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

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.

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.

Experiments in Integer Linear Programming in Computational Biology
Simons Institute for Computational Theory, UC Berkeley. June 29, 2017 (Invited Lecture)

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)

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)

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 twentyfive 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.

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)

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).

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)

GWAS for Compound Heterozygous Traits: Phenotypic Distance and Integer Linear Programming
Talk given at the Langleyfest celebration for Chuck Langley. Asilomar Conference
Ceneter, May 23, 2015.

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)

A Simpler SubCubicTime RNA Folding Algorithm
Israel Stringology Meeting  The Gadifest (Invited Lecture)
The Dead Sea, Israel
January 5, 2015

The MultiState Perfect Phylogeny Problem: Modeling Infinite Alleles
University of Illinois, Chicago
September 15, 2014

Propagandizing for Integer Programming in Computational Biology (Invited Lecture)
Oxford University Conference on Population Genomics
July, 2014
 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
 Recent Progress on MultiState Perfect Phylogeny
Computer Science Dept. UC Santa Barbara (Invited Lecture)
November 5, 2012
 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
 Two New Algorithms for Phylogenetics and RNA structure
M.I.T. CSAIL Computational Biology Seminar, Cambrige MA
August 6, 2012
 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
 Recent Results in MultiState Perfect Phylogeny
Israel Stringology Conference, Tzfat Israel (Invited Lecture)
June 4, 2012

Overview of Phylogenetic Networks with Recombination
University of Oregon, Institute of Ecology and Evolution (Invited Lecture)
May 8, 2012
 What are Math and Computer Science Doing in Biology?
Denison University, March 29, 2012 (A Doris G. Gordon Lecture)
Gordon
Lecture Series
 Eight hour minicourse on ReCombinatorics
2012 INTERNATIONAL WINTER SCHOOL IN
Methods in Bioinformatics,
Tarragona, Spain, February 2024, 2012 (Invited lectures)
 Recent Progress on MultiState 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

MultiState Perfect Phylogeny Via Chordal Graph Theory
UC Berkeley, Dept. Mathematics, Computational Biology Seminar
February 17, 2010

The MultiState Perfect Phylogeny Problem: The Chordal Graph Approach
UCLA, Computational Biology Seminar (Invited Lecture)
December 6, 2009

The MultiState Perfect Phylogeny Problem
Iowa State, Computational Biology Seminar, November 18, 2009 (Invited Lecture)

A simple, practical and complete O(n^3/ log n)time Algorithm for RNA folding using the FourRussians Speedup
WABI 2009 Conference, U. Penn, September 13, 2009
Talk given by Yelena Frid

Generalizing the SplitEquivalence Theorem and FourGametes Condition:
Perfect Phylogeny on ThreeState Characters
WABI 2009 Conference, U. Penn, September 12, 2009
Talk given by Fumei Lam

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.

Two Solutions in Search of Killer Apps.
April 27, 2009, DIMACS Workshop on Algorithms in Human Population Genomics
Rutgers University

Combinatorial Optimization in Computational Biology
Conference on Optimization and Systems Biology (Keynote Lecture)
Lijiang, China, November 1, 2008

ReCombinatorics
June 17, 2008 Pisa Italy,
Combinatorial Pattern Matching (CPM) 2008 (Keynote Lecture)
 Graph Theory in Computational Biology
Graph Theory
Four hour tutorial presented at Miami University, Oxford Ohio, May 15, 2008 (Invited Lectures)
 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 multistate perfect phylogeny
problem.

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)

ReCombinatorics: Combinatorial Algorithms for Studying
The History of Recombination in Populations.
(Miller Distinguished Lecture)
Iowa State Univeristy.
October 11, 2007
 Integer Programming for NPhard 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 fourstate 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
 Algorithms for Reconstructing Recombination Histories in Populations
University of Glasgow, Scotland, August 31, 2007
 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
 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
 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
 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)
 Algorithms for Estimating and Reconstructing Recombinations in Populations
North Carolina State University, Research Triangle Distinguished Lecture Series, February 19, 2007
(Distinguished Lecture)
 Algorithms for Reconstructing Recombinations in Populations
Georgia State University, Molecular Basis of Disease Lecture Series, February 1, 2007 (Distinguished Lecture)

Progress on Combinatorial Haplotyping .
Recomb Satellite Conference on SNPs and Haplotyping, USC, January 28, 2007 (Invited Lecture)
 Introduction to Algorithms for Reconstructing Recombinations in Populations
INCOB06, Fifth International Conference on Bioinformatics, New Delhi, December 20, 2006 (Plenary Lecture)

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).
 Adventures in Combinatorial Haplotyping.
UCSD Computer Science, October 9, 2006 (Distinguished Lecture)
 Efficient Computation of Minimium Recombination
with Genotypes (not Haplotypes).
Presented at the CSB Conference, Stanford Univ. August 2006
Talk presented by Yufeng Wu

Combinatorial Optimization Problems from Population Genomics
Given at The First Ohio Collaborative Conference on Bioinformatics
Ohio University, June 30, 2006 (Keynote Lecture)
OCCBIO Website

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

Algorithms to Distinguish the Role of GeneConversion from Single Crossover Recombination
in SNP sequences in Populations
given at RECOMB 2006, April 1, 2006 in Venice, Italy.

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).
Online 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)

Reconstructing Ancestral Recombination Graphs
Given at Henri Poincare Institute, Paris June 2005 at the Conference on Mathematics of Evolution and Phylogeny (Invited Lecture).

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.

A LinearTime Algorithm for Perfect Phylogeny Haplotyping
Given by Z. Ding at MIT, May 2005 at the Conference on Research in Computational Biology, RECOMB 2005.

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.

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
 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 2021, 2004, Rutgers University
The German Bioinformatics Conference, Bielefeld University, October 4, 2004 (Plenary Lecture)
 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

COMBINATORIAL OPTIMIZATION IN COMPUTATIONAL BIOLOGY
SIAM Workshop on Combinatorial Scientific Computing, Feb. 27, 2004,
San Francisco
(Plenary Lecture)
 Efficient Reconstruction of Phylogenetic
Networks with Constrained Recombination,
University of Illinois, UrbanaChampaign, 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)
 Empirical Evaluation of Perfect Phylogeny Haplotyping and Haplotypers
ICTAI, November 3, 2003 (Plenary Lecture)
Cocoon, July 2003 Big Sky Montana (Plenary Lecture)
 Haplotyping by Pure Parsimony
CPM 2003 June 26, Morelia Mexico
 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)
 Combinatorial Approaches to Haplotyping
November 22, 2002 DIMACS Conference on Haplotypes and SNPs, Rutgers University
June 18, 2003, Cancer Center, University of Wisconsin, Madison
 Combinatorial Optimization in Molecular Biology (90 min. tutorial)
November 18, 2002 INFORMS Annual Meeting, San Jose CA.
 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.
 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.
 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:

2002 TUTORIAL ON COMBINATORIAL ALGORITHMS IN COMPUTATIONAL BIOLOGY, INFORMS National Conference, San Jose, CA
(Invited Tutorial)

2002 SEQUENCE ANALYSIS IN BIOINFORMATICS.
at Triosieme Cycle Romand d'informatique  Ecole de Printemps, Les Diablorets, Switzerland, March 78.
(Invited Lectures)

2000 OPTIMAL HAPLOTYPING.
Case Western Symposium on Computational Genetics
(Invited Lecture)

1998 ALGORITHMIC ASPECTS OF MOLECULAR SEQUENCE COMPARISON.
at CISM/Unesco summerschool on
bioinformatics/computational biology. Udine, Italy
June 1020, 1998
(Invited Lectures)

1997 PARAMETRIC SEQUENCE ALIGNMENT FOR BIOSEQUENCES.
The Fifth International Conference on
Parametric Optimization. October 1997, Tokyo, Japan.
(Special Invited Lecture)

1995 A SHORT COURSE ON COMBINATORIAL SEQUENCE ANALYSIS IN BIOLOGY.
CPM Summer School, Helsinki, Finland, June.
(Invited lectures)

1994 WHAT IS THE ROLE OF DISCRETE STRING ALGORITHMS AND ALGORITHMISTS IN
COMPUTATIONAL MOLECULAR BIOLOGY?
DIMACS,
RutgersPrinceton NSF Center, Special year on Mathematical support for molecular biology, September 28.
(Distinguished Lecture)

1994 A TUTORIAL ON SEQUENCE ANALYSIS.
Presented at the Sandia Symposium on Computational Molecular Biology, Albuquerque, NM, June.
(Invited Lecture)

1994 RECONSTRUCTING THE HISTORY OF CROSSOVERS.
Presented at the USC Workshop of Genome Rearrangements, Los Angeles, CA, March.
(Invited Lecture)

1994 NEW RESULTS IN SEQUENCE ANALYSIS.
Presented at the SIAM Conference on Discrete Math, Albuquerque, NM, June.
(Invited Lecture)

1990 NEW USES FOR SUFFIX TREES AND LEAST COMMON ANCESTOR ALGORITHMS.
Presented at the Mathematical Approaches to DNA Conference, Santa Fe, NM.
(Invited Lecture)

1990 NEW ALGORITHMS FOR DNA SEQUENCE ANALYSIS AND ALIGNMENT.
Presented at the SIAM National Meeting, Chicago, IL.
(Invited Lecture)
This research was partially supported by NSF grants ITR9723346,
SEIBIO 0513910, CCF0515378, IIS0803564, CCF1017580 and NSF IIS1219278.
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