Brenda Andrews(University of Toronto)
Exploring genetic networks and biological pathways using yeast functional genomics
Determining how combinations of genetic variants or perturbations manifest themselves, particularly in the context of human disease, is a formidable challenge. To define general principles of genetic networks, our group has focused on the systematic identification of genetic interactions in the budding yeast. Synthetic genetic array (SGA) analysis provides a high throughput approach for systematic analysis of genetic interactions in budding yeast. We have used SGA analysis to generate a large-scale view of synthetic lethal interactions in yeast, assessing both essential and non-essential genes. We estimate that a global synthetic lethal genetic network will contain on the order of 200 000 genetic interactions, and we are testing this prediction by using SGA to complete the synthetic lethal map. We have also expanded our SGA platform to encompass other types of genetic interactions and to include cell biological phenotypes and quantitative read-outs of the activity of specific biological pathways.

Andrew G. Clark (Cornell University)
Comparative genomic imprinting
RNA-seq provides an efficient way to examine differential allelic expression across all genes with sufficient levels of expression. By performing RNA-seq in F1 progeny from reciprocal crosses of two inbred divergent strains, it becomes possible to infer differential parent-of-origin expression (genomic imprinting). We have done this with a focus on placental tissues of embryonic origin, seeking to understand evolutionary principles of genes that undergo imprinting. Comparison of human, mouse and horse reveals a striking observation - that there is considerable fluidity in the imprinting status of genes across mammals. These data provide a rich resource for understanding both molecular and evolutionary determinants of differential allelic expression and genomic imprinting.

Nicolas Corradi (University of Ottawa)
Beauty and drama in the microbial genomics universe
In the last two decades, the knowledge we have acquired by studying the genomes of laboratory model species has filled our undergraduate biology books with a "universal" conception of the structure and content of a "eukaryotic" genome. Such models, however, represent only a tiny fraction of the overall biodiversity that is present on Earth, leading to the provocative question: do model eukaryotic genomes represent exceptions rather than the rule in the "genomics" universe? Here, I will introduce the highly diverse genomic features that are sparked by several intriguing microbial eukaryotes, commonly referred to as "protists". In particular, I will discuss the genomic features assumed to be typical among eukaryotes in light of our increasing knowledge of the natural diversity, structure and content of protists' genomes.

Jan Dvorak (University of California at Davis)
Chromosome number evolution in the grass family
Dysploidy is a change in the chromosome number in a genome without a significant loss or duplication of genetic information in the genome. Comparisons of rice, sorghum, and Brachypodium distachyon genome sequences and Triticeae comparative genetic maps showed that the common ancestor of grass subfamilies Panicoideae, Ehrhartoideae, and Pooideae had 12 chromosomes. This state is preserved in the rice genome. This chromosome number was reduced to x = 7 in the wheat lineage, x = 5 in the Brachypodium lineage, x = 10 in the sorghum lineage, and x = 9 and in the finger millet lineage. All these dysploid reductions took place by insertion of an entire chromosome into the centromere of another chromosome. I will discuss the mechanism and significance of this process for genome evolution in the grass family.

Aoife McLysaght (University of Dublin)
Evolution of new genes
The most common mechanism of origin of new genes is by gene duplication, however other mechanisms are also operating including de novo origins of protein-coding genes from non-coding DNA. In this talk I will explore the constraints acting on the duplication of dosage-balanced genes and the interesting evolutionary implications of this. I will also present evidence for the de novo origin of mammalian protein-coding genes.

Nicholas Putnam (Rice University)
Long time scale evolution of metazoan genome organization.
Chromosome scale genome organization is conserved from the eumetazoan ancestor in several contemporary animal phyla, and apparently lost in others. This conservation allows us to reconstruct chromosomal gene complements for ancient animal ancestors, and to identify specific events of genome rearrangement along ancestral lineages. These reconstructions can be used to constrain models of genome evolution. We have developed new tests that suggest the observed conservation is the result of selection acting to preserve functional features of genome organization, rather than the slow decay of a neutral feature of the ancestral genome.

SCHEDULE (all talks in Desmarais room 12102)

RECOMB CG 2010 program

Friday evening, October 8
20:00-22:00 Reception

Saturday, October 9
8:00 Breakfast
8:45 Welcome
9:00 Brenda Andrews, Exploring genetic networks and biological pathways using yeast functional genomics
10:00 Emmanuel Mongin, Ken Dewar and Mathieu Blanchette. Mapping association between long-range cis-regulatory regions and their target genes using comparative genomics
10:30 Coffee (Room 12110)
11:00 Mukul S. Bansal, J. Peter Gogarten and Ron Shamir. Detecting highways of horizontal gene transfer
11:30 Stéphane Aris-Brosou. A simple measure of the dynamics of segmented genomes: an application to influenza
12:00 Hugo Devillers, Hélène Chiapello, Sophie Schbath and Meriem El Karoui. Assessing the robustness of complete bacterial genome segmentations
12:30 Lunch (Room 12110) and posters (Room 12120)
14:00 Andrew G, Clark, Comparative genomic imprinting
15:00 Jakub Kovác, Marília Braga and Jens Stoye. The problem of chromosome reincorporation in DCJ sorting and halving
15:30 Coffee (Room 12110)
16:00 Yves Gagnon, Olivier Tremblay Savard, Denis Bertrand and Nadia El-Mabrouk. Advances on genome duplication distances
16:30 Robert Warren and David Sankoff. Genome aliquoting revisited
17:00 Atheer Matroud, Michael Hendy and Christopher Tuffley. An algorithm to solve the motif alignment problem for approximate nested tandem repeats
19:30 Supper

Sunday, October 10
8:00 Breakfast
8:45 Jan Dvorak, Chromosome number evolution in the grass family
9:45 Ulisses Dias, Zanoni Dias and João Carlos Setubal. A simulation tool for the study of symmetric genomic inversions in bacteria
10:15 Coffee (Room 12110)
10:30 Max Alekseyev and Pavel Pevzner. Limited lifespan of fragile regions in mammalian evolution
11:00 Oliver Attie and Sophia Yancopoulos. Bounding generalized transpositions in genome rearrangements by DCJ
11:30 Marília Braga. On sorting genomes with DCJ and indels
12:00 Andrew Wei Xu. On Exploring phylogenetic patterns
12:30 Lunch (Room 12110) and posters (Room 12120)
14:00 Aoife Mclysaght, Evolution of new genes
15:00 Jean-Philippe Doyon, Céline Scornavacca, K. Yu. Gorbunov, Gergely J. Szöllösi, Vincent Ranwez and Vincent Berry. An efficient algorithm for gene/species trees parsimonious reconciliation with losses, duplications and transfers
15:30 Coffee (Room 12110)
16:00Yu Lin, Vaibhav Rajan and Bernard Moret. Fast and accurate phylogenetic reconstruction from high-resolution whole-genome data and a novel robustness estimator
16:30 Aïda Ouangraoua, Krister Swenson and Cedric Chauve. An approximation algorithm for computing a parsimonious first speciation in the gene duplication model
17:00 Yu Lin and Bernard Moret. A new genomic evolutionary model for rearrangements, duplications, and losses that applies across eukaryotes and prokaryotes
19:30 Banquet

Monday, October 11
8:00 Breakfast
9:00 Nicholas Putnam, Long time scale evolution of metazoan genome organization
10:00 Roland Wittler and Jens Stoye. Consistency of sequence-based gene clusters
10:30 Coffee (Room 12110)
11:00 Katharina Jahn. Efficient computation of approximate gene clusters based on reference occurrences
11:30 Ján Manuch and Murray Patterson. The complexity of the gapped consecutive-ones property problem for matrices of bounded maximum degree
12:00 Minghui Jiang. The zero exemplar distance problem
12:30 Lunch (Room 12110) and posters (Room 12120)
14:00 Nicolas Corradi, Beauty and drama in the microbial genomics universe
15:00 Aïda Ouangraoua, Anne Bergeron and Krister Swenson. Ultra-perfect sorting scenarios
15:30 Coffee (Room 12110)
16:00 Ghada Badr, Krister Swenson and David Sankoff. Listing all parsimonious reversal sequences: new algorithms and perspectives
16:30 Raluca Uricaru, Alban Mancheron and Eric Rivals. Novel definition and algorithm for chaining fragments with proportional overlaps
17:00 Haitao Jiang, Chunfang Zheng, David Sankoff and Binhai Zhu. Scaffold filling under the breakpoint distance