Agenda 2011

First Session

Chair: Javier Herrero

Welcome note

Orthology vs Not orthology
Erik Sonnhammer

Conceptual Framework and Pilot Study to Benchmarking Phylogenomic Databases Based on Reference Gene Trees
Brigitte Boeckmann, Marc Robinson-Rechavi, Ioannis Xenarios, Christophe Dessimoz

Groups of orthologs: objectives and definitions
Christophe Dessimoz

Homology within multi-domain families
Dannie Durand

Second Session

Chair: Erik Sonnhammer

Orthology Inference Using Hidden Markov Models
Ingo Ebersberger

Genes in the orthology twilight zone
Radek Szklarczyk

Taxonomic classification of metagenomics sequences
Ikuo Uchiyama

Third Session

Chair: David Roos

Prediction of orthology and paralogy based on gene phylogenies
Toni Gabaldón

OrthoDB: Correlating traits of gene retention, sequence divergence, duplicability and essentiality
Evgenia V. Kriventseva

Ruchira S. Datta, Kimmen Sjölander

Fourth Session

Chair: Dannie Durand

Phylogenetic placement of sequences using a graph alignment algorithm
Ari Löytynoja, Albert J. Vilella, Nick Goldman

Detection and handling of split genes in phylogenetic studies
Thomas Maurel, Albert Vilella, Javier Herrero

P-POD, the Princeton Protein Orthology Database
Michael S. Livstone, Rose Oughtred, Sven Heinicke, Benjamin Vernot, Curtis Huttenhower, Dannie Durand, Kara Dolinski

An ensemble method for the identification of plant orthologs
Michiel Van Bel, Sebastian Proost, Yves Van de Peer, Klaas Vandepoele

Fifth Session

Chair: Kimmen Sjölander

The protein barcode: capturing evolutionary histories in vertebrates
Benjamin Linard

Gene families as meta-communities in a similarity network
Vincent Miele

Exploiting Orthology for Data Mining – Experience from the Eukaryotic Pathogen Genome Database ( and the Drug Target Prioritization Database (
David Roos

Pan-Taxonomic Compara & HMMs
Andy Yates


Reference proteome and Benchmarking Workshop (I)

Chair: Maria Martin

Generation of the Reference proteome sets for the QfO consortium
UniProt reference proteomes
Eleanor Stanley, Alan Wilter Sousa da Silva, Benoit Bely, Maria Jesus Martin

Representative Proteomes
Raja Mazumder

Reference proteome and Benchmarking Workshop (II)

Chair: Christophe Dessimoz

Web Service for Assessment of Orthology Predictions
Adrian Altenhoff, Christophe Dessimoz

Orthology of proteins with promiscuous domains
Jacob Joseph, Dannie Durand

Function Prediction

Chair: Mike Cherry

Integrating expression data with sequence orthology to predict functional homologs across plant species
Sara Movahedi, Michiel Van Bel, Yves Van de Peer, Klaas Vandepoele

Using evolutionary reconstructions to infer gene function
Paul D. Thomas, Pascale Gaudet, Suzanna Lewis

Quality of electronic Gene Ontology annotations
Nives Škunca, Adrian Altenhoff and Christophe Dessimoz

Standardised Formats

Chair:Erik Sonhammer

Determination of functional ncRNA orthology

Chair:Javier Herrero

Strategies for assessing similarity

Chair: Toni Gabaldón

Ancestral HMMs and their Use to Detect Distant Homologs
Jean-Baka Domelevo Entfellner, Olivier Gascuel

Tina Koestler

Handling alternative transcripts

Chair: Brigitte Boeckmann

Round table discussion + concluding remarks