Selected Recent Talks - Slides (often more than used in the talk)
September 2019 - D. Gusfield

1. A tutorial on Integer Linear Programming in Computational and Systems Biology
   Two hour tutorial at the ACM BCB conference September 7, 2019 in Niagara Falls, NY. This is a somewhat revised version extracted from the tutorial in Turku, listed next.
   
   
2. A tutorial on Integer Linear Programming in Computational Biology
   Three hour invited (plenary) tutorial at the conference Computability in Europe, June 15, 16 2017, in Turku Finland.
   
   
3. Experiments in Integer Linear Programming in Computational Biology
   Simons Institute for Computational Theory, UC Berkeley. June 29, 2017 (Invited Lecture)
   
   
4. The History Bound and Integer Linear Programming
   Given at the BIRS Mathematics Centre, Banff, Canada.
   Conference on Phylogenetics and Phylogenetic Networks, February 15, 2017 (Invited Lecture)
   
   
5. GWAS for Compound Heterozygous Traits: Phenotypic Distance and Integer Linear Programming
   Given at the Institute of Mathematical Sciences, Chennai, India.
   Conference on Computational Biology, December 11, 2016 (Invited Lecture)
   
   
6. Integer Programming in Computational Biology
   Given at the Chennai Mathematical Institute, Chennai, India.
   Rangoli of Algorithms Conference, December 12, 2016 (Invited Lecture)
   
   The lecture was from noon to 1pm. Cyclone Vardah - the most powerful cyclone to hit Chennai in twenty-five years - was expected to hit Chennai at noon, and hit just as I was ending my talk. The wind and rain broke through the windows in the theater and flooded the stage during the 2pm talk. We waited out the storm, moved to a different room and restarted the talks at 7pm - the show went on.
   
   
7. ReCombinatorics: Introduction to Recombination and Phylogenetic Networks
   Given at the National Centre for Biological Sciences, Bangalore, India.
   Conference on Theoretical Computer Science and Biology, December 19, 2016 (Invited Lecture)
   
   
8. Fundamentals of Stringology
   Three hour tutorial given at the Bootcamp for the Algorithms in Genomics program. Simons Institute for Computational Theory. UC Berkeley, January 2016 (Invited Lectures).
   
   
9. GWAS for Compound Heterozygous Traits: Phenotypic Distance and Integer Linear Programming
   In the special program on Phylogenetic Networks, Institute for Mathematics Science, National Univeristy of Singapore, July 27, 2015 (Invited Lecture)
   
   
10. GWAS for Compound Heterozygous Traits: Phenotypic Distance and Integer Linear Programming
    
    Talk given at the Langley-fest celebration for Chuck Langley. Asilomar Conference Ceneter, May 23, 2015.
    
    
11. Phylogenetics from the viewpoint of chordal Graphs
    powerpoint
    Safra Distinguished Lecture, U. of Tel Aviv, Israel (Distinguished Lecture)
    January 8, 2015 (These are the slides. Unfortunately, I had to cancel the lecture at the last minute)
    
    
12. A Simpler Sub-Cubic-Time RNA Folding Algorithm
    Israel Stringology Meeting -- The Gadi-fest (Invited Lecture)
    The Dead Sea, Israel
    January 5, 2015
    
    
13. The Multi-State Perfect Phylogeny Problem: Modeling Infinite Alleles
    University of Illinois, Chicago
    September 15, 2014
    
    
14. Propagandizing for Integer Programming in Computational Biology (Invited Lecture)
    Oxford University Conference on Population Genomics
    July, 2014
    
    
15. Three Algorithmic Results of Possible Use in Synthetic Biology, and then something that I actually do understand
    IEEE International Conference on Computational Advances in Bio and Medical Sciences (Keynote Lecture)
    New Orleans, LA
    June 12, 2013
    
    
16. Recent Progress on Multi-State Perfect Phylogeny
    Computer Science Dept. UC Santa Barbara (Invited Lecture)
    November 5, 2012
    
    
17. Phylogenetic Networks with Recombination
    Given at the workshop: The Future of Phylogenetic Networks, Lorentz Center University of Leiden, The Netherlands (Invited Lecture)
    October 17, 2012
    
    
18. Two New Algorithms for Phylogenetics and RNA structure
    M.I.T. CSAIL Computational Biology Seminar, Cambrige MA
    August 6, 2012
    
    
19. Three Algorithmic Results of Possible Use in Synthetic Biology
    ISMB Conference, Special Interest Group on Biological Systems Design, Long Beach CA. (Keynote Lecture)
    July 13, 2012
    
    
20. Recent Results in Multi-State Perfect Phylogeny
    Israel Stringology Conference, Tzfat Israel (Invited Lecture)
    June 4, 2012
    
    
21. Overview of Phylogenetic Networks with Recombination
    University of Oregon, Institute of Ecology and Evolution (Invited Lecture)
    May 8, 2012
    
    
22. What are Math and Computer Science Doing in Biology?
    Denison University, March 29, 2012 (A Doris G. Gordon Lecture)
    Gordon Lecture Series
    
    
23. Eight hour mini-course on ReCombinatorics
    2012 INTERNATIONAL WINTER SCHOOL IN Methods in Bioinformatics,
    Tarragona, Spain, February 20-24, 2012 (Invited lectures)
    
    
24. Recent Progress on Multi-State Perfect Phylogeny
    Workshop on Phylogenetics
    Isaac Newton Institute for Mathematical Science (Keynote Lecture),
    Cambridge University, June 20, 2011
    
    Online video of the talk can be found at
    video of the talk
    
    
25. Multi-State Perfect Phylogeny Via Chordal Graph Theory
    UC Berkeley, Dept. Mathematics, Computational Biology Seminar
    February 17, 2010
    
    
26. The Multi-State Perfect Phylogeny Problem: The Chordal Graph Approach
    UCLA, Computational Biology Seminar (Invited Lecture)
    December 6, 2009
    
    
27. The Multi-State Perfect Phylogeny Problem
    Iowa State, Computational Biology Seminar, November 18, 2009 (Invited Lecture)
    
    
28. 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
    
    
29. 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
    
    
30. 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.
    
    
31. Two Solutions in Search of Killer Apps.
    April 27, 2009, DIMACS Workshop on Algorithms in Human Population Genomics
    Rutgers University
    
    
32. Combinatorial Optimization in Computational Biology
    Conference on Optimization and Systems Biology (Keynote Lecture)
    Lijiang, China, November 1, 2008
    
    
33. ReCombinatorics
    June 17, 2008 Pisa Italy,
    Combinatorial Pattern Matching (CPM) 2008 (Keynote Lecture)
    
    
34. Graph Theory in Computational Biology
    Graph Theory
    Four hour tutorial presented at Miami University, Oxford Ohio, May 15, 2008 (Invited Lectures)
    
    
35. 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.
    
    
36. 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 (Invited Lecture)
    
    
37. ReCombinatorics: Combinatorial Algorithms for Studying The History of Recombination in Populations. (Miller Distinguished Lecture)
    Iowa State Univeristy. October 11, 2007
    
    
38. 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. (Invited Lecture)
    
    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
    
    
39. Algorithms for Reconstructing Recombination Histories in Populations
    University of Glasgow, Scotland, August 31, 2007
    
    
40. 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
    
    
41. 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
    
    
42. 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
    
    
43. 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 (Invited Lecture)
    
    
44. Algorithms for Estimating and Reconstructing Recombinations in Populations
    North Carolina State University, Research Triangle Distinguished Lecture Series, February 19, 2007 (Distinguished Lecture)
    
    
45. Algorithms for Reconstructing Recombinations in Populations
    Georgia State University, Molecular Basis of Disease Lecture Series, February 1, 2007 (Distinguished Lecture)
    
    
46. Progress on Combinatorial Haplotyping .
    Recomb Satellite Conference on SNPs and Haplotyping, USC, January 28, 2007 (Invited Lecture)
    
    
47. Introduction to Algorithms for Reconstructing Recombinations in Populations
    INCOB06, Fifth International Conference on Bioinformatics, New Delhi, December 20, 2006 (Plenary Lecture)
    
    
48. 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).
    
    
49. Adventures in Combinatorial Haplotyping.
    UCSD Computer Science, October 9, 2006 (Distinguished Lecture)
    
    
50. Efficient Computation of Minimium Recombination with Genotypes (not Haplotypes).
    Presented at the CSB Conference, Stanford Univ. August 2006
    Talk presented by Yufeng Wu
    
    
51. Combinatorial Optimization Problems from Population Genomics
    Given at The First Ohio Collaborative Conference on Bioinformatics Ohio University, June 30, 2006 (Keynote Lecture)
    OCCBIO Website
    
    
52. 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
    
    
53. 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.
    
    
54. 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 (Invited Lectures).
    
    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)
    
    
55. Reconstructing Ancestral Recombination Graphs
    Given at Henri Poincare Institute, Paris June 2005 at the Conference on Mathematics of Evolution and Phylogeny (Invited Lecture).
    
    
56. 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.
    
    
57. 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.
    
    
58. 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.
    
    
59. 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
    
    
60. 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)
    
    
61. 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 (Invited Lecture)
    USC February, 2004
    UC Berkeley, Mathematics Department, October 22, 2003
    
    
62. COMBINATORIAL OPTIMIZATION IN COMPUTATIONAL BIOLOGY
    SIAM Workshop on Combinatorial Scientific Computing, Feb. 27, 2004, San Francisco (Plenary Lecture)
    
    
63. 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)
    
    
64. Empirical Evaluation of Perfect Phylogeny Haplotyping and Haplotypers
    ICTAI, November 3, 2003 (Plenary Lecture)
    Cocoon, July 2003 Big Sky Montana (Plenary Lecture)
    
    
65. Haplotyping by Pure Parsimony
    CPM 2003 June 26, Morelia Mexico
    
    
66. 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 (Invited Lecture)
    November 27, 2002 UC San Diego, Computer Science Department
    October 21, University of Washington, Computer Science Department (Invited Lecture)
    
    
67. Combinatorial Approaches to Haplotyping
    November 22, 2002 DIMACS Conference on Haplotypes and SNPs, Rutgers University
    June 18, 2003, Cancer Center, University of Wisconsin, Madison
    
    
68. Combinatorial Optimization in Molecular Biology (90 min. tutorial)
    November 18, 2002 INFORMS Annual Meeting, San Jose CA.
    
    
69. 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.
    
    
70. 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.
    
    
71. 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.
    
    

    Older Invited Lectures:

72. 2002 TUTORIAL ON COMBINATORIAL ALGORITHMS IN COMPUTATIONAL BIOLOGY, INFORMS National Conference, San Jose, CA (Invited Tutorial)
    
    
73. 2002 SEQUENCE ANALYSIS IN BIOINFORMATICS. at Triosieme Cycle Romand d'informatique - Ecole de Printemps, Les Diablorets, Switzerland, March 7-8. (Invited Lectures)
    
    
74. 2000 OPTIMAL HAPLOTYPING. Case Western Symposium on Computational Genetics (Invited Lecture)
    
    
75. 1998 ALGORITHMIC ASPECTS OF MOLECULAR SEQUENCE COMPARISON. at CISM/Unesco summer-school on bioinformatics/computational biology. Udine, Italy June 10-20, 1998 (Invited Lectures)
    
    
76. 1997 PARAMETRIC SEQUENCE ALIGNMENT FOR BIOSEQUENCES. The Fifth International Conference on Parametric Optimization. October 1997, Tokyo, Japan. (Special Invited Lecture)
    
    
77. 1995 A SHORT COURSE ON COMBINATORIAL SEQUENCE ANALYSIS IN BIOLOGY. CPM Summer School, Helsinki, Finland, June. (Invited lectures)
    
    
78. 1994 WHAT IS THE ROLE OF DISCRETE STRING ALGORITHMS AND ALGORITHMISTS IN COMPUTATIONAL MOLECULAR BIOLOGY?
    DIMACS, Rutgers-Princeton NSF Center, Special year on Mathematical support for molecular biology, September 28. (Distinguished Lecture)
    
    
79. 1994 A TUTORIAL ON SEQUENCE ANALYSIS.
    Presented at the Sandia Symposium on Computational Molecular Biology, Albuquerque, NM, June. (Invited Lecture)
    
    
80. 1994 RECONSTRUCTING THE HISTORY OF CROSS-OVERS.
    Presented at the USC Workshop of Genome Rearrangements, Los Angeles, CA, March. (Invited Lecture)
    
    
81. 
    1994 NEW RESULTS IN SEQUENCE ANALYSIS.
    Presented at the SIAM Conference on Discrete Math, Albuquerque, NM, June. (Invited Lecture)
    
    
82. 
    1990 NEW USES FOR SUFFIX TREES AND LEAST COMMON ANCESTOR ALGORITHMS.
    Presented at the Mathematical Approaches to DNA Conference, Santa Fe, NM. (Invited Lecture)
    
    
83. 1990 NEW ALGORITHMS FOR DNA SEQUENCE ANALYSIS AND ALIGNMENT.
    Presented at the SIAM National Meeting, Chicago, IL. (Invited Lecture)