Network Biology Lab - User contributions [en]

People:YH Ko

2013-07-24T08:12:52Z

Younko: /* Publications */

{|
|[[File:Younhee ko.jpg|150px]]
|
===Younhee Ko ===
*Postdoctoral researcher, Department of Biotechnology, Yonsei University (10/2011 ~ Present)
*Postdoctoral researcher, Institute for Genomics Biology, University of Illinois at Urbana-Champaign, (01/2011 ~ 08/2011)
*PhD in Computer Science, University of Illinois at Urbana-Champaign, 2010
**Advisor: Prof. ChengXiang Zhai, Department of Computer Science
**Co-Advisor: Prof. Sandra Rodriguez-Zas, Department of Animal Science
**Co-Advisor: Prof. Nathan Price, Department of Chemical and Biomolecular Engineering
*M.S. in CSE, Korea University, 2003
**Advisor: Prof. Hyeoncheol Kim
*B.S. in CSE, Korea University, 2001

|}

==Current Research Interests==
*Systems Biology and computational biology
**Transcriptional Regulation Network, Cell type identification and analysis of network morphology of Human Brain, Immune cell responses from viral infection
*Biological data mining and data integration

==Publications==
Book Chapter
* S. L. Rodriguez-Zas, '''Y. Ko'''. Applied Statistics for Network Biology: Methods in Systems Biology,
Chapter: Elucidation of General and Condition-dependent Gene Pathways Using Mixture Models and
Bayesian Networks. '''''Wiley''''', 91-103, 2011.

Journal Articles
*'''Y. Ko''', S. A. Ament, J. A. Eddy, J. Cabellero, J. C. Earls, L. Hood and N. D. Price. Cell-type specific genes show striking and distinct patterns of spatial expression in the mouse brain. '''''PNAS''''' 110(8):3095-3100, 2013 [http://www.ncbi.nlm.nih.gov/pubmed/23386717 pubmed] [[media:PNAS-2013-Ko-18548-53.pdf|pdf]]
*J. C. Earls, J. A. Eddy, C. Funk, '''Y. Ko''', A. Magis, and N .D. Price, AUREA: An open-source software system for accurate and user-friendly identification of relative expression molecular signatures, ''''' BMC Bioinformatics''''',14:78 , 2013
*A. Magis, J. Earls, '''Y. Ko''', J. Eddy and N. Price. Graphics processing unit implementations of relative expression analysis algorithms enable dramatic computational speedup, '''''Bioinformatics''''', 2011
*'''Y. Ko''', C.Zhai and S. L. Rodriguez-Zas. Discovery of gene network variability across samples representing multiple classes, '''''IJBRA''''', 2010
*'''Y. Ko''', C.Zhai and S. L. Rodriguez-Zas. Inference of gene pathways using mixture Bayesian networks, '''''BMC Systems Biology''''', 3:54, 2009 '''''Marked as highly accessed'''''
*S. L. Rodriguez-Zas, '''Y. Ko''', H. A. Adams and B. R. Southey. Advancing the understanding of the embryo transcriptome co-regulation using meta-, functional, and gene network analysis tools, '''''Reproduction''''',135:213-224, 2008
*'''Y. Ko''', H. Kim and W. Lee. Frequent Itemset Search Using LSI Similarity, '''''Journal of Korean Association of Computer Education''''', 6:2, 2003

Referred Conference Papers
*S. Kim, J. Kim, '''Y. Ko''', S. Hwang and J. Han.PerRank:Personalized Rank Retrieval with Categorical and Numerical Attributes, WAIM, 2008
*'''Y. Ko''', C. Zhai and S. L. Rodriguez-Zas. Inference of Gene Pathways using Gaussian Mixture Models, IEEE BIBM, 2007
*'''Y. Ko''', H. Kim. An effcient algorithm to search frequent itemsets using TID Lists, KISS, 2002
*'''Y. Ko''', H. Kim and W. Lee. Design and Implementation of a XML Editor For DataBases, KISS, 2001

People:YH Ko

2013-05-23T06:59:15Z

Younko: /* Younhee Ko (고윤희) */

{|
|[[File:Younhee ko.jpg|150px]]
|
===Younhee Ko ===
*Postdoctoral researcher, Department of Biotechnology, Yonsei University (10/2011 ~ Present)
*Postdoctoral researcher, Institute for Genomics Biology, University of Illinois at Urbana-Champaign, (01/2011 ~ 08/2011)
*PhD in Computer Science, University of Illinois at Urbana-Champaign, 2010
**Advisor: Prof. ChengXiang Zhai, Department of Computer Science
**Co-Advisor: Prof. Sandra Rodriguez-Zas, Department of Animal Science
**Co-Advisor: Prof. Nathan Price, Department of Chemical and Biomolecular Engineering
*M.S. in CSE, Korea University, 2003
**Advisor: Prof. Hyeoncheol Kim
*B.S. in CSE, Korea University, 2001

|}

==Current Research Interests==
*Systems Biology and computational biology
**Transcriptional Regulation Network, Cell type identification and analysis of network morphology of Human Brain, Immune cell responses from viral infection
*Biological data mining and data integration

==Publications==
Book Chapter
* S. L. Rodriguez-Zas, '''Y. Ko'''. Applied Statistics for Network Biology: Methods in Systems Biology,
Chapter: Elucidation of General and Condition-dependent Gene Pathways Using Mixture Models and
Bayesian Networks. '''''Wiley''''', 91-103, 2011.

Journal Articles
*'''Y. Ko''', S. A. Ament, J. A. Eddy, J. Cabellero, J. C. Earls, L. Hood and N. D. Price. Cell-type specific genes show striking and distinct patterns of spatial expression in the mouse brain. '''''PNAS''''' 110(8):3095-3100, 2013 [http://www.ncbi.nlm.nih.gov/pubmed/23386717 pubmed] [[media:PNAS-2013-Ko-18548-53.pdf|pdf]]
*J. C. Earls, J. A. Eddy, C. Funk, '''Y. Ko''', A. Magis, and N .D. Price, AUREA: An open-source software system for accurate and user-friendly identification of relative expression molecular signatures, ''''' BMC Bioinformatics''''',14:78 , 2013
*A. Magis, J. Earls, '''Y. Ko''', J. Eddy and N. Price. Graphics processing unit implementations of relative expression analysis algorithms enable dramatic computational speedup, '''''Bioinformatics''''', 2011
*'''Y. Ko''', C.Zhai and S. L. Rodriguez-Zas. Discovery of variation in the co-expression patterns of gene pathways across biological replicates, '''''IJBRA''''', 2010
*'''Y. Ko''', C.Zhai and S. L. Rodriguez-Zas. Inference of gene pathways using mixture Bayesian networks, '''''BMC Systems Biology''''', 3:54, 2009 '''''Marked as highly accessed'''''
*S. L. Rodriguez-Zas, '''Y. Ko''', H. A. Adams and B. R. Southey. Advancing the understanding of the embryo transcriptome co-regulation using meta-, functional, and gene network analysis tools, '''''Reproduction''''',135:213-224, 2008
*'''Y. Ko''', H. Kim and W. Lee. Frequent Itemset Search Using LSI Similarity, '''''Journal of Korean Association of Computer Education''''', 6:2, 2003

Referred Conference Papers
*S. Kim, J. Kim, '''Y. Ko''', S. Hwang and J. Han.PerRank:Personalized Rank Retrieval with Categorical and Numerical Attributes, WAIM, 2008
*'''Y. Ko''', C. Zhai and S. L. Rodriguez-Zas. Inference of Gene Pathways using Gaussian Mixture Models, IEEE BIBM, 2007
*'''Y. Ko''', H. Kim. An effcient algorithm to search frequent itemsets using TID Lists, KISS, 2002
*'''Y. Ko''', H. Kim and W. Lee. Design and Implementation of a XML Editor For DataBases, KISS, 2001

People:YH Ko

2013-05-23T06:58:42Z

Younko: /* Younhee Ko */

{|
|[[File:Younhee ko.jpg|150px]]
|
===Younhee Ko (고윤희) ===
*Postdoctoral researcher, Department of Biotechnology, Yonsei University (10/2011 ~ Present)
*Postdoctoral researcher, Institute for Genomics Biology, University of Illinois at Urbana-Champaign, (01/2011 ~ 08/2011)
*PhD in Computer Science, University of Illinois at Urbana-Champaign, 2010
**Advisor: Prof. ChengXiang Zhai, Department of Computer Science
**Co-Advisor: Prof. Sandra Rodriguez-Zas, Department of Animal Science
**Co-Advisor: Prof. Nathan Price, Department of Chemical and Biomolecular Engineering
*M.S. in CSE, Korea University, 2003
**Advisor: Prof. Hyeoncheol Kim
*B.S. in CSE, Korea University, 2001

|}

==Current Research Interests==
*Systems Biology and computational biology
**Transcriptional Regulation Network, Cell type identification and analysis of network morphology of Human Brain, Immune cell responses from viral infection
*Biological data mining and data integration

==Publications==
Book Chapter
* S. L. Rodriguez-Zas, '''Y. Ko'''. Applied Statistics for Network Biology: Methods in Systems Biology,
Chapter: Elucidation of General and Condition-dependent Gene Pathways Using Mixture Models and
Bayesian Networks. '''''Wiley''''', 91-103, 2011.

Journal Articles
*'''Y. Ko''', S. A. Ament, J. A. Eddy, J. Cabellero, J. C. Earls, L. Hood and N. D. Price. Cell-type specific genes show striking and distinct patterns of spatial expression in the mouse brain. '''''PNAS''''' 110(8):3095-3100, 2013 [http://www.ncbi.nlm.nih.gov/pubmed/23386717 pubmed] [[media:PNAS-2013-Ko-18548-53.pdf|pdf]]
*J. C. Earls, J. A. Eddy, C. Funk, '''Y. Ko''', A. Magis, and N .D. Price, AUREA: An open-source software system for accurate and user-friendly identification of relative expression molecular signatures, ''''' BMC Bioinformatics''''',14:78 , 2013
*A. Magis, J. Earls, '''Y. Ko''', J. Eddy and N. Price. Graphics processing unit implementations of relative expression analysis algorithms enable dramatic computational speedup, '''''Bioinformatics''''', 2011
*'''Y. Ko''', C.Zhai and S. L. Rodriguez-Zas. Discovery of variation in the co-expression patterns of gene pathways across biological replicates, '''''IJBRA''''', 2010
*'''Y. Ko''', C.Zhai and S. L. Rodriguez-Zas. Inference of gene pathways using mixture Bayesian networks, '''''BMC Systems Biology''''', 3:54, 2009 '''''Marked as highly accessed'''''
*S. L. Rodriguez-Zas, '''Y. Ko''', H. A. Adams and B. R. Southey. Advancing the understanding of the embryo transcriptome co-regulation using meta-, functional, and gene network analysis tools, '''''Reproduction''''',135:213-224, 2008
*'''Y. Ko''', H. Kim and W. Lee. Frequent Itemset Search Using LSI Similarity, '''''Journal of Korean Association of Computer Education''''', 6:2, 2003

Referred Conference Papers
*S. Kim, J. Kim, '''Y. Ko''', S. Hwang and J. Han.PerRank:Personalized Rank Retrieval with Categorical and Numerical Attributes, WAIM, 2008
*'''Y. Ko''', C. Zhai and S. L. Rodriguez-Zas. Inference of Gene Pathways using Gaussian Mixture Models, IEEE BIBM, 2007
*'''Y. Ko''', H. Kim. An effcient algorithm to search frequent itemsets using TID Lists, KISS, 2002
*'''Y. Ko''', H. Kim and W. Lee. Design and Implementation of a XML Editor For DataBases, KISS, 2001

People:YH Ko

2013-03-07T01:36:10Z

Younko: /* Publications */

{|
|[[File:Younhee ko.jpg|150px]]
|
===Younhee Ko===
*Postdoctoral researcher, Department of Biotechnology, Yonsei University (10/2011 ~ Present)
*Postdoctoral researcher, Institute for Genomics Biology, University of Illinois at Urbana-Champaign, (01/2011 ~ 08/2011)
*PhD in Computer Science, University of Illinois at Urbana-Champaign, 2010
**Advisor: Prof. ChengXiang Zhai, Department of Computer Science
**Co-Advisor: Prof. Sandra Rodriguez-Zas, Department of Animal Science
**Co-Advisor: Prof. Nathan Price, Department of Chemical and Biomolecular Engineering
*M.S. in CSE, Korea University, 2003
**Advisor: Prof. Hyeoncheol Kim
*B.S. in CSE, Korea University, 2001

|}

==Current Research Interests==
*Systems Biology and computational biology
**Transcriptional Regulation Network, Cell type identification and analysis of network morphology of Human Brain, Immune cell responses from viral infection
*Biological data mining and data integration

==Publications==
Book Chapter
* S. L. Rodriguez-Zas, '''Y. Ko'''. Applied Statistics for Network Biology: Methods in Systems Biology,
Chapter: Elucidation of General and Condition-dependent Gene Pathways Using Mixture Models and
Bayesian Networks. '''''Wiley''''', 91-103, 2011.

Journal Articles
*'''Y. Ko''', S. A. Ament, J. A. Eddy, J. Cabellero, J. C. Earls, L. Hood and N. D. Price. Cell-type specific genes show striking and distinct patterns of spatial expression in the mouse brain. '''''PNAS''''' 110(8):3095-3100, 2013 [http://www.ncbi.nlm.nih.gov/pubmed/23386717 pubmed] [[media:PNAS-2013-Ko-18548-53.pdf|pdf]]
*J. C. Earls, J. A. Eddy, C. Funk, '''Y. Ko''', A. Magis, and N .D. Price, AUREA: An open-source software system for accurate and user-friendly identification of relative expression molecular signatures, ''''' BMC Bioinformatics''''',14:78 , 2013
*A. Magis, J. Earls, '''Y. Ko''', J. Eddy and N. Price. Graphics processing unit implementations of relative expression analysis algorithms enable dramatic computational speedup, '''''Bioinformatics''''', 2011
*'''Y. Ko''', C.Zhai and S. L. Rodriguez-Zas. Discovery of variation in the co-expression patterns of gene pathways across biological replicates, '''''IJBRA''''', 2010
*'''Y. Ko''', C.Zhai and S. L. Rodriguez-Zas. Inference of gene pathways using mixture Bayesian networks, '''''BMC Systems Biology''''', 3:54, 2009 '''''Marked as highly accessed'''''
*S. L. Rodriguez-Zas, '''Y. Ko''', H. A. Adams and B. R. Southey. Advancing the understanding of the embryo transcriptome co-regulation using meta-, functional, and gene network analysis tools, '''''Reproduction''''',135:213-224, 2008
*'''Y. Ko''', H. Kim and W. Lee. Frequent Itemset Search Using LSI Similarity, '''''Journal of Korean Association of Computer Education''''', 6:2, 2003

Referred Conference Papers
*S. Kim, J. Kim, '''Y. Ko''', S. Hwang and J. Han.PerRank:Personalized Rank Retrieval with Categorical and Numerical Attributes, WAIM, 2008
*'''Y. Ko''', C. Zhai and S. L. Rodriguez-Zas. Inference of Gene Pathways using Gaussian Mixture Models, IEEE BIBM, 2007
*'''Y. Ko''', H. Kim. An effcient algorithm to search frequent itemsets using TID Lists, KISS, 2002
*'''Y. Ko''', H. Kim and W. Lee. Design and Implementation of a XML Editor For DataBases, KISS, 2001

People:YH Ko

2013-03-07T01:35:31Z

Younko: /* Publications */

{|
|[[File:Younhee ko.jpg|150px]]
|
===Younhee Ko===
*Postdoctoral researcher, Department of Biotechnology, Yonsei University (10/2011 ~ Present)
*Postdoctoral researcher, Institute for Genomics Biology, University of Illinois at Urbana-Champaign, (01/2011 ~ 08/2011)
*PhD in Computer Science, University of Illinois at Urbana-Champaign, 2010
**Advisor: Prof. ChengXiang Zhai, Department of Computer Science
**Co-Advisor: Prof. Sandra Rodriguez-Zas, Department of Animal Science
**Co-Advisor: Prof. Nathan Price, Department of Chemical and Biomolecular Engineering
*M.S. in CSE, Korea University, 2003
**Advisor: Prof. Hyeoncheol Kim
*B.S. in CSE, Korea University, 2001

|}

==Current Research Interests==
*Systems Biology and computational biology
**Transcriptional Regulation Network, Cell type identification and analysis of network morphology of Human Brain, Immune cell responses from viral infection
*Biological data mining and data integration

==Publications==
Book Chapter
* S. L. Rodriguez-Zas, '''Y. Ko'''. Applied Statistics for Network Biology: Methods in Systems Biology,
Chapter: Elucidation of General and Condition-dependent Gene Pathways Using Mixture Models and
Bayesian Networks. '''''Wiley''''', 91-103, 2011.

Journal Articles
*'''Y. Ko''', S. A. Ament, J. A. Eddy, J. Cabellero, J. C. Earls, L. Hood and N. D. Price. Cell-type specific genes show striking and distinct patterns of spatial expression in the mouse brain. '''''PNAS''''' 110(8):3095-3100 (2013) [http://www.ncbi.nlm.nih.gov/pubmed/23386717 pubmed] [[media:PNAS-2013-Ko-18548-53.pdf|pdf]]
*J. C. Earls, J. A. Eddy, C. Funk, '''Y. Ko''', A. Magis, and N .D. Price, AUREA: An open-source software system for accurate and user-friendly identification of relative expression molecular signatures, ''''' BMC Bioinformatics''''',14:78 ,2013
*A. Magis, J. Earls, '''Y. Ko''', J. Eddy and N. Price. Graphics processing unit implementations of relative expression analysis algorithms enable dramatic computational speedup, '''''Bioinformatics''''', 2011
*'''Y. Ko''', C.Zhai and S. L. Rodriguez-Zas. Discovery of variation in the co-expression patterns of gene pathways across biological replicates, '''''IJBRA''''', 2010
*'''Y. Ko''', C.Zhai and S. L. Rodriguez-Zas. Inference of gene pathways using mixture Bayesian networks, '''''BMC Systems Biology''''', 3:54, 2009 '''''Marked as highly accessed'''''
*S. L. Rodriguez-Zas, '''Y. Ko''', H. A. Adams and B. R. Southey. Advancing the understanding of the embryo transcriptome co-regulation using meta-, functional, and gene network analysis tools, '''''Reproduction''''',135:213-224, 2008
*'''Y. Ko''', H. Kim and W. Lee. Frequent Itemset Search Using LSI Similarity, '''''Journal of Korean Association of Computer Education''''', 6:2, 2003

Referred Conference Papers
*S. Kim, J. Kim, '''Y. Ko''', S. Hwang and J. Han.PerRank:Personalized Rank Retrieval with Categorical and Numerical Attributes, WAIM, 2008
*'''Y. Ko''', C. Zhai and S. L. Rodriguez-Zas. Inference of Gene Pathways using Gaussian Mixture Models, IEEE BIBM, 2007
*'''Y. Ko''', H. Kim. An effcient algorithm to search frequent itemsets using TID Lists, KISS, 2002
*'''Y. Ko''', H. Kim and W. Lee. Design and Implementation of a XML Editor For DataBases, KISS, 2001

People:YH Ko

2013-03-06T00:57:02Z

Younko:

{|
|[[File:Younhee ko.jpg|150px]]
|
===Younhee Ko===
*Postdoctoral researcher, Department of Biotechnology, Yonsei University (10/2011 ~ Present)
*Postdoctoral researcher, Institute for Genomics Biology, University of Illinois at Urbana-Champaign, (01/2011 ~ 08/2011)
*PhD in Computer Science, University of Illinois at Urbana-Champaign, 2010
**Advisor: Prof. ChengXiang Zhai, Department of Computer Science
**Co-Advisor: Prof. Sandra Rodriguez-Zas, Department of Animal Science
**Co-Advisor: Prof. Nathan Price, Department of Chemical and Biomolecular Engineering
*M.S. in CSE, Korea University, 2003
**Advisor: Prof. Hyeoncheol Kim
*B.S. in CSE, Korea University, 2001

|}

==Current Research Interests==
*Systems Biology and computational biology
**Transcriptional Regulation Network, Cell type identification and analysis of network morphology of Human Brain, Immune cell responses from viral infection
*Biological data mining and data integration

==Publications==
Book Chapter
* S. L. Rodriguez-Zas, '''Y. Ko'''. Applied Statistics for Network Biology: Methods in Systems Biology,
Chapter: Elucidation of General and Condition-dependent Gene Pathways Using Mixture Models and
Bayesian Networks. '''''Wiley''''', 91-103, 2011.

Journal Articles
*'''Y. Ko''', S. A. Ament, J. A. Eddy, J. Cabellero, J. C. Earls, L. Hood and N. D. Price. Cell-type specific genes show striking and distinct patterns of spatial expression in the mouse brain. '''''PNAS''''' 110(8):3095-3100 (2013) [http://www.ncbi.nlm.nih.gov/pubmed/23386717 pubmed] [[media:PNAS-2013-Ko-18548-53.pdf|pdf]]
*J. C. Earls, J. A. Eddy, C. Funk, '''Y. Ko''', A. Magis, and N .D. Price, AUREA: An open-source software system for accurate and user-friendly identification of relative expression molecular signatures, (Accepted to '''''BMC Bioinformatics''''', 2013)
*A. Magis, J. Earls, '''Y. Ko''', J. Eddy and N. Price. Graphics processing unit implementations of relative expression analysis algorithms enable dramatic computational speedup, '''''Bioinformatics''''', 2011
*'''Y. Ko''', C.Zhai and S. L. Rodriguez-Zas. Discovery of variation in the co-expression patterns of gene pathways across biological replicates, '''''IJBRA''''', 2010
*'''Y. Ko''', C.Zhai and S. L. Rodriguez-Zas. Inference of gene pathways using mixture Bayesian networks, '''''BMC Systems Biology''''', 3:54, 2009 '''''Marked as highly accessed'''''
*S. L. Rodriguez-Zas, '''Y. Ko''', H. A. Adams and B. R. Southey. Advancing the understanding of the embryo transcriptome co-regulation using meta-, functional, and gene network analysis tools, '''''Reproduction''''',135:213-224, 2008
*'''Y. Ko''', H. Kim and W. Lee. Frequent Itemset Search Using LSI Similarity, '''''Journal of Korean Association of Computer Education''''', 6:2, 2003

Referred Conference Papers
*S. Kim, J. Kim, '''Y. Ko''', S. Hwang and J. Han.PerRank:Personalized Rank Retrieval with Categorical and Numerical Attributes, WAIM, 2008
*'''Y. Ko''', C. Zhai and S. L. Rodriguez-Zas. Inference of Gene Pathways using Gaussian Mixture Models, IEEE BIBM, 2007
*'''Y. Ko''', H. Kim. An effcient algorithm to search frequent itemsets using TID Lists, KISS, 2002
*'''Y. Ko''', H. Kim and W. Lee. Design and Implementation of a XML Editor For DataBases, KISS, 2001

People:YH Ko

2013-03-05T08:09:03Z

Younko: /* Publications */

{|
|[[File:Younhee ko.jpg|150px]]
|
===Younhee Ko===
*Postdoctoral researcher, Department of Biotechnology, Yonsei University (10/2011 ~ Present)
*Postdoctoral researcher, Institute for Genomics Biology, University of Illinois at Urbana-Champaign, (01/2011 ~ 08/2011)
*PhD in Computer Science, University of Illinois at Urbana-Champaign, 2010
**Advisor: Prof. ChengXiang Zhai, Department of Computer Science
**Co-Advisor: Prof. Sandra Rodriguez-Zas, Department of Animal Science
**Co-Advisor: Prof. Nathan Price, Department of Chemical and Biomolecular Engineering
*M.S. in CSE, Korea University, 2003
**Advisor: Prof. Hyeoncheol Kim
*B.S. in CSE, Korea University, 2001

|}

==Current Research Interests==
*Systems Biology and computational biology
**Transcriptional Regulation Network, Cell type identification and analysis of network morphology of Human Brain, Immune cell responses from viral infection
*Biological data mining and data integration

==Publications==
Book Chapter
* S. L. Rodriguez-Zas, '''Y. Ko'''. Applied Statistics for Network Biology: Methods in Systems Biology,
Chapter: Elucidation of General and Condition-dependent Gene Pathways Using Mixture Models and
Bayesian Networks. Wiley, 91-103, 2011.

Journal Articles
*'''Y. Ko''', S. A. Ament, J. A. Eddy, J. Cabellero, J. C. Earls, L. Hood and N. D. Price. Cell-type specific genes show striking and distinct patterns of spatial expression in the mouse brain. '''''PNAS''''' 110(8):3095-3100 (2013) [http://www.ncbi.nlm.nih.gov/pubmed/23386717 pubmed] [[media:PNAS-2013-Ko-18548-53.pdf|pdf]]
*J. C. Earls, J. A. Eddy, C. Funk, '''Y. Ko''', A. Magis, and N .D. Price, AUREA: An open-source software system for accurate and user-friendly identification of relative expression molecular signatures, (Accepted to BMC Bioinformatics, 2013)
*A. Magis, J. Earls, '''Y. Ko''', J. Eddy and N. Price. Graphics processing unit implementations of relative expression analysis algorithms enable dramatic computational speedup, Bioinformatics, 2011
*'''Y. Ko''', C.Zhai and S. L. Rodriguez-Zas. Discovery of variation in the co-expression patterns of gene pathways across biological replicates, IJBRA, 2010
*'''Y. Ko''', C.Zhai and S. L. Rodriguez-Zas. Inference of gene pathways using mixture Bayesian networks, BMC Systems Biology, 3:54, 2009 Marked as highly accessed
*S. L. Rodriguez-Zas, '''Y. Ko''', H. A. Adams and B. R. Southey. Advancing the understanding of the embryo transcriptome co-regulation using meta-, functional, and gene network analysis tools, Reproduction,135:213-224, 2008
*'''Y. Ko''', H. Kim and W. Lee. Frequent Itemset Search Using LSI Similarity, Journal of Korean Association of Computer Education, 6:2, 2003

Referred Conference Papers
*S. Kim, J. Kim, '''Y. Ko''', S. Hwang and J. Han.PerRank:Personalized Rank Retrieval with Categorical and Numerical Attributes, WAIM, 2008
*'''Y. Ko''', C. Zhai and S. L. Rodriguez-Zas. Inference of Gene Pathways using Gaussian Mixture Models, IEEE BIBM, 2007
*'''Y. Ko''', H. Kim. An effcient algorithm to search frequent itemsets using TID Lists, KISS, 2002
*'''Y. Ko''', H. Kim and W. Lee. Design and Implementation of a XML Editor For DataBases, KISS, 2001

People:YH Ko

2013-03-05T08:07:25Z

Younko: /* Publications */

{|
|[[File:Younhee ko.jpg|150px]]
|
===Younhee Ko===
*Postdoctoral researcher, Department of Biotechnology, Yonsei University (10/2011 ~ Present)
*Postdoctoral researcher, Institute for Genomics Biology, University of Illinois at Urbana-Champaign, (01/2011 ~ 08/2011)
*PhD in Computer Science, University of Illinois at Urbana-Champaign, 2010
**Advisor: Prof. ChengXiang Zhai, Department of Computer Science
**Co-Advisor: Prof. Sandra Rodriguez-Zas, Department of Animal Science
**Co-Advisor: Prof. Nathan Price, Department of Chemical and Biomolecular Engineering
*M.S. in CSE, Korea University, 2003
**Advisor: Prof. Hyeoncheol Kim
*B.S. in CSE, Korea University, 2001

|}

==Current Research Interests==
*Systems Biology and computational biology
**Transcriptional Regulation Network, Cell type identification and analysis of network morphology of Human Brain, Immune cell responses from viral infection
*Biological data mining and data integration

==Publications==
Book Chapter
* S. L. Rodriguez-Zas, '''Y. Ko'''. Applied Statistics for Network Biology: Methods in Systems Biology,
Chapter: Elucidation of General and Condition-dependent Gene Pathways Using Mixture Models and
Bayesian Networks. Wiley, 91-103, 2011.

Journal Articles
*'''Y. Ko''', S. A. Ament, J. A. Eddy, J. Cabellero, J. C. Earls, L. Hood and N. D. Price. Cell-type specific genes show striking and distinct patterns of spatial expression in the mouse brain. '''''PNAS''''' 110(8):3095-3100 (2013)
[http://www.ncbi.nlm.nih.gov/pubmed/23386717 pubmed] [[media:PNAS-2013-Ko-18548-53.pdf|pdf]]
*J. C. Earls, J. A. Eddy, C. Funk, '''Y. Ko''', A. Magis, and N .D. Price, AUREA: An open-source software system for accurate and user-friendly identification of relative expression molecular signatures, (Accepted to BMC Bioinformatics, 2013)
*A. Magis, J. Earls, '''Y. Ko''', J. Eddy and N. Price. Graphics processing unit implementations of relative expression analysis algorithms enable dramatic computational speedup, Bioinformatics, 2011
*'''Y. Ko''', C.Zhai and S. L. Rodriguez-Zas. Discovery of variation in the co-expression patterns of gene pathways across biological replicates, IJBRA, 2010
*'''Y. Ko''', C.Zhai and S. L. Rodriguez-Zas. Inference of gene pathways using mixture Bayesian networks, BMC Systems Biology, 3:54, 2009 Marked as highly accessed
*S. L. Rodriguez-Zas, '''Y. Ko''', H. A. Adams and B. R. Southey. Advancing the understanding of the embryo transcriptome co-regulation using meta-, functional, and gene network analysis tools, Reproduction,135:213-224, 2008
*'''Y. Ko''', H. Kim and W. Lee. Frequent Itemset Search Using LSI Similarity, Journal of Korean Association of Computer Education, 6:2, 2003

Referred Conference Papers
*S. Kim, J. Kim, '''Y. Ko''', S. Hwang and J. Han.PerRank:Personalized Rank Retrieval with Categorical and Numerical Attributes, WAIM, 2008
*'''Y. Ko''', C. Zhai and S. L. Rodriguez-Zas. Inference of Gene Pathways using Gaussian Mixture Models, IEEE BIBM, 2007
*'''Y. Ko''', H. Kim. An effcient algorithm to search frequent itemsets using TID Lists, KISS, 2002
*'''Y. Ko''', H. Kim and W. Lee. Design and Implementation of a XML Editor For DataBases, KISS, 2001

People:YH Ko

2013-03-05T08:06:49Z

Younko: /* Publications */

{|
|[[File:Younhee ko.jpg|150px]]
|
===Younhee Ko===
*Postdoctoral researcher, Department of Biotechnology, Yonsei University (10/2011 ~ Present)
*Postdoctoral researcher, Institute for Genomics Biology, University of Illinois at Urbana-Champaign, (01/2011 ~ 08/2011)
*PhD in Computer Science, University of Illinois at Urbana-Champaign, 2010
**Advisor: Prof. ChengXiang Zhai, Department of Computer Science
**Co-Advisor: Prof. Sandra Rodriguez-Zas, Department of Animal Science
**Co-Advisor: Prof. Nathan Price, Department of Chemical and Biomolecular Engineering
*M.S. in CSE, Korea University, 2003
**Advisor: Prof. Hyeoncheol Kim
*B.S. in CSE, Korea University, 2001

|}

==Current Research Interests==
*Systems Biology and computational biology
**Transcriptional Regulation Network, Cell type identification and analysis of network morphology of Human Brain, Immune cell responses from viral infection
*Biological data mining and data integration

==Publications==
Book Chapter
* S. L. Rodriguez-Zas, '''Y. Ko'''. Applied Statistics for Network Biology: Methods in Systems Biology,
Chapter: Elucidation of General and Condition-dependent Gene Pathways Using Mixture Models and
Bayesian Networks. Wiley, 91-103, 2011.

Journal Articles
*'''Y. Ko''', S. A. Ament, J. A. Eddy, J. Cabellero, J. C. Earls, L. Hood and N. D. Price. Cell-type specific genes show striking and distinct patterns of spatial expression in the mouse brain. '''''PNAS''''' 110(8):3095-3100 (2013)

*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/23386717 pubmed] [[media:PNAS-2013-Ko-18548-53.pdf|pdf]]

*J. C. Earls, J. A. Eddy, C. Funk, '''Y. Ko''', A. Magis, and N .D. Price, AUREA: An open-source software system for accurate and user-friendly identification of relative expression molecular signatures, (Accepted to BMC Bioinformatics, 2013)
*A. Magis, J. Earls, '''Y. Ko''', J. Eddy and N. Price. Graphics processing unit implementations of relative expression analysis algorithms enable dramatic computational speedup, Bioinformatics, 2011
*'''Y. Ko''', C.Zhai and S. L. Rodriguez-Zas. Discovery of variation in the co-expression patterns of gene pathways across biological replicates, IJBRA, 2010
*'''Y. Ko''', C.Zhai and S. L. Rodriguez-Zas. Inference of gene pathways using mixture Bayesian networks, BMC Systems Biology, 3:54, 2009 Marked as highly accessed
*S. L. Rodriguez-Zas, '''Y. Ko''', H. A. Adams and B. R. Southey. Advancing the understanding of the embryo transcriptome co-regulation using meta-, functional, and gene network analysis tools, Reproduction,135:213-224, 2008
*'''Y. Ko''', H. Kim and W. Lee. Frequent Itemset Search Using LSI Similarity, Journal of Korean Association of Computer Education, 6:2, 2003

Referred Conference Papers
*S. Kim, J. Kim, '''Y. Ko''', S. Hwang and J. Han.PerRank:Personalized Rank Retrieval with Categorical and Numerical Attributes, WAIM, 2008
*'''Y. Ko''', C. Zhai and S. L. Rodriguez-Zas. Inference of Gene Pathways using Gaussian Mixture Models, IEEE BIBM, 2007
*'''Y. Ko''', H. Kim. An effcient algorithm to search frequent itemsets using TID Lists, KISS, 2002
*'''Y. Ko''', H. Kim and W. Lee. Design and Implementation of a XML Editor For DataBases, KISS, 2001

People:YH Ko

2013-03-05T08:03:05Z

Younko:

{|
|[[File:Younhee ko.jpg|150px]]
|
===Younhee Ko===
*Postdoctoral researcher, Department of Biotechnology, Yonsei University (10/2011 ~ Present)
*Postdoctoral researcher, Institute for Genomics Biology, University of Illinois at Urbana-Champaign, (01/2011 ~ 08/2011)
*PhD in Computer Science, University of Illinois at Urbana-Champaign, 2010
**Advisor: Prof. ChengXiang Zhai, Department of Computer Science
**Co-Advisor: Prof. Sandra Rodriguez-Zas, Department of Animal Science
**Co-Advisor: Prof. Nathan Price, Department of Chemical and Biomolecular Engineering
*M.S. in CSE, Korea University, 2003
**Advisor: Prof. Hyeoncheol Kim
*B.S. in CSE, Korea University, 2001

|}

==Current Research Interests==
*Systems Biology and computational biology
**Transcriptional Regulation Network, Cell type identification and analysis of network morphology of Human Brain, Immune cell responses from viral infection
*Biological data mining and data integration

==Publications==
Book Chapter
* S. L. Rodriguez-Zas, '''Y. Ko'''. Applied Statistics for Network Biology: Methods in Systems Biology,
Chapter: Elucidation of General and Condition-dependent Gene Pathways Using Mixture Models and
Bayesian Networks. Wiley, 91-103, 2011.

Journal Articles
*'''Y. Ko''', S. A. Ament, J. A. Eddy, J. Cabellero, J. C. Earls, L. Hood and N. D. Price. Cell-type specific genes show striking and distinct patterns of spatial expression in the mouse brain. '''''PNAS''''' 110(8):3095-3100 (2013)
*J. C. Earls, J. A. Eddy, C. Funk, '''Y. Ko''', A. Magis, and N .D. Price, AUREA: An open-source software system for accurate and user-friendly identification of relative expression molecular signatures, (Accepted to BMC Bioinformatics, 2013)
*A. Magis, J. Earls, '''Y. Ko''', J. Eddy and N. Price. Graphics processing unit implementations of relative expression analysis algorithms enable dramatic computational speedup, Bioinformatics, 2011
*'''Y. Ko''', C.Zhai and S. L. Rodriguez-Zas. Discovery of variation in the co-expression patterns of gene pathways across biological replicates, IJBRA, 2010
*'''Y. Ko''', C.Zhai and S. L. Rodriguez-Zas. Inference of gene pathways using mixture Bayesian networks, BMC Systems Biology, 3:54, 2009 Marked as highly accessed
*S. L. Rodriguez-Zas, '''Y. Ko''', H. A. Adams and B. R. Southey. Advancing the understanding of the embryo transcriptome co-regulation using meta-, functional, and gene network analysis tools, Reproduction,135:213-224, 2008
*'''Y. Ko''', H. Kim and W. Lee. Frequent Itemset Search Using LSI Similarity, Journal of Korean Association of Computer Education, 6:2, 2003

Referred Conference Papers
*S. Kim, J. Kim, '''Y. Ko''', S. Hwang and J. Han.PerRank:Personalized Rank Retrieval with Categorical and Numerical Attributes, WAIM, 2008
*'''Y. Ko''', C. Zhai and S. L. Rodriguez-Zas. Inference of Gene Pathways using Gaussian Mixture Models, IEEE BIBM, 2007
*'''Y. Ko''', H. Kim. An effcient algorithm to search frequent itemsets using TID Lists, KISS, 2002
*'''Y. Ko''', H. Kim and W. Lee. Design and Implementation of a XML Editor For DataBases, KISS, 2001

People:YH Ko

2013-02-11T10:21:42Z

Younko: /* Publications */

{|
|[[File:Younhee ko.jpg|150px]]
|
===Younhee Ko===
*Postdoctoral researcher, Department of Biotechnology, Yonsei University (10/2011 ~ Present)
*Postdoctoral researcher, Institute for Genomics Biology, University of Illinois at Urbana-Champaign, (01/2011 ~ 08/2011)
*PhD in Computer Science, University of Illinois at Urbana-Champaign, 2010
**Advisor: Prof. ChengXiang Zhai, Department of Computer Science
**Co-Advisor: Prof. Sandra Rodriguez-Zas, Department of Animal Science
**Co-Advisor: Prof. Nathan Price, Department of Chemical and Biomolecular Engineering
*M.S. in CSE, Korea University, 2003
**Advisor: Prof. Hyeoncheol Kim
*B.S. in CSE, Korea University, 2001

|}

==Current Research Interests==
*Systems Biology and computational biology
**Transcriptional Regulation Network, Cell type identification and analysis of network morphology of Human Brain, Immune cell responses from viral infection
*Biological data mining and data integration

==Publications==
Book Chapter
* S. L. Rodriguez-Zas, '''Y. Ko'''. Applied Statistics for Network Biology: Methods in Systems Biology,
Chapter: Elucidation of General and Condition-dependent Gene Pathways Using Mixture Models and
Bayesian Networks. Wiley, 91-103, 2011.

Journal Articles
*'''Y. Ko''', S. A. Ament, J. A. Eddy, J. Cabellero, J. C. Earls, L. Hood and N. D. Price. Cell-type specific genes show striking and distinct patterns of spatial expression in the mouse brain. PNAS 2013 ; published ahead of print February 5, 2013, doi:10.1073/pnas.1222897110
*J. C. Earls, J. A. Eddy, C. Funk, '''Y. Ko''', A. Magis, and N .D. Price, AUREA: An open-source software system for accurate and user-friendly identification of relative expression molecular signatures, (Accepted to BMC Bioinformatics, 2013)
*A. Magis, J. Earls, '''Y. Ko''', J. Eddy and N. Price. Graphics processing unit implementations of relative expression analysis algorithms enable dramatic computational speedup, Bioinformatics, 2011
*'''Y. Ko''', C.Zhai and S. L. Rodriguez-Zas. Discovery of variation in the co-expression patterns of gene pathways across biological replicates, IJBRA, 2010
*'''Y. Ko''', C.Zhai and S. L. Rodriguez-Zas. Inference of gene pathways using mixture Bayesian networks, BMC Systems Biology, 3:54, 2009 Marked as highly accessed
*S. L. Rodriguez-Zas, '''Y. Ko''', H. A. Adams and B. R. Southey. Advancing the understanding of the embryo transcriptome co-regulation using meta-, functional, and gene network analysis tools, Reproduction,135:213-224, 2008
*'''Y. Ko''', H. Kim and W. Lee. Frequent Itemset Search Using LSI Similarity, Journal of Korean Association of Computer Education, 6:2, 2003

Referred Conference Papers
*S. Kim, J. Kim, '''Y. Ko''', S. Hwang and J. Han.PerRank:Personalized Rank Retrieval with Categorical and Numerical Attributes, WAIM, 2008
*'''Y. Ko''', C. Zhai and S. L. Rodriguez-Zas. Inference of Gene Pathways using Gaussian Mixture Models, IEEE BIBM, 2007
*'''Y. Ko''', H. Kim. An effcient algorithm to search frequent itemsets using TID Lists, KISS, 2002
*'''Y. Ko''', H. Kim and W. Lee. Design and Implementation of a XML Editor For DataBases, KISS, 2001

People:YH Ko

2013-02-11T10:21:25Z

Younko: /* Publications */

{|
|[[File:Younhee ko.jpg|150px]]
|
===Younhee Ko===
*Postdoctoral researcher, Department of Biotechnology, Yonsei University (10/2011 ~ Present)
*Postdoctoral researcher, Institute for Genomics Biology, University of Illinois at Urbana-Champaign, (01/2011 ~ 08/2011)
*PhD in Computer Science, University of Illinois at Urbana-Champaign, 2010
**Advisor: Prof. ChengXiang Zhai, Department of Computer Science
**Co-Advisor: Prof. Sandra Rodriguez-Zas, Department of Animal Science
**Co-Advisor: Prof. Nathan Price, Department of Chemical and Biomolecular Engineering
*M.S. in CSE, Korea University, 2003
**Advisor: Prof. Hyeoncheol Kim
*B.S. in CSE, Korea University, 2001

|}

==Current Research Interests==
*Systems Biology and computational biology
**Transcriptional Regulation Network, Cell type identification and analysis of network morphology of Human Brain, Immune cell responses from viral infection
*Biological data mining and data integration

==Publications==
Book Chapter
* S. L. Rodriguez-Zas, '''Y. Ko'''. Applied Statistics for Network Biology: Methods in Systems Biology,
Chapter: Elucidation of General and Condition-dependent Gene Pathways Using Mixture Models and
Bayesian Networks. Wiley, 91-103, 2011.

Journal Articles
*'''Y. Ko''', S. A. Ament, J. A. Eddy, J. Cabellero, J. C. Earls, L. Hood and N. D. Price. Cell-type specific genes show striking and distinct patterns of spatial expression in the mouse brain. PNAS 2013 ; published ahead of print February 5, 2013, doi:10.1073/pnas.1222897110
*J. C. Earls, J. A. Eddy, C. Funk, '''Y. Ko''', A. Magis, and N .D. Price, AUREA: An open-source software system for accurate and user-friendly identification of relative expression molecular signatures, (Accepted to BMC Bioinformatics, 2013)
*A. Magis, J. Earls, '''Y. Ko''', J. Eddy and N. Price. Graphics processing unit implementations of relative expression analysis algorithms enable dramatic computational speedup, Bioinformatics, 2011
*'''Y. Ko''', C.Zhai and S. L. Rodriguez-Zas. Discovery of variation in the co-expression patterns of gene pathways across biological replicates, IJBRA, 2010
*'''Y. Ko''', C.Zhai and S. L. Rodriguez-Zas. Inference of gene pathways using mixture Bayesian networks, BMC Systems Biology, 3:54, 2009 Marked as highly accessed
*S. L. Rodriguez-Zas, '''Y. Ko''', H. A. Adams and B. R. Southey. Advancing the understanding of the embryo transcriptome co-regulation using meta-, functional, and gene network analysis tools, Reproduction,135:213-224, 2008
*'''Y. Ko''', H. Kim and W. Lee. Frequent Itemset Search Using LSI Similarity, Journal of Korean Association of Computer Education, 6:2, 2003

Referred Conference Papers
*S. Kim, J. Kim, '''Y. Ko''', S. Hwang and J. Han.PerRank:Personalized Rank Retrieval with Categorical and Numerical Attributes, WAIM, 2008
*'''Y. Ko''', C. Zhai and S. L. Rodriguez-Zas. Inference of Gene Pathways using Gaussian Mixture Models, IEEE BIBM, 2007
*'''Y. Ko''', H. Kim. An effcient algorithm to search frequent itemsets using TID Lists, KISS, 2002
*'''Y. Ko''', H. Kim and W. Lee. Design and Implementation of a XML Editor For DataBases, KISS, 2001