Arbor 3D: an interactive environment for examining phylogenetic and taxonomic trees in multiple dimensions. - Derek A. Ruths; Edward S. Chen; Leland Ellis (Bioinform., 2000)

RIATA-HGT: A Fast and Accurate Heuristic for Reconstructing Horizontal Gene Transfer. - Luay Nakhleh; Derek A. Ruths; Li-San Wang (COCOON, 2005)

Recombination and phylogeny: effects and detection. - Derek A. Ruths; Luay Nakhleh (Int. J. Bioinform. Res. Appl., 2005)

RECOMP: A Parsimony-Based Method for Detecting Recombination. - Derek A. Ruths; Luay Nakhleh (APBC, 2006)

Techniques for Assessing Phylogenetic Branch Support: A Performance Study. - Derek A. Ruths; Luay Nakhleh (APBC, 2006)

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)

Identifiability Issues in Phylogeny-Based Detection of Horizontal Gene Transfer. - Cuong Than; Derek A. Ruths; Hideki Innan; Luay Nakhleh (Comparative Genomics, 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)

Confounding Factors in HGT Detection: Statistical Error, Coalescent Effects, and Multiple Solutions. - Cuong Than; Derek A. Ruths; Hideki Innan; Luay Nakhleh (J. Comput. Biol., 2007)

PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships. - Cuong Than; Derek A. Ruths; Luay Nakhleh (BMC Bioinform., 2008)

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)

GS2: an efficiently computable measure of GO-based similarity of gene sets. - Troy A. Ruths; Derek A. Ruths; Luay Nakhleh (Bioinform., 2009)