Ghent University Academic Bibliography

Advanced

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

Kristoffer Forslund, Cecile Pereira, Salvador Capella-Gutierrez, Alan Sousa da Silva, Adrian Altenhoff, Jaime Huerta-Cepas, Matthieu Muffato, Mateus Patricio, Klaas Vandepoele UGent, Ingo Ebersberger, et al. (2018) BIOINFORMATICS. 34(2). p.323-329
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 orthology 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.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
keyword
FUNCTIONAL ANNOTATIONS, SEQUENCE, TREE
journal title
BIOINFORMATICS
Bioinformatics
volume
34
issue
2
pages
7 pages
publisher
Oxford Univ Press
place of publication
Oxford
Web of Science type
Article
Web of Science id
000419593000027
ISSN
1367-4803
1460-2059
DOI
10.1093/bioinformatics/btx542
project
Bioinformatics: from nucleotids to networks (N2N)
language
English
UGent publication?
yes
classification
U
id
8558082
handle
http://hdl.handle.net/1854/LU-8558082
date created
2018-04-03 09:46:40
date last changed
2018-04-03 09:46:40
@article{8558082,
  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 orthology 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.},
  author       = {Forslund, Kristoffer and Pereira, Cecile and Capella-Gutierrez, Salvador and Sousa da Silva, Alan and Altenhoff, Adrian and Huerta-Cepas, Jaime and Muffato, Matthieu and Patricio, Mateus and Vandepoele, Klaas and Ebersberger, Ingo and Blake, Judith and Fernandez Breis, Jesualdo Tomas and Boeckmann, Brigitte and Gabaldon, Toni and Sonnhammer, Erik and Dessimoz, Christophe and Lewis, Suzanna},
  issn         = {1367-4803},
  journal      = {BIOINFORMATICS},
  keyword      = {FUNCTIONAL ANNOTATIONS,SEQUENCE,TREE},
  language     = {eng},
  number       = {2},
  pages        = {323--329},
  publisher    = {Oxford Univ Press},
  title        = {Gearing up to handle the mosaic nature of life in the quest for orthologs},
  url          = {http://dx.doi.org/10.1093/bioinformatics/btx542},
  volume       = {34},
  year         = {2018},
}

Chicago
Forslund, Kristoffer, Cecile Pereira, Salvador Capella-Gutierrez, Alan Sousa da Silva, Adrian Altenhoff, Jaime Huerta-Cepas, Matthieu Muffato, et al. 2018. “Gearing up to Handle the Mosaic Nature of Life in the Quest for Orthologs.” Bioinformatics 34 (2): 323–329.
APA
Forslund, K., Pereira, C., Capella-Gutierrez, S., Sousa da Silva, A., Altenhoff, A., Huerta-Cepas, J., Muffato, M., et al. (2018). Gearing up to handle the mosaic nature of life in the quest for orthologs. BIOINFORMATICS, 34(2), 323–329.
Vancouver
1.
Forslund K, Pereira C, Capella-Gutierrez S, Sousa da Silva A, Altenhoff A, Huerta-Cepas J, et al. Gearing up to handle the mosaic nature of life in the quest for orthologs. BIOINFORMATICS. Oxford: Oxford Univ Press; 2018;34(2):323–9.
MLA
Forslund, Kristoffer, Cecile Pereira, Salvador Capella-Gutierrez, et al. “Gearing up to Handle the Mosaic Nature of Life in the Quest for Orthologs.” BIOINFORMATICS 34.2 (2018): 323–329. Print.