Probability and Statistics in Complex Systems: Genomics, Networks, and Financial Engineering, September 1, 2003 - June 30, 2004

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 Wednesday Thursday Friday
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

NAME	DEPARTMENT	AFFILIATION
Scot Adams	Institute for Mathematics and its Applications	University of Minnesota
Soohan Ahn	Department of Statistics	Seoul National University
Max Alekseyev	Department of Finance	University of California, San Diego
Yusuf Altundas	Institute for Mathematics and its Applications	Schlumberger-Doll
Greg Anderson	School of Mathematics	University of Minnesota
Douglas Arnold	Institute for Mathematics and its Applications	University of Minnesota
Donald Aronson	Institute for Mathematics and its Applications	University of Minnesota
Lars Arvestad	Stockholm Bioinformatics Center	Royal Institute of Technology (KTH)
Gerard Awanou	Institute for Mathematics and its Applications	University of Minnesota
Pierre Baldi	Department of Information and Computer Science	University of California, Irvine
Karen Ball	Institute for Mathematics and its Applications	University of Minnesota
Antar Bandyopadhyay	Institute for Mathematics and its Applications	University of Minnesota
Anne Bergeron	Laboratoire de combinatoire et d'informatique math	University of Quebec
Ann-Charlotte Berglund	Stockholm Bioinformatics Center	University of Stockholm
Guillaume Bourque	Centre de Recherches Mathématiques	University of Montreal
Maury Bramson	School of Mathematics	University of Minnesota
Olga Brezhneva	Institute for Mathematics and its Applications	University of Minnesota
Fiona Brinkman	Department of Molecular Biology and Biochemistry	Simon Fraser University
Steven Cannon	Department of Plant Biology	University of Minnesota
Alberto Caprara	Viale Risorgimento, 2	Università di Bologna
Dimitra Chalkia	Department of Biology	Pennsylvania State University
Laura Chihara	Department of Mathematics	Carleton College
Avril Coghlan	Department of Genetics	Trinity College
Dannie Durand	Departments of Biological Sciences and Computer Science	Carnegie Mellon University
Evan Eichler		Case Western Reserve University
Nadia El-Mabrouk	Informatique et recherche opérationnelle	University of Montreal
Scott Fahrenkrug	Department of Animal Science	University of Minnesota
David Fernández-Baca	Department of Computer Science	Iowa State University
Allan Force	Department of Molecular Genetics	Virginia Mason Research Center
Shmuel Friedland	Department of Mathematics, Statistics, and Computer Science	University of Illinois at Chicago
Tim Garoni	Institute for Mathematics and its Applications	University of Minnesota
Anant Godbole	Department of Mathematics	East Tennessee State University
Steve Goldstein	Department of Biotechnology Center	University of Wisconsin-Madison
Josefa Gonzalez	Departament de Genetica i de Microbiologia	Autonomous University of Barcelona
Balaji Gopalakrishnan	Institute for Mathematics and its Applications	University of Minnesota
Roderic Guigó	Grup de Recerca en Informatica Biomedica	Instituto Municipal de Investigación Mèdica (IMIM)
Chuan-Hsiang Han	Institute for Mathematics and its Applications	University of Minnesota
Tzvika Hartman	Department of Applied Mathematics and Computer Science	Weizmann Institute of Science
Dirk Holste	Department of Biology	Massachusetts Institute of Technology
Elizabeth Housworth	Department of Mathematics	Indiana University
Fern Hunt	Mathematical and Computational Sciences Division	National Institute of Standards and Technology
Naresh Jain	School of Mathematics	University of Minnesota
Lili Ju	Institute for Mathematics and its Applications	University of Minnesota
Sabera Kazi	Wireless and RF Solutions	Honeywell
Christina Kendziorski	Department of Biostatistics and Medical Informatic	University of Wisconsin-Madison
Mohammad Khan	Department of Mathematics	Kent State University
Dohyun Kim	Department of Statistics	Seoul National University
Thomas Kurtz	Department of Mathematics	University of Wisconsin-Madison
Jens Lagergren	Stockholm Bioinformatics Center	Royal Institute of Technology (KTH)
Bret Larget	Department of Statistics and Botany	University of Wisconsin-Madison
Emmanuelle Lerat	Biométrie et Biologie Évolutive	Université Claude-Bernard (Lyon I)
C. Linder	Department of Integrated Biology	University of Texas at Austin
Bill Long		CRAY Inc
Michael Lynch	Department of Biology	Indiana University
Wojciech Makalowski	Department of Biology	Pennsylvania State University
Bob Mau	Department of AHABS / Oncology	University of Wisconsin-Madison
Georgiana May	Department of Ecology and Evolutionary Biology	University of Minnesota
Aoife McLysaght	Department of Genetics	Trinity College
Joao Meidanis	Institute of Computing	State University of Campinas (UNICAMP)
Daniel Miranker	Department of Computer Science	University of Texas at Austin
Julia Mixtacki	Fakultät für Mathematik	Universität Bielefeld
Bernard Moret	Department of Computer Science	University of New Mexico
James Mullikin	National Human Genome Research Institute	National Institutes of Health
Bill Murphy	Laboratory of Genomic Diversity	National Cancer Institute
Gene Myers		Celera Genomics Corporation
Luay Nakhleh	Department of Computer Science	University of Texas at Austin
Haewon Nam	Institute of Mathematics and Statistics	University of Minnesota
Michael Newton	Department of Statistics	University of Wisconsin-Madison
Amir Niknejad	Department of Mathematics	University of Illinois at Chicago
Nikolas Nikolaidis	IMEG and Department of Biology	Pennsylvania State University
Stephen O'Brien	Laboratory of Genomic Diversity	National Cancer Institute
Ross Overbeek	Mathematics and Computer Science Division	Argonne National Laboratory
Wei Pan	Division of Biostatistics	University of Minnesota
Pavel Pevzner	Department of Computer Science and Engineering	University of California, San Diego
Ron Pinter	Department of Computer Science	Technion-Israel Institute of Technology
Lea Popovic	Institute for Mathematics and its Applications	University of Minnesota
Juan Poyatos	Department of Structual and Computational Biology Program	Spanish National Cancer Centre (CNIO)
Raj Rajagopal	Department of Genomics and Proteomics	3M
Grzegorz Rempala	Department of Mathematics	University of Louisville
David Sankoff	Department of Mathematics & Statistics	University of Ottawa
Fadil Santosa	Institute for Mathematics and its Applications	University of Minnesota
Arnd Scheel	School of Mathematics	University of Minnesota
Jeanette Schmidt		Incyte Corporation
Jennifer Seffernick	Department of Biochemistry and Molecular Biophysics	University of Minnesota
Igor Sharakhov	Department of Biology/Biological Sciences	University of Notre Dame
Amal Shervington	Department of Biological Sciences	University of Central Lancashire
Jens Stoye	Technische Fakultät	Universität Bielefeld
Jijun Tang		University of New Mexico
Eric Tannier	Biométrie et Biologie Évolutive	Université Claude-Bernard (Lyon I)
Glenn Tesler	Department of Mathematics	University of California, San Diego
Peter Tiffin	Department of Plant Biology	University of Minnesota
Elisabeth Tillier	Cancer Institute	Princess Margaret Hospital
Ali Tofigh	Department of Numerical Analysis and Computer Science, NADA	Royal Institute of Technology (KTH)
Vamsi Veeramachaneni	Department of Biology	Pennsylvania State University
Jing Wang	Institute for Mathematics and its Applications	University of Minnesota
Li-San Wang	Department of Computer Science	University of Texas at Austin
Tandy Warnow	Department of Computer Science	University of Texas at Austin
Derek Wildman	Center for Molecular Medicine and Genetics	Wayne State University
Tiffani Williams	Department of Computer Science	University of New Mexico
Stephen Willson	Department of Mathematics	Iowa State University
Ken Wolfe	Department of Genetics	Trinity College
Stacia Wyman	Department of Computer Science	University of Texas at Austin
Weijia Xu	Department of Computer Science	University of Texas at Austin
Fan Yang	Department of Statistics	University of Minnesota
Yuhong Yang	Department of Statistics	Iowa State University
Ofer Zeitouni	School of Mathematics	University of Minnesota
Weixiong Zhang	Department of Computer Science and Genetics	Washington University
Yongqian Zhang	Department of Animal Science	University of Minnesota
Jun Zhao	Institute of Mathematics and its Application	University of Minnesota