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Major Research Thrusts

PROGRESS REVIEW Mike Langston’s Research Team Department of Computer Science University of Tennessee 11 June 2003.

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Major Research Thrusts

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  1. PROGRESS REVIEWMike Langston’s Research TeamDepartment of Computer ScienceUniversity of Tennessee11 June 2003

  2. Team Members in AttendanceFaisal Abu-Khzam, Nicole Baldwin, Rebecca Collins, Mahesh Dorai, Mike Langston, Lan Lin, Jon Scharff, Pushkar Shanbhag, Henry Suters Team Members AbsentJohn Eblen, Xinxia Peng, Chris Symons

  3. Major Research Thrusts • Basic Research - Algorithm Design and Analysis - Fixed-Parameter Tractability - Novel Tools and Techniques • Applied Research - Bioinformatics Toolchains - Computational Grids, Parallel Architectures and Hardware Acceleration - Highly-Scalable Implementations

  4. Bioinformatics Short Course17 June to 11 July University of TennesseeOrganized by Jay SnoddyAttendees Nicole Baldwin, Rebecca Collins, Jon Scharff, Xinxia Peng, Chris Symons

  5. Tutorial on Modern Concepts in Biology for Mathematical and Physical Scientists23 June to 3 JulyPrinceton UniversityOrganized by BioMaPS/DIMACSAttendees Faisal Abu-Khzam, Lan Lin

  6. Update for Faisal Abu-Khzam • Working with Ottawa on Clustal XP portal • Upgrading vertex cover codes • Representing team at FPT workshop in Germany • Transitioning to bioinformatics role with Jay Snoddy • Co-chairing HICSS with Mike Langston • Defending PhD thesis on 19 June ---- good luck Faisal!

  7. Update for Nicole Baldwin • Working on new clique implementations - small cliques via direct algorithms - maximal and maximum cliques • Use genomics and proteomics knowledge - applications include phylogeny, microarray analysis, motif finding and SELDI • For details, see: Nicole's Slides

  8. Update for Rebecca Collins • Investigating Dinic’s algorithm for simple network flow (see Hochbaum) • Incorporating it into our vertex cover kernelization suite • Determining how it stacks up against Bill Cook’s Linear Programming • For details, see: Rebecca's notes

  9. Update for Mahesh Dorai • Some progress, some stumbling blocks • For details, see: Mahesh's report

  10. Update for John Eblen • Investigating new clique implementations - medium-sized cliques - the independent set problem • Examining the “gene trolling” problem • Preparing to enter the PhD program this fall

  11. Update for Lan Lin • Looking at interleaving, especially for vertex cover • Studying dominating and dominated set • Also considering “gene trolling” • For details, see: Lan's slides

  12. Update for Xinxia Peng • Exploring opportunities for graph algorithms in the context of important problems of bioinformatics • Possibilities include pattern recognition, data mining, and general operations of interest on data organized along the lines of GeneKeyDB • A theme worth pursuing is GRN homology

  13. Update for Jon Scharff • Working with Mike Langston and Mike Leuze on UT-ORNL summer internship • Putting a front end on existing software • Looking at the problem of adding a GUI • Developing new motif finding algorithms and codes • For details, see: Jon's notes

  14. Update for Pushkar Shanbhag • Assisting Faisal with vertex cover codes • Maintaining and updating sequential versions • Adding queue manager to parallel versions • Defending PILOT -- good luck Pushkar!

  15. Update for Henry Suters • Implementing crown decomposition rules • Testing against kernelization alternatives • Systematically exploring general utility • For details, see: Henry's write-up

  16. Update for Chris Symons • Working on hitting set - new kernelization and branching rules - sequential and parallel implementations • Serving as team expert for GRNs • Participating in clique implementations • Representing team at FPT workshop in Canada

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