2nd  RECOMB Comparative Genomics Satellite Workshop
16-19 October 2004
University of Bologna Residential Center
Bertinoro (Forlì), Italy		 bertinoro

What the Meeting is About

The workshop will consist of invited talks as well as talks selected based on submitted abstracts

The increasing availability of complete genomes from diverse organisms offers unprecedented research opportunities. Intergenomic comparison of various kinds of maps is revelatory of many types of genomic events central to biological, medical and bioinformatics research in the post-genomic era. Computational biology has a key role to play in many aspects of this work: understanding patterns and processes of genomic evolution, mapping genome-level mutational events, and the effective use of these maps by bioinformatics tools. Genomic data offer an alternative approach to phylogenetic reconstruction, based on genome-level events rather than nucleotide or amino-acid substitutions.

The core of comparative genome analysis is the establishment of the correspondence between genes (orthology analysis) or other genomic features indifferent organisms. It is these intergenomic maps that make it possible to trace the evolutionary processes responsible for the divergence of two genomes. A multitude of evolutionary events acting at various organizational levels shape genome evolution. At the lowest level, point mutations affect individual nucleotides. At a higher level, large chromosomal segments undergo duplication, lateral transfer, inversion, transposition, deletion and insertion. Ultimately, whole genomes are involved in processes of hybridization, polyploidization and endosymbiosis, often leading to rapid speciation. The complexity of genome evolution poses many exciting challenges to developers of mathematical models and algorithms, who have recourse to a spectra of algorithmic, statistical and mathematical techniques, 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.

The RECOMB Satellite Workshop on Comparative Genomics is a forum on all aspects and components of this field, ranging from new quantitative discoveries about genome structure and process to theorems on the complexity of computational problems inspired by genome comparison.

The first RECOMB satellite workshop on Comparative Genomics was held in Minneapolis in 2003.

Talk Schedule: The submitted papers are listed by first author but may be presented by another  author. Most titles can be found below. There is a reception 6-9 pm Saturday October 16.
16
17
18
19
20

Sat
Sun
Mon
Tue
Wed
08.00-09.00 arrivals breakfast
09.00-10.00 Henrik Kaessman Martin Lercher
 Ben Raphael
 departures
10.00-10.25 Berard et al.
 Song et al.
 Buhler et al
10.25-10.50 coffee  coffee  coffee 
10.50-11.15 Sharakhov et al.
Hoberman et al.
 Caspi et al.
11.15-11.40 Pinter Mau et al.
 Dubchak et al.
11.40-12.15 Miklos et al.
 Gorecki et al.
 Choi et al.
12.30-13.30 lunch! lunch! lunch!
14.00-15.00 Marie-France Sagot
 Mathieu Blanchette
 Bill Martin
15.00-15.25 A. Bashir et al.
 Sankoff, Lefebvre et al.
 Sankoff and Mazowita
15.25-15.50 coffee coffee Taneri et al.
 15.50-16.50
Daniela Delneri
 Graziano Pezole
 coffee

Important Dates

Submission Deadline:
 September 3, 2004
Notifications to Authors:
 September 16, 2004
Arrival: October 16, 2004
Departure: October 19 or 20, 2004

Location

The meeting will be held in the small medieval hilltop town of Bertinoro. This town is in Emilia Romagna about 50km east of Bologna at an elevation of about 230m.  Here is a map putting it in context. It is easily reached by train and taxi from Bologna and is close to many splendid Italian locations such as Ravenna, a treasure trove of byzantine art and history, and the Republic of San Marino (all within 35km) as well as some less well-known locations like the thermal springs of Fratta Terme and the castle and monastic gardens of Monte Maggio.  Bertinoro can also be a base for visiting some of the better-known Italian locations such as Padua, Ferrara, Vicenza, Venice, Florence and Siena.

Bertinoro itself is picturesque, with many narrow streets and walkways winding around the central peak.  The meeting will be held in a redoubtable ex-Episcopal fortress that has been converted by the University of Bologna into a modern conference center with computing facilities and Internet access.  From the fortress you can enjoy a beautiful the vista that stretches from the Tuscan Apennines to the Adriatic coast.

How to Reach Bertinoro

List of Invited Speakers


We will also have the following shorter sessions talks chosen based on submitted abstracts.

Authors: Pawel Gorecki and Jerzy Tiuryn
Title: On the structure of reconciliations

Authors: David Sankoff and Matthew Mazowita
Title: Estimators of translocations and inversions in comparative maps

Authors:  Nan Song, George Davis, and  Dannie Durand
Title: Homology Identification Strikes Back: The Challenge of Multi-Domain Proteins

Authors: Sharakhov IV*, Kayondo J, Sharakhova M, Lobo NF,Goeddel L,
Williams DW,Collins FH, Besansky NJ
Title: Comparative Analysis of the 2La Inversion Breakpoints in the Anopheles gambiae Complex

Authors: Istvan Miklos  and Jotun Hein
Title: Genome Rearrangement in Mitochondria and Its Computational Biology

Authors: Ron Y. Pinter
Title: Recent algorithmic developments in length-weighted genomic rearrangements

Authors: Severine Berard, Anne Bergeron and Cedric Chauve
Title: Conservation of Combinatorial Structures in Evolution Scenarios

Authors: A. Bashir, C. Ye, A. Price, and V. Bafna
Title: Orthologous Repeats and Phylogenetic Inference

Authors: Rose Hoberman,  David Sankoff, and Dannie Durand
Title: Calculating the Significance of Max-Gap Gene Clusters

Authors: I. Dubchak, M.Brudno, A.Poliakov, Andrey Kislyuk, Mukund Sundararajan, Serafim Batzoglou
Title: Glocal (global/local) alignment methods for comparison of DNA sequences and whole-genome assemblies utilized in VISTA tools

Authors:  Bob Mau, Aaron E. Darling, Nicole T. Perna
Title: Identifying evolutionarily conserved segments among   multiple divergent and rearranged genomes

Authors:  JeongHyeon Choi, Kwangmin Choi, Hwan-Gue Cho, and Sun Kim
Title: Multiple Genome Alignment by Clustering Pairwise Matches

Authors: Anat Caspi*, Lior Pachter
Title: Using Global Alignment to identify Transposable elements.

Authors: David Sankoff, Jean-Francois Lefebvre, Elisabeth Tillier, Adrian Maler, and Nadia El-Mabrouk
Title: The distribution of inversion lengths in prokaryotes

Authors: Bahar Taneri, Alexey Novoradovsky, Ben Snyder, Terry Gaasterland
Title: Databases for comparative analysis of human-mouse orthologous alternative splicing.

Authors: Jeremy Buhler and Rachel Nordgren
Title: Toward a Phylogenetically Aware Algorithm for Fast DNA Similarity Search

Submission

Please send files for final version to jensl@nada.kth.se and copy right from to Jens Lagergren, SBC, KTH/Albanova, 106 91 Stockholm,  Sweden.

Program committee

Cost

The workshop fee is 250 euros for early registration (before October 7) and 300 euros for late registration (October 7 and after)

Full Board Accommodation

The daily fee includes full board accommodation and coffee breaks and it is: Euros 115.00 for single room accommodation, per person, per day; Euros 105.00 for accommodation in a double room, per person, per day

BICI-UNESCO(ROSTE) Grants: A limited number of BICI-UNESCO (ROSTE) grants are available for student and young researchers. To apply, please follow the directions on the registration page.

Registration

Organization and Sponsorship

Scientific Organizing Committee Jens Lagergren, Stockholm Bioinformatics Center & KTH
Aoife McLysaght, Trinity College
Nancy Moran, University of Arizona
Bernard Moret, University of New Mexico
David Sankoff, University of Ottawa
Local Organization
Andrea Bandini, Elena Della Godenza, Centro Congressi di Bertinoro
Sponsored by BICI   Bertinoro International Center for Informatics