derek ruths || network dynamics

Publications

Tenure: the academician's dream

Peer-reviewed Papers | Book Chapters | Articles & Essays | Invited Talks | Presentations & Posters

Peer-reviewed Papers

  1. W. Liu, F. A. Zamal, and D. Ruths. “Using social media to infer gender composition of commuter populations.” When the City Meets the Citizen Workshop, ICWSM 2012. pdf
  2. F. A. Zamal, W. Liu, and D. Ruths. “Homophily and Latent Attribute Inference: Inferring Latent Attributes of Twitter Users from Neighbors.” ICWSM 2012. pdf
  3. M. Perreault and D. Ruths. “The Effect of Mobile Platforms on Twitter Content Generation.” ICWSM 2011. pdf
  4. D. Ruths and F. A. Zamal. “A method for the automated, reliable retrieval of publication-citation records.” PLoS ONE 5(8): e12133. doi:10.1371/journal.pone.0012133, 2010. open-access
  5. D. Ruths and L. Nakhleh. “Deriving predictive models of signaling network dynamics from qualitative experimental data.” Computation Systems Bioinformatics (CSB 2010), Stanford, CA, 2010. pdf
  6. T. Ruths, D. Ruths, and L. Nakhleh. “GS2: An efficiently computable measure of GO-based similarity of gene sets.” Bioinformatics, 25(9):1178-1184, 2009. open-access
  7. M Fete, H. van Bokloven, S. Clements, F. McKeon, D. R. Roop, M. I. Koster, C. Missero, L. D. Attardi, V. A. Lombillo, E. Ratoviski, M. Julapalli, D. Ruths, V. P. Sybert, E. C. Siegfried, A. F. Bree. “Conference Report: International Research Symposium on Ankyloblepharon-Ectodermal Defects-Clift Lip and/or Palate (AEC) Syndrome.” American Journal of Medical Genetics, 149A(9):1885-1893, 2009.
  8. C. Than, D. Ruths, L. Nakhleh. “PhyloNet: A Software Package for Analyzing and Reconstructing Reticulate Evolutionary Relationships.” BMC Bioinformatics, 9:322, 2008. open-access
  9. D. Ruths and M. Maas. “Novel Graph-theoretic Analysis of Roads in Late Antiquity.” Proceedings of the Conference on Highways and Byways, To appear, 2008.
  10. D. Ruths, L. Nakhleh, P. T. Ram. “Rapidly exploring structural and dynamic properties of signaling networks using PathwayOracle.” BMC Systems Biology, 2:76, 2008. open-access
  11. D. Ruths, M. Muller, J. T. Tseng, L. Nakhleh, and P. T. Ram. “The Signaling Petri Net-Based Simulator: A Non-Parametric Strategy for Characterizing the Dynamics of Cell-Specific Signaling Networks.” PLoS Computational Biology, 4(2):e1000005, 2008. open-access
  12. C. Than, D. Ruths, H. Innan, L. Nakhleh. “Confounding Factors in HGT Detection: Statistical Error, Coalescent Effects, and Multiple Solutions.” Journal of Computational Biology, 14(4):517-535, 2007. pdf
  13. D. Ruths, J. T. Tseng, L. Nakhleh, P. T. Ram. “De novo Signaling Pathway Predictions based on Protein-Protein Interaction, Targeted Therapy and Protein Microarray Analysis.” Proceedings of the RECOMB Satellite Workshop on Systems Biology and Proteomics. Lecture Nodes in Bioinformatics (LNBI #4463), 61-72, 2007. pdf
  14. C. Than, D. Ruths, H. Innan, and L. Nakhleh. “Identifiability Issues in Phylogeny-based Detection of Horizontal Gene Transfer.” Proceedings of the 4th RECOMB Comparative Genomics Satellite Workshop, (LNBI 4205):215-229, 2006. pdf
  15. D. Ruths, L. Nakhleh, M. S. Iyengar, S. A. G. Reddy, and P. T. Ram. “Graph-theoretic Hypothesis Generation in Biological Signaling Networks.” Journal of Computational Biology. 13(9):1546-1557, 2006. pdf
  16. D. Ruths and L. Nakhleh. “Techniques for Assessing Phylogenetic Branch Support: A Performance Study.” Proceedings of the 4th Asia Pacific Bioinformatics Conference (APBC2006), 187-196, 2006. pdf
  17. D. Ruths and L. Nakhleh. “RECOMP: A Parsimony-based Method for Detecting Recombination.” Proceedings of the 4th Asia-Pacific Bioinformatics Conference, (APBC2006), 59-68, 2006. pdf
  18. L. Nakhleh, D. Ruths, and L.S. Wang. “RIATA-HGT: A Fast and Accurate Heuristic for Reconstructing Horizontal Gene Transfer.” Proceedings of the 11th International Computing and Combinatorics Conference (LNCS 3595), 84-93, 2005. pdf
  19. D. Ruths and L. Nakhleh. “Recombination and Phylogeny: Effects and Detection.” International Journal on Bioinformatics Research and Applications, 1(2):202-212, 2005. pdf
  20. J. M. Tour, W. L Van Zandt, C. P. Husband, S. M. Husband, E. C. Libby, D. Ruths, K. K. Young, L. S. Wilson, P. D. Franzon, and D. P. Nackashi. “Nanocell Logic Gates for Molecular Computing.” IEEE Transations on Nanotechnology. 1(2):100-109, 2002.
  21. D. Ruths, E. Chen, and L. Ellis. “Arbor3D: An Interactive Environment for Examining Phylogenetic and Taxonomic Trees in Multiple Dimensions.” Bioinformatics. 16(11): 1003-1009. 2000. pdf
  22. D. Ruths, E. Chen, and L. Ellis. “A Virtual Genome Environment for the Visualization and Navigation of Genomic Data.” Proceedings of the 4th International Immersive Projection Technology Workshop. Iowa State University. Ames, Iowa. 2000. pdf

Book Chapters

  1. L. Nakhleh, D. Ruths, and H. Innan. “Gene Trees, Species Trees, and Species Networks.” Editors R. Guerra and D. Allison. In Meta-analysis and Combining Information in Genetics. 2005.

Articles & Essays

  1. D. Ruths. “Zombies at war.” Armed Forces Journal, October 2008.

Invited Talks

  1. D. Ruths. “From Military Spagetti to Military Strategy.” IMA Workshop on Network Links: Connecting Social, Communication, and Biological Network Analysis, 1 March 2012.
  2. D. Ruths. “A Model of Social Network Formation.” University of Toronto Computer Science Department, 7 November 2011.
  3. D. Ruths. “Social processes and obesity.” Canadian Obesity Network Workshop, 28 April 2011.
  4. D. Ruths. “Models of signaling networks from semi-quantitative data.” Barbados Cancer Workshop, 3 February 2011.
  5. D. Ruths. “Spoons, Cancer, and Civilization.” TEDxMcGill, 20 November 2010.
  6. D. Ruths. “Modeling biochemical network dynamics using qualitative experimental data.” MIT Bioinformatics Seminar, 20 November 2009.
  7. D. Ruths. “Perspectives on modeling biochemical network dynamics.” Merck Frosst Pharmeceutical, November 17 2009.
  8. D. Ruths. “Applications of social network models to understanding childhood obesity.” Montreal Brain-to-Society Childhood Obesity Workshop, November 12 2009.
  9. D. Ruths. “Models of biochemical network dynamics from qualitative experimental data.” Microsoft Research at Cambridge, 10 March 2009.
  10. D. Ruths. “Models of biochemical network dynamics from qualitative experimental data.” School of Computer Science, McGill University, 24 February 2009.
  11. D. Ruths. “Models of biochemical network dynamics from qualitative experimental data.” Lane Center for Computational Biology, Carnegie Mellon University, 27 January 2009.
  12. D. Ruths. “Predicting insurgent group structure and behavior.” Central Intelligence Agency, 10 September 2008.
  13. D. Ruths. “The Signaling Petri Net: An Executable Model of Signaling Network Dynamics.” Brown University, 4 April 2008.
  14. D. Ruths. “PathwayOracle: Software for Elucidating the Systems Function of Signaling Networks.” Bertinoro Computational Biology Meeting, Italy, 12-15 May 2007.
  15. D. Ruths. “Contextual Collaboration.” Collaborate West Conference. Anaheim, California. 4 November 2002.
  16. D. Ruths. “Applications for Contextual Collaboration.” International Cadence User Group Conference. San Jose, California. 18 September 2002.
  17. D. Ruths. “Data-centric Collaboration.” InterDoc Conference. Quebec, Canada. 5 July 2002.
  18. D. Ruths. “Contextual Collaboration.” Collaborate East Conference. Boston, Massachusetts. 25 June 2002.
  19. D. Ruths. “Making Applications Collaborative.” TACCAS Conference. South Padre, Texas. 20 May 2002.

Presentations & Posters

  1. D. Ruths, B. Kogut, M. Conover, and D. Lazer. “The Political Coloring of Corporate Boards.” Workshop on Information in Networks, 30 September 2011.
  2. D. Ruths, B. Kogut, M. Conover, and D. Lazer. “Do Corporate Board Interlocks Shape Political Campaign Contribution Behavior?” Political Networks Conference, 19 June 2011.
  3. D. Ruths. “Network Generation Mechanisms and the Twitter Online Network.” Sunbelt Conference on Networks, Riva del Garda, Italy, July 1-4, 2010.
  4. D. Ruths, D. Lazer. Enduring Patterns of Campaign Contribution Networks.” Political Networks Conference, Duke, May 19-21, 2010.
  5. D. Ruths. “Identifying and Modeling Network Generation Mechanisms.” Netsci Conference, Northeastern, May 10-14, 2010.
  6. D. Ruths, C. Bronk, D. Subramanian. “Analysis of Associational Networks Embedded in Terrorist Events.” Networks in Political Science Conference, Harvard, June 13-14, 2008.
  7. D. Ruths and M. Maas. “Novel Graph-theoretic Analysis of Roads in Late Antiquity.” Conference on Highways and Byways, Brown University, 2008.
  8. D. Ruths, J. T. Tseng, L. Nakhleh, P. T. Ram. “De novo Signaling Pathway Predictions based on Protein-Protein Interaction, Targeted Therapy and Protein Microarray Analysis.” RECOMB Satellite Workshop on Systems Biology and Proteomics, 2007.
  9. D. Ruths and L. Nakhleh. “Techniques for Assessing Phylogenetic Branch Support: A Performance Study.” 4th Asia Pacific Bioinformatics Conference (APBC2006), 2006.
  10. D. Ruths and L. Nakhleh. “RECOMP: A Parsimony-based Method for Detecting Recombination.” 4th Asia-Pacific Bioinformatics Conference, (APBC2006), 2006.
  11. L. Nakhleh, D. Ruths, and L.S. Wang. ”RIATA-HGT: A Fast and Accurate Heuristic for Reconstructing Horizontal Gene Transfer.” 11th International Computing and Combinatorics Conference (LNCS 3595), 2005.