1996).
|}

==Current Research Interests==
*Biological data mining, integration, interpretation, hypothesis generation
*Genotype-phenotype mapping by various biological data and modeling algorithms

==Publications==
* Peggy I Wang, '''Sohyun Hwang (co-first)''', Rodney P Kincaid, Christopher S Sullivan, Insuk Lee, and Edward M Marcotte. RIDDLE: Reflective diffusion and local extension reveal functional associations for unannotated gene sets via proximity in a gene network. '''''Genome Biology''''', 13:R125, 2012. [http://www.ncbi.nlm.nih.gov/pubmed/23268829 pubmed]
* '''Sohyun Hwang''', Seung Y. Rhee, Edwawrd M. Marcotte, and Insuk Lee. "Systematic prediction of candidate gene function associated to phenotype traits using the probabilistic functional gene network of Arabidopsis thaliana", '''''Nature Protocols''''', 6:1429-1442, 2011. [http://www.ncbi.nlm.nih.gov/pubmed/22042862 pubmed] [[media:PNAS-2011-Lee-18548-53.pdf|pdf]]
* Insuk Lee, Young-Su Seo, Dusical Coltrane, '''Sohyun Hwang''', Taeyun Oh, Edward M. Marcotte, Pamela C Ronald, "Genetic dissection of the biotic stress response using a genome-scale gene network for rice", '''''PNAS''''' 108(45):18548-53, 2011.
* Young-Su Seo, Mawsheng Chen, Laura E Bartley, Muho Han, Ki-Hong Jung, Inusk Lee, Harkamal Walia, Xia Xu, Peijian Cao, Wei Bai, Rajeshwari Ramanan, Fawn Amonpant, Loganathan Arul, Patrick E Canlas, Randy Ruan, Chang-Jin Park, Xuewei Chen, '''Sohyun Hwang''', Jong-Seong, Jeon, Pamela C Ronald, “Towards Establishment of a Rice Stress Response Interactome” '''''PLoS Genetics''''', 7(4):e1002020, 2011.
* '''Sohyun Hwang''', Sangwoo Kim, Heesung Shim, Doheon Lee, “Context-dependent transcriptional regulations between signal transduction pathways”, '''''BMC Bioinformatics''''', 12:19, 2011.
* '''Sohyun Hwang''', Seung-Woo Son, Sang Cheol Kim, Young Joo Kim, Hawoong Jeong and Doheon Lee, “A protein interaction network associated with asthma”, '''''J. of Theor. Biol.''''', Vol 252, Issue 4, pp 722-731, 2008. ''(Yonhap news reported “Asthma candidate genes have been identified by bioinformatics” as a creditable achievement in June 2008.)''
* Jin Ok Yang, '''Sohyun Hwang (Co-first)''', Jeongsu Oh, Jong Bhak and Tae-Kwon Sohn, “An integrated database-pipeline system for studying single nucleotide polymorphisms and disease”, '''''BMC Bioinformatics''''', vol 9, Suppl 12: S19, 2008.
* Jung Kyoon Choi, '''Sohyun Hwang''', Young-Joon Kim, “Stochastic and regulatory role of chromatin silencing in genomic response to environmental changes”, '''''PLoS ONE''''', Vol 3, No. 8: e3002. 2008.
* Jungsun Park, '''Sohyun Hwang (Co-first)''', Yong Seok Lee, Sang-Cheol Kim and Doheon Lee, “SNP@Ethnos: a database of ethnically variant single-nucleotide polymorphisms”, '''''Nucleic Acids Res.''''' Vol. 35, Database issue D711-D715, 2006.
* Hyojin Kang, Taehui Hong, Won-Hyung Chung, Younguk Kim, Jinhee Jung, '''Sohyun Hwang''', Areum Han and Young Joo Kim, “D2GSNP: a web server for the selection of single nucleotide polymorphisms within human disease genes”, '''''Genomics & Informatics''''', Vol. 4, No. 1, pp 45-47, 2006.
* Seong-Bae Park, '''Sohyun Hwang''', and Byoung-Tak Zhang, “Classification of Human Papillomavirus (HPV) Risk Type via Text Mining”, '''''Genomics & Informatics''''', Vol. 1, No. 2, pp. 80-86, 2003.
* '''Sohyun Hwang''', Jaehong Suh and Cheol O. Joe, “Estrogen inhibits Bcl-2 expression and stimulate apoptosis mediated by 2,3,7,8-Tetrachlorodibenzo-p-dioxin.” '''''J. Toxicol. Pub. Health''''' vol. 19 No. 4, pp 325-330, 2003.

People:SH Hwang

2013-01-22T04:48:38Z

Winnie: /* Publications */

{|
|[[File:People_SYHwang.JPG|150px]]
|
===Sohyun Hwang===
*'''Ph.D.''', ''KAIST'', Dept of Bio and Brain Engineering(09/2004 - 02/2010). 
Dissertation: System level identification of interactions between cell signaling pathways. 
*'''M.S.''', ''KAIST'', Dept of Biology (03/2000 - 02/2002). 
Thesis: Regulation of apoptosis by 2,3,7,8-tetrachlorodibenzo-p-dioxin in MCF-7 cells.
*'''B.S''', ''KAIST'', Dept of Biology (03/1996 - 02/2000).
*''Hansung Science High School'' (03/1994 - 02/1996).
|}

==Current Research Interests==
*Biological data mining, integration, interpretation, hypothesis generation
*Genotype-phenotype mapping by various biological data and modeling algorithms

==Publications==
* Peggy I Wang, '''Sohyun Hwang (co-first)''', Rodney P Kincaid, Christopher S Sullivan, Insuk Lee, and Edward M Marcotte. RIDDLE: Reflective diffusion and local extension reveal functional associations for unannotated gene sets via proximity in a gene network. '''''Genome Biology''''', 13:R125, 2012. [http://www.ncbi.nlm.nih.gov/pubmed/23268829 pubmed]
* '''Sohyun Hwang''', Seung Y. Rhee, Edwawrd M. Marcotte, and Insuk Lee. "Systematic prediction of candidate gene function associated to phenotype traits using the probabilistic functional gene network of Arabidopsis thaliana", '''''Nature Protocols''''', 6:1429-1442, 2011.
* Insuk Lee, Young-Su Seo, Dusical Coltrane, '''Sohyun Hwang''', Taeyun Oh, Edward M. Marcotte, Pamela C Ronald, "Genetic dissection of the biotic stress response using a genome-scale gene network for rice", '''''PNAS''''' 108(45):18548-53, 2011.
* Young-Su Seo, Mawsheng Chen, Laura E Bartley, Muho Han, Ki-Hong Jung, Inusk Lee, Harkamal Walia, Xia Xu, Peijian Cao, Wei Bai, Rajeshwari Ramanan, Fawn Amonpant, Loganathan Arul, Patrick E Canlas, Randy Ruan, Chang-Jin Park, Xuewei Chen, '''Sohyun Hwang''', Jong-Seong, Jeon, Pamela C Ronald, “Towards Establishment of a Rice Stress Response Interactome” '''''PLoS Genetics''''', 7(4):e1002020, 2011.
* '''Sohyun Hwang''', Sangwoo Kim, Heesung Shim, Doheon Lee, “Context-dependent transcriptional regulations between signal transduction pathways”, '''''BMC Bioinformatics''''', 12:19, 2011.
* '''Sohyun Hwang''', Seung-Woo Son, Sang Cheol Kim, Young Joo Kim, Hawoong Jeong and Doheon Lee, “A protein interaction network associated with asthma”, '''''J. of Theor. Biol.''''', Vol 252, Issue 4, pp 722-731, 2008. ''(Yonhap news reported “Asthma candidate genes have been identified by bioinformatics” as a creditable achievement in June 2008.)''
* Jin Ok Yang, '''Sohyun Hwang (Co-first)''', Jeongsu Oh, Jong Bhak and Tae-Kwon Sohn, “An integrated database-pipeline system for studying single nucleotide polymorphisms and disease”, '''''BMC Bioinformatics''''', vol 9, Suppl 12: S19, 2008.
* Jung Kyoon Choi, '''Sohyun Hwang''', Young-Joon Kim, “Stochastic and regulatory role of chromatin silencing in genomic response to environmental changes”, '''''PLoS ONE''''', Vol 3, No. 8: e3002. 2008.
* Jungsun Park, '''Sohyun Hwang (Co-first)''', Yong Seok Lee, Sang-Cheol Kim and Doheon Lee, “SNP@Ethnos: a database of ethnically variant single-nucleotide polymorphisms”, '''''Nucleic Acids Res.''''' Vol. 35, Database issue D711-D715, 2006.
* Hyojin Kang, Taehui Hong, Won-Hyung Chung, Younguk Kim, Jinhee Jung, '''Sohyun Hwang''', Areum Han and Young Joo Kim, “D2GSNP: a web server for the selection of single nucleotide polymorphisms within human disease genes”, '''''Genomics & Informatics''''', Vol. 4, No. 1, pp 45-47, 2006.
* Seong-Bae Park, '''Sohyun Hwang''', and Byoung-Tak Zhang, “Classification of Human Papillomavirus (HPV) Risk Type via Text Mining”, '''''Genomics & Informatics''''', Vol. 1, No. 2, pp. 80-86, 2003.
* '''Sohyun Hwang''', Jaehong Suh and Cheol O. Joe, “Estrogen inhibits Bcl-2 expression and stimulate apoptosis mediated by 2,3,7,8-Tetrachlorodibenzo-p-dioxin.” '''''J. Toxicol. Pub. Health''''' vol. 19 No. 4, pp 325-330, 2003.

People:SH Hwang

2013-01-22T04:45:17Z

Winnie: /* Publications */

{|
|[[File:People_SYHwang.JPG|150px]]
|
===Sohyun Hwang===
*'''Ph.D.''', ''KAIST'', Dept of Bio and Brain Engineering(09/2004 - 02/2010). 
Dissertation: System level identification of interactions between cell signaling pathways. 
*'''M.S.''', ''KAIST'', Dept of Biology (03/2000 - 02/2002). 
Thesis: Regulation of apoptosis by 2,3,7,8-tetrachlorodibenzo-p-dioxin in MCF-7 cells.
*'''B.S''', ''KAIST'', Dept of Biology (03/1996 - 02/2000).
*''Hansung Science High School'' (03/1994 - 02/1996).
|}

==Current Research Interests==
*Biological data mining, integration, interpretation, hypothesis generation
*Genotype-phenotype mapping by various biological data and modeling algorithms

==Publications==
* Peggy I Wang, '''Sohyun Hwang (co-first)''', Rodney P Kincaid, Christopher S Sullivan, Insuk Lee, and Edward M Marcotte. RIDDLE: Reflective diffusion and local extension reveal functional associations for unannotated gene sets via proximity in a gene network. '''''Genome Biology''''', 13:R125, 2012.
* '''Sohyun Hwang''', Seung Y. Rhee, Edwawrd M. Marcotte, and Insuk Lee. "Systematic prediction of candidate gene function associated to phenotype traits using the probabilistic functional gene network of Arabidopsis thaliana", '''''Nature Protocols''''', 6:1429-1442, 2011.
* Insuk Lee, Young-Su Seo, Dusical Coltrane, '''Sohyun Hwang''', Taeyun Oh, Edward M. Marcotte, Pamela C Ronald, "Genetic dissection of the biotic stress response using a genome-scale gene network for rice", '''''PNAS''''' 108(45):18548-53, 2011.
* Young-Su Seo, Mawsheng Chen, Laura E Bartley, Muho Han, Ki-Hong Jung, Inusk Lee, Harkamal Walia, Xia Xu, Peijian Cao, Wei Bai, Rajeshwari Ramanan, Fawn Amonpant, Loganathan Arul, Patrick E Canlas, Randy Ruan, Chang-Jin Park, Xuewei Chen, '''Sohyun Hwang''', Jong-Seong, Jeon, Pamela C Ronald, “Towards Establishment of a Rice Stress Response Interactome” '''''PLoS Genetics''''', 7(4):e1002020, 2011.
* '''Sohyun Hwang''', Sangwoo Kim, Heesung Shim, Doheon Lee, “Context-dependent transcriptional regulations between signal transduction pathways”, '''''BMC Bioinformatics''''', 12:19, 2011.
* '''Sohyun Hwang''', Seung-Woo Son, Sang Cheol Kim, Young Joo Kim, Hawoong Jeong and Doheon Lee, “A protein interaction network associated with asthma”, '''''J. of Theor. Biol.''''', Vol 252, Issue 4, pp 722-731, 2008. ''(Yonhap news reported “Asthma candidate genes have been identified by bioinformatics” as a creditable achievement in June 2008.)''
* Jin Ok Yang, '''Sohyun Hwang (Co-first)''', Jeongsu Oh, Jong Bhak and Tae-Kwon Sohn, “An integrated database-pipeline system for studying single nucleotide polymorphisms and disease”, '''''BMC Bioinformatics''''', vol 9, Suppl 12: S19, 2008.
* Jung Kyoon Choi, '''Sohyun Hwang''', Young-Joon Kim, “Stochastic and regulatory role of chromatin silencing in genomic response to environmental changes”, '''''PLoS ONE''''', Vol 3, No. 8: e3002. 2008.
* Jungsun Park, '''Sohyun Hwang (Co-first)''', Yong Seok Lee, Sang-Cheol Kim and Doheon Lee, “SNP@Ethnos: a database of ethnically variant single-nucleotide polymorphisms”, '''''Nucleic Acids Res.''''' Vol. 35, Database issue D711-D715, 2006.
* Hyojin Kang, Taehui Hong, Won-Hyung Chung, Younguk Kim, Jinhee Jung, '''Sohyun Hwang''', Areum Han and Young Joo Kim, “D2GSNP: a web server for the selection of single nucleotide polymorphisms within human disease genes”, '''''Genomics & Informatics''''', Vol. 4, No. 1, pp 45-47, 2006.
* Seong-Bae Park, '''Sohyun Hwang''', and Byoung-Tak Zhang, “Classification of Human Papillomavirus (HPV) Risk Type via Text Mining”, '''''Genomics & Informatics''''', Vol. 1, No. 2, pp. 80-86, 2003.
* '''Sohyun Hwang''', Jaehong Suh and Cheol O. Joe, “Estrogen inhibits Bcl-2 expression and stimulate apoptosis mediated by 2,3,7,8-Tetrachlorodibenzo-p-dioxin.” '''''J. Toxicol. Pub. Health''''' vol. 19 No. 4, pp 325-330, 2003.

People:SH Hwang

2013-01-22T04:44:12Z

Winnie: /* Publications */

{|
|[[File:People_SYHwang.JPG|150px]]
|
===Sohyun Hwang===
*'''Ph.D.''', ''KAIST'', Dept of Bio and Brain Engineering(09/2004 - 02/2010). 
Dissertation: System level identification of interactions between cell signaling pathways. 
*'''M.S.''', ''KAIST'', Dept of Biology (03/2000 - 02/2002). 
Thesis: Regulation of apoptosis by 2,3,7,8-tetrachlorodibenzo-p-dioxin in MCF-7 cells.
*'''B.S''', ''KAIST'', Dept of Biology (03/1996 - 02/2000).
*''Hansung Science High School'' (03/1994 - 02/1996).
|}

==Current Research Interests==
*Biological data mining, integration, interpretation, hypothesis generation
*Genotype-phenotype mapping by various biological data and modeling algorithms

==Publications==
* Peggy I Wang, '''Sohyun Hwang''' (co-first), Rodney P Kincaid, Christopher S Sullivan, Insuk Lee, and Edward M Marcotte. RIDDLE: Reflective diffusion and local extension reveal functional associations for unannotated gene sets via proximity in a gene network. '''''Genome Biology''''', 13:R125, 2012.
* '''Sohyun Hwang''', Seung Y. Rhee, Edwawrd M. Marcotte, and Insuk Lee. "Systematic prediction of candidate gene function associated to phenotype traits using the probabilistic functional gene network of Arabidopsis thaliana", '''''Nature Protocols''''', 6:1429-1442, 2011.
* Insuk Lee, Young-Su Seo, Dusical Coltrane, '''Sohyun Hwang''', Taeyun Oh, Edward M. Marcotte, Pamela C Ronald, "Genetic dissection of the biotic stress response using a genome-scale gene network for rice", '''''PNAS''''' 108(45):18548-53, 2011.
* Young-Su Seo, Mawsheng Chen, Laura E Bartley, Muho Han, Ki-Hong Jung, Inusk Lee, Harkamal Walia, Xia Xu, Peijian Cao, Wei Bai, Rajeshwari Ramanan, Fawn Amonpant, Loganathan Arul, Patrick E Canlas, Randy Ruan, Chang-Jin Park, Xuewei Chen, '''Sohyun Hwang''', Jong-Seong, Jeon, Pamela C Ronald, “Towards Establishment of a Rice Stress Response Interactome” '''''PLoS Genetics''''', 2011 (Accepted).
* '''Sohyun Hwang''', Sangwoo Kim, Heesung Shim, Doheon Lee, “Context-dependent transcriptional regulations between signal transduction pathways”, '''''BMC Bioinformatics''''', 12:19, 2011.
* '''Sohyun Hwang''', Seung-Woo Son, Sang Cheol Kim, Young Joo Kim, Hawoong Jeong and Doheon Lee, “A protein interaction network associated with asthma”, '''''J. of Theor. Biol.''''', Vol 252, Issue 4, pp 722-731, 2008. ''(Yonhap news reported “Asthma candidate genes have been identified by bioinformatics” as a creditable achievement in June 2008.)''
* Jin Ok Yang, '''Sohyun Hwang (Co-first)''', Jeongsu Oh, Jong Bhak and Tae-Kwon Sohn, “An integrated database-pipeline system for studying single nucleotide polymorphisms and disease”, '''''BMC Bioinformatics''''', vol 9, Suppl 12: S19, 2008.
* Jung Kyoon Choi, '''Sohyun Hwang''', Young-Joon Kim, “Stochastic and regulatory role of chromatin silencing in genomic response to environmental changes”, '''''PLoS ONE''''', Vol 3, No. 8: e3002. 2008.
* Jungsun Park, '''Sohyun Hwang (Co-first)''', Yong Seok Lee, Sang-Cheol Kim and Doheon Lee, “SNP@Ethnos: a database of ethnically variant single-nucleotide polymorphisms”, '''''Nucleic Acids Res.''''' Vol. 35, Database issue D711-D715, 2006.
* Hyojin Kang, Taehui Hong, Won-Hyung Chung, Younguk Kim, Jinhee Jung, '''Sohyun Hwang''', Areum Han and Young Joo Kim, “D2GSNP: a web server for the selection of single nucleotide polymorphisms within human disease genes”, '''''Genomics & Informatics''''', Vol. 4, No. 1, pp 45-47, 2006.
* Seong-Bae Park, '''Sohyun Hwang''', and Byoung-Tak Zhang, “Classification of Human Papillomavirus (HPV) Risk Type via Text Mining”, '''''Genomics & Informatics''''', Vol. 1, No. 2, pp. 80-86, 2003.
* '''Sohyun Hwang''', Jaehong Suh and Cheol O. Joe, “Estrogen inhibits Bcl-2 expression and stimulate apoptosis mediated by 2,3,7,8-Tetrachlorodibenzo-p-dioxin.” '''''J. Toxicol. Pub. Health''''' vol. 19 No. 4, pp 325-330, 2003.

People:SH Hwang

2013-01-22T04:43:16Z

Winnie: /* Publications */

{|
|[[File:People_SYHwang.JPG|150px]]
|
===Sohyun Hwang===
*'''Ph.D.''', ''KAIST'', Dept of Bio and Brain Engineering(09/2004 - 02/2010). 
Dissertation: System level identification of interactions between cell signaling pathways. 
*'''M.S.''', ''KAIST'', Dept of Biology (03/2000 - 02/2002). 
Thesis: Regulation of apoptosis by 2,3,7,8-tetrachlorodibenzo-p-dioxin in MCF-7 cells.
*'''B.S''', ''KAIST'', Dept of Biology (03/1996 - 02/2000).
*''Hansung Science High School'' (03/1994 - 02/1996).
|}

==Current Research Interests==
*Biological data mining, integration, interpretation, hypothesis generation
*Genotype-phenotype mapping by various biological data and modeling algorithms

==Publications==
* Peggy I Wang, '''Sohyun Hwang'''(co-first), Rodney P Kincaid, Christopher S Sullivan, Insuk Lee, and Edward M Marcotte. RIDDLE: Reflective diffusion and local extension reveal functional associations for unannotated gene sets via proximity in a gene network. '''''Genome Biology''''', 13:R125, 2012.
* '''Sohyun Hwang''', Seung Y. Rhee, Edwawrd M. Marcotte, and Insuk Lee. "Systematic prediction of candidate gene function associated to phenotype traits using the probabilistic functional gene network of Arabidopsis thaliana", '''''Nature Protocols''''', 6:1429-1442, 2011.
* Insuk Lee, Young-Su Seo, Dusical Coltrane, '''Sohyun Hwang''', Taeyun Oh, Edward M. Marcotte, Pamela C Ronald, "Genetic dissection of the biotic stress response using a genome-scale gene network for rice", '''''PNAS''''', 2011.
* Young-Su Seo, Mawsheng Chen, Laura E Bartley, Muho Han, Ki-Hong Jung, Inusk Lee, Harkamal Walia, Xia Xu, Peijian Cao, Wei Bai, Rajeshwari Ramanan, Fawn Amonpant, Loganathan Arul, Patrick E Canlas, Randy Ruan, Chang-Jin Park, Xuewei Chen, '''Sohyun Hwang''', Jong-Seong, Jeon, Pamela C Ronald, “Towards Establishment of a Rice Stress Response Interactome” '''''PLoS Genetics''''', 2011 (Accepted).
* '''Sohyun Hwang''', Sangwoo Kim, Heesung Shim, Doheon Lee, “Context-dependent transcriptional regulations between signal transduction pathways”, '''''BMC Bioinformatics''''', 12:19, 2011.
* '''Sohyun Hwang''', Seung-Woo Son, Sang Cheol Kim, Young Joo Kim, Hawoong Jeong and Doheon Lee, “A protein interaction network associated with asthma”, '''''J. of Theor. Biol.''''', Vol 252, Issue 4, pp 722-731, 2008. ''(Yonhap news reported “Asthma candidate genes have been identified by bioinformatics” as a creditable achievement in June 2008.)''
* Jin Ok Yang, '''Sohyun Hwang (Co-first)''', Jeongsu Oh, Jong Bhak and Tae-Kwon Sohn, “An integrated database-pipeline system for studying single nucleotide polymorphisms and disease”, '''''BMC Bioinformatics''''', vol 9, Suppl 12: S19, 2008.
* Jung Kyoon Choi, '''Sohyun Hwang''', Young-Joon Kim, “Stochastic and regulatory role of chromatin silencing in genomic response to environmental changes”, '''''PLoS ONE''''', Vol 3, No. 8: e3002. 2008.
* Jungsun Park, '''Sohyun Hwang (Co-first)''', Yong Seok Lee, Sang-Cheol Kim and Doheon Lee, “SNP@Ethnos: a database of ethnically variant single-nucleotide polymorphisms”, '''''Nucleic Acids Res.''''' Vol. 35, Database issue D711-D715, 2006.
* Hyojin Kang, Taehui Hong, Won-Hyung Chung, Younguk Kim, Jinhee Jung, '''Sohyun Hwang''', Areum Han and Young Joo Kim, “D2GSNP: a web server for the selection of single nucleotide polymorphisms within human disease genes”, '''''Genomics & Informatics''''', Vol. 4, No. 1, pp 45-47, 2006.
* Seong-Bae Park, '''Sohyun Hwang''', and Byoung-Tak Zhang, “Classification of Human Papillomavirus (HPV) Risk Type via Text Mining”, '''''Genomics & Informatics''''', Vol. 1, No. 2, pp. 80-86, 2003.
* '''Sohyun Hwang''', Jaehong Suh and Cheol O. Joe, “Estrogen inhibits Bcl-2 expression and stimulate apoptosis mediated by 2,3,7,8-Tetrachlorodibenzo-p-dioxin.” '''''J. Toxicol. Pub. Health''''' vol. 19 No. 4, pp 325-330, 2003.

People:SH Hwang

2011-11-14T08:03:29Z

Winnie: /* Publications */

{|
|[[File:People_SYHwang.JPG|150px]]
|
===Sohyun Hwang===
*'''Ph.D.''', ''KAIST'', Dept of Bio and Brain Engineering(09/2004 - 02/2010). 
Dissertation: System level identification of interactions between cell signaling pathways. 
*'''M.S.''', ''KAIST'', Dept of Biology (03/2000 - 02/2002). 
Thesis: Regulation of apoptosis by 2,3,7,8-tetrachlorodibenzo-p-dioxin in MCF-7 cells.
*'''B.S''', ''KAIST'', Dept of Biology (03/1996 - 02/2000).
*''Hansung Science High School'' (03/1994 - 02/1996).
|}

==Current Research Interests==
*Biological data mining, integration, interpretation, hypothesis generation
*Genotype-phenotype mapping by various biological data and modeling algorithms

==Publications==
* '''Sohyun Hwang''', Seung Y. Rhee, Edwawrd M. Marcotte, and Insuk Lee. "Systematic prediction of candidate gene function associated to phenotype traits using the probabilistic functional gene network of Arabidopsis thaliana", '''''Nature Protocols''''', 6:1429-1442, 2011.
* Insuk Lee, Young-Su Seo, Dusical Coltrane, '''Sohyun Hwang''', Taeyun Oh, Edward M. Marcotte, Pamela C Ronald, "Genetic dissection of the biotic stress response using a genome-scale gene network for rice", '''''PNAS''''' (Accepted), 2011.
* Young-Su Seo, Mawsheng Chen, Laura E Bartley, Muho Han, Ki-Hong Jung, Inusk Lee, Harkamal Walia, Xia Xu, Peijian Cao, Wei Bai, Rajeshwari Ramanan, Fawn Amonpant, Loganathan Arul, Patrick E Canlas, Randy Ruan, Chang-Jin Park, Xuewei Chen, '''Sohyun Hwang''', Jong-Seong, Jeon, Pamela C Ronald, “Towards Establishment of a Rice Stress Response Interactome” '''''PLoS Genetics''''', 2011 (Accepted).
* '''Sohyun Hwang''', Sangwoo Kim, Heesung Shim, Doheon Lee, “Context-dependent transcriptional regulations between signal transduction pathways”, '''''BMC Bioinformatics''''', 12:19, 2011.
* '''Sohyun Hwang''', Seung-Woo Son, Sang Cheol Kim, Young Joo Kim, Hawoong Jeong and Doheon Lee, “A protein interaction network associated with asthma”, '''''J. of Theor. Biol.''''', Vol 252, Issue 4, pp 722-731, 2008. ''(Yonhap news reported “Asthma candidate genes have been identified by bioinformatics” as a creditable achievement in June 2008.)''
* Jin Ok Yang, '''Sohyun Hwang (Co-first)''', Jeongsu Oh, Jong Bhak and Tae-Kwon Sohn, “An integrated database-pipeline system for studying single nucleotide polymorphisms and disease”, '''''BMC Bioinformatics''''', vol 9, Suppl 12: S19, 2008.
* Jung Kyoon Choi, '''Sohyun Hwang''', Young-Joon Kim, “Stochastic and regulatory role of chromatin silencing in genomic response to environmental changes”, '''''PLoS ONE''''', Vol 3, No. 8: e3002. 2008.
* Jungsun Park, '''Sohyun Hwang (Co-first)''', Yong Seok Lee, Sang-Cheol Kim and Doheon Lee, “SNP@Ethnos: a database of ethnically variant single-nucleotide polymorphisms”, '''''Nucleic Acids Res.''''' Vol. 35, Database issue D711-D715, 2006.
* Hyojin Kang, Taehui Hong, Won-Hyung Chung, Younguk Kim, Jinhee Jung, '''Sohyun Hwang''', Areum Han and Young Joo Kim, “D2GSNP: a web server for the selection of single nucleotide polymorphisms within human disease genes”, '''''Genomics & Informatics''''', Vol. 4, No. 1, pp 45-47, 2006.
* Seong-Bae Park, '''Sohyun Hwang''', and Byoung-Tak Zhang, “Classification of Human Papillomavirus (HPV) Risk Type via Text Mining”, '''''Genomics & Informatics''''', Vol. 1, No. 2, pp. 80-86, 2003.
* '''Sohyun Hwang''', Jaehong Suh and Cheol O. Joe, “Estrogen inhibits Bcl-2 expression and stimulate apoptosis mediated by 2,3,7,8-Tetrachlorodibenzo-p-dioxin.” '''''J. Toxicol. Pub. Health''''' vol. 19 No. 4, pp 325-330, 2003.

People:SH Hwang

2011-11-14T08:00:09Z

Winnie: /* Publications */

{|
|[[File:People_SYHwang.JPG|150px]]
|
===Sohyun Hwang===
*'''Ph.D.''', ''KAIST'', Dept of Bio and Brain Engineering(09/2004 - 02/2010). 
Dissertation: System level identification of interactions between cell signaling pathways. 
*'''M.S.''', ''KAIST'', Dept of Biology (03/2000 - 02/2002). 
Thesis: Regulation of apoptosis by 2,3,7,8-tetrachlorodibenzo-p-dioxin in MCF-7 cells.
*'''B.S''', ''KAIST'', Dept of Biology (03/1996 - 02/2000).
*''Hansung Science High School'' (03/1994 - 02/1996).
|}

==Current Research Interests==
*Biological data mining, integration, interpretation, hypothesis generation
*Genotype-phenotype mapping by various biological data and modeling algorithms

==Publications==
* '''Sohyun Hwang''', Seung Y. Rhee, Edwawrd M. Marcotte, and Insuk Lee. "Systematic prediction of candidate gene function associated to phenotype traits using the probabilistic functional gene network of Arabidopsis thaliana", Nature Protocols, 6:1429-1442, 2011.
* Insuk Lee, Young-Su Seo, Dusical Coltrane, '''Sohyun Hwang''', Taeyun Oh, Edward M. Marcotte, Pamela C Ronald, "Genetic dissection of the biotic stress response using a genome-scale gene network for rice", PNAS (Accepted), 2011.
* Young-Su Seo, Mawsheng Chen, Laura E Bartley, Muho Han, Ki-Hong Jung, Inusk Lee, Harkamal Walia, Xia Xu, Peijian Cao, Wei Bai, Rajeshwari Ramanan, Fawn Amonpant, Loganathan Arul, Patrick E Canlas, Randy Ruan, Chang-Jin Park, Xuewei Chen, '''Sohyun Hwang''', Jong-Seong, Jeon, Pamela C Ronald, “Towards Establishment of a Rice Stress Response Interactome” PLoS Genetics, 2011 (Accepted).
* '''Sohyun Hwang''', Sangwoo Kim, Heesung Shim, Doheon Lee, “Context-dependent transcriptional regulations between signal transduction pathways”, BMC Bioinformatics, 12:19, 2011.
* '''Sohyun Hwang''', Seung-Woo Son, Sang Cheol Kim, Young Joo Kim, Hawoong Jeong and Doheon Lee, “A protein interaction network associated with asthma”, J. of Theor. Biol., Vol 252, Issue 4, pp 722-731, 2008. ''(Yonhap news reported “Asthma candidate genes have been identified by bioinformatics” as a creditable achievement in June 2008.)''
* Jin Ok Yang, '''Sohyun Hwang (Co-first)''', Jeongsu Oh, Jong Bhak and Tae-Kwon Sohn, “An integrated database-pipeline system for studying single nucleotide polymorphisms and disease”, BMC Bioinformatics, vol 9, Suppl 12: S19, 2008.
* Jung Kyoon Choi, '''Sohyun Hwang''', Young-Joon Kim, “Stochastic and regulatory role of chromatin silencing in genomic response to environmental changes”, PLoS ONE, Vol 3, No. 8: e3002. 2008.
* Jungsun Park, '''Sohyun Hwang (Co-first)''', Yong Seok Lee, Sang-Cheol Kim and Doheon Lee, “SNP@Ethnos: a database of ethnically variant single-nucleotide polymorphisms”, Nucleic Acids Res. Vol. 35, Database issue D711-D715, 2006.
* Hyojin Kang, Taehui Hong, Won-Hyung Chung, Younguk Kim, Jinhee Jung, '''Sohyun Hwang''', Areum Han and Young Joo Kim, “D2GSNP: a web server for the selection of single nucleotide polymorphisms within human disease genes”, Genomics & Informatics, Vol. 4, No. 1, pp 45-47, 2006.
* Seong-Bae Park, '''Sohyun Hwang''', and Byoung-Tak Zhang, “Classification of Human Papillomavirus (HPV) Risk Type via Text Mining”, Genomics & Informatics, Vol. 1, No. 2, pp. 80-86, 2003.
* '''Sohyun Hwang''', Jaehong Suh and Cheol O. Joe, “Estrogen inhibits Bcl-2 expression and stimulate apoptosis mediated by 2,3,7,8-Tetrachlorodibenzo-p-dioxin.” J. Toxicol. Pub. Health vol. 19 No. 4, pp 325-330, 2003.

Publications

2011-10-04T01:55:02Z

Winnie: /* 2011 */

==2011==
*26. Sohyun Hwang, Seung Y. Rhee, Edward M. Marcotte, and '''Insuk Lee'''. Systematic prediction of candidate gene function associated to phenotype traits using the probabilistic functional gene network of Arabidopsis thaliana. '''''Nature Protocols''''' 6:1429-1442 (2011) [[media:2011.08.25.online.nprot.2011.372.pdf|pdf]]

*25. '''Insuk Lee''', Probabilistic functional gene societies. '''''Progress in Biophysics and Molecular Biology''''' 106:435-442 (2011) [http://www.ncbi.nlm.nih.gov/pubmed/21281658 pubmed] [[media:Publications_023_n.pdf|pdf]]

*24. '''Insuk Lee''', U. Martin Blom, Peggy I. Wang, Jung Eun Shim, and Edward M. Marcotte. Prioritizing candidate disease genes by network-based boosting of genome-wide association data. '''''Genome Research''''' 21:1109-1121 (2011) [http://www.ncbi.nlm.nih.gov/pubmed/21536720 pubmed] [[media:Publications_025_n.pdf|pdf]]

*23. Young-Su Seo, Mawsheng Chern, Laura E. Bartley, Muho Han, Ki-Hong Jung, '''Insuk Lee''', Harkamal Walia, Todd Richter, Xia Xu, Peijian Cao, Wei Bai, Rajeshwari Ramanan, Fawn Amonpant, Loganathan Arul, Patrick E. Canlas, Randy Ruan, Chang-Jin Park, Xuewel Chen, Sohyun Hwang, Jong-Seong Jeon, and Pamela C. Ronald. Towards establishment of a rice stress response interactome. '''''PLoS Genetics''''' 7(4):e1002020 (2011) [http://www.ncbi.nlm.nih.gov/pubmed/21533176 pubmed] [[media:Publications_024.pdf|pdf]]

==2010==
*22. Ni Huang, '''Insuk Lee''', Edward M.Marcotte, Matthew E.Hurles, Characterising and predicting haploinsufficiency in the human genome, '''''PLoS Genet.''''' 6(10):e1001154(2010) [http://www.ncbi.nlm.nih.gov/pubmed/20976243 pubmed] [[media:Publications_022.pdf|pdf]]

*21. Eiru Kim, Jaeyoon Shin and '''Insuk Lee''', Assessment of effectiveness of the network-guided genetic screen, '''''Mol Biosyst.''''' 6:1803-1806(2010) [http://www.ncbi.nlm.nih.gov/pubmed/20697632 pubmed] [[media:Publications_021.pdf|pdf]]

*20. '''Insuk Lee''', Ben Lehner, Tanya Vavouri, Junha Shin, Andrew G. Fraser, and Edward M. Marcotte, Predicting genetic modifier loci using functional gene networks, '''''Genome Research''''', 20:1143-1153(2010) . co-corresponding author [http://www.ncbi.nlm.nih.gov/pubmed/20538624 pubmed] [[media:Publications_020.pdf|pdf]]

*19. '''Insuk Lee''', Bindu Ambaru, Pranjali Thakkar, Edward M Marcotte, Seung Y Rhee, Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana, '''''Nature Biotechnology''''', 28:149-156 (2010). ''co-corresponding author'' [http://www.ncbi.nlm.nih.gov/pubmed/20118918 pubmed] [[media:Publications_019.pdf|pdf]]
==2009==
*18. '''Insuk Lee''' and Edward Marcotte. Effects of functional bias on supervised learning of a gene network model. '''In Methods in Molecular Biology''' Vol. 541, Computational Systems Biology (ed. R. Ireton, K. Montgomery, J. McDermott, R. Samudrala, R. Bumgarner). Totowa, THE HUMANA. p463-475 (2009) [http://www.ncbi.nlm.nih.gov/pubmed/19381535 pubmed] [[media:Publications_018.pdf|pdf]]

*17. Zhihua Li, '''Insuk Lee''', Emily Moradi, Nai-Jung Hung, Arlen W. Johnson, Edward M. Marcotte, Rational Extension of the Ribosome Biogenesis Pathway Using Network-Guided Genetics, '''''PLoS Biology''''', 7(10):e1000213 (2009) [http://www.ncbi.nlm.nih.gov/pubmed/19806183 pubmed] [[media:Publications_017.pdf|pdf]]

*16. Ryan S. Gray, Philip B. Abitua, Bogdan J. Wlodarczyk, Heather L. Szabo-Rogers, Otis Blanchard, '''Insuk Lee''', Greg S. Weiss, Karen J. Liu, Edward M. Marcotte, John B. Wallingford, Richard H. Finnell. The planar cell polarity effector protein Fuz is essential for targeted membrane trafficking, ciliogenesis, and mouse embryonic development, '''''Nature Cell Biology''''' 11:1225-32 (2009) '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/19767740 pubmed] [[media:Publications_016.pdf|pdf]]
==2008==
*15. Ben Lehner and '''Insuk Lee'''. Network-guided genetic screening: building, testing, and using gene networks to predict gene function. '''''Brief. Funct. Genomic. Proteomic'''''. 7:217-227 (2008). '''''co-corresponding author''''' [http://www.ncbi.nlm.nih.gov/pubmed/18445637 pubmed] [[media:Publications_015.pdf|pdf]]

*14. '''Insuk Lee''' and Edward Marcotte. Integrating Functional Genomics Data. '''In Methods in Molecular Biology''' Vol. 453, Bioinformatics Vol. II (ed. Jonathan Keith). Totowa, THE HUMANA. p267-278 (2008) [http://www.ncbi.nlm.nih.gov/pubmed/18712309 pubmed] [[media:Publications_014.pdf|pdf]]

*13. '''Insuk Lee''', Ben Lehner, Catriona Crombie, Wendy Wong, Andrew G. Fraser, Edward M. Marcotte. A single gene network accurately predicts phenotypic effects of gene perturbation in ''Caenorhabditis elegans''. '''''Nature Genetics''''' 40:181-188 (2008). '''''*Cover story''''' [http://www.ncbi.nlm.nih.gov/pubmed/18223650 pubmed] [[media:Publications_013.pdf|pdf]] This paper was the subject of the following commentary (Natalie de Souza, Networking on organism. Nature Methods 5:217), and minireviews (Von Stetina S. E. and Mango S. E. Wormnet: a crystal ball for Caenorhabditis elegans. Genome Biology 9:226. Borgwardt K. Predicting phenotypic effects of gene perturbations in C. elegans using an integrated network model. BioEssays 30:707)
==Before 2007==
*12. '''Insuk Lee''', Rammohan Narayanaswamy, Edward Marcotte. Bioinformatic prediction of yeast gene function. '''In METHOD IN MICROBIOLOGY''' Vol. 36, Yeast Gene Analysis (ed. Ian Stansfield and Mike Stark), Elsevier. p597-628, (2007) [[media:Publications_012.pdf|pdf]]

*11. Kris McGary, '''Insuk Lee''', Edward M. Marcotte. Broad network-based predictability of S. cerevisiae gene loss-of-function phenotypes. '''''Genome Biology''''' 8:R258 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/18053250 pubmed] [[media:Publications_011.pdf|pdf]]

*10. '''Insuk Lee''', Zhihua Li, and Edward M. Marcotte. An improved bias-reduced probabilistic functional gene network of baker’s yeast ''Saccharomyces cerevisiae''. '''''PLOS One''''' 2:e988 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17912365 pubmed] [[media:Publications_010.pdf|pdf]]

*9. Hart G. Traver, '''Insuk Lee''', Edward Marcotte. A high-accuracy consensus map of yeast protein complexes reveals modular nature of gene essentiality. '''''BMC Bioinformatic''''' 8:236 (2007) [http://www.ncbi.nlm.nih.gov/pubmed/17605818 pubmed] [[media:Publications_009.pdf|pdf]]

*8. Insuk Lee, Shailesh V. Date, Alex T. Adai, Edward Marcotte. A Probabilistic functional network of yeast genes. '''''Science''''' 306:1555-1558, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15567862 pubmed] [[media:Publications_008.pdf|pdf]]

*7. Bork, P., Jensen, L.J., Von Mering, C., Ramani, A.K., '''Lee I''', Marcotte, E.M. Protein interaction networks from yeast to human. '''''Curr. Opin. Struct. Biol.''''' 14:292-9, (2004) [http://www.ncbi.nlm.nih.gov/pubmed/15193308 pubmed] [[media:Publications_007.pdf|pdf]]

*6. '''Insuk Lee''' and Rasika Harshey. Patterns of Sequence conservation at termini of LTR retrotransposons and DNA transposons in the human genome: Lessons from phage Mu. '''''Nucleic Acids Res.''''' 31:4531-4540, (2003)

*5. '''Insuk Lee''' and Rasika Harshey. The conserved CA/TG motif at Mu termini: T specifies stable transpososome assembly. '''''J. Mol. Biol.''''' 330:261-275, (2003)

*4. '''Insuk Lee''' and Rasika Harshey. Importance of the conserved CA dinucleotide at Mu termini. '''''J. Mol. Biol.''''' 314:433-444, (2001)

*3. Xue, Y., Bai, X., '''Lee, I.''', Kallstrom, G., Ho, J., Brown, J., Stevens, A., and Johnson, A. W. Saccharomyces cerevisiae RAI1 (YGL246c) is homologous to human DOM3Z and encodes a protein that binds the nuclear exoribonuclease Rat1p. '''''Mol. Cell. Biol.''''' 20:4006-4015, (2000)

*2. Liu, J., Gong, Y., Prakash, O., Wen, L., '''Lee, I'''., Huang J.,-K., and Krishnamoorthi, R. NMR studies of internal dynamics of serine proteinase protein inhibitors: Binding region mobilities of intact and reactive-site hydrolyzed CMTI-III of the squash family and comparison with those of counterparts of CMTI-V of the potato I family. '''''Protein Science''''' 7:132-141, (1998)

*1. Wen, L., '''Lee, I.''', Chen, G., Huang, J.,-K., Gong, Y., and Krishnamoorthi, R. Changing the inhibitory specificity and function of CMTI-V by site-directed mutagenesis. '''''Biochem. Biophys. Res. Commun.''''' 207:897-902, (1995)

People:SH Hwang

2011-02-21T08:32:30Z

Winnie:

{|
|[[File:People_SYHwang.JPG|150px]]
|
===Sohyun Hwang===
*'''Ph.D.''', ''KAIST'', Dept of Bio and Brain Engineering(09/2004 - 02/2010). 
Dissertation: System level identification of interactions between cell signaling pathways. 
*'''M.S.''', ''KAIST'', Dept of Biology (03/2000 - 02/2002). 
Thesis: Regulation of apoptosis by 2,3,7,8-tetrachlorodibenzo-p-dioxin in MCF-7 cells.
*'''B.S''', ''KAIST'', Dept of Biology (03/1996 - 02/2000).
*''Hansung Science High School'' (03/1994 - 02/1996).
|}

==Current Research Interests==
*Biological data mining, integration, interpretation, hypothesis generation
*Genotype-phenotype mapping by various biological data and modeling algorithms

==Publications==
* Young-Su Seo, Mawsheng Chen, Laura E Bartley, Muho Han, Ki-Hong Jung, Inusk Lee, Harkamal Walia, Xia Xu, Peijian Cao, Wei Bai, Rajeshwari Ramanan, Fawn Amonpant, Loganathan Arul, Patrick E Canlas, Randy Ruan, Chang-Jin Park, Xuewei Chen, '''Sohyun Hwang''', Jong-Seong, Jeon, Pamela C Ronald, “Towards Establishment of a Rice Stress Response Interactome” PLoS Genetics, 2011 (Accepted).
* '''Sohyun Hwang''', Sangwoo Kim, Heesung Shim, Doheon Lee, “Context-dependent transcriptional regulations between signal transduction pathways”, BMC Bioinformatics, 12:19, 2011.
* '''Sohyun Hwang''', Seung-Woo Son, Sang Cheol Kim, Young Joo Kim, Hawoong Jeong and Doheon Lee, “A protein interaction network associated with asthma”, J. of Theor. Biol., Vol 252, Issue 4, pp 722-731, 2008. ''(Yonhap news reported “Asthma candidate genes have been identified by bioinformatics” as a creditable achievement in June 2008.)''
* Jin Ok Yang, '''Sohyun Hwang (Co-first)''', Jeongsu Oh, Jong Bhak and Tae-Kwon Sohn, “An integrated database-pipeline system for studying single nucleotide polymorphisms and disease”, BMC Bioinformatics, vol 9, Suppl 12: S19, 2008.
* Jung Kyoon Choi, '''Sohyun Hwang''', Young-Joon Kim, “Stochastic and regulatory role of chromatin silencing in genomic response to environmental changes”, PLoS ONE, Vol 3, No. 8: e3002. 2008.
* Jungsun Park, '''Sohyun Hwang (Co-first)''', Yong Seok Lee, Sang-Cheol Kim and Doheon Lee, “SNP@Ethnos: a database of ethnically variant single-nucleotide polymorphisms”, Nucleic Acids Res. Vol. 35, Database issue D711-D715, 2006.
* Hyojin Kang, Taehui Hong, Won-Hyung Chung, Younguk Kim, Jinhee Jung, '''Sohyun Hwang''', Areum Han and Young Joo Kim, “D2GSNP: a web server for the selection of single nucleotide polymorphisms within human disease genes”, Genomics & Informatics, Vol. 4, No. 1, pp 45-47, 2006.
* Seong-Bae Park, '''Sohyun Hwang''', and Byoung-Tak Zhang, “Classification of Human Papillomavirus (HPV) Risk Type via Text Mining”, Genomics & Informatics, Vol. 1, No. 2, pp. 80-86, 2003.
* '''Sohyun Hwang''', Jaehong Suh and Cheol O. Joe, “Estrogen inhibits Bcl-2 expression and stimulate apoptosis mediated by 2,3,7,8-Tetrachlorodibenzo-p-dioxin.” J. Toxicol. Pub. Health vol. 19 No. 4, pp 325-330, 2003.

People:SH Hwang

2010-05-17T05:11:19Z

Winnie: /* Publication */

People:SH Hwang

2010-05-17T05:11:05Z

Winnie:

People:SH Hwang

2010-05-17T04:45:31Z

Winnie:

{|
|[[File:People_SYHwang.JPG|150px]]
|NBL NBL NBL NBL NBL NBL NBL NBL NBL NBL NBL NBL NBL NBL NBL NBL NBL NBL NBL NBL NBL NBL NBL NBL NBL NBL NBL NBL NBL NBL NBL NBL NBL NBL NBL NBL NBL NBL NBL NBL NBL NBL NBL
NBL NBL NBL NBL NBL
|}

Welcome to Yonsei Network Biotechnology Loboratory!

2010-03-17T04:06:33Z

Winnie:

{|align = "left"
|[[File : Main_photo02.jpg|370px|main_photo]]
|
===oral presentation===
<pre>
***TY Oh
***HH Kim
JE Shim
SG Ji
SH Hwang
AR Cho
JH Shin
</pre>
===address===
<pre>
134 Shinchon-dong, Seodaemun-gu, Seoul 120-749, Korea
</pre>
===phone===
<pre>
+82-70-8625-5205
</pre>
|}