• Dynamic Modeling of Robotic Fish with a Flexible Caudal Fin
  Jianxun Wang, Philip K. McKinley, and Xiaobo Tan
  In Proceedings of the 5th Annual Dynamic Systems and Control Conference, Ft. Lauderdale, Florida, USA, October 2012. (Accepted to appear)
  



• Evolution of Network Construction and Data Distribution in Digital Organisms
  David B. Knoester and Philip K. McKinley
  In Proceedings of the Sixth IEEE International Conference on Self-Adaptive and Self-Organizing Systems, Lyon, France, September 2012. (Accepted to appear)
  



• A Taxonomy of Uncertainty for Dynamically Adaptive Systems
  Andres J. Ramirez and Betty H. C. Cheng
  In Proceedings of the International Symposium on Software Engineering for Adaptive and Self-Managed Systems (SEAMS), Zurich, Switzerland, June 2012.
  



• Genetic Variation and the Evolution of Consensus in Digital Organisms
  David B. Knoester, Heather J. Goldsby, and Philip K. McKinley
  IEEE Transactions on Evolutionary Computation, 2012. (Accepted to appear)
  



• Evolution of Resistance to Quorum Quenching in Digital Organisms
  B. E. Beckmann, David B. Knoester, B. D. Connelly, C. M. Waters, and Philip K. McKinley
  Artificial Life, 2012. (Accepted to appear)
  



• The SEEDS Platform for Evolutionary and Ecological Simulations
  Brian D. Connelly, Luis Zaman, and Philip K. McKinley
  In Proceedings of the Evolutionary Computation Software Systems Workshop, Philadelphia, Pennsylvania, July 2012.
  



• Evolutionary design and experimental validation of a flexible caudal fin for robotic fish
  Anthony Clark, Jared Moore, Jianxun Wang, Xiaobo Tan, and Philip McKinley
  In Proceedings of the Thirteenth International Conference on the Synthesis and Simulation of Living Systems, East Lansing, Michigan, USA, July 2012. (Best Paper Award)
  



• Evolving Flexible Joint Morphologies
  Jared M. Moore and Philip K. McKinley
  In Proceedings of the ACM Genetic and Evolutionary Computation Conference (GECCO-2012), Philadelphia, Pennsylvania, July 2012.
  



• Exploring the Evolution of Internal Control Structure using Digital Enzymes (poster summary)
  C. Byers, B. H. C. Cheng, and P. K. McKinley
  In Proceedings of the ACM Genetic and Evolutionary Computation Conference (GECCO-2012), Philadelphia, Pennsylvania, July 2012.
  



• Applying Evolutionary Computation To Mitigate Uncertainty in Dynamically Adaptive, High-Assurance Middleware
  P. K. McKinley, B. H. C. Cheng, A. J. Ramirez, and A. C. Jensen
  Journal of Internet Services and Applications, Special Issue on The Future of Middleware, 3(1):51--58, 2012.
  



• Automatically Exploring How Uncertainty Impacts the Behavior of Dynamically Adaptive Systems
  A. J. Ramirez, A. C. Jensen, B. H.C. Cheng, and D. B. Knoester
  In Proceedings of the 26th International Conference on Automated Software Engineering, Lawrence, Kansas, November 2011.
  



• Neuroevolution of Controllers for Self-Organizing Mobile Ad Hoc Networks
  David B. Knoester and Philip K. McKinley
  In Proceedings of the Fifth IEEE International Conference on Self-Adaptive and Self-Organizing Systems, Ann Arbor, Michigan, October 2011.
  



• An Evolutionary Approach to Network Self-Organization and Resilient Data Diffusion
  Andres J. Ramirez, Betty H. C. Cheng, and Philip K. Mckinley
  In Proceedings of the Fifth IEEE International Conference on Self-Adaptive and Self-Organizing Systems, Ann Arbor, Michigan, October 2011.
  



• Automatic Derivation of Utility Functions for Monitoring Software Requirements
  Andres J. Ramirez and Betty H. C. Cheng
  In Proceedings of the ACM/IEEE International Conference on Model Driven Engineering Languages and Systems (MODELS 2011), Wellington, New Zealand, pages 501--516, October 2011.
  



• A Toolchain for the Detection of Structural and Behavioral Latent System Properties
  Adam Jensen, Betty H. C. Cheng, Heather J. Goldsby, and Edward Nelson)
  In Proceedings of the ACM/IEEE International Conference on Model Driven Engineering Languages and Systems (MODELS 2011), Wellington, New Zealand, pages 683--698, October 2011. (Best Paper Nomination)
  



• Digital Enzymes: Agents of Reaction Inside Robotic Controllers for the Foraging Problem
  Chad M. Byers, Betty H. C. Cheng, and Philip K. McKinley
  In Proceedings of the ACM Genetic and Evolutionary Computation Conference (GECCO-2011), Dublin, Ireland, pages 243--250, July 2011. (Best Paper Nomination)
  



• Modeling the Evolutionary Dynamics of Plasmids in Spatial Populations
  Brian D. Connelly, Luis Zaman, Philip K. McKinley, and and Charles Ofria
  In Proceedings of the ACM Genetic and Evolutionary Computation Conference (GECCO-2011), Dublin, Ireland, pages 227--233, July 2011.
  



• Effects of Biased Group Selection on Cooperative Predation in Digital Organisms (poster summary)
  Daniel Couvertier and Philip K. McKinley
  In Proceedings of the ACM Genetic and Evolutionary Computation Conference (GECCO-2011), Dublin, Ireland, pages 23--24, July 2011.
  



• An Aspect-Oriented Approach for Implementing Evolutionary Computation Applications
  Andres J. Ramirez, Adam C. Jensen, and Betty H. C. Cheng
  In Proceedings of the 10th International Conference on Aspect-Oriented Software Development (AOSD-11), Porto de Galinhas, Pernambuco, Brazil projects = AWARE, others?, pages 153--164, March 2011.
  



• Transparent Shaping: A Methodology for Adding Adaptive Behavior to Existing Software Systems and Applications
  S. M. Sadjadi, P. K. McKinley, and B. H. C. Cheng
  In W. Eric Wong and Bojan Cukic, editors,Adaptive Control Approach for Software Quality Improvement, pages 77--114. World Scientific, 2011.
  



• On the Performance of Indirect Encoding Across the Continuum of Regularity
  J. Clune, K. O. Stanley, R. T. Pennock, and C. Ofria
  IEEE Transactions on Evolutionary Computation, 15(3):346--367, 2011.
  



• Selective pressures for accurate altruism targeting: evidence from digital evolution for difficult-to-test aspects of inclusive fitness theory
  Jeff Clune, Heather J. Goldsby, Charles Ofria, and Robert T. Pennock
  Proceedings of the Royal Society B, 278:666--674, 2011.
  



• Plato: A Genetic Algorithm Approach to Run-Time Reconfiguration in Autonomic Computing Systems
  Andres J. Ramirez, David B. Knoester, Betty H. C. Cheng, and Philip K. McKinley
  Cluster Computing, 14(3), 2011.
  



• Evolution of Synchronization and Desynchronization in Digital Organisms
  D. B. Knoester and Philip K. McKinley
  Artificial Life, 17(1):1--20, 2011.
  



• RELAX: A language to address uncertainty in self-adaptive systems requirement
  Jon Whittle, Pete Sawyer, Nelly Bencomo, Betty Cheng, and Jean-Michel Bruel
  Requirements Engineering, 15:177--196, 2010.
  



• Adaptive Monitoring of Software Requirements
  Andres J. Ramirez, Betty H. C. Cheng, and and Philip K. McKinley
  In Proceedings of the First International Workshop on Requirements at Run Time, Sydney, Australia, pages 41--50, October 2010.
  



• Evolutionary dynamics, epistatic interactions, and biological information
  C. C. Strelioff, C. Ofria, and R. E. Lenski
  Journal of Theoretical Biology, 266:584--594, 2010.
  



• Automatically Discovering Properties that Specify the Latent Behavior of UML Models
  Heather J. Goldsby and Betty H. C. Cheng
  In Proceedings of the ACM/IEEE International Conference on Model Driven Engineering Languages and Systems (MoDELS 2010), Oslo, Norway, October 2010.
  



• Social Structure and the Maintenance of Biodiversity
  B. Connelly, L. Zaman, C. Ofria, and P. McKinley
  In Proceedings of the 12th International Conference on the Synthesis and Simulation of Living Systems (ALIFE XII), Odense, Denmark, pages 461--468, August 2010.
  



• Resource Abundance Promotes the Evolution of Public Goods Cooperation
  B. D. Connelly, B. E. Beckmann, and P. K. McKinley
  In Proceedings of the ACM Genetic and Evolutionary Computation Conference (GECCO-2010), Portland, Oregon, pages 143--150, July 2010. (Best Paper Award)
  



• On the Use of Genetic Programming for Automated Refactoring and the Introduction of Design Patterns
  A. C. Jensen and B. H. C. Cheng
  In Proceedings of the ACM Genetic and Evolutionary Computation Conference (GECCO-2010), Portland, Oregon, July 2010.
  



• Neuroevolution of Mobile Ad Hoc Networks
  D. B. Knoester, H. J. Goldsby, and P. K. McKinley
  In Proceedings of the ACM Genetic and Evolutionary Computation Conference (GECCO-2010), Portland, Oregon, pages 603--610, July 2010.
  



• Investigating Whether HyperNEAT Produces Modular Neural Networks
  J. Clune, B. E. Beckmann, P. K. McKinley, and C. Ofria
  In Proceedings of the ACM Genetic and Evolutionary Computation Conference (GECCO-2010), Portland, Oregon, pages 235--642, July 2010.
  



• Evolution of Division of Labor in Genetically Homogenous Groups
  H. J. Goldsby, D. B. Knoester, and C. Ofria
  In Proceedings of the ACM Genetic and Evolutionary Computation Conference (GECCO-2010), Portland, Oregon, July 2010.
  



• Automatically Generating Adaptive Logic to Balance Non-functional Tradeoffs During Reconfiguration
  Andres J. Ramirez, Betty H. C. Cheng, Philip K. McKinley, and Benjamin E. Beckmann
  In Proceedings of the 7th International Conference on Autonomic Computing, Washington, DC, pages 225--234, June 2010.
  



• Design Patterns for Developing Dynamically Adaptive Systems
  Andres J. Ramirez and Betty H. C. Cheng
  In Proceedings of the Workshop on Software Engineering for Adaptive and Self-Managed Systems (SEAMS), Capetown, South Africa, pages 49--58, May 2010 projects = AWARE, others?.
  



• Automatically Discovering Properties That Specify the Latent Behavior of UML Models
  Heather Goldsby and Betty H. C. Cheng
  In Proceedings of the ACM/IEEE International Conference on Model Driven Engineering Languages and Systems (MODELS 2010), Capetown, South Africa, pages 316--330, May 2010.
  



• A Goal-Based Modeling Approach to Develop Requirements of an Adaptive System with Environmental Uncertainty
  Betty H. C. Cheng, Pete Sawyer, Nelly Bencomo, and Jon Whittle
  In Proceedings of the ACM/IEEE 12th International Conference on Model Driven Engineering Languages and Systems (MoDELS), Denver, Colorado, pages 468--483, October 2009.
  



• Evolving Virtual Fireflies
  David B. Knoester and Philip K. McKinley
  In Proceedings of the 10th European Conference on Artificial Life, Budapest, Hungary, September 2009.
  



• Analytical Modeling and Experimental Studies of Robotic Fish Turning
  X. Tan, M. Carpenter, J. Thon, and F. Alequin-Ramos
  In Proceedings of the 2010 IEEE International Conference on Robotics and Automation, Anchorage, AK, pages 102--108, 2010.
  



• Ensemble extraction for classification and detection of bird species
  E. P. Kasten, P. K. McKinley, and S. H. Gage
  Ecological Informatics, 5:153--166, 2010.
  



• Evolving Social Behavior in Adverse Environments
  Brian D. Connelly and Philip K. McKinley
  In Proceedings of the 10th European Conference on Artificial Life, Budapest, Hungary, September 2009.
  



• HybrID: A Hybridization of Indirect and Direct Encodings for Evolutionary Computation
  Jeff Clune, Benjamin E. Beckmann, Charles Ofria, and Robert T. Pennock
  In Proceedings of the 10th European Conference on Artificial Life, Budapest, Hungary, September 2009.
  



• The Evolution of Division of Labor
  Heather Goldsby, David B. Knoester, Jeff Clune, Philip K. McKinley, and Charles Ofria
  In Proceedings of the 10th European Conference on Artificial Life, Budapest, Hungary, September 2009.
  



• Evolution of Probabilistic Consensus in Digital Organisms
  David B. Knoester and Philip K. McKinley
  In Proceedings of the Third IEEE International Conference on Self-Adaptive and Self-Organizing Systems, San Francisco, California, September 2009.
  



• Effects of Communication Impairments on Quorum Sensing (poster summary)
  Benjamin E. Beckmann, David B. Knoester, and Philip K. McKinley
  In Proceedings of the Third IEEE International Conference on Self-Adaptive and Self-Organizing Systems, San Francisco, California, September 2009.
  



• Evolving Quorum Sensing in Digital Organisms
  Benjamin E. Beckmann and Philip K. McKinley
  In Proceedings of the ACM Genetic and Evolutionary Computation Conference (GECCO-2009), Montreal, Canada, July 2009.
  



• Evolution of Robust Data Distribution Among Digital Organisms
  David B. Knoester, Andres Ramirez, Philip K. McKinley, and Betty H. C. Cheng
  In Proceedings of the ACM Genetic and Evolutionary Computation Conference (GECCO-2009), Montreal, Canada, July 2009. (Best Paper Nomination)
  



• Transparent autonomization of CORBA
  S. M. Sadjadi and P. K. McKinley
  Computer Networks, 53(10):1570--1586, July 2009.
  



• Applying Genetic Algorithms to Decision Making in Autonomic Computing Systems
  Andres Ramirez, David Knoester, Betty H. C. Cheng, and Philip K. McKinley
  In Proceedings of the 6th IEEE International Conference on Autonomic Computing and Communications, Barcelona, Spain, June 2009. (Best Paper Award)
  



• Design Patterns for Developing Dynamically Adaptive Systems (poster summary)
  Andres Ramirez and Betty H. C. Cheng
  In Proceedings of the 6th IEEE International Conference on Autonomic Computing and Communications, Barcelona, Spain, June 2009.
  



• Evolving Coordinated Quadruped Gaits with the HyperNEAT Generative Encoding
  Jeff Clune, Benjamin E. Beckmann, Charles Ofria, and Robert T. Pennock
  In Proceedings of the 2009 IEEE Congress on Evolutionary Computation (CEC), Trondheim, Norway, May 2009.
  



• Modular Verification of Dynamically Adaptive Systems
  Ji Zhang, Heather J. Goldsby, and Betty H. C. Cheng
  In Proceedings of the ACM International Conference on Aspect-Oriented Software Development (AOSD 2009), Charlottesville, Virginia, March 2009.
  



• Digital Evolution of Quorum Sensing and its Applications
  Benjamin E. Beckmann and Philip K. McKinley
  In Proceedings of the Complex Systems Advanced Academic Workshop, Ann Arbor, Michigan, May 2009.
  



• Applying Digital Evolution to the Design of Self-Adaptive Software
  Benjamin Beckmann, Laura Grabowski, Philip McKinley, and Charles Ofria
  In Proceedings of the 2009 IEEE Symposium on Artificial Life, Nashville, Tennessee, March 2009.
  



• Evolving Cooperative Pheromone Usage in Digital Organisms
  Brian D. Connelly, Philip K. McKinley, and Benjamin E. Beckmann
  In Proceedings of the 2009 IEEE Symposium on Artificial Life, Nashville, Tennessee, March 2009.
  



• Research Directions in Requirements Engineering
  Betty H. C. Cheng and Joanne M. Atlee
  In K.J. Lyytinen, P. Loucopoulos, J. Mylopoulos, and W. Robinson, editors,Design Requirements Engineering: A Ten-Year Perspective, pages 11--43. Springer, 2009.
  



• Automatically Generating Behavioral Models of Adaptive Systems to Address Uncertainty
  Heather Goldsby and Betty H. C. Cheng
  In Proceedings of the ACM/IEEE 12th International Conference on Model Driven Engineering Languages and Systems (MoDELS), pages 568--583, October 2008. (Selected as one of the Best Papers)
  



• Evolution of Adaptive Population Control in Multi-agent Systems
  Benjamin E. Beckmann and Philip K. McKinley
  In Proceedings of the Second IEEE International Conference on Self-Adaptive and Self-Organizing Systems (SASO), Venice, Italy, pages 181--190, October 2008.
  



• Dynamis: Dynamic Overlay Service Composition for Distributed Stream Processing
  Farshad A. Samimi and Philip K. McKinley
  In Proceedings of the 20th International Conference on Software Engineering and Knowledge Engineering, San Fransisco, California, pages 881--886, July 2008.
  



• Cooperative Network Construction using Digital Germlines
  David B. Knoester, Philip K. McKinley, and Charles A. Ofria
  In Proceedings of the ACM Genetic and Evolutionary Computation Conference (GECCO-2008), Atlanta, Georgia, July 2008.
  



• Selection for Group-Level Efficiency Leads to Self-Regulation of Population Size
  Benjamin E. Beckmann, Philip K. McKinley, and Charles Ofria
  In Proceedings of the ACM Genetic and Evolutionary Computation Conference (GECCO-2008), Atlanta, Georgia, July 2008.
  



• Avida-MDE: A Digital Evolution Approach to Generating Models of Adaptive System Behavior
  Heather Goldsby and Betty H. C. Cheng
  In Proceedings of the ACM Genetic and Evolutionary Computation Conference (GECCO-2008), Atlanta, Georgia, July 2008.
  



• Autonomic software development methodology based on Darwinian evolution (poster summary)
  Benjamin E. Beckmann, Laura M. Grabowski, Philip K. McKinley, and Charles Ofria
  In Proceedings of the 5th IEEE International Conference on Autonomic Computing, Chicago, Illinois, June 2008.
  



• Digital Evolution of Behavioral Models for Autonomic Systems
  Heather J. Goldsby, Betty H. C. Cheng, Philip K. McKinley , David B. Knoester, and Charles Ofria
  In Proceedings of the 5th IEEE International Conference on Autonomic Computing, Chicago, Illinois, June 2008. (Best Paper Award)
  



• Goal-Based Modeling of Dynamically Adaptive System Requirements
  Heather J. Goldsby, Pete Sawyer, Nelly Bencomo, Betty H. C. Cheng , and Danny Hughes
  In Proceedings of the 15th IEEE International Conference on Engineering of Computer-Based Systems (ECBS 2008), Belfast, Northern Ireland, March 2008.
  



• Harnessing Digital Evolution
  Philip K. McKinley, Betty H. C. Cheng, Charles Ofria, David Knoester, Benjamin Beckmann, and Heather Goldsby
  IEEE Computer, 41(1), January 2008.
  



• Service Clouds: Distributed Infrastructure for Adaptive Communication Services
  F. A. Samimi, P. K. McKinley, S. M. Sadjadi, C. Tang, J. K. Shapiro, and Z. Zhou
  IEEE Transactions on Network and Service Management, 4(2):84--95, 2007.
  



• Evolution of Adaptive Sleep Response in Digital Organisms
  Benjamin Beckmann, Philip K. McKinley, and Charles A. Ofria
  In Proceedings of the 9th European Conference on Artificial Life, Lisbon, Portugal, September 2007.
  



• Directed Evolution of Communication and Cooperation in Digital Organisms
  David B. Knoester, Philip K. McKinley, Benjamin Beckmann, and Charles A. Ofria
  In Proceedings of the 9th European Conference on Artificial Life, Lisbon, Portugal, September 2007.
  



• Using Group Selection to Evolve Leadership in Populations of Self-Replicating Digital Organisms
  David B. Knoester, Philip K. McKinley, and Charles Ofria
  In Proceedings of the ACM Genetic and Evolutionary Computation Conference (GECCO-2007), London, UK, July 2007.
  



• Evolution of Cooperative Information Gathering in Self-Replicating Digital Organisms
  Benjamin Beckmann, Philip K. McKinley, David B. Knoester, and Charles Ofria
  In Proceedings of the First IEEE International Conference on Self-Adaptive and Self-Organizing Systems (SASO), Boston, Massachusetts, July 2007.
  



• Automated Ensemble Extraction and Analysis of Acoustic Data Streams
  Eric P. Kasten, Philip K. McKinley, and Stuart H. Gage
  In Proceedings of the First International Workshop on Distributed Event Processing, Systems and Applications (DEPSA), in conjunction with ICDCS 2007, Toronto, Ontario, Canada, June 2007.
  



• Digitally Evolving Models for Dynamically Adaptive Systems
  H. J. Goldsby, D. B. Knoester, B. H. C. Cheng, P. K. McKinley, and C. A. Ofria
  In Proceedings of the ICSE Workshop on Software Engineering for Adaptive and Self-Managing Systems (SEAMS), Minneapolis, Minnesota, May 2007.
  



• Applying Digital Evolution to the Design of Self-Adaptive ULS Systems (Position Paper)
  P. K. McKinley, B. H. C. Cheng, and C. A. Ofria
  In Proceedings of the ICSE Workshop on Software Technologies for Ultra-Large-Scale (ULS) Systems, Minneapolis, Minnesota, May 2007.
  



• Topology-aware overlay path probing
  Chiping Tang and Philip K. McKinley
  Computer Communications, 30(9):1994--2009, 2007.
  



• MESO: Supporting Online Decision Making in Autonomic Computing Systems
  Eric P. Kasten and Philip K. McKinley
  IEEE Transactions on Knowledge and Data Engineering, 19(4):485--499, April 2007.
  



• Specifying Real-Time Properties in Autonomic Systems
  J. Zhang, Z. Zhou, B. H. C. Cheng, and P. K. McKinley
  Innovations in Systems and Software Engineering, 3(1):3--16, March 2007.
  

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