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

Fall 2003

IMA Workshop 2:

IMA/RECOMB Satellite Workshop on Comparative Genomics

October 20-24, 2003

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

Schedule	Participants	Registration	Feedback
Abstracts
Material from Talks
Group Photo

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, 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