derek ruths || network dynamics

Publications

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

Peer-reviewed Papers

  1. C. Campbell, S. Alcott, J. Ruths, D. Ruths, K. Shea, R. Albert. “Correlations in the degeneracy of structurally controllable topologies for networks” Scientific Reports (7), 2017.
  2. J. Thomas, S. Ghosh, D. Parek, D. Ruths, J. Ruths. “Robustness of Network Controllability to Degree-Based Edge Attacks” Complex Networks, 2016.
  3. E. Newell and D. Ruths. “How one microtask affects another” CHI, 2016.
  4. E. Newell, S. Dimitrov, A. Piper, D. Ruths. “To Buy or to Read: How a Platform Shapes Reviewing Behavior” ICWSM, 2016.
  5. E. Newell, D. Jurgens, H. M. Saleem, H. Vala, J. Sassine, C. Armstrong, D. Ruths. “User Migration in Online Social Networks: A Case Study on Reddit During a Period of Community Unrest” ICWSM, 2016.
  6. H. Vala, S. Dimitrov, D. Jurgens, A. Piper, D. Ruths. “Annotating characters in literary corpora: A scheme, the CHARLES tool, and an annotated novel” LREC 2016.
  7. D. Ruths and J. Ruths. “Estimating the minimum control count of random network models” Scientific Reports (6), 2016.
  8. D. Jurgens, T. Finethy, C. Armstrong, D. Ruths. “Everyone’s Invited: A New Paradigm for Evaluation on Non-transferable Datasets” ICWSM Workshop on Standards and Practices in Large-Scale Social Media Research, 2015. (PDF)
  9. D. Jurgens, T. Finethy, J. McCorriston, Y. T. Xu, D. Ruths. “Geolocation Prediction in Twitter Using Social Networks: A Critical Analysis and Review of Current Practice” ICWSM, 2015. (PDF)
  10. D. Jurgens, J. McCorriston, D. Ruths. An Analysis of Exercising Behavior in Online Populations. ICWSM, 2015. (PDF)
  11. J. McCorriston, D. Jurgens, D. Ruths. “Organizations are Users Too: Characterizing and Detecting the Presence of Organizations on Twitter” ICWSM, 2015. (PDF)
  12. S. Dimitrov, A. Piper, D. Ruths. “Goodreads vs. Amazon: The Effect of Decoupling Book Reviewing and Book Selling” ICWSM, 2015. (PDF)
  13. H. M. Saleem and D. Ruths. “Tackling the challenges of situational awareness extraction in Twitter with an adaptive approach” HumTech 2015.
  14. D. Ruths and J. Pfeffer. “Social media for large studies of behavior” Science, 346(6213):1063-1064. 2014. (Summary | Reprint | Full Text)
  15. D. Parekh, D. Ruths, and J. Ruths. “Reachability-based Robustness of Network Controllability under Node and Edge Attacks” International Workshop on Complex Networks and their Applications @ SITIS 2014.
  16. D. Jurgens, S. Dimitrov, and D. Ruths. “Twitter Users #CodeSwitch Hashtags! #MoltoImportante #wow” First Workshop on Computational Approaches to Code Switching @ EMNLP 2014. (PDF)
  17. H. M. Saleem, Y. Xu, and D. Ruths. “Novel Situational Information in Mass Emergencies: What does Twitter Provide?” HumTech 2014. (PDF)
  18. H. M. Saleem, Y. Xu, and D. Ruths. “Effects of Disaster Characteristics on Twitter event signatures” HumTech 2014. (PDF)
  19. J. Ruths and D. Ruths. “Control Profiles of Complex Networks” Science, 2014. (Online)
  20. M. Ciot, M. Sonderegger, and D. Ruths. “Gender Inference on Twitter in Non-English Contexts” EMNLP 2013. (PDF)
  21. R. Cohen and D. Ruths. “Political Orientation Inference on Twitter: It’s Not Easy!” ICWSM 2013. (PDF)
  22. M. Misiewicz, M. Dery, B. Foveau, J. Jodoin, D. Ruths, and A. C. LeBlanc. “Identification of a novel Endoplasmic Reticulum Stress Response Element regulated by XBP1.” Journal of Biological Chemistry, 2013. (Online)
  23. J. Ruths and D. Ruths. “Robustness of Network Controllability under Edge Removal.” CompleNet, 2013.
  24. W. Liu and D. Ruths. “What’s in a name? Using first names as features for gender inference in Twitter.” Symposium on Analyzing Microtext, Stanford University, 2013. (PDF)
  25. F. A. Zamal and D. Ruths. “On the Contributions of Topology to Transcriptional Regulatory Network Robustness.” BMC Bioinformatics, 13:318, 2012. (Open-access)
  26. V. Calcagno, E. Demoinet, K. Gollner, L. Guidi, D. Ruths, and C. de Mazancourt. “Flows of Research Manuscripts Among Scientific Journals Reveal Hidden Submission Patterns.” Science 338(6110):1065-1069, 2012. (Online)
  27. 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)
  28. F. A. Zamal, W. Liu, and D. Ruths. “Homophily and Latent Attribute Inference: Inferring Latent Attributes of Twitter Users from Neighbors.” ICWSM 2012. (PDF)
  29. D. Ruths and M. Maas. “Novel Graph-theoretic Analysis of Roads in Late Antiquity.” in Highways, Byways, and Road Systems in the Pre-Modern World, 2012.
  30. Y. Lu, M. Muller, D. Smith, B. Dutta, K. Komurov, S. Iadevaia, D. Ruths, J-T. Tseng, S. Yu, Q. Yu, L. Nakhleh, G. Balazsi, J. Donnelly, M. Schurdak, S. Morgan-Lappe, S. Fesik, P. T. Ram and G. B. Mills. “Kinome siRNA-phosphoproteomic screen identifies networks regulating AKT signaling.” Oncogene 30:4567-4577, 2011. (Online)
  31. M. Perreault and D. Ruths. “The Effect of Mobile Platforms on Twitter Content Generation.” ICWSM 2011. (PDF)
  32. 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)
  33. 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)
  34. 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)
  35. 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.
  36. C. Than, D. Ruths, L. Nakhleh. “PhyloNet: A Software Package for Analyzing and Reconstructing Reticulate Evolutionary Relationships.” BMC Bioinformatics, 9:322, 2008. open-access
  37. 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)
  38. 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)
  39. 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)
  40. 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)
  41. 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)
  42. 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)
  43. 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)
  44. 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)
  45. 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)
  46. D. Ruths and L. Nakhleh. “Recombination and Phylogeny: Effects and Detection.” International Journal on Bioinformatics Research and Applications, 1(2):202-212, 2005. (PDF)
  47. 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.
  48. 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)
  49. 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. C. Bronk and D. Ruths. “Quantitative Modeling of Violent Group Behavior using Open-Source Intelligence.” Editors K. Desouza and E. Johnston. In Policy Informatics, MIT Press, Forthcoming.
  2. 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. “The Promises and Pitfalls of Demographic Inference on Social Media.” MIT Media Lab, 10 January 2014.
  2. “The Promises and Pitfalls of Demographic Inference on Social Media.” Computer Science Department, Northeastern University, 9 January 2014.
  3. “Interpreting large textual and graphical corpora using crowd sourcing.” Ephemera: Current and Future Workshop, Rice University, 7 December 2013.
  4. “The Promises and Pitfalls of Demographic Inference on Social Media.” Microsoft Research, Seattle, 22 October 2013.
  5. “Distinguishing and Estimating Mechanisms of Social Network Formation.” Dartmouth Interdisciplinary Network Research Group, Dartmouth University, 11 October 2013.
  6. “The Promises and Pitfalls of Demographic Inference on Social Media.” Columbia Computer Science Department, Columbia University, 3 October 2013.
  7. “The origins of robustness in biochemical networks.” Workshop on Evolution and Transcriptional Gene Regulation, Bellairs Research Center, 22 April 2013.
  8. “The role of computational network analysis in the humanities.” Workshop on Digitalization in Humanities, Rice University, 5 April 2013.
  9. “Recent advances in semantic analysis of social media.” Public Safety Canada’s Kanishka Conference, Ottawa, 9 November 2012.
  10. “The future of demographic inference in Twitter.” Computer Science Department, Simon-Frasier University, 26 October 2012.
  11. “The role of social media in crisis response.” Canadian Risk and Hazards Network Annual Conference, Vancouver, 25 October 2012.
  12. “Mapping urban populations using Twitter.” NSF Specialist Meeting on Mapping Ideas: Discovering Information Landscapes, San Diego, 1-2 August 2012.
  13. “Network science and history.” NEH Seminar on Communication, Empire, and the City of Rome, Rome, 2 July 2012.
  14. “Social media and social mobilization.” Public Safety Canada’s Cross-Cultural Security Round Table Meeting, Niagara Falls, 9-10 June 2012.
  15. “Introducing the Zen Network Library for Python.” Sage Days, 9 May 2012.
  16. “Computational tools for hypothesis generation with the Afghanistan COIN Strategy Map.” IMA Workshop on Network Links: Connecting Social, Communication, and Biological Network Analysis. 27 February – 2 March 2012.
  17. “Homophily and Political Orientation on Twitter.” US Department of Defense Strategic Multilayer Assessment Briefing, NIH Campus, Maryland, 14 February 2012.
  18. “A Model of Social Network Formation.” University of Toronto Computer Science Department, 7 November 2011.
  19. “Social processes and obesity.” Canadian Obesity Network Workshop, 28 April 2011.
  20. “Models of signaling networks from semi-quantitative data.” Barbados Cancer Workshop, 3 February 2011.
  21. “Spoons, Cancer, and Civilization.” TEDxMcGill, 20 November 2010.
  22. “Modeling biochemical network dynamics using qualitative experimental data.” MIT Bioinformatics Seminar, 20 November 2009.
  23. “Perspectives on modeling biochemical network dynamics.” Merck Frosst Pharmeceutical, November 17 2009.
  24. “Applications of social network models to understanding childhood obesity.” Montreal Brain-to-Society Childhood Obesity Workshop, November 12 2009.
  25. “Models of biochemical network dynamics from qualitative experimental data.” Microsoft Research at Cambridge, 10 March 2009.
  26. “Models of biochemical network dynamics from qualitative experimental data.” School of Computer Science, McGill University, 24 February 2009.
  27. “Models of biochemical network dynamics from qualitative experimental data.” Lane Center for Computational Biology, Carnegie Mellon University, 27 January 2009.
  28. “Predicting insurgent group structure and behavior.” Central Intelligence Agency, 10 September 2008.
  29. “The Signaling Petri Net: An Executable Model of Signaling Network Dynamics.” Brown University, 4 April 2008.
  30. “PathwayOracle: Software for Elucidating the Systems Function of Signaling Networks.” Bertinoro Computational Biology Meeting, Italy, 12-15 May 2007.
  31. “Contextual Collaboration.” Collaborate West Conference. Anaheim, California. 4 November 2002.
  32. “Applications for Contextual Collaboration.” International Cadence User Group Conference. San Jose, California. 18 September 2002.
  33. “Data-centric Collaboration.” InterDoc Conference. Quebec, Canada. 5 July 2002.
  34. “Contextual Collaboration.” Collaborate East Conference. Boston, Massachusetts. 25 June 2002.
  35. “Making Applications Collaborative.” TACCAS Conference. South Padre, Texas. 20 May 2002.

Presentations & Posters

  1. M. Ciot, M. Sonderegger, D. Ruths. “Gender Inference of Twitter Users in Non-English Contexts.” Conference on Empirical methods in Natural Language Processing, 2013.
  2. W. Liu, F. A. Zamal, D. Ruths. “Political Orientation on Twitter: Polarization and Echo Chambers.” Workshop on Information in Networks, 2013.
  3. R. Cohen and D. Ruths. “Inference of political orientation on Twitter: It’s not easy!” International Conference on Weblogs and Social Media, 2013.
  4. B. Deverett and D. Ruths. “Human strategies for the perception of network visualizations.” Workshop on Information in Networks, 28-29 September 2012.
  5. D. Ruths. “A First-look at Patterns of Giving among Individual Campaign Contributors.” Political Networks Conference, Bloomington, Indiana, 26-29 June 2012.
  6. M. Ciot, D. Ruths, D. Lazer. “Occupations and Campaign Contributions.” Political Networks Conference, Boulder, Colorado, 15-16 June 2012.
  7. F.A. Zamal, W. Liu, and D. Ruths. “Political Orientation on Twitter.” Political Networks Conference, Boulder, Colorado, 15-16 June 2012.
  8. W. Liu, F. A. Zamal, and D. Ruths. “Using homphily to boost latent attribute detection algorithm performance.” Sunbelt Conference on Social Network Analysis, Redondo Beach, 14-17 March 2012.
  9. D. Ruths, B. Kogut, M. Conover, and D. Lazer. “The Political Coloring of Corporate Boards.” Workshop on Information in Networks, 30 September 2011.
  10. D. Ruths, B. Kogut, M. Conover, and D. Lazer. “Do Corporate Board Interlocks Shape Political Campaign Contribution Behavior?” Political Networks Conference, 19 June 2011.
  11. D. Ruths. “Network Generation Mechanisms and the Twitter Online Network.” Sunbelt Conference on Networks, Riva del Garda, Italy, 1-4 July 2010.
  12. D. Ruths, D. Lazer. “Enduring Patterns of Campaign Contribution Networks.” Political Networks Conference, Duke, 19-21 May 2010.
  13. D. Ruths. “Identifying and Modeling Network Generation Mechanisms.” NetSci Conference, Northeastern, 10-14 May 2010.
  14. D. Ruths, C. Bronk, D. Subramanian. “Analysis of Associational Networks Embedded in Terrorist Events.” Networks in Political Science Conference, Harvard, 13-14 June 2008.
  15. D. Ruths and M. Maas. “Novel Graph-theoretic Analysis of Roads in Late Antiquity.” Conference on Highways and Byways, Brown University, 4-6 April 2008.
  16. 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.
  17. D. Ruths and L. Nakhleh. “Techniques for Assessing Phylogenetic Branch Support: A Performance Study.” 4th Asia Pacific Bioinformatics Conference (APBC2006), 2006.
  18. D. Ruths and L. Nakhleh. “RECOMP: A Parsimony-based Method for Detecting Recombination.” 4th Asia-Pacific Bioinformatics Conference, (APBC2006), 2006.
  19. 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.

Dissertations

  • “Deriving Executable Models of Biochemical Network Dynamics from Qualitative Data and Network Connectivity.” PhD Thesis, April 2009. Advisor: Luay Nakhleh.
  • “Applications of Phylogenetic Incongruence to Detecting and Reconstructing Recombination and Horizontal Gene Transfer.” Master’s Thesis, Nov 2005. Advisor: Luay Nakhleh.