Selected Recent Talks - Powerpoint Slides (often more than used in the talk)
January 2010 - D. Gusfield

1. The Multi-State Perfect Phylogeny Problem: The Chordal Graph Approach
   UCLA, December 6, 2009
   
   
2. The Multi-State Perfect Phylogeny Problem
   Iowa State, Computational Biology Seminar, November 18, 2009
   
   
3. A simple, practical and complete O(n^3/ log n)-time Algorithm for RNA folding using the Four-Russians Speedup
   WABI 2009 Conference, U. Penn, September 13, 2009
   Talk given by Yelena Frid
   
   
4. Generalizing the Split-Equivalence Theorem and Four-Gametes Condition: Perfect Phylogeny on Three-State Characters
   WABI 2009 Conference, U. Penn, September 12, 2009
   Talk given by Fumei Lam
   
   
5. The Multistate Perfect Phylogeny Problem with Missing and Removable and Data; Solutions via Integer Linear Programming and Perfect Graph Theory.
   Recomb 2009, May 2009
   Tucson, AZ.
   
   
6. Two Solutions in Search of Killer Apps.
   April 27, 2009, DIMACS Workshop on Algorithms in Human Population Genomics
   Rutgers University
   
   
7. Combinatorial Optimization in Computational Biology
   Conference on Optimization and Systems Biology (Keynote Lecture)
   Lijiang, China, November 1, 2008
   
   
8. ReCombinatorics
   June 17, 2008 Pisa Italy,
   Combinatorial Pattern Matching (CPM) 2008 (Keynote Lecture)
   
   
9. Graph Theory in Computational Biology
   Graph Theory
   Four hour tutorial presented at Miami University, Oxford Ohio, May 15, 2008
   
   
10. Expanded Graph Theory in Computational Biology
    Topics added to previous lecture
    September 2009. I will extend these lectures as additional material is developed. Here I have added new material on the chordal graph view of the multi-state perfect phylogeny problem.
    
    
11. ReCombinatorics: Combinatorial Algorithms for Studying The History of Recombination in Populations.
    ReCombinatorics
    UC Irvine, Institute for Genomics and Bioinformatics, Feb. 7, 2008 (Distinguished Lecture)
    MITACS Bioinformatics Series, Vancouver BC, November 29, 2007
    
    
12. ReCombinatorics: Combinatorial Algorithms for Studying The History of Recombination in Populations. (Miller Distinguished Lecture)
    Iowa State Univeristy. October 11, 2007
    
    
13. Integer Programming for NP-hard Phylogenetic (and Population Genetic) Problems
    Workshop on Challenges in Phylogenetics, Isaac Newton Institute for Mathematical Science, Cambridge University, September 4, 2007.
    
    This talk extends to three and four-state characters, the work reported in the July 16 COCOON talk and paper on binary characters.
    The slides posted here somewhat updated since the Cambridge workshop.
    Online video of the talk can be found at
    video of the talk
    
    
14. Algorithms for Reconstructing Recombination Histories in Populations
    University of Glasgow, Scotland, August 31, 2007
    
    
15. Integer Programming for Phylogenetic and Population Genetic Problems with Complex Data
    18'th Annual Symposium on Computing and Combinatorics (COCOON), Banff, Canada, July 16, 2007
    
    
16. A New Recombination Lower Bound and the Minimum Perfect Phylogenetic Forest Problem
    18'th Annual Symposium on Computing and Combinatorics (COCOON), Banff, Canada, July 16, 2007
    
    
17. Improved Algorithms for Inferring the Minimum Mosaic of a Set of Recombinants
    Talk given by Yufeng Wu. 18th Annual Symposium on Combinatorial Pattern Matching (CPM), London, Canada, July 10, 2007
    
    
18. An Overview of Algorithms for Reconstructing Recombinations in Populations
    Symposium on Information Technology in the Life Sciences, University of Mayaguez, Puerto Rico, February 22, 2007
    
    
19. Algorithms for Estimating and Reconstructing Recombinations in Populations
    North Carolina State University, Research Triangle Distinguished Lecture Series, February 19, 2007 (Distinguished Lecture)
    
    
20. Algorithms for Reconstructing Recombinations in Populations
    Georgia State University, Molecular Basis of Disease Lecture Series, February 1, 2007 (Distinguished Lecture)
    
    
21. Progress on Combinatorial Haplotyping .
    Recomb Satellite Conference on SNPs and Haplotyping, USC, January 28, 2007
    
    
22. Introduction to Algorithms for Reconstructing Recombinations in Populations
    INCOB06, Fifth International Conference on Bioinformatics, New Delhi, December 20, 2006 (Plenary Lecture)
    
    
23. Efficient and Practical Algorithms for Reconstructing the History of Recombinations in a Population.
    IASTED Conference on Computational and Systems Biology, Dallas Texas, November 13, 2006 (Keynote Lecture).
    
    
24. Adventures in Combinatorial Haplotyping.
    UCSD Computer Science, October 9, 2006 (Distinguished Lecture)
    
    
25. Efficient Computation of Minimium Recombination with Genotypes (not Haplotypes).
    Presented at the CSB Conference, Stanford Univ. August 2006
    Talk presented by Yufeng Wu
    
    
26. Combinatorial Optimization Problems from Population Genomics
    Given at The First Ohio Collaborative Conference on Bioinformatics Ohio University, June 30, 2006 (Keynote Lecture)
    OCCBIO Website
    
    
27. Algorithms to Reconstruct the History of Recombinations in Populations
    Given at The Second International Workshop on Bioinformatics Research and Applications, University of Reading, England, May 29, 2006 (Keynote Lecture)
    IWBRA Website
    
    
28. Algorithms to Distinguish the Role of Gene-Conversion from Single Crossover Recombination in SNP sequences in Populations
    given at RECOMB 2006, April 1, 2006 in Venice, Italy.
    
    
29. Structured Pattern Detection and Exploitation
    Three hours of lectures given at the workshop on The Analysis of Patterns held at Centre "Ettore Majorana" for Scientific Culture, Erice, Italy, October 28 - November 6, 2005.
    
    On-line video of the lecture (and of the other lecturers) can be found at
    Link to video webpage (don't worry, downloading does not begin with this click)
    
    
30. Reconstructing Ancestral Recombination Graphs
    Given at Henri Poincare Institute, Paris June 2005 at the Conference on Mathematics of Evolution and Phylogeny.
    
    
31. Efficient Computation of Close Upper and Lower Bounds on the Number of Recombinations Needed in the Evolution Biological Sequences
    Given by Yun S. Song at the 2005 ISMB Conference, June 2005.
    
    
32. A Linear-Time Algorithm for Perfect Phylogeny Haplotyping
    Given by Z. Ding at MIT, May 2005 at the Conference on Research in Computational Biology, RECOMB 2005.
    
    
33. A Fundamental Decomposition Theory for Phylogenetic Networks and Incompatible Characters
    Given at MIT, May 2005 at the Conference on Research in Computational Biology, RECOMB 2005.
    
    
34. Closer Upper and Lower Bounds on the Number of Needed Recombinations in the Evolution of Biological Sequences
    March 17, 2005
    U.C. Berkeley Statistical Genetics Seminar
    
    
35. Optimal, Efficient Reconstruction of Phylogenetic Networks with Constrained and Unconstrained Recombination (Updated Version),
    2005 UT/ORNL/KBRIN Bioinformatics Summit, April 2, 2005 (Plenary Lecture)
    DIMACS Workshop on Reticulated Evolution, September 20-21, 2004, Rutgers University
    The German Bioinformatics Conference, Bielefeld University, October 4, 2004 (Plenary Lecture)
    
    
36. Optimal, Efficient Reconstruction of Phylogenetic Networks with Constrained and Unconstrained Recombination (algorithms and decomposition theory),
    Phylogenetic Combinatorics and Applications, Linaes Bioinformatics Center, Uppsala Sweden, July 2004
    USC February, 2004
    UC Berkeley, Mathematics Department, October 22, 2003
    
    
37. COMBINATORIAL OPTIMIZATION IN COMPUTATIONAL BIOLOGY
    SIAM Workshop on Combinatorial Scientific Computing, Feb. 27, 2004, San Francisco (Plenary Lecture)
    
    
38. Efficient Reconstruction of Phylogenetic Networks with Constrained Recombination,
    University of Illinois, Urbana-Champaign, Computer Science Department, October 10, 2003
    IEEE CSB Bioinformatics Conference, August 14, 2003, Stanford, CA.
    Genome Center, University of Wisconsin, June 18, 2003
    U.C. Berkeley, I.E.O.R. Department, March 31, 2003
    U.C. Riverside Genetics Graduate Group Retreat, March 21, 2003, (Keynote Lecture)
    
    
39. Empirical Evaluation of Perfect Phylogeny Haplotyping and Haplotypers
    ICTAI, November 3, 2003 (Plenary Lecture)
    Cocoon, July 2003 Big Sky Montana (Plenary Lecture)
    
    
40. Haplotyping by Pure Parsimony
    CPM 2003 June 26, Morelia Mexico
    
    
41. Haplotyping via Perfect Phylogeny - A Direct Approach
    Feb. 28, 2003 Carnegie Mellon, Frontiers in Computational Molecular Biology (Merck Distinguished Lecture Series)
    Feb. 13, 2003 Johns Hopkins, Center for Genetic Medicine
    January 29, 2003 UC Riverside, Computer Science Department
    November 27, 2002 UC San Diego, Computer Science Department
    October 21, University of Washington, Computer Science Department
    
    
42. Combinatorial Approaches to Haplotyping
    November 22, 2002 DIMACS Conference on Haplotypes and SNPs, Rutgers University
    June 18, 2003, Cancer Center, University of Wisconsin, Madison
    
    
43. Combinatorial Optimization in Molecular Biology (90 min. tutorial)
    November 18, 2002 INFORMS Annual Meeting, San Jose CA.
    
    
44. String Barcoding: Uncovering Optimal Virus Signatures
    October 22, 2002 Institute for Systems Biology, Seattle Washington
    
    Sam Rash created these slides and gave this talk at RECOMB in April 2002.
    At the Institute for Systems Biology, I also gave a short talk on the Partition Distance Problem in Clusting and Genetics, but I have no powerpoint for that. See the Recent Papers list for the paper.
    
    
45. Suffix Trees Come of Age in Bioinformatics
    August 15, 2002 CSB02 Bioinformatics Conference, Stanford, CA. (Invited Lecture).
    
    This is an overview of some new uses of suffix trees and arrays in Bioinformatics. There are about 40 new papers in this area since 1997. I had intended to write a survey for the conference as well, but it never happened, and probably never will happen - there is just too much new, good work out there.
    
    
46. Haplotyping as Perfect Phylogeny
    May 3, 2002 UC Berkeley, Statistical Genetics and Genomics Colloquium.
    April 17, 2002 RECOMB Conference on Computational Biology, Washington DC.
    March 4, 2002, Oxford University, Bioinformatics/Statistical Genetics Seminar
    
    This talk uses the Graph Realization approach (based on Matroid theory) to solve the Perfect Phylogeny Haplotyping Problem, rather than the Direct Approach in the later talks listed above.