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IMA Workshop 2:
IMA/RECOMB Satellite Workshop on Comparative Genomics
October 20-24, 2003


Probability and Statistics in Complex Systems: Genomics, Networks, and Financial Engineering, September 1, 2003 - June 30, 2004
Jointly sponsored by RECOMB and IMA.

Organizers:

Jens Lagergren
Department of Numerical Analysis and Computer Science
Royal Institute of Technology in Stockholm
jensl@nada.kth.se
http://www.nada.kth.se/~jensl/index-en.html

Bernard M.E. Moret
Department of Computer Science
University of New Mexico
moret@cs.unm.edu
http://www.cs.unm.edu/~moret/

and

David Sankoff
Department of Mathematics and Statistics
University of Ottawa
sankoff@uottawa.ca
http://www.crm.umontreal.ca/cgi/qui?sankoff

We have made a call for posters. Click here for information.

The increasing availability of complete genomes from diverse organisms offers unprecedented opportunities. Exploitation of the full power intergenomic comparative maps for all types of genomic events will be central in biological, medical and bioinformatics research in the post-genomic era. Several areas are crucial to the success of this enterprise, for instance: understanding patterns and processes of genome evolutionary change, mapping genomic mutational events, and the utilization of such maps as bioinformatics tools. Genomic data also facilitates phylogeny reconstruction based on genomic mutational events rather than nucleotide substitution.

The kernel of comparative genome analysis is the establishment of the correspondence (orthology analysis) between genes in different genomes. It is such intergenomic maps that make it possible to translate information from one organism to another. Genome evolution is shaped by a multitude of evolutionary events acting at various organizational levels. On a low level point mutations affect individual nucleotides. On a higher level genome segments are affected by processes such as duplication, lateral transfer, inversion, transposition, deletion and insertion. Finally, the whole genome is influenced by speciation and hybridization of organism lineages. The complexity of genome evolution poses a serious challenge in developing mathematical models and algorithms. Fortunately, there is a spectra of algorithmic techniques that can be applied to problems from this domain, ranging from exact, heuristic, fixed parameter and approximation algorithms for problems based on parsimony models to Monte Carlo Markov Chain algorithms for Bayesian analysis of problems based on probabilistic models.

WORKSHOP SCHEDULE
Monday Tuesday
MONDAY, OCTOBER 20
All talks are in Lecture Hall EE/CS 3-180 unless otherwise noted.
8:30 Coffee and Registration

Reception Room EE/CS 3-176

9:15 Douglas N. Arnold, Scot Adams, and Organizers Welcome and Introduction
9:30 Michael Lynch
Indiana University

The Origins of Genome Complexity

Slides:   html    pdf    ps    ppt

10:20
Discussion
10:30 Coffee Break Reception Room EE/CS 3-176
11:00 Nadia El-Mabrouk
University of Montreal

Reconstructing the Ancestor of a Modern Genome with Multigene Families

Slides:   html    pdf    ps    ppt

11:50
Discussion
12:00
Lunch Break
1:30 Roderic Guigó
Institut Municipal d'Investigacio Medica (IMIM/UPF/CRG)

Comparative Gene Prediction

Slides:   html    pdf    ps    ppt

2:20
Discussion
2:30 Coffee Break Reception Room EE/CS 3-176
3:00 Guillaume Bourque
Universite de Montreal

A Comparative Approach for Multiple Gene Network Inference Using Time-Series Gene Expression Data

Slides:   html    pdf    ps    ppt

3:20
Discussion
3:30 Avril Coghlan
Trinity College Dublin, Ireland

Origins of Recently Gained Introns in Caenorhabditis

Slides:   html    pdf    ps    ppt

3:50
Discussion
4:00 Igor V. Sharakhov
University of Notre Dame

High Rates of Genome Rearrangements in Malaria Mosquitoes, Anopheles gambiae and A. funestus

Slides:   html    pdf    ps    ppt

4:20
Discussion
4:30 SECOND CHANCES, i.e., speakers of the day respond to further questions, suggestions, re-frame their main points, look toward future directions.
5:00 Group photo here  
5:10

IMA Tea/Reception (with POSTER SESSION)
400 Lind Hall

Max Alekseyev
University of California, San Diego
Genome Halving Problem
Lars Arvestad
Royal Institute of Technology (KTH)
New Methods for Estimating Amino Acid Replacement Rates
Anne Bergeron
Universite du Quebec a Montreal  
Easy Ways to Clear Hurdles
Steven B. Cannon
University of Minnesota
Distinguishing Orthologs from paralogs by Integrating Comparative Genome Data and Gene Phylogenies
Dimitra Chalkia
The Pennsylvania State University
Phylogenetic Analysis of Formin Homology Proteins in Arabidopsis Thaliana and Oryza Sativa
Ramana V. Davuluri
Ohio State University
Mammalian Promoter Database: A Computational Platform for Comparative Genomics of Mammalian Transcriptional Regulation
Anant Godbole
East Tennessee State University
Distributional Approximations in Genome Reconstruction
Steve Goldstein
University of Wisconsin-Madison
Graph Compression Algorithms for Efficiently Comparing Genomes
Josefa González
Universitat Autònoma de Barcelona
Duplicative and Conservative Transpositions of the Larval Serum Protein 1 Genes in the Genus Drosophila
Tzvika Hartman
Weizmann Institute of Science, Rehovot, Israel
A Simpler 1.5-Approximation Algorithm for Sorting by Transpositions
Robert (Bob) Mau
University of Wisconsin-Madison
Inferring Orthologous Regions via a Pseudo-Gibbs Sampler: Finding the Pieces of the Rearrangement Puzzle
Daniel P. Miranker
University of Texas - Austin
Application of MoBIoS for Conserved Primer Pair Discovery
William J. Murphy
National Cancer Institute - Frederick
Reconstructing the Genomic Architecture of Mammalian Ancestors Using Multispecies Comparative Maps
Luay Nakhleh
The University of Texas at Austin
Reconstructing Reticulate Evolution in Species
Nikolas Nikolaidis
Pennsylvania State University
Evolution of the Hsp70 Gene Superfamily in Two Sibling Species of Nematodes Caenorhabditis elegans and C. briggsae
Ron Y. Pinter
Technion, Israel Institute of Technology
Evaluating a Class of Length-Sensitive Algorithms for Sorting by Reversal
Amal A. Shervington
University of Central Lancashire
Induced CYP1A1 Gene Expression in Lung Cancer Cell Lines
Derek E. Wildman
Wayne St. University School of Medicine
An Objective View of Humankind's Place in Primate Evolution
Tiffani L. Williams
University of New Mexico
Searching for Optimal Trees Under Maximum Parsimony
Stacia K. Wyman
University of Texas at Austin
Comparative Chloroplast Genomics of Seed Plants: Annotation and Analysis of Genomic Sequences
TUESDAY, OCTOBER 21
All talks are in Lecture Hall EE/CS 3-180 unless otherwise noted.
9:00 Coffee Reception Room EE/CS 3-176
9:30 Bret Larget
University of Wisconsin - Madison

A Statistical Approach to the Estimation of Phylogeny from Genome Arrangements

Slides:   pdf

10:20
Discussion
10:30 Coffee Break Reception Room EE/CS 3-176
11:00 Li-San Wang
University of Pennsylvania

Distance-Based Genome Rearrangement Phylogeny

Slides:   html    pdf    ps    ppt

11:50
Discussion
12:00
Lunch Break
1:30 Stephen J. O'Brien
Laboratory of Genomic Diversity, National Cancer Institute-Frederick
The Landscape of Comparative Genomics in Mammals
2:20
Discussion
2:30 Coffee Break Reception Room EE/CS 3-176
3:00 Pavel A. Pevzner
University of California San Diego
Transforming Men into Mice: Lessons from Human and Mouse Genomic Sequences
3:50
Discussion
4:00 Coffee Break Reception Room EE/CS 3-176
4:30 SECOND CHANCES, i.e., speakers of the day respond to further questions, suggestions, re-frame their main points, look toward future directions.
WEDNESDAY, OCTOBER 22
All talks are in Lecture Hall EE/CS 3-180 unless otherwise noted.
9:00 Coffee Reception Room EE/CS 3-176
9:30 Elisabeth R.M. Tillier
Ontario Cancer Institute / University of Toronto
Models and Methods for Phylogenomics
10:20
Discussion
10:30 Coffee Break Reception Room EE/CS 3-176
11:00 Aoife McLysaght
Trinity College Dublin, Ireland

Poxviruses and Adaptive Genome Evolution

Slides:   html    pdf    ps    ppt

11:50
Discussion
12:00
Lunch Break
1:30 Dannie Durand
Carnegie Mellon University

Gene Clusters in Comparative Genomics: Accident or Design?

Slides:   pdf

2:20
Discussion
2:30 Coffee Break Reception Room EE/CS 3-176
3:00 Ross Overbeek
Fellowship for Interpretation of Genomes (FIG)

Exploiting Gene Clusters to Curate Annotations

Slides:   html    pdf    ps    ppt

3:50
Discussion
4:00 Coffee Break Reception Room EE/CS 3-176
4:30 SECOND CHANCES, i.e., speakers of the day respond to further questions, suggestions, re-frame their main points, look toward future directions.
THURSDAY, OCTOBER 23
All talks are in Lecture Hall EE/CS 3-180 unless otherwise noted.
9:00 Coffee Reception Room EE/CS 3-176
9:15 Ron Y. Pinter
Technion, Israel Institute of Technology

Evaluating a Class of Length-Sensitive Algorithms for Sorting by Reversal

Slides:    html    pdf    ps    ppt

9:35
Discussion
9:45 Jijun Tang and Bernard M.E. Moret
University of New Mexico

Large-scale Phylogeny Reconstruction from Arbitrary Gene-order Data

Slides:   pdf

10:05
Discussion
10:15 Allan G. Force
Benaroya Research Institute at Virginia Mason

Origin of Subfunctions and Modular Genes

Slides:   html    pdf    ps    ppt

10:35
Discussion
10:45 Coffee Break Reception Room EE/CS 3-176
11:00 Elizabeth Ann Housworth
Indiana University

Measures of Conserved Synteny

Slides:   html    pdf    ps    ppt

11:50
Discussion
12:00
Lunch Break
1:30 Fiona Brinkman
Simon Fraser University

Analysis of Horizontal Gene Transfers of Potential Relevance to Microbial Virulence

Slides:   html    pdf    ps    ppt

2:20
Discussion
2:30 Coffee Break Reception Room EE/CS 3-176
3:00 Emmanuelle Lerat
University of Arizona
Lateral Gene Transfers and Organismal Phylogeny in Bacteria: Implications for Ancestral Genome Reconstruction
3:50
Discussion
4:00 Coffee Break Reception Room EE/CS 3-176
4:30 SECOND CHANCES, i.e., speakers of the day respond to further questions, suggestions, re-frame their main points, look toward future directions.
6:00 Workshop Dinner Gardens of Salonica
19 Fifth Street NE, Minneapolis
Tel (612) 378-0611
FRIDAY, OCTOBER 24
All talks are in Lecture Hall EE/CS 3-180 unless otherwise noted.
9:00 Coffee Reception Room EE/CS 3-176
9:30 Kenneth H. Wolfe
University of Dublin, Trinity College
Genome Evolution and Sorting Out Ancient Polyploidy in Yeasts
10:20
Discussion
10:30 Coffee Break Reception Room EE/CS 3-176
11:00 Jens Lagergren
SBC (Stockholm Bioinformatics Center), & KTH (Kunliga Tekniska Högskolan)
Bayesian Gene/Species Tree Reconciliation and Orthology Analysis Using MCMC
11:50
Discussion
12:00
Lunch Break
1:30 Evan Eichler
Case Western Reserve University
Recent Segmental Duplications and the Fragile Breakage Model of Human Genome Evolution
2:20
Discussion
2:30 Coffee Break Reception Room EE/CS 3-176
3:00 SECOND CHANCES, i.e., speakers of the day respond to further questions, suggestions, re-frame their main points, look toward future directions.
3:30
Concluding Remarks by Organizers
3:40
End of Workshop

LIST OF CONFIRMED PARTICIPANTS

NAMEDEPARTMENTAFFILIATION
Scot AdamsInstitute for Mathematics and its Applications University of Minnesota, Twin Cities
Soohan AhnDepartment of Statistics Seoul National University
Max AlekseyevDepartment of Finance University of California, San Diego
Yusuf Bilgin AltundasInstitute for Mathematics and its Applications Schlumberger-Doll
Greg AndersonSchool of Mathematics University of Minnesota, Twin Cities
Douglas ArnoldInstitute for Mathematics and its Applications University of Minnesota, Twin Cities
Donald AronsonInstitute for Mathematics and its Applications University of Minnesota, Twin Cities
Lars ArvestadStockholm Bioinformatics Center Royal Institute of Technology (KTH)
Gerard AwanouInstitute for Mathematics and its Applications University of Minnesota, Twin Cities
Pierre BaldiDepartment of Information and Computer Science University of California, Irvine
Karen BallInstitute for Mathematics and its Applications University of Minnesota, Twin Cities
Antar BandyopadhyayInstitute for Mathematics and its Applications University of Minnesota, Twin Cities
Anne BergeronLaboratoire de combinatoire et d'informatique math University of Quebec
Ann-Charlotte BerglundStockholm Bioinformatics Center University of Stockholm
Guillaume BourqueCentre de Recherches Mathématiques University of Montreal
Maury BramsonSchool of Mathematics University of Minnesota, Twin Cities
Olga BrezhnevaInstitute for Mathematics and its Applications University of Minnesota, Twin Cities
Fiona BrinkmanDepartment of Molecular Biology and Biochemistry Simon Fraser University
Steven CannonDepartment of Plant Biology University of Minnesota, Twin Cities
Alberto CapraraViale Risorgimento, 2 Università di Bologna
Dimitra ChalkiaDepartment of Biology The Pennsylvania State University
Laura ChiharaDepartment of Mathematics Carleton College
Avril CoghlanDepartment of Genetics Trinity College
Dannie DurandDepartments of Biological Sciences and Computer Science Carnegie Mellon University
Evan Eichler Case Western Reserve University
Nadia El-MabroukInformatique et recherche opérationnelle University of Montreal
Scott FahrenkrugDepartment of Animal Science University of Minnesota, Twin Cities
David Fernández-BacaDepartment of Computer Science Iowa State University
Allan ForceDepartment of Molecular Genetics Virginia Mason Research Center
Shmuel FriedlandDepartment of Mathematics, Statistics, and Computer Science University of Illinois, Chicago
Tim GaroniInstitute for Mathematics and its Applications University of Minnesota, Twin Cities
Anant GodboleDepartment of Mathematics East Tennessee State University
Steve GoldsteinDepartment of Biotechnology Center University of Wisconsin, Madison
Josefa GonzalezDepartament de Genetica i de Microbiologia Autonomous University of Barcelona
Balaji GopalakrishnanInstitute for Mathematics and its Applications University of Minnesota, Twin Cities
Roderic GuigóGrup de Recerca en Informatica Biomedica Instituto Municipal de Investigación Mèdica (IMIM)
Chuan-Hsiang HanInstitute for Mathematics and its Applications University of Minnesota, Twin Cities
Tzvika HartmanDepartment of Applied Mathematics and Computer Science Weizmann Institute of Science
Dirk HolsteDepartment of Biology Massachusetts Institute of Technology
Elizabeth HousworthDepartment of Mathematics Indiana University
Fern HuntMathematical and Computational Sciences Division National Institute of Standards and Technology
Naresh JainSchool of Mathematics University of Minnesota, Twin Cities
Lili JuInstitute for Mathematics and its Applications University of Minnesota, Twin Cities
Sabera KaziWireless and RF Solutions Honeywell
Christina KendziorskiDepartment of Biostatistics and Medical Informatic University of Wisconsin, Madison
Mohammad KhanDepartment of Mathematics Kent State University
Dohyun KimDepartment of Statistics Seoul National University
Thomas KurtzDepartment of Mathematics University of Wisconsin, Madison
Jens LagergrenStockholm Bioinformatics Center Royal Institute of Technology (KTH)
Bret LargetDepartment of Statistics and Botany University of Wisconsin, Madison
Emmanuelle LeratBiométrie et Biologie Évolutive Université Claude-Bernard (Lyon I)
C. LinderDepartment of Integrated Biology University of Texas, Austin
Bill Long CRAY Inc
Michael LynchDepartment of Biology Indiana University
Wojciech MakalowskiDepartment of Biology The Pennsylvania State University
Bob MauDepartment of AHABS / Oncology University of Wisconsin, Madison
Georgiana MayDepartment of Ecology and Evolutionary Biology University of Minnesota, Twin Cities
Aoife McLysaghtDepartment of Genetics Trinity College
Joao MeidanisInstitute of Computing State University of Campinas (UNICAMP)
Daniel MirankerDepartment of Computer Science University of Texas, Austin
Julia MixtackiFakultät für Mathematik Universität Bielefeld
Bernard MoretDepartment of Computer Science University of New Mexico
James MullikinNational Human Genome Research Institute National Institutes of Health
Bill MurphyLaboratory of Genomic Diversity National Cancer Institute
Gene Myers Celera Genomics Corporation
Luay NakhlehDepartment of Computer Science University of Texas, Austin
Haewon NamInstitute of Mathematics and Statistics University of Minnesota, Twin Cities
Michael NewtonDepartment of Statistics University of Wisconsin, Madison
Amir NiknejadDepartment of Mathematics University of Illinois, Chicago
Nikolas NikolaidisIMEG and Department of Biology The Pennsylvania State University
Stephen O'BrienLaboratory of Genomic Diversity National Cancer Institute
Ross OverbeekMathematics and Computer Science Division Argonne National Laboratory
Wei PanDivision of Biostatistics University of Minnesota, Twin Cities
Pavel PevznerDepartment of Computer Science and Engineering University of California, San Diego
Ron PinterDepartment of Computer Science Technion-Israel Institute of Technology
Lea PopovicInstitute for Mathematics and its Applications University of Minnesota, Twin Cities
Juan PoyatosDepartment of Structual and Computational Biology Program Spanish National Cancer Centre (CNIO)
Raj RajagopalDepartment of Genomics and Proteomics 3M
Grzegorz RempalaDepartment of Mathematics University of Louisville
David SankoffDepartment of Mathematics & Statistics University of Ottawa
Fadil SantosaInstitute for Mathematics and its Applications University of Minnesota, Twin Cities
Arnd ScheelSchool of Mathematics University of Minnesota, Twin Cities
Jeanette Schmidt Incyte Corporation
Jennifer SeffernickDepartment of Biochemistry and Molecular Biophysics University of Minnesota, Twin Cities
Igor SharakhovDepartment of Biology/Biological Sciences University of Notre Dame
Amal ShervingtonDepartment of Biological Sciences University of Central Lancashire
Jens StoyeTechnische Fakultät Universität Bielefeld
Jijun Tang University of New Mexico
Eric TannierBiométrie et Biologie Évolutive Université Claude-Bernard (Lyon I)
Glenn TeslerDepartment of Mathematics University of California, San Diego
Peter TiffinDepartment of Plant Biology University of Minnesota, Twin Cities
Elisabeth TillierCancer Institute Princess Margaret Hospital
Ali TofighDepartment of Numerical Analysis and Computer Science, NADA Royal Institute of Technology (KTH)
Vamsi VeeramachaneniDepartment of Biology The Pennsylvania State University
Jing WangInstitute for Mathematics and its Applications University of Minnesota, Twin Cities
Li-San WangDepartment of Computer Science University of Texas, Austin
Tandy WarnowDepartment of Computer Science University of Texas, Austin
Derek WildmanCenter for Molecular Medicine and Genetics Wayne State University
Tiffani WilliamsDepartment of Computer Science University of New Mexico
Stephen WillsonDepartment of Mathematics Iowa State University
Ken WolfeDepartment of Genetics Trinity College
Stacia WymanDepartment of Computer Science University of Texas, Austin
Weijia XuDepartment of Computer Science University of Texas, Austin
Fan YangDepartment of Statistics University of Minnesota, Twin Cities
Yuhong YangDepartment of Statistics Iowa State University
Ofer ZeitouniSchool of Mathematics University of Minnesota, Twin Cities
Weixiong ZhangDepartment of Computer Science and Genetics Washington University
Yongqian ZhangDepartment of Animal Science University of Minnesota, Twin Cities
Jun ZhaoInstitute of Mathematics and its Application University of Minnesota, Twin Cities
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