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Large-scale assignment of orthology: back to phylogenetics?
Toni Gabaldón
Genome Biol. 2008; 9(10): 235. Published online 2008 October 30. doi: 10.1186/gb-2008-9-10-235
PMCID:
PMC2760865
Abstract Full Text PDF–119K

Is Cited by the Following 29 Articles in this Archive:

Toward community standards in the quest for orthologs
Christophe Dessimoz, Toni Gabaldón, David S. Roos, Erik L. L. Sonnhammer, Javier Herrero, the Quest for Orthologs Consortium, Adrian Altenhoff, Rolf Apweiler, Michael Ashburner, Judith Blake, Brigitte Boeckmann, Alan Bridge, Elspeth Bruford, Mike Cherry, Matthieu Conte, Durand Dannie, Ruchira Datta, Christophe Dessimoz, Jean-Baka Domelevo Entfellner, Ingo Ebersberger, Toni Gabaldón, Michael Galperin, Javier Herrero, Jacob Joseph, Tina Koestler, Evgenia Kriventseva, Odile Lecompte, Jack Leunissen, Suzanna Lewis, Benjamin Linard, Michael S. Livstone, Hui-Chun Lu, Maria Martin, Raja Mazumder, David Messina, Vincent Miele, Matthieu Muffato, Guy Perrière, Marco Punta, David Roos, Mathieu Rouard, Thomas Schmitt, Fabian Schreiber, Alan Silva, Kimmen Sjölander, Nives Škunca, Erik Sonnhammer, Eleanor Stanley, Radek Szklarczyk, Paul Thomas, Ikuo Uchiyama, Michiel Van Bel, Klaas Vandepoele, Albert J. Vilella, Andrew Yates, Evgeny Zdobnov
Bioinformatics. 2012 March 15; 28(6): 900–904. Published online 2012 February 12. doi: 10.1093/bioinformatics/bts050
PMCID:
PMC3307119
Abstract Full Text PDF–99K
Dissecting Plant Genomes with the PLAZA Comparative Genomics Platform
Michiel Van Bel, Sebastian Proost, Elisabeth Wischnitzki, Sara Movahedi, Christopher Scheerlinck, Yves Van de Peer, Klaas Vandepoele
Plant Physiol. 2012 February; 158(2): 590–600. Published online 2011 December 23. doi: 10.1104/pp.111.189514
PMCID:
PMC3271752
Free in PMC on 2013/02/01
A novel substitution matrix fitted to the compositional bias in Mollicutes improves the prediction of homologous relationships
Claire Lemaitre, Aurélien Barré, Christine Citti, Florence Tardy, François Thiaucourt, Pascal Sirand-Pugnet, Patricia Thébault
BMC Bioinformatics. 2011; 12: 457. Published online 2011 November 24. doi: 10.1186/1471-2105-12-457
PMCID:
PMC3248887
Abstract Full Text PDF–658K Supplementary Material
Genome-Wide Detection of Gene Extinction in Early Mammalian Evolution
Shigehiro Kuraku, Shigeru Kuratani
Genome Biol Evol. 2011; 3: 1449–1462. Published online 2011 November 17. doi: 10.1093/gbe/evr120
PMCID:
PMC3296468
Abstract Full Text PDF–1.4M
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges
Sean Powell, Damian Szklarczyk, Kalliopi Trachana, Alexander Roth, Michael Kuhn, Jean Muller, Roland Arnold, Thomas Rattei, Ivica Letunic, Tobias Doerks, Lars J. Jensen, Christian von Mering, Peer Bork
Nucleic Acids Res. 2012 January; 40(D1): D284–D289. Published online 2011 November 16. doi: 10.1093/nar/gkr1060
PMCID:
PMC3245133
Abstract Full Text PDF–5.0M
Orthology prediction methods: A quality assessment using curated protein families
Kalliopi Trachana, Tomas A Larsson, Sean Powell, Wei-Hua Chen, Tobias Doerks, Jean Muller, Peer Bork
Bioessays. 2011 October; 33(10): 769–780. doi: 10.1002/bies.201100062
PMCID:
PMC3193375
Abstract Full Text PDF–486K Supplementary Material
Phylogenetic Relationships within the Opisthokonta Based on Phylogenomic Analyses of Conserved Single-Copy Protein Domains
Guifré Torruella, Romain Derelle, Jordi Paps, B. Franz Lang, Andrew J. Roger, Kamran Shalchian-Tabrizi, Iñaki Ruiz-Trillo
Mol Biol Evol. 2012 February; 29(2): 531–544. Published online 2011 July 18. doi: 10.1093/molbev/msr185
PMCID:
PMC3350318
Free in PMC on 2013/02/01
Identification and Characterization of NF-Y Transcription Factor Families in the Monocot Model Plant Brachypodium distachyon
Shuanghe Cao, Roderick W. Kumimoto, Chamindika L. Siriwardana, Jan R. Risinger, Ben F. Holt, III
PLoS One. 2011; 6(6): e21805. Published online 2011 June 30. doi: 10.1371/journal.pone.0021805
PMCID:
PMC3128097
Abstract Full Text PDF–1.3M Supplementary Material
Computational methods for Gene Orthology inference
David M. Kristensen, Yuri I. Wolf, Arcady R. Mushegian, Eugene V. Koonin
Brief Bioinform. 2011 September; 12(5): 379–391. Published online 2011 June 17. doi: 10.1093/bib/bbr030
PMCID:
PMC3178053
Free in PMC on 2012/09/01
When orthologs diverge between human and mouse
Walid H. Gharib, Marc Robinson-Rechavi
Brief Bioinform. 2011 September; 12(5): 436–441. Published online 2011 June 15. doi: 10.1093/bib/bbr031
PMCID:
PMC3178054
Abstract Full Text PDF–91K
Testing the Ortholog Conjecture with Comparative Functional Genomic Data from Mammals
Nathan L. Nehrt, Wyatt T. Clark, Predrag Radivojac, Matthew W. Hahn
PLoS Comput Biol. 2011 June; 7(6): e1002073. Published online 2011 June 9. doi: 10.1371/journal.pcbi.1002073
PMCID:
PMC3111532
Abstract Full Text PDF–516K Supplementary Material
Finding Single Copy Genes Out of Sequenced Genomes for Multilocus Phylogenetics in Non-Model Fungi
Nicolas Feau, Thibaut Decourcelle, Claude Husson, Marie-Laure Desprez-Loustau, Cyril Dutech
PLoS One. 2011; 6(4): e18803. Published online 2011 April 13. doi: 10.1371/journal.pone.0018803
PMCID:
PMC3076447
Abstract Full Text PDF–1.0M Supplementary Material
CycADS: an annotation database system to ease the development and update of BioCyc databases
Augusto F. Vellozo, Amélie S. Véron, Patrice Baa-Puyoulet, Jaime Huerta-Cepas, Ludovic Cottret, Gérard Febvay, Federica Calevro, Yvan Rahbé, Angela E. Douglas, Toni Gabaldón, Marie-France Sagot, Hubert Charles, Stefano Colella
Database (Oxford) 2011; 2011: bar008. Published online 2011 April 7. doi: 10.1093/database/bar008
PMCID:
PMC3072769
Abstract Full Text PDF–572K
OrthoInspector: comprehensive orthology analysis and visual exploration
Benjamin Linard, Julie D Thompson, Olivier Poch, Odile Lecompte
BMC Bioinformatics. 2011; 12: 11. Published online 2011 January 10. doi: 10.1186/1471-2105-12-11
PMCID:
PMC3024942
Abstract Full Text PDF–1.4M Supplementary Material
MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score
Leszek P. Pryszcz, Jaime Huerta-Cepas, Toni Gabaldón
Nucleic Acids Res. 2011 March; 39(5): e32. Published online 2010 December 11. doi: 10.1093/nar/gkq953
PMCID:
PMC3061081
Abstract Full Text PDF–6.4M Supplementary Material
OMA 2011: orthology inference among 1000 complete genomes
Adrian M. Altenhoff, Adrian Schneider, Gaston H. Gonnet, Christophe Dessimoz
Nucleic Acids Res. 2011 January; 39(Database issue): D289–D294. Published online 2010 November 27. doi: 10.1093/nar/gkq1238
PMCID:
PMC3013747
Abstract Full Text PDF–7.5M
PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions
Jaime Huerta-Cepas, Salvador Capella-Gutierrez, Leszek P. Pryszcz, Ivan Denisov, Diego Kormes, Marina Marcet-Houben, Toni Gabaldón
Nucleic Acids Res. 2011 January; 39(Database issue): D556–D560. Published online 2010 November 11. doi: 10.1093/nar/gkq1109
PMCID:
PMC3013701
Abstract Full Text PDF–4.3M
MetaPIGA v2.0: maximum likelihood large phylogeny estimation using the metapopulation genetic algorithm and other stochastic heuristics
Raphaël Helaers, Michel C Milinkovitch
BMC Bioinformatics. 2010; 11: 379. Published online 2010 July 15. doi: 10.1186/1471-2105-11-379
PMCID:
PMC2912891
Abstract Full Text PDF–6.0M
Dating and functional characterization of duplicated genes in the apple (Malus domestica Borkh.) by analyzing EST data
Javier Sanzol
BMC Plant Biol. 2010; 10: 87. Published online 2010 May 14. doi: 10.1186/1471-2229-10-87
PMCID:
PMC3095355
Abstract Full Text PDF–4.9M Supplementary Material
SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction
Raffi Hagopian, John R. Davidson, Ruchira S. Datta, Bushra Samad, Glen R. Jarvis, Kimmen Sjölander
Nucleic Acids Res. 2010 July 1; 38(Web Server issue): W29–W34. Published online 2010 April 29. doi: 10.1093/nar/gkq298
PMCID:
PMC2896197
Abstract Full Text PDF–8.8M
Getting Started in Gene Orthology and Functional Analysis
Gang Fang, Nitin Bhardwaj, Rebecca Robilotto, Mark B. Gerstein
PLoS Comput Biol. 2010 March; 6(3): e1000703. Published online 2010 March 26. doi: 10.1371/journal.pcbi.1000703
PMCID:
PMC2845645
Full Text PDF–430K Supplementary Material
Genome Sequence of the Pea Aphid Acyrthosiphon pisum
The International Aphid Genomics Consortium
PLoS Biol. 2010 February; 8(2): e1000313. Published online 2010 February 23. doi: 10.1371/journal.pbio.1000313
PMCID:
PMC2826372
Abstract Full Text PDF–1.3M Supplementary Material
2× genomes - depth does matter
Michel C Milinkovitch, Raphaël Helaers, Eric Depiereux, Athanasia C Tzika, Toni Gabaldón
Genome Biol. 2010; 11(2): R16. Published online 2010 February 9. doi: 10.1186/gb-2010-11-2-r16
PMCID:
PMC2872876
Abstract Full Text PDF–1.0M
ETE: a python Environment for Tree Exploration
Jaime Huerta-Cepas, Joaquín Dopazo, Toni Gabaldón
BMC Bioinformatics. 2010; 11: 24. Published online 2010 January 13. doi: 10.1186/1471-2105-11-24
PMCID:
PMC2820433
Abstract Full Text PDF–623K
InParanoid 7: new algorithms and tools for eukaryotic orthology analysis
Gabriel Östlund, Thomas Schmitt, Kristoffer Forslund, Tina Köstler, David N. Messina, Sanjit Roopra, Oliver Frings, Erik L. L. Sonnhammer
Nucleic Acids Res. 2010 January; 38(Database issue): D196–D203. Published online 2010 January. doi: 10.1093/nar/gkp931
PMCID:
PMC2808972
Abstract Full Text PDF–5.2M
Phylogenomics of the oxidative phosphorylation in fungi reveals extensive gene duplication followed by functional divergence
Marina Marcet-Houben, Giuseppe Marceddu, Toni Gabaldón
BMC Evol Biol. 2009; 9: 295. Published online 2009 December 21. doi: 10.1186/1471-2148-9-295
PMCID:
PMC2803194
Abstract Full Text PDF–1.0M Supplementary Material
Historical Constraints on Vertebrate Genome Evolution
Michel C. Milinkovitch, Raphaël Helaers, Athanasia C. Tzika
Genome Biol Evol. 2010; 2: 13–18. Published online 2009 December 18. doi: 10.1093/gbe/evp052
PMCID:
PMC2839353
Abstract Full Text PDF–357K
Joining forces in the quest for orthologs
Toni Gabaldón, Christophe Dessimoz, Julie Huxley-Jones, Albert J Vilella, Erik LL Sonnhammer, Suzanna Lewis
Genome Biol. 2009; 10(9): 403. Published online 2009 September 29. doi: 10.1186/gb-2009-10-9-403
PMCID:
PMC2768974
Abstract Full Text PDF–171K
The Tree versus the Forest: The Fungal Tree of Life and the Topological Diversity within the Yeast Phylome
Marina Marcet-Houben, Toni Gabaldón
PLoS ONE. 2009; 4(2): e4357. Published online 2009 February 3. doi: 10.1371/journal.pone.0004357
PMCID:
PMC2629814
Abstract Full Text PDF–280K Supplementary Material
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