Clare's Home Page (archive, partial, from Bowdoin) Clare Bates Congdon Visiting Associate Professor Department of Computer Science, Bowdoin College, Brunswick, Maine
contact me:	email:	congdon@bowdoin.edu
	phone:	207.725.3824 (I check messages irregularly... email is usually the best way to reach me)
	sue's phone:	207.725.3567 (Sue Theberge is the CS Department Coordinator)
	cs dept. fax:	207.725.3750
	us mail:	Clare Bates Congdon, Computer Science, Bowdoin College, 8650 College Station, Brunswick, ME 04011-8486
find me:	office:	109 Banister Hall (Yes, that's the Chapel. I'm at the back on the side by the polar bear statue)
	lab:	108 Banister Hall

Teaching and Mentoring

• I enjoy working with motivated students on independent-study projects relating to my interests and expertise, particularly in bioinformatics and evolutionary computation (which includes the agents/games work). I'll also consider other projects, including (but not limited to) scientific modelling, visualization, and interactive art.
• Here are some past independent-study projects I've supervised
• I am also often able to employ students to help with bioinformatics research, particularly in the summers.
• My students can be high-achievers. Those who wish to put in the time and effort regularly present their work at conferences, are co-authors on peer-reviewed publications, and win competitions and awards.
• I am also happy to mentor students who are less confident in their skills and are less clear on their ambitions. Some of us are new to computing or bioinformatics and some of us are late bloomers.

Research

	GAMI: genetic algorithms for motif inference Synopsis: In this project, we develop computational tools to infer regulatory regions in noncoding DNA, based on conservation over evolutionary time, and including biochemical data from the ENCODE project. Current and recent collaborators: Leif Oxburgh, Carol Kim, Jim Coffman Current staff and students: Craig Lessard, Sam McFarland, Brenna Gardner, Naomi Heuer, Amanda Castonguay, Ben Congdon-Jones With Carol Kim's lab at the University of Maine, we have computationally identified regulatory elements for CFTR, the gene responsible for cystic fibrosis, and completed preliminary biological validations of these. With Jim Coffman's lab at the Mount Desert Island Biological Lab, we have computationally identified regulatory regions for FOXJ1, a gene important in cilia development, and completed preliminary biological validations of these. With Leif Oxburgh's lab at the Maine Medical Center Research Institute, we have computationally identified regulatory regions for PDGFRb, a gene critical to kidney development, and completed preliminary biological validations of these.
	GPS: Genome Pattern Scan Synopsis: In this project, we develop computational tools that identify genes that might be influenced by specific regulatory factors (specified by the user). Collaborators: Leif Oxburgh, Mary Ann Asson-Batres Staff and students: Sam McFarland, Craig Lessard, Jen Fetting With Leif Oxburgh's lab at the Maine Medical Center Research Institute, we are working to identify genes that might be regulated by FOXD1. With Mary Ann Asson-Batres of Tennessee State University and Doug Sawyer of the Maine Medical Center Research Institute, we are working to identify genes that might be regulated by the presence of Vitamin A.
	Gaphyl: genetic algorithms for phylogenetics Synopsis: Find the most plausible evolutionary relationships among species Staff and students: Emily Greenfest, Josh Ladieu, Kevin Septor, Lunn Sawyer

	REALM: A Rule-Based Evolutionary Computation Agent that Learns to Play Mario Synopsis: Using an evolutionary computation approach to learn to play Mario. Masters project by Slawomir Bojarski
	RAMP: A Rule-Based Agent for Ms. PacMan Synposis: As of 2008, the best artificial agent for Ms. PacMan, with a high score of 25,520; winner of the WCCI 2008 Ms. PacMan competition Masters project by Alan Fitzgerald Contributors: Peter Kemeraitis Base code and competetion run by Simon Lucas
	Learning to Play Unreal Synposis: Development of Chimera, an evolutionary approach to learning rule-based systems and Agent Smith, an agent to play Unreal. A hand-coded version of Agent Smith won the CEC 2009 Unreal Tournament competition. Independent study project by Ryan Small

• I am supported by an NIH COBRE Grant (NIGMS 8-P20-GM103534-02), “Quantitative Biology Research Institute”, Dr. Christopher Amos, Dartmouth Medical School, PI. This grant teams Biologists and Quantitative researchers (such as myself) to investigate the interactions between genes and the environment.
• I am also PI on an NSF CAREER grant (953495), which is focused on the use of evolutionary computation for bioinformatics.
• I am also a Co-PI on NSF TUES award (1245635), Infusing Creative Thinking Into STEM Education, which is focused on teaching STEM faculty the steps of the creative process, and helping them to create activities using these ideas for their USM classes.

• I am a Visiting Scientist at MMCRI, the Maine Medical Center Research Institute in Scarborough, Maine
• I am an Adjunct Research Professor of Public Health at The University of Southern Maine in Portland, Maine
• I am an Adjunct Associate Professor and a seasonal investigator at the Mount Desert Island Biological Lab in Salisbury Cove, Maine

• Member, IEEE Computational Intelligence Society Task force on the ethical and social implications of Computational Intelligence
• Associate Editor, IEEE Transactions on Evolutionary Computation
• Associate Editor, IEEE Transactions on Computational Intelligence and AI in Games
• IEEE CIS BBTC I was Chair of the IEEE Computational Intelligence Society Bioinformatics and Bioengineering Technical Committee (two one-year terms, 2011 and 2012)
• IEEE CIS GTC I was Vice Chair of the IEEE Computational Intelligence Society Games Technical Committee (two one-year terms, 2013 and 2014))
• ACM/IEEE TCBB I serve on the steering committee of the ACM/IEEE Transactions in Computational Biology and Bioinformatics journal.
• I have helped organize a number of international conferences, including:
  CIBCB: I was the General Chair of CIBCB '11, Computational Intelligence in Bioinformatics and Computational Biology (and was Evolutionary Computation Technical Chair for CIBCB '10, and Publicity Chair in '07 and Proceedings Chair in '08). (This is an IEEE conference.)
  GECCO: I was co-chair of the Undergraduate Research Workshop (with Frank Moore and Jennifer Seitzer), and was co-chair of the Bioinformatics and Computational Biology track for GECCO, the Genetic and Evolutionary Computation Conference. (This is an ACM conference.)
  Congress on Evolutionary Computation: I am Workshops Chair (with Fahmida Chowdhury) for CEC 2011, the Congress on Evolutionary Computation, and Co-Chair (with Bobby Bryant) of the Special Session on Evolutionary Computation and Games. (This is an IEEE conference.)
  
  

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