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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

Is Cited by the Following 17 Articles in this Archive:

Iterative orthology prediction uncovers new mitochondrial proteins and identifies C12orf62 as the human ortholog of COX14, a protein involved in the assembly of cytochrome c oxidase
Radek Szklarczyk, Bas FJ Wanschers, Thomas D Cuypers, John J Esseling, Moniek Riemersma, Mariël AM van den Brand, Jolein Gloerich, Edwin Lasonder, Lambert P van den Heuvel, Leo G Nijtmans, Martijn A Huynen
Genome Biol. 2012; 13(2): R12. Published online 2012 February 22. doi: 10.1186/gb-2012-13-2-r12
PMCID:
PMC3334569
Abstract Full Text PDF–3.1M Supplementary Material
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
Roundup 2.0: enabling comparative genomics for over 1800 genomes
Todd F. DeLuca, Jike Cui, Jae-Yoon Jung, Kristian Che St. Gabriel, Dennis P. Wall
Bioinformatics. 2012 March 1; 28(5): 715–716. Published online 2012 January 13. doi: 10.1093/bioinformatics/bts006
PMCID:
PMC3289913
Abstract Full Text PDF–71K
InterEvol database: exploring the structure and evolution of protein complex interfaces
Guilhem Faure, Jessica Andreani, Raphaël Guerois
Nucleic Acids Res. 2012 January; 40(D1): D847–D856. Published online 2011 November 2. doi: 10.1093/nar/gkr845
PMCID:
PMC3245184
Abstract Full Text PDF–4.7M
An integrative approach to ortholog prediction for disease-focused and other functional studies
Yanhui Hu, Ian Flockhart, Arunachalam Vinayagam, Clemens Bergwitz, Bonnie Berger, Norbert Perrimon, Stephanie E Mohr
BMC Bioinformatics. 2011; 12: 357. Published online 2011 August 31. doi: 10.1186/1471-2105-12-357
PMCID:
PMC3179972
Abstract Full Text PDF–825K Supplementary Material
Domain architecture conservation in orthologs
Kristoffer Forslund, Isabella Pekkari, Erik LL Sonnhammer
BMC Bioinformatics. 2011; 12: 326. Published online 2011 August 5. doi: 10.1186/1471-2105-12-326
PMCID:
PMC3215765
Abstract Full Text PDF–409K Supplementary Material
Ortholog identification in the presence of domain architecture rearrangement
Kimmen Sjölander, Ruchira S. Datta, Yaoqing Shen, Grant M. Shoffner
Brief Bioinform. 2011 September; 12(5): 413–422. Published online 2011 June 28. doi: 10.1093/bib/bbr036
PMCID:
PMC3178056
Abstract Full Text PDF–343K
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
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
Nonadaptive origins of interactome complexity
Ariel Fernández, Michael Lynch
Nature. Author manuscript; available in PMC 2011 December 23.
Published in final edited form as: Nature. 2011 May 18; 474(7352): 502–505. doi: 10.1038/nature09992
PMCID:
PMC3121905
Abstract Full Text PDF–1.3M Supplementary Material
Representative Proteomes: A Stable, Scalable and Unbiased Proteome Set for Sequence Analysis and Functional Annotation
Chuming Chen, Darren A. Natale, Robert D. Finn, Hongzhan Huang, Jian Zhang, Cathy H. Wu, Raja Mazumder
PLoS One. 2011; 6(4): e18910. Published online 2011 April 27. doi: 10.1371/journal.pone.0018910
PMCID:
PMC3083393
Abstract Full Text PDF–702K Supplementary Material
IsoBase: a database of functionally related proteins across PPI networks
Daniel Park, Rohit Singh, Michael Baym, Chung-Shou Liao, Bonnie Berger
Nucleic Acids Res. 2011 January; 39(Database issue): D295–D300. Published online 2010 December 16. doi: 10.1093/nar/gkq1234
PMCID:
PMC3013743
Abstract Full Text PDF–3.0M
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
Predicting phenotypic traits of prokaryotes from protein domain frequencies
Thomas Lingner, Stefanie Mühlhausen, Toni Gabaldón, Cedric Notredame, Peter Meinicke
BMC Bioinformatics. 2010; 11: 481. Published online 2010 September 24. doi: 10.1186/1471-2105-11-481
PMCID:
PMC2955703
Abstract Full Text PDF–353K Supplementary Material
GreenPhylDB v2.0: comparative and functional genomics in plants
Mathieu Rouard, Valentin Guignon, Christelle Aluome, Marie-Angélique Laporte, Gaëtan Droc, Christian Walde, Christian M. Zmasek, Christophe Périn, Matthieu G. Conte
Nucleic Acids Res. 2011 January; 39(Database issue): D1095–D1102. Published online 2010 September 22. doi: 10.1093/nar/gkq811
PMCID:
PMC3013755
Abstract Full Text PDF–4.8M
Bayesian Markov Random Field Analysis for Protein Function Prediction Based on Network Data
Yiannis A. I. Kourmpetis, Aalt D. J. van Dijk, Marco C. A. M. Bink, Roeland C. H. J. van Ham, Cajo J. F. ter Braak
PLoS One. 2010; 5(2): e9293. Published online 2010 February 24. doi: 10.1371/journal.pone.0009293
PMCID:
PMC2827541
Abstract Full Text PDF–1.1M Supplementary Material
Identification of mammalian orthologs using local synteny
Jin Jun, Ion I Mandoiu, Craig E Nelson
BMC Genomics. 2009; 10: 630. Published online 2009 December 23. doi: 10.1186/1471-2164-10-630
PMCID:
PMC2807883
Abstract Full Text PDF–521K Supplementary Material
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