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Overview

This site provides my review on biological network research and some software that I wrote for network analysis.

Software

This software package contains some C++ and PERL programs that are useful for studying biological networks, especially protein interaction networks and gene coexpression 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 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.

Program 'wdk':
This program calculate the shortest-path distance for a weighted, undirected network. It outputs a distance matrix and the shortest-paths.

Program 'ms02':
This program generate a MS02 network null model.

All programs have been tested in LINUX and cygwin(simulated Linux in Windows) environments.

Reference:
1)Qin H, Lu HH, Wu WB, Li WH. Evolution of the yeast protein interaction network. 

  PNAS, 2003, 100(22):12820-4  PDF

2)Maslov S, Sneppen K. Specificity and stability in topology of protein networks. 

  Science. 2002, 296(5569):910-3.

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. PDF

This project is partially supported by the Spelman College and by the following grants:

  • 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


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