De Novo Signaling Pathway Predictions Based on Protein-Protein Interaction, Targeted Therapy and Protein Microarray Analysis. - Derek A. Ruths; Jen-Te Tseng; Luay Nakhleh; Prahlad T. Ram (Systems Biology and Computational Proteomics, 2006)

Hypothesis Generation in Signaling Networks. - Derek A. Ruths; Luay Nakhleh; M. Sriram Iyengar; Shrikanth A. G. Reddy; Prahlad T. Ram (J. Comput. Biol., 2006)

Rapidly exploring structural and dynamic properties of signaling networks using PathwayOracle. - Derek A. Ruths; Luay Nakhleh; Prahlad T. Ram (BMC Syst. Biol., 2008)

The Signaling Petri Net-Based Simulator: A Non-Parametric Strategy for Characterizing the Dynamics of Cell-Specific Signaling Networks. - Derek A. Ruths; Melissa Muller; Jen-Te Tseng; Luay Nakhleh; Prahlad T. Ram (PLoS Comput. Biol., 2008)

Patterns of human gene expression variance show strong associations with signaling network hierarchy. - Kakajan Komurov; Prahlad T. Ram (BMC Syst. Biol., 2010)

Use of Data-Biased Random Walks on Graphs for the Retrieval of Context-Specific Networks from Genomic Data. - Kakajan Komurov; Michael A. White; Prahlad T. Ram (PLoS Comput. Biol., 2010)