Publications

2012

  • B. D. Connelly, “Ecological effects on the evolution of cooperative behaviors,” PhD Thesis, 2012.
    [Bibtex]
    @phdthesis{connelly2012ecological,
    author={Connelly, Brian D.},
    title={Ecological Effects on the Evolution of Cooperative Behaviors},
    school={Michigan State University},
    year={2012},
    month={April}
    }
  • [PDF] B. E. Beckmann, D. B. Knoester, B. D. Connelly, C. M. Waters, and P. K. McKinley, “Evolution of resistance to quorum quenching in digital organisms,” Artificial life, pp. 1-20, 2012.
    [Bibtex]
    @article{beckmann2012evolution,
    title={Evolution of resistance to quorum quenching in digital organisms},
    author={Beckmann, Benjamin E. AND Knoester, David B. AND Connelly, Brian D. AND Waters, Christopher M. AND McKinley, Philip K.},
    journal={Artificial Life},
    year={2012},
    pages={1--20},
    }
  • [PDF] B. D. Connelly, L. Zaman, and P. K. McKinley, “The seeds platform for evolutionary and ecological simulations,” in Proceedings of the genetic and evolutionary computation conference, 2012, pp. 133-140.
    [Bibtex]
    @inproceedings{connelly2012seeds,
    author={Connelly, Brian D. AND Zaman, Luis AND McKinley, Philip K.},
    title={The SEEDS Platform for Evolutionary and Ecological Simulations},
    year={2012},
    booktitle={Proceedings of the Genetic and Evolutionary Computation Conference},
    pages={133--140}
    }

2011

  • [PDF] B. D. Connelly, L. Zaman, P. K. McKinley, and C. Ofria, “Modeling the evolutionary dynamics of plasmids in spatial populations,” in Proceedings of the genetic and evolutionary computation conference, 2011, pp. 227-233.
    [Bibtex]
    @inproceedings{connelly2011modeling,
    author={Connelly, Brian D. AND Zaman, Luis AND McKinley, Philip K. AND Ofria, Charles},
    title={Modeling the Evolutionary Dynamics of Plasmids in Spatial Populations},
    year={2011},
    booktitle={Proceedings of the Genetic and Evolutionary Computation Conference},
    pages={227--233}
    }

2010

  • [PDF] B. D. Connelly, B. E. Beckmann, and P. K. McKinley, “Resource abundance promotes the evolution of public goods cooperation,” in Proceedings of the genetic and evolutionary computation conference, 2010, pp. 143-150.
    [Bibtex]
    @inproceedings{connelly2010resource,
    author={Connelly, Brian D. AND Beckmann, Benjamin E. AND McKinley, Philip K.},
    title={Resource Abundance Promotes the Evolution of Public Goods Cooperation},
    year={2010},
    booktitle={Proceedings of the Genetic and Evolutionary Computation Conference},
    pages={143--150}
    }
  • [PDF] B. D. Connelly, L. Zaman, C. Ofria, and P. K. McKinley, “Social structure and the maintenance of biodiversity,” in Proceedings of the 12th international conference on the synthesis and simulation of living systems (alife), 2010, pp. 461-468.
    [Bibtex]
    @inproceedings{connelly2010social,
    title={Social Structure and the Maintenance of Biodiversity},
    author={Connelly, Brian D. AND Zaman, Luis AND Ofria, Charles AND McKinley, Philip K.},
    booktitle={Proceedings of the 12th International Conference on the Synthesis and Simulation of Living Systems (ALIFE)},
    year={2010},
    pages={461--468}
    }

2009

  • [PDF] B. D. Connelly, P. K. McKinley, and B. E. Beckmann, “Evolving cooperative pheromone usage in digital organisms,” in Proceedings of ieee symposium on artificial life, 2009, pp. 184-191.
    [Bibtex]
    @inproceedings{connelly2009aevolving,
    author={Connelly, Brian D. AND McKinley, Philip K. AND Beckmann, Benjamin E.},
    title={Evolving Cooperative Pheromone Usage in Digital Organisms},
    booktitle={Proceedings of IEEE Symposium on Artificial Life},
    year={2009},
    pages={184--191},
    language={English}
    }
  • [PDF] B. D. Connelly and P. K. McKinley, “Evolving social behavior in adverse environments,” in Proceedings of 10th european conference on articial life, 2009, pp. 498-498.
    [Bibtex]
    @inproceedings{connelly2009evolving,
    author={Connelly, Brian D. AND McKinley, Philip K.},
    title={Evolving Social Behavior in Adverse Environments},
    year={2009},
    pages={498--498},
    booktitle={Proceedings of 10th European Conference on Articial Life}
    }

2008

  • [PDF] M. Feig, S. Tanizaki, J. Chocholousova, M. Sayadi, J. W. Clifford, B. D. Connelly, S. Mukherjee, and S. M. Law, “Simulating biomolecules in cellular environments,” in Proceedings of the nic workshop, from computational biophysics to systems biology (cbsb08), 2008, pp. 23-39.
    [Bibtex]
    @inproceedings{feig2008simulating,
    title={Simulating Biomolecules in Cellular Environments},
    author={Feig, Michael AND Tanizaki, Seiichiro AND Chocholousova, Jana AND Sayadi, Maryam AND Clifford, Jacob W. AND Connelly, Brian D. AND Mukherjee, Shayantani AND Law, Sean M.},
    booktitle={Proceedings of the NIC Workshop, From Computational Biophysics to Systems Biology (CBSB08)},
    pages={23--39},
    year={2008}
    }
  • [PDF] S. Tanizaki, J. W. Clifford, B. D. Connelly, and M. Feig, “Conformational sampling of peptides in cellular environments,” Biophysical journal, vol. 94, iss. 3, pp. 747-759, 2008.
    [Bibtex]
    @article{tanizaki2008conformational,
    title={Conformational sampling of peptides in cellular environments},
    author={Tanizaki, Seiichiro AND Clifford, Jacob W. AND Connelly, Brian D. AND Feig, Michael},
    journal={Biophysical Journal},
    volume={94},
    number={3},
    pages={747--759},
    year={2008},
    publisher={Elsevier}
    }

2006

  • [PDF] B. D. Connelly, C. W. Bowron, L. Xiao, P. Tan, and C. Wang, “Adaptively routing P2P queries using association analysis,” in Proceedings of the 2006 international conference on parallel processing, 2006, pp. 281-288.
    [Bibtex]
    @inproceedings{connelly2006adaptively,
    title={Adaptively Routing {P2P} Queries Using Association Analysis},
    author={Connelly, Brian D. AND Bowron, Christopher W. AND Xiao, Li AND Tan, Pang-Ning AND Wang, Chen},
    booktitle={Proceedings of the 2006 International Conference on Parallel Processing},
    pages={281--288},
    year={2006}
    }

2005

  • B. D. Connelly, “A distributed approach to managing large simulation data sets,” Master Thesis, 2005.
    [Bibtex]
    @MastersThesis{connelly2005distributed,
    author={Connelly, Brian D.},
    title={A distributed approach to managing large simulation data sets},
    school={Michigan State University},
    year={2005},
    month={May},
    }