Network Biology Lab - User contributions [en]

Services

2014-01-14T06:50:35Z

Hanhaekim:

__NOTOC__
==Genome-scale gene networks for model organisms==
[[file:Tools_RiceNetLogo.jpg|150px|link=http://www.functionalnet.org/ricenet]] Functional gene network for ''Oryza sativa''. Version 1 (18,377 genes, 588,221 links)

[[file:Tools_HumanNetLogo.jpg|150px|link=http://www.functionalnet.org/humannet]] Functional gene network for ''Homo sapiens''. Version 1 (16,242 genes, 476,399 links)

[[file:Tools_AraNetLogo.jpg|150px|link=http://www.functionalnet.org/aranet]] Functional gene network for ''Arabidopsis thaliana''. Version 1 (19,647 genes, 1,062,222 links)

[[file:Tools_WormNetLogo.jpg|150px|link=http://www.functionalnet.org/wormnet]] Functional gene network for ''Caenorhabditis elegans''. Version 2 (15,139 genes, 999,367 links)

[[File:Tools_YesatNetLogo.jpg|150px|link=http://www.inetbio.org/yeastnet]] Functional gene network for ''Saccharomyces cerevisiae''. Version 3 (5,818 genes, 362,512 links)

==A network-assisted Gene Set Analysis server==
[[File:Riddle cover title.jpg|150px|link=http://www.functionalnet.org/riddle]] RIDDLE: Reflective diffusion and local extension

==A web-based instant protein network modeler for newly sequenced species==
[[File:Jiffynetlogo4 small.jpg |150px|link=http://www.jiffynet.org]] JiffyNet: an instant network builder

Services

2014-01-14T06:48:27Z

Hanhaekim:

__NOTOC__
==Genome-scale gene networks for model organisms==
[[file:Tools_RiceNetLogo.jpg|150px|link=http://www.functionalnet.org/ricenet]] Functional gene network for ''Oryza sativa''. Version 1 (18,377 genes, 588,221 links)

[[file:Tools_HumanNetLogo.jpg|150px|link=http://www.functionalnet.org/humannet]] Functional gene network for ''Homo sapiens''. Version 1 (16,242 genes, 476,399 links)

[[file:Tools_AraNetLogo.jpg|150px|link=http://www.functionalnet.org/aranet]] Functional gene network for ''Arabidopsis thaliana''. Version 1 (19,647 genes, 1,062,222 links)

[[file:Tools_WormNetLogo.jpg|150px|link=http://www.functionalnet.org/wormnet]] Functional gene network for ''Caenorhabditis elegans''. Version 2 (15,139 genes, 999,367 links)

[[file:Tools YeastNetLogo.jpg|150px|link=http://www.inetbio.org/yeastnet]] Functional gene network for ''Saccharomyces cerevisiae''. Version 3 (5,818 genes, 362,512 links)

==A network-assisted Gene Set Analysis server==
[[File:Riddle cover title.jpg|150px|link=http://www.functionalnet.org/riddle]] RIDDLE: Reflective diffusion and local extension

==A web-based instant protein network modeler for newly sequenced species==
[[File:Jiffynetlogo4 small.jpg |150px|link=http://www.jiffynet.org]] JiffyNet: an instant network builder

File:Tools YesatNetLogo.jpg

2014-01-14T06:43:27Z

Hanhaekim:

Services

2014-01-14T06:34:25Z

Hanhaekim:

__NOTOC__
==Genome-scale gene networks for model organisms==
[[file:Tools_RiceNetLogo.jpg|150px|link=http://www.functionalnet.org/ricenet]] Functional gene network for ''Oryza sativa''. Version 1 (18,377 genes, 588,221 links)

[[file:Tools_HumanNetLogo.jpg|150px|link=http://www.functionalnet.org/humannet]] Functional gene network for ''Homo sapiens''. Version 1 (16,242 genes, 476,399 links)

[[file:Tools_AraNetLogo.jpg|150px|link=http://www.functionalnet.org/aranet]] Functional gene network for ''Arabidopsis thaliana''. Version 1 (19,647 genes, 1,062,222 links)

[[file:Tools_WormNetLogo.jpg|150px|link=http://www.functionalnet.org/wormnet]] Functional gene network for ''Caenorhabditis elegans''. Version 2 (15,139 genes, 999,367 links)

[[file:Tools_YeastNetLogo.jpg|150px|link=http://www.inetbio.org/yeastnet]] Functional gene network for ''Saccharomyces cerevisiae''. Version 3 (5,818 genes, 362,512 links)

==A network-assisted Gene Set Analysis server==
[[File:Riddle cover title.jpg|150px|link=http://www.functionalnet.org/riddle]] RIDDLE: Reflective diffusion and local extension

==A web-based instant protein network modeler for newly sequenced species==
[[File:Jiffynetlogo4 small.jpg |150px|link=http://www.jiffynet.org]] JiffyNet: an instant network builder

Publications

2014-01-08T08:10:14Z

Hanhaekim:

*[http://scholar.google.com/citations?user=3uHQIOkAAAAJ Google Scholar citation report]
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}}

* '*' co-corresponding authorship
==2014==
*34. Junha Shin, Tak Lee, Hanhae Kim and '''Insuk Lee''', Complementarity between distance- and probability-based methods of gene neighbourhood identification for pathway reconstruction. '''''Mol. BioSyst.''''', 10 (1), 24 - 29., (2014) [http://www.ncbi.nlm.nih.gov/pubmed/24194096 Pubmed]
*33. 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''''' 42 (D1): D731-D736., (2014) [http://www.ncbi.nlm.nih.gov/pubmed/24165882 Pubmed]

==2013==
*32. Eiru Kim, Hanhae Kim and '''Insuk Lee''', JiffyNet: a web-based instant protein network modeler for newly sequenced species. '''''Nucleic Acids Research''''' 41 (W1): W192-W197., (2013) [http://www.ncbi.nlm.nih.gov/pubmed/23685435 Pubmed][http://nar.oxfordjournals.org/content/early/2013/05/17/nar.gkt419.full.pdf+html pdf]
*31. '''Insuk Lee''', Network approaches to the genetic dissection of phenotypes in animals and humans. '''''Animal Cells and Systems''''' Vol.17,No.2,75-79(2013)[http://www.tandfonline.com/doi/abs/10.1080/19768354.2013.789076 Link]

==2012==
*30. Peggy I Wang, Sohyun Hwang, 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]
*29. Lee Chae*, '''Insuk Lee*''', Junha Shin, and Seung Yon Rhee*. Towards understanding how molecular networks evolve in plant. '''''Current Opinion in Plant Biology''''' 15:177-184 (2012)[http://www.ncbi.nlm.nih.gov/pubmed/22280840 pubmed] [[media:CurrOpinPlantBiol 15-177.pdf|pdf]]
*28. Stephanie M. Quanbeck, Libuse Brachova, Alexis A. Campbell, Xin Guan, Ann Perera, Kun He, Seung Y. Rhee, Preeti Bais, Julie A. Dickerson, Philip Dixon, Gert Wohlgemuth, Oliver Fiehn, Lenore Barken, Iris Lange, B. Markus Lange, '''Insuk Lee''', Diego Cortes, Carolina Salazar, Joel Shuman, Vladimir Shulaev, David V. Huhman, Lloyd W. Sumner, Mary R. Roth, Ruth Welti, Hilal Ilarslan, Eve S. Wurtele, and Basil J. Nikolau. Metabolomics as a hypothesis-generating functional genomics tool for the annotation of Arabidopsis thaliana genes of “unknown function”. '''''Frontiers in Plant Science''''' 3:1-12 (2012) [http://www.ncbi.nlm.nih.gov/pubmed/22645570/ pubmed][[media:Fpls-03-00015.pdf|pdf]]

==2011==
*27. '''Insuk Lee*''', Young-Su Seo, Dusica Coltrane, Sohyun Hwang, Taeyun Oh, Edward M. Marcotte*, and Pamela C. Ronald*. Genetic dissection of the biotic stress response using a genome-scale gene network for rice. '''''PNAS''''' 108(45):18548-53 (2011) [http://www.ncbi.nlm.nih.gov/pubmed/22042862 pubmed] [[media:PNAS-2011-Lee-18548-53.pdf|pdf]]

*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) [http://www.ncbi.nlm.nih.gov/pubmed/21886106 pubmed][[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'''''. 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]]<br />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:HH Kim

2010-05-20T02:51:49Z

Hanhaekim: /* HANHAE KIM */

[[File:Example.jpg]]===HANHAE KIM===
*'''M.S. Candidate''', Yonsei University, College of Life Science and Biotechnology, Department of Biotechnology (08/2009 - ).
*'''B.Eng''', Yonsei University, School of Engineering, Department of Biotechnology (03/2002 - 08/2009).

<pre>
*E-mail : kimhanhae@gmail.com

People:HH Kim

2010-05-20T02:51:21Z

Hanhaekim: /* HANHAE KIM */

===HANHAE KIM===
*'''M.S. Candidate''', Yonsei University, College of Life Science and Biotechnology, Department of Biotechnology (08/2009 - ).
*'''B.Eng''', Yonsei University, School of Engineering, Department of Biotechnology (03/2002 - 08/2009).

<pre>
*E-mail : kimhanhae@gmail.com

People:HH Kim

2010-05-20T02:51:14Z

Hanhaekim: /* HANHAE KIM */

People:HH Kim

2010-05-20T02:51:05Z

Hanhaekim: /* ARA CHO */

People:HH Kim

2010-05-20T02:49:50Z

Hanhaekim:

===ARA CHO===
*'''M.S. Candidate''', ''Yonsei Univ'', College of Life Science and Biotechnology, Dept of Biotechnology (08/2009 - )
*'''B.S.,''' ''Yonsei Univ'', College of Life Science and Biotechnology, Dept of Biology (03/2004 - 08/2008).

<pre>
*E-mail : kimhanhae@gmail.com
</pre>
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