======== 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__// **PHOG**\\ //__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 (EuPathDB.org) and the Drug Target Prioritization Database (TDRtargets.org)**\\ //__David Roos__// **Pan-Taxonomic Compara & HMMs**\\ //__Andy Yates__// ====== Workshops ====== ===== 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// **rEvolver**\\ //__Tina Koestler__// ===== Handling alternative transcripts ===== Chair: Brigitte Boeckmann ====== Round table discussion + concluding remarks ======