PROGRAM INFORMATION

KEYNOTE SPEAKERS

CONTRIBUTED PAPERS

SCHEDULE

KEYNOTE SPEAKERS

 Richard Durbin (Welcome Trust Sanger institute)
Jotun Hein (Department of Statistics University of Oxford, UK)
Laurence Hurst (Department of Biology and Biochemistry University of Bath, UK)
Csaba Pál (Evolutionary Systems Biology Group Biological Research Center, Szeged, Hungary)
Lisa Stubbs (Genome Biology group)
Jeroen Raes (EMBL Heidelberg)

CONTRIBUTED PAPERS
  • Aida Ouangraoua and Anne Bergeron. Parking functions, labeled trees and DCJ sorting scenarios
  • Guillaume Blin and Jens Stoye. Finding Nested Common Intervals Efficiently
  • Cedric Chauve, Tamon Stephen, Utz-Uwe Haus and Vivija You. Minimal Conflicting Sets for the Consecutive Ones Property in ancestral genome reconstruction
  • Eric Tannier. Yeast ancestral genome reconstructions: the possibilities of computational methods
  • Tomas Vinar, Bronislava Brejova, Giltae Song and Adam Siepel. Reconstructing Histories of Complex Gene Clusters on a Phylogeny
  • Andrew Wei Xu. DCJ median problems on linear multichromosomal genomes: graph representation and fast exact solutions
  • Tamir Tuller, Hadas Birin, Martin Kupiec and Eytan Ruppin. Co-evolutionary Models for Reconstructing Ancestral Genomic Sequences: Computational Issues and Biological examples
  • Paul Medvedev and Jens Stoye. Rearrangement Models and Single-Cut Operations
  • Marilia Braga and Jens Stoye. Counting All DCJ Sorting Scenarios
  • Chih-Hao Hsu, Yu Zhang, Ross Hardison and Webb Miller. Whole-Genome Analysis of Gene Conversion Events
  • Minmei Hou, Cathy Riemer, Piotr Berman, Ross Hardison and Webb Miller. Aligning two genomic sequences that contain duplications
  • Giltae Song, Louxin Zhang, Tomas Vinar and Webb Miller. Inferring the Recent Duplication History of a Gene Cluster
  • Zhenyu Yang and David Sankoff. Natural parameter values for generalized gene adjacency
  • Zaky Adam and David Sankoff. A statistically fair comparison of ancestral genome reconstructions, based on breakpoint and rearrangement distances
  • Sébastien Angibaud, Guillaume Fertin, Annelyse Thévenin and Stéphane Vialette. Pseudo-boolean programming for partially ordered genomes
  • Dale Richardson and Thomas Wiehe. Properties of sequence conservation in upstream regulatory and protein coding sequences among paralogs in Arabidopsis thaliana
  • Guylaine Poisson, Mahdi Belcaid and Anne Bergeron. Comparative genomics and extensive recombinations in phage communities
  • Xiao Liu and Neil Clarke. Transcription factor binding probabilities in orthologous promoters: an alignment-free approach to the inference of functional regulatory targets
  • Joao Delgado, Ines Lynce and Vasco Manquinho. Computing the Summed Adjacency Disruption Number between Two Genomes with Duplicate Genes using Pseudo-Boolean Optimization
Schedule

Sunday, Sept 27

8:00- REGISTRATION

9:00-10:00 Invited speaker: Lisa Stubbs, KRAB-ZNF transcription factors and the evolution of mammalian regulatory networks

10:00-10:30 COFFEE

10:30-10:55 Eric Tannier, Yeast ancestral genome reconstructions: the possibilities of computational methods
10:55-11:20 Zhenyu Yang and David Sankoff, Natural parameter values for generalized gene adjacency
11:20-11:45 Aida Ouangraoua and Anne Bergeron Parking functions, labeled trees and DCJ sorting scenarios and Marilia Braga and Jens Stoye Counting All DCJ Sorting Scenarios (Joint presentation)
11:45-12:10 Cedric Chauve, Tamon Stephen, Utz-Uwe Haus and Vivija You. Minimal Conflicting Sets for the Consecutive Ones Property in ancestral genome reconstruction

12:10-14:00 LUNCH

14:00-15:00 Invited speaker: Csaba Pál Evolution of cellular networks in microbes
15:00-15:25 Guillaume Blin and Jens Stoye Finding Nested Common Intervals Efficiently

15:25-17:30 Poster session and Wine & Cheese party

19:00-21:00 Facultative program: Széchenyi thermal bath

Monday, Sept 28

9:00-10:00 Invited speaker: Laurance Hurst Why there is more to gene evolution than protein function: splicing, nucleosomes and dual-coding sequence

10:00-10:30 COFFEE

10:30-10:55 Minmei Hou, Cathy Riemer, Piotr Berman, Ross Hardison and Webb Miller Aligning two genomic sequences that contain duplications
10:55-11:20 Giltae Song, Louxin Zhang, Tomas Vinar and Webb Miller Inferring the Recent Duplication History of a Gene Cluster
11:20-11:45 Sébastien Angibaud, Guillaume Fertin, Annelyse Thévenin and Stéphane Vialette Pseudo-boolean programming for partially ordered genomes
11:45-12:10 Joao Delgado, Ines Lynce and Vasco Manquinho Computing the Summed Adjacency Disruption Number between Two Genomes with Duplicate Genes using Pseudo-Boolean Optimization

12:10-14:00 LUNCH

14:00-15:00 Invited speaker: Jeroen Raes Untangling microbial communities sing metagenomics - from oceans to the human body
15:00-15:25 Tomas Vinar, Bronislava Brejova, Giltae Song and Adam Siepel Reconstructing Histories of Complex Gene Clusters on a Phylogeny

15:25-15:55 COFFEE

15:55-16:20 Andrew Wei Xu DCJ median problems on linear multichromosomal genomes: graph representation and fast exact solutions
16:20-16:45 Paul Medvedev and Jens Stoye Rearrangement Models and Single-Cut Operations

20:00-23:00 CONFERENCE DINNER, Kiskakukk Restaurant

Tuesday, Sept 29

9:00-10:00 Invited speaker: Richard Durbin TBA

10:00-10:30 COFFEE

10:30-10:55 Tamir Tuller, Hadas Birin, Martin Kupiec and Eytan Ruppin Co-evolutionary Models for Reconstructing Ancestral Genomic Sequences: Computational Issues and Biological examples
10:55-11:20 Chih-Hao Hsu, Yu Zhang, Ross Hardison and Webb Miller Whole-Genome Analysis of Gene Conversion Events
11:20-11:45 Zaky Adam and David Sankoff A statistically fair comparison of ancestral genome reconstructions, based on breakpoint and rearrangement distances
11:45-12:10 Guylaine Poisson, Mahdi Belcaid and Anne Bergeron Comparative genomics and extensive recombinations in phage communities

12:10-14:00 LUNCH

14:00-15:00 Invited speaker: Jotun Hein Statistical alignment and footprinting
15:00-15:25 Dale Richardson and Thomas Wiehe Properties of sequence conservation in upstream regulatory and protein coding sequences among paralogs in Arabidopsis thaliana
15:25-15:50 Xiao Liu and Neil Clarke Transcription factor binding probabilities in orthologous promoters: an alignment-free approach to the inference of functional regulatory targets