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Journal Articles Bioinformatics Year : 2018

Gearing up to handle the mosaic nature of life in the quest for orthologs

1 EMBL - European Molecular Biology Laboratory [Heidelberg]
2 UF - University of Florida [Gainesville]
3 I2BC - Institut de Biologie Intégrative de la Cellule
4 BioInfo - LRI - Bioinformatique (LRI)
5 UPF - Universitat Pompeu Fabra [Barcelona]
6 SIB - Swiss Institute of Bioinformatics [Lausanne]
7 CRG - Centre for Genomic Regulation
8 EMBL-EBI - European Bioinformatics Institute [Hinxton]
9 PSB Center - Center for Plant Systems Biology
10 Senckenberg Climate and Research
11 Applied Bioinformatics
12 USC - University of Southern California
13 Department of Computer Science
14 LBCMCP - Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération
15 BPGE - Bioinformatique, phylogénie et génomique évolutive [LBBE]
16 HMS - Harvard Medical School [Boston]
17 UMR AGAP - Amélioration génétique et adaptation des plantes méditerranéennes et tropicales
18 Universidad de Murcia
19 NCBI - National Center for Biotechnology Information
20 University of Geneva Medical School
21 GRAS - Genome Resource and Analysis Unit
22 IGBMC - Institut de Génétique et de Biologie Moléculaire et Cellulaire
23 CNRS - Centre National de la Recherche Scientifique
24 MAB - Méthodes et Algorithmes pour la Bioinformatique
25 Comparative Bioinformatics
26 LBBE - Laboratoire de Biométrie et Biologie Evolutive - UMR 5558
27 DEE - Department of Ecology and Evolution [UNIL, Lausanne] = Département d'écologie et évolution
28 LBNL - Lawrence Berkeley National Laboratory [Berkeley]
29 UZH - Universität Zürich [Zürich] = University of Zurich
30 Dstl - Defence Science and Technology Laboratory
31 SIB - Swiss Institute of Bioinformatics [Genève]
32 Medical School
Alan Sousa da Silva
  • Function : Author
Mateus Patricio
  • Function : Author
Klaas Vandepoele
Judith Blake
  • Function : Author
Suzanna Lewis
  • Function : Author
Carla Bello
  • Function : Author
Edward Chalstrey
  • Function : Author
Hirokazu Chiba
  • Function : Author
Oscar Conchillo-Solé
  • Function : Author
Dannie Durand
  • Function : Author
Natasha Glover
  • Function : Author
Alexander Hauser
  • Function : Author
Davide Heller
  • Function : Author
Mateus Kaduk
  • Function : Author
Jan Koch
  • Function : Author
Jeremy Levy
  • Function : Author
Benjamin Liebeskind
  • Function : Author
Marc Marcet-Houben
  • Function : Author
Martin Kauffmann
Claire Mcwhite
  • Function : Author
Sergei Mekhedov
  • Function : Author
Steven Müller
  • Function : Author
El-Mabrouk Nadia
  • Function : Author
Cedric Notredame
  • Function : Author
  • PersonId : 955125
Ivana Pilizota
  • Function : Author
Henning Redestig
  • Function : Author
Nives Škunca
  • Function : Author
Martin Steinegger
  • Function : Author
Ernst Thuer
  • Function : Author
Clément Train
  • Function : Author
Ikuo Uchiyama
  • Function : Author
Lucas Wittwer
  • Function : Author
Bethan Yates
  • Function : Author
Evgeny Zdobnov
  • Function : Author
  • PersonId : 971004
Robert Waterhouse
  • Function : Author

Abstract

The Quest for Orthologs (QfO) is an open collaboration framework for experts in comparative phylogenomics and related research areas who have an interest in highly accurate orthology predictions and their applications. We here report highlights and discussion points from the QfO meeting 2015 held in Barcelona. Achievements in recent years have established a basis to support developments for improved orthology prediction and to explore new approaches. Central to the QfO effort is proper benchmarking of methods and services, as well as design of standardized datasets and standardized formats to allow sharing and comparison of results. Simultaneously, analysis pipelines have been improved, evaluated and adapted to handle large datasets. All this would not have occurred without the long-term collaboration of Consortium members. Meeting regularly to review and coordinate complementary activities from a broad spectrum of innovative researchers clearly benefits the community. Highlights of the meeting include addressing sources of and legitimacy of disagreements between orthology calls, the context dependency of orthology definitions, special challenges encountered when analyzing very anciently rooted orthologies, orthology in the light of whole-genome duplications, and the concept of orthologous versus paralogous relationships at different levels, including domain-level orthology. Furthermore, particular needs for different applications (e.g. plant genomics, ancient gene families and others) and the infrastructure for making orthol-ogy inferences available (e.g. interfaces with model organism databases) were discussed, with several ongoing efforts that are expected to be reported on during the upcoming 2017 QfO meeting.
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hal-01758841 , version 1 (20-12-2019)

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Kristoffer Forslund, Cécile Pereira, Salvador Capella-Gutiérrez, Alan Sousa da Silva, Adrian M Altenhoff, et al.. Gearing up to handle the mosaic nature of life in the quest for orthologs. Bioinformatics, 2018, 34 (2), pp.323-329. ⟨10.1093/bioinformatics/btx542⟩. ⟨hal-01758841⟩
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