CV Brian D. Connelly, PhD

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Current Address (map):
Department of Biology
University of Washington
Box 351800
Seattle, WA 98105 USA
Contact:
Email: .
Lab Phone: +1 (206) 221-7026
Web: http://bconnelly.net

Education

2012
Ph.D. in Computer Science; Ecology, Evolutionary Biology, and Behavior
Dissertation: Ecological Effects on the Evolution of Cooperative Behaviors
Advisor: Philip K. McKinley
Michigan State University, East Lansing, MI USA
2005
M.S. in Computer Science
Thesis: A Distributed Approach to Managing Large Simulation Data Sets
Advisors: Li Xiao and Michael Feig
Michigan State University, East Lansing, MI USA
2002
B.S. in Computer Science
Minors in German and Psychology
Purdue University, West Lafayette, IN USA

Professional Experience

2013—2015
NSF Postdoctoral Research Fellow (PRFB)
Project: The Co-Evolution of Cooperation and Communication in Quorum Sensing Systems
Mentors: Benjamin Kerr (University of Washington) and Michael Doebeli (University of British Columbia)
2012—2013
Postdoctoral Research Associate, BEACON Center for the Study of Evolution in Action
Research: The Evolution of Cooperation and Quorum Sensing
Michigan State University and University of Washington
2011—2012
Graduate Research Assistant, BEACON Center for the Study of Evolution in Action
Research: Ecological effects on the evolution of cooperation and bacterial biofilm formation
Michigan State University, East Lansing, MI USA
2009—2011
Graduate Research Assistant, Department of Computer Science and Engineering
Research: Ecological effects on the evolution of cooperation and bacterial biofilm formation
Michigan State University, East Lansing, MI USA
2008
Lead Teaching Assistant, Department of Computer Science and Engineering
Technical Computing and Problem Solving (CSE 131)
Responsibilities: Managed group of 17 teaching assistants, designed biweekly labs and quizzes, designed midterm examiniations, taught biweekly labs, assisted in weekly lectures, held office hours, grading
Michigan State University, East Lansing, MI USA
2005—2006,
2007—2008
Teaching Assistant, Department of Computer Science and Engineering
Technical Computing and Problem Solving (CSE 131)
Responsibilities: Taught biweekly labs, assisted in lectures, held office hours, grading
Michigan State University, East Lansing, MI USA
2007—2009
Graduate Research Assistant, Department of Computer Science and Engineering
Research: The evolution of cooperative behaviors
Michigan State University, East Lansing, MI USA
2003—2007
Graduate Research Assistant, Department of Biochemistry and Molecular Biology
Project: The Analysis and Management of Large Molecular Dynamics Simulation Data Sets
Michigan State University, East Lansing, MI USA
2000
Software Engineering Internship, Intel Corporation
Responsibilites: Software development, research, design of project distribution system
Hillsboro, OR USA
1999—2000
2001—2002
Teaching Assistant, Department of Computer Science
Problem Solving and Programming (CS 180)
Responsibilities: Taught weekly labs, developed class projects, grading
Purdue University, West Lafayette, IN USA

Publications

2012
Brian D. Connelly, Luis Zaman, and Philip K. McKinley. The SEEDS platform for evolutionary and ecological simulations. In Proceedings of the Genetic and Evolutionary Computation Conference, pages 133–140, 2012.
Benjamin E. Beckmann, David B. Knoester, Brian D. Connelly, Christopher M. Waters, and Philip K. McKinley. Evolution of resistance to quorum quenching in digital organisms. Artificial Life, pages 1–20, 2012.
Brian D. Connelly. Ecological Effects on the Evolution of Cooperative Behaviors. PhD thesis, Michigan State University, April 2012.
2011
Brian D. Connelly, Luis Zaman, Philip K. McKinley, and Charles Ofria. Modeling the evolutionary dynamics of plasmids in spatial populations. In Proceedings of the Genetic and Evolutionary Computation Conference, pages 227–233, 2011.
2010
Brian D. Connelly, Luis Zaman, Charles Ofria, and Philip 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), pages 461–468, 2010.
Brian D. Connelly, Benjamin E. Beckmann, and Philip K. McKinley. Resource abundance promotes the evolution of public goods cooperation. In Proceedings of the Genetic and Evolutionary Computation Conference, pages 143–150, 2010.
2009
Brian D. Connelly and Philip K. McKinley. Evolving social behavior in adverse environments. In Proceedings of 10th European Conference on Articial Life, pages 498–498, 2009.
Brian D. Connelly, Philip K. McKinley, and Benjamin E. Beckmann. Evolving cooperative pheromone usage in digital organisms. In Proceedings of IEEE Symposium on Artificial Life, pages 184–191, 2009.
2008
Michael Feig, Seiichiro Tanizaki, Jana Chocholousova, Maryam Sayadi, Jacob W. Clifford, Brian D. Connelly, Shayantani Mukherjee, and Sean M. Law. Simulating biomolecules in cellular environments. In Proceedings of the NIC Workshop, From Computational Biophysics to Systems Biology (CBSB08), pages 23–39, 2008.
Seiichiro Tanizaki, Jacob W. Clifford, Brian D. Connelly, and Michael Feig. Conformational sampling of peptides in cellular environments. Biophysical Journal, 94(3):747–759, 2008.
2006
Brian D. Connelly, Christopher W. Bowron, Li Xiao, Pang-Ning Tan, and Chen Wang. Adaptively routing P2P queries using association analysis. In Proceedings of the 2006 International Conference on Parallel Processing, pages 281–288, 2006.
2005
Brian D. Connelly. A distributed approach to managing large simulation data sets. Master’s thesis, Michigan State University, May 2005.

Awards and Honors

2014
Google Research Cloud Services Award
Brian D. Connelly, Sylvie Estrella, and Benjamin Kerr: Expanding the Scale of Eco-Evolutionary Models.
2013
NSF Postdoctoral Research Fellowship in Biology
2012
Outstanding Graduate Student
Department of Computer Science and Engineering, Michigan State University
Outstanding Service Award
Department of Computer Science and Engineering, Michigan State University
Nominee, Fitch-Beach Outstanding Graduate Research Award
College of Engineering, Michigan State University
2010
Best Paper
Resource Abundance Promotes the Evolution of Public Goods Cooperation
Genetic and Evolutionary Computation Conference (GECCO) 2010
2006
Best Poster, Third Place
Adaptively Routing P2P Queries Using Association Analysis
Department of Computer Science and Engineering, Michigan State University
2004
Graduate Research Fellowship Award
Project: The Simulation Database (SimDB) for Comparing Molecular Dynamics Simulations
Quantitative Biology and Modeling Initiative, Michigan State University.

Teaching Experience

2014
Mentor, Worked with two zoology and one computer science graduate students to conduct course research project modeling the evolution of pheromone-based navigation for Multi-disciplinary Research Methods for the Study of Evolution at BEACON Center for the Study of Evolution in Action
2013
Tutorial Instructor, Data Visualization! How to convey scientific datasets through plots, movies, and interaction.
BEACON Center for the Study of Evolution in Action Congress 2013.
Mentor, Worked with two undergraduate students to conduct research and gain experience through Biology 482: Independent Research in Experimental Evolutionary Ecology at the University of Washington
2012
Mentor, Worked with a Lansing, Michigan area high school biology teacher to develop and conduct experimental evolution studies and corresponding classroom materials as part of the Research Experience for Teachers program at MSU
Seminar Organizer, Organized, led, and developed BEACON Toolkit, a seminar series introducing computational techniques to researchers in evolutionary biology and ecology
2011
Tutorial Instructor, SEEDS: Life off The Grid
BEACON Center of the Study of Evolution in Action
2008
Lead Teaching Assistant, Technical Computing and Problem Solving (MSU CSE 131)
Managed group of 17 teaching assistants, designed biweekly labs and quizzes, designed midterm examinations, taught biweekly labs, assisted in weekly lectures, grading
2005—2008
Teaching Assistant, Technical Computing and Problem Solving (MSU CSE 131)
Taught biweekly labs, assisted in lectures, grading
1999—2002
Teaching Assistant, Problem Solving and Programming (Purdue CS 180)
Taught weekly labs, developed class projects, grading

Service Activities

University Committee Service

2014—2015
Biology Department Representative, University of Washington Postdoctoral Association
2013—2014
Postdoc Representative, UW Biology Faculty Appointments Committee
2011
Co-founder, BEACON Students and Postdocs Association
2011—2012
Graduate Student Representative, MSU College of Engineering Research Committee
2011
Graduate Student Representative, MSU College of Engineering Graduate Studies Committee
2009—2012
Chair, MSU CSE Graduate Students Association
2009—2010
Graduate Student Representative, MSU CSE Computing Environment Committee
2007—2008
Graduate Student Representative, MSU CSE Graduate Studies and Research Committee
2006—2007
Graduate Student Representative, MSU CSE Faculty Meetings
2004—2012
MSU CSE Graduate Students Association

Conference Program Committee Membership

2015
Artificial Life/Robotics/Evolvable Hardware Track, Genetic and Evolutionary Computation Conference (GECCO)
2014
Fourteenth International Conference on the Synthesis and Simulation of Living Systems (ALIFE)
Artificial Life/Robotics/Evolvable Hardware Track, Genetic and Evolutionary Computation Conference (GECCO)
2013
Artificial Life/Robotics/Evolvable Hardware Track, Genetic and Evolutionary Computation Conference (GECCO)
Generative and Developmental Systems Track, Genetic and Evolutionary Computation Conference (GECCO)
2012
Thirteenth International Conference on the Synthesis and Simulation of Living Systems (ALIFE)
Artificial Life/Robotics/Evolvable Hardware Track, Genetic and Evolutionary Computation Conference (GECCO)

Education Outreach

2014
Science Fair Judge, Jane Addams K-8 School in Seattle, WA
Judge for Biology Graduate Student Symposium, University of Washington
2013
Science Fair Judge, Jane Addams K-8 School in Seattle, WA
2012
Developed and taught BEACON Tools: A seminar series introducing computational tools for data-driven science to students, postdocs, and faculty of BEACON Center
Taught third grade students from East Lansing, MI how computers can be used to study evolution
Worked with MSU’s Graduate Women In Science showing high school students science and engineering using computers, robots, and digital evolution as part of the NSF-sponsored College Ambition Program
2011
Taught first grade students from East Lansing, MI how computers can be used to study evolution

External Activities

2013—
Volunteer, Decibel International Festival of Electronic Music Performance, Visual Art and New Media
2002—
Volunteer cabin counselor for Hoosier Burn Camp, a camp for child burn survivors

Software Contributions

Primary Developer, SEEDS Platform for computational ecology and evolution
Primary Developer, growthcurve, an R package for analyzing biological growth curves
Primary Developer, PlateTools for reading, manipulating, and analyzing microplate data
Primary Developer, pushoverr, an R package for sending notifications
Developer, Avida Digital Evolution Platform
See briandconnelly on GitHub for additional software

Presentations

2013
Conference Presentation, The Co-Evolution of Cooperation and Communication in Quorum Sensing Systems
BEACON Congress 2013
Guest Lecture, Digital Evolution
Evolutionary Biology (UW Biology 354)
Guest Blog Post, When Cooperation Means Just Saying No
BEACON Center for the Study of Evolution in Action
Invited Talk, Ecological Effects on the Evolution of Cooperation
North Carolina A&T State University
2011
Guest Lecture, Ecological Effects on the Evolution of Cooperative Behavior
Evolutionary Dynamics and Modeling (MSU MMG 982)
Conference Presentation, Modeling the Evolutionary Dynamics of Plasmids in Spatial Populations
Genetic and Evolutionary Computation Conference (GECCO), Dublin, Ireland
Guest Blog Post, The Role of Environment in the Evolution of Cooperation
BEACON Center of the Study of Evolution in Action
Invited Talk, Social Structure and the Maintenance of Biodiversity
BEACON Center of the Study of Evolution in Action
Guest Lecture, Evolving Cooperative Behaviors
Advanced Topics in Distributed Computing Systems (MSU CSE 912)
2010
Invited Talk, Environmental Resource Abundance and the Evolution of Cooperation
BEACON Center of the Study of Evolution in Action
Conference Presentation, Social Structure and the Maintenance of Biodiversity
12th International Conference on the Synthesis and Simulation of Living Systems (ALIFE), Odense, Denmark
Conference Presentation, Resource Abundance Promotes the Evolution of Public Goods Cooperation
PLACE
2009
Conference Presentation, Evolving Cooperative Pheromone Usage in Digital Organisms
IEEE Symposium Series on Computational Intelligence in Nashville, TN USA
2007
Guest Lecture, Peer-to-Peer Networks
Computer Networks (MSU CSE 422)

References

Available upon request