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}
}

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},
}

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

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

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}
}

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

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}
}

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

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}
}

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

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},
}