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— agenda_qf2 [2017/02/17 17:46] (current)
Cécile Pereira created
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 +======== 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 ======
 +