Main»Home Page

Home Page


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


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.

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

There are {$TotalCount} visits since Oct 6, 2008.