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Main.HomePage History
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June 06, 2011, at 11:41 PM
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!!Overview
This site provides my review on biological network research and some software that I wrote for network analysis.
!! Software
June 04, 2011, at 11:55 AM
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This project is partially supported by the Spelman College and by the following grants:
* [[http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1022294 | NSF Award #1022294]] RUI: Testing the network hypothesis of Cellular Aging in Saccharomyces Cerevisiae, 2010-2012
* NSF Award #0837075, Computing in Life Sciences Through Hands-on Experience and Case Studies at Tuskegee University, 2009-2010
%width=70px% http://bioinformatics.org/ctls/nsflogo.jpeg %width=80px% %width=40px% http://bioinformatics.org/ctls/spelman.jpg \\
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There are '''{$TotalCount}''' visits since Oct 6, 2008. October 08, 2008, at 04:42 PM
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1)Qin H, Lu HH, Wu WB, Li WH. [[Evolution of the yeast protein interaction network->http://www.pnas.org/cgi/content/full/100/22/12820]].
PNAS, 2003, 100(22):12820-4
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1)Qin H, Lu HH, Wu WB, Li WH. Evolution of the yeast protein interaction network.
PNAS, 2003, 100(22):12820-4 [[http://www.pnas.org/cgi/content/full/100/22/12820| PDF ]]
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3)Qin H, Yang Li, Detection of Changes in Transitive Associations by Shortest-path Analysis of Protein Interaction Networks Integrated with Gene Expression Profiles. BMEI (1) 2008, 418-423. [[http://doi.ieeecomputersociety.org/10.1109/BMEI.2008.157 | PDF ]]
April 09, 2006, at 12:20 AM
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1)Qin H, Lu HH, Wu WB, Li WH. Evolution of the yeast protein interaction network. to:
1)Qin H, Lu HH, Wu WB, Li WH. [[Evolution of the yeast protein interaction network->http://www.pnas.org/cgi/content/full/100/22/12820]]. Changed lines 17-18 from:
[[http://www.pnas.org/cgi/content/full/100/22/12820]]
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March 23, 2006, at 02:38 PM
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February 20, 2006, at 08:18 PM
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This software package contains some C++ and PERL programs that are useful for studying biological networks, especially protein interaction networks.
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This software package contains some C++ and PERL programs that are useful for studying biological networks, especially protein interaction networks and gene coexpression networks.
February 17, 2006, at 10:11 AM
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All programs have been tested in LINUX and [[cygwin]](simulated Linux in Windows) environments.
February 17, 2006, at 10:00 AM
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This program calculate the shortest-path for all pairwise combinations within a input list of proteins. The network is input in pairwise format. This network is unweighted and undirected. The outputs are the shortest-path distance matrix, the number of shortes-path in a distance matrix, and a detail file that contains all the shortest-path between for all the combinations.
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This program calculate the shortest-path for all pairwise combinations within a input list of proteins. The network is input in pairwise format. This network is unweighted and undirected. The outputs are the shortest-path distance matrix, the number of shortes-path in a distance matrix, and a detail file that contains all the shortest-path for all the combinations.
February 16, 2006, at 12:00 PM
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This program generate MS02 network null model.
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This program generate a MS02 network null model.
February 16, 2006, at 11:59 AM
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[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11988575&query_hl=4&itool=pubmed_docsum]] February 16, 2006, at 11:59 AM
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PNAS, 2003, 100(22):12820-4
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PNAS, 2003, 100(22):12820-4
[[http://www.pnas.org/cgi/content/full/100/22/12820]]
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[[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11988575&query_hl=4&itool=pubmed_docsum]] February 16, 2006, at 11:55 AM
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This software package some C++ and PERL programs that are useful for biological network analysis, especially protein interaction networks.
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This software package contains some C++ and PERL programs that are useful for studying biological networks, especially protein interaction networks.
February 16, 2006, at 11:46 AM
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This program calculate the shortest-path for all pairwise combinations within a input list of proteins. The network is input in pairwise format. This network is unweighted and undirectional. The outputs are the shortest-path distance matrix, the number of shortes-path in a distance matrix, and a detail file that contains all the shortest-path between for all the combinations.
to:
This program calculate the shortest-path for all pairwise combinations within a input list of proteins. The network is input in pairwise format. This network is unweighted and undirected. The outputs are the shortest-path distance matrix, the number of shortes-path in a distance matrix, and a detail file that contains all the shortest-path between for all the combinations.
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This program calculate the shortest-path distance for a weighted network. It outputs a distance matrix and the shortest-paths.
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This program calculate the shortest-path distance for a weighted, undirected network. It outputs a distance matrix and the shortest-paths.
February 16, 2006, at 11:45 AM
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This software package some C++ and PERL programs that are useful for biological netwokr analysis, especially protein interaction networks.
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This software package some C++ and PERL programs that are useful for biological network analysis, especially protein interaction networks.
February 16, 2006, at 11:38 AM
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February 16, 2006, at 11:37 AM
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This software package some C++ and PERL programs that are useful for biological netwokr analysis, especially protein interaction networks.
Program 'dk':
This program calculate the shortest-path for all pairwise combinations within a input list of proteins. The network is input in pairwise format. This network is unweighted and undirectional. The outputs are the shortest-path distance matrix, the number of shortes-path in a distance matrix, and a detail file that contains all the shortest-path between for all the combinations.
Program 'wdk':
This program calculate the shortest-path distance for a weighted network. It outputs a distance matrix and the shortest-paths.
Program 'ms02':
This program generate MS02 network null model.
Reference:
1)Qin H, Lu HH, Wu WB, Li WH. Evolution of the yeast protein interaction network.
PNAS, 2003, 100(22):12820-4
2)Maslov S, Sneppen K. Specificity and stability in topology of protein networks.
Science. 2002, 296(5569):910-3.
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