Gabriel F. Berriz, John E. Beaver, Can Cenik, Murat Tasan, and Frederick P. Roth. Next generation software for functional trend analysis. Bioinformatics, 25(22):3043–3044, November 2009.

Fan Chung. The heat kernel as the pagerank of a graph. Proceedings of the National Academy of Sciences, 104(50):19735–19740, December 2007.

U. Karaoz, T. M. Murali, S. Letovsky, Y. Zheng, C. Ding, C. R. Cantor, and S. Kasif. Whole-genome annotation by using evidence integration in functional-linkage networks.. Proc Natl Acad Sci U S A, 101(9):2888–2893, March 2004.

S.Y. Kim and D.J. Volsky. PAGE: parametric analysis of gene set enrichment. BMC Bioinformatics, 6:144, 2005.

K. Komurov, M. A. White, and P. T. Ram. Use of data-biased random walks on graphs for the retrieval of context-specific networks from genomic data. PLoS Comput Biol, 6(8), 2010.

Yong Lu, Roni Rosenfeld, Itamar Simon, Gerard J. Nau, and Ziv Bar-Joseph. A probabilistic generative model for GO enrichment analysis. Nucl. Acids Res., 36(17):e109+, October 2008.

S. Mostafavi, D. Ray, D. Warde-Farley, C. Grouios, and Q. Morris. GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function. Genome Biol, 9 Suppl 1:S4, 2008.

T M. Murali and Simon Kasif. Extracting conserved gene expression motifs from gene expression data. In Proceedings of the Pacific Symposium on Biocomputing, pages 77–88, 2003.

T. M. Murali, Chang-Jiun Wu, and Simon Kasif. The art of gene function prediction. Nature Biotechnology, 24(12):1474–1475, December 2006.

T. M. Murali, Matthew D. Dyer, David Badger, Brett M. Tyler, and Michael G. Katze. Network-Based prediction and analysis of HIV dependency factors. PLoS Comput Biol, 7(9):e1002164+, September 2011.

E. Nabieva, K. Jim, A. Agarwal, B. Chazelle, and M. Singh. Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps. Bioinformatics, 21 Suppl 1:i302–i310, June 2005.

Daniela Nitsch, Joana Goncalves, Fabian Ojeda, Bart de Moor, and Yves Moreau. Candidate gene prioritization by network analysis of differential expression using machine learning approaches. BMC Bioinformatics, 11(1):460+, September 2010.

Lawrence Page, Sergey Brin, Rajeev Motwani, and Terry Winograd. The PageRank citation ranking: Bringing order to the web. Technical Report 1999-66, Stanford InfoLab, November 1999.

Christopher L. Poirel, Clifford C. Owens III, and T. M. Murali. Network-based functional enrichment. BMC Bioinformatics, 12(Suppl 13):S14, 2011.

Oron Vanunu, Oded Magger, Eytan Ruppin, Tomer Shlomi, and Roded Sharan. Associating genes and protein complexes with disease via network propagation. PLoS Comput Biol, 6(1):e1000641+, January 2010.

Christof Winter, Glen Kristiansen, Stephan Kersting, Janine Roy, Daniela Aust, Thomas Knösel, Petra Rümmele, Beatrix Jahnke, Vera Hentrich, Felix Rückert, Marco Niedergethmann, Wilko Weichert, Marcus Bahra, Hans J. Schlitt, Utz Settmacher, Helmut Friess, Markus Büchler, Hans-Detlev Saeger, Michael Schroeder, Christian Pilarsky, and Robert Grützmann. Google goes cancer: Improving outcome prediction for cancer patients by network-based ranking of marker genes. PLoS Comput Biol, 8(5):e1002511+, May 2012.

D. Zhou, O. Bousquet, T. N. Lal, J. Weston, and B. Scholkopf. Learning with local and global consistency. Advances in Neural Information Processing Systems, 16:321–328, 2004.