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Benchmarking ortholog identification methods using functional genomics data
Tim Hulsen, Martijn A Huynen, Jacob de Vlieg, Peter MA Groenen
Genome Biol. 2006; 7(4): R31. Published online 2006 April 13. doi: 10.1186/gb-2006-7-4-r31
PMCID:
PMC1557999
Abstract Full Text PDF–297K Supplementary Material

Is Cited by the Following 51 Articles in this Archive:

Comparative Analysis of Gene Content Evolution in Phytoplasmas and Mycoplasmas
Ling-Ling Chen, Wan-Chia Chung, Chan-Pin Lin, Chih-Horng Kuo
PLoS One. 2012; 7(3): e34407. Published online 2012 March 27. doi: 10.1371/journal.pone.0034407
PMCID:
PMC3313985
Abstract Full Text PDF–453K 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
Identifying Single Copy Orthologs in Metazoa
Christopher J. Creevey, Jean Muller, Tobias Doerks, Julie D. Thompson, Detlev Arendt, Peer Bork
PLoS Comput Biol. 2011 December; 7(12): e1002269. Published online 2011 December 1. doi: 10.1371/journal.pcbi.1002269
PMCID:
PMC3228760
Abstract Full Text PDF–1.3M Supplementary Material
ApicoAlign: an alignment and sequence search tool for apicomplexan proteins
Jamshaid Ali, Umadevi Paila, Akash Ranjan
BMC Genomics. 2011; 12(Suppl 3): S6. Published online 2011 November 30. doi: 10.1186/1471-2164-12-S3-S6
PMCID:
PMC3333189
Abstract Full Text PDF–811K Supplementary Material
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
Organ and Cell Type–Specific Complementary Expression Patterns and Regulatory Neofunctionalization between Duplicated Genes in Arabidopsis thaliana
Shao-Lun Liu, Gregory J. Baute, Keith L. Adams
Genome Biol Evol. 2011; 3: 1419–1436. Published online 2011 November 4. doi: 10.1093/gbe/evr114
PMCID:
PMC3243486
Abstract Full Text PDF–775K
Sequence variability of Rhizobiales orthologs and relationship with physico-chemical characteristics of proteins
Humberto Peralta, Gabriela Guerrero, Alejandro Aguilar, Jaime Mora
Biol Direct. 2011; 6: 48. Published online 2011 October 4. doi: 10.1186/1745-6150-6-48
PMCID:
PMC3198989
Abstract Full Text PDF–1.6M Supplementary Material
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
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
IONS: Identification of Orthologs by Neighborhood and Similarity—an Automated Method to Identify Orthologs in Chromosomal Regions of Common Evolutionary Ancestry and its Application to Hemiascomycetous Yeasts
Marie-Line Seret, Philippe V. Baret
Evol Bioinform Online. 2011; 7: 123–133. Published online 2011 August 30. doi: 10.4137/EBO.S7465
PMCID:
PMC3169350
Abstract Full Text PDF–749K Supplementary Material
Mitochondrial genome deletions and minicircles are common in lice (Insecta: Phthiraptera)
Stephen L Cameron, Kazunori Yoshizawa, Atsushi Mizukoshi, Michael F Whiting, Kevin P Johnson
BMC Genomics. 2011; 12: 394. Published online 2011 August 4. doi: 10.1186/1471-2164-12-394
PMCID:
PMC3199782
Abstract Full Text PDF–512K Supplementary Material
Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees
Brigitte Boeckmann, Marc Robinson-Rechavi, Ioannis Xenarios, Christophe Dessimoz
Brief Bioinform. 2011 September; 12(5): 423–435. Published online 2011 July 7. doi: 10.1093/bib/bbr034
PMCID:
PMC3178055
Abstract Full Text PDF–580K
Positional orthology: putting genomic evolutionary relationships into context
Colin N. Dewey
Brief Bioinform. 2011 September; 12(5): 401–412. Published online 2011 June 24. doi: 10.1093/bib/bbr040
PMCID:
PMC3178058
Abstract Full Text PDF–304K
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
OrthoList: A Compendium of C. elegans Genes with Human Orthologs
Daniel D. Shaye, Iva Greenwald
PLoS One. 2011; 6(5): e20085. Published online 2011 May 25. doi: 10.1371/journal.pone.0020085
PMCID:
PMC3102077
Abstract Full Text PDF–530K Supplementary Material
QuartetS: a fast and accurate algorithm for large-scale orthology detection
Chenggang Yu, Nela Zavaljevski, Valmik Desai, Jaques Reifman
Nucleic Acids Res. 2011 July; 39(13): e88. Published online 2011 May 13. doi: 10.1093/nar/gkr308
PMCID:
PMC3141274
Abstract Full Text PDF–368K Supplementary Material
Unexpected complexity of the Reef-Building Coral Acropora millepora transcription factor network
Taewoo Ryu, Charalampos Harris Mavromatis, Till Bayer, Christian R Voolstra, Timothy Ravasi
BMC Syst Biol. 2011; 5: 58. Published online 2011 April 28. doi: 10.1186/1752-0509-5-58
PMCID:
PMC3096595
Abstract Full Text PDF–8.8M Supplementary Material
Evaluating Ortholog Prediction Algorithms in a Yeast Model Clade
Leonidas Salichos, Antonis Rokas
PLoS One. 2011; 6(4): e18755. Published online 2011 April 13. doi: 10.1371/journal.pone.0018755
PMCID:
PMC3076445
Abstract Full Text PDF–1.0M Supplementary Material
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
Multi-species integrative biclustering
Peter Waltman, Thadeous Kacmarczyk, Ashley R Bate, Daniel B Kearns, David J Reiss, Patrick Eichenberger, Richard Bonneau
Genome Biol. 2010; 11(9): R96. Published online 2010 September 29. doi: 10.1186/gb-2010-11-9-r96
PMCID:
PMC2965388
Abstract Full Text PDF–2.6M Supplementary Material
Computational analysis of LexA regulons in Cyanobacteria
Shan Li, Minli Xu, Zhengchang Su
BMC Genomics. 2010; 11: 527. Published online 2010 September 29. doi: 10.1186/1471-2164-11-527
PMCID:
PMC3091678
Abstract Full Text PDF–2.8M Supplementary Material
The Extinction Dynamics of Bacterial Pseudogenes
Chih-Horng Kuo, Howard Ochman
PLoS Genet. 2010 August; 6(8): e1001050. Published online 2010 August 5. doi: 10.1371/journal.pgen.1001050
PMCID:
PMC2916853
Abstract Full Text PDF–451K Supplementary Material
Orthology confers intron position conservation
Anna Henricson, Kristoffer Forslund, Erik LL Sonnhammer
BMC Genomics. 2010; 11: 412. Published online 2010 July 2. doi: 10.1186/1471-2164-11-412
PMCID:
PMC2996940
Abstract Full Text PDF–1.7M Supplementary Material
Dissecting spatio-temporal protein networks driving human heart development and related disorders
Kasper Lage, Kjeld Møllgård, Steven Greenway, Hiroko Wakimoto, Joshua M Gorham, Christopher T Workman, Eske Bendsen, Niclas T Hansen, Olga Rigina, Francisco S Roque, Cornelia Wiese, Vincent M Christoffels, Amy E Roberts, Leslie B Smoot, William T Pu, Patricia K Donahoe, Niels Tommerup, Søren Brunak, Christine E Seidman, Jonathan G Seidman, Lars A Larsen
Mol Syst Biol. 2010; 6: 381. Published online 2010 June 22. doi: 10.1038/msb.2010.36
PMCID:
PMC2913399
Abstract Full Text PDF–2.8M Supplementary Material
Identification of BERP (brain-expressed RING finger protein) as a p53 target gene that modulates seizure susceptibility through interacting with GABAA receptors
Carol C. Cheung, Caimei Yang, Thorsten Berger, Kathrin Zaugg, Patrick Reilly, Andrew J. Elia, Andrew Wakeham, Annick You-Ten, Ning Chang, Lijun Li, Qi Wan, Tak Wah Mak
Proc Natl Acad Sci U S A. 2010 June 29; 107(26): 11883–11888. Published online 2010 June 11. doi: 10.1073/pnas.1006529107
PMCID:
PMC2900672
Abstract Full Text PDF–651K Supplementary Material
Dynamic Zebrafish Interactome Reveals Transcriptional Mechanisms of Dioxin Toxicity
Andrey Alexeyenko, Deena M. Wassenberg, Edward K. Lobenhofer, Jerry Yen, Elwood Linney, Erik L. L. Sonnhammer, Joel N. Meyer
PLoS One. 2010; 5(5): e10465. Published online 2010 May 5. doi: 10.1371/journal.pone.0010465
PMCID:
PMC2864754
Abstract Full Text PDF–2.4M Supplementary Material
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
Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates
Zhengdong D Zhang, Adam Frankish, Toby Hunt, Jennifer Harrow, Mark Gerstein
Genome Biol. 2010; 11(3): R26. Published online 2010 March 8. doi: 10.1186/gb-2010-11-3-r26
PMCID:
PMC2864566
Abstract Full Text PDF–1.3M Supplementary Material
FUNGIpath: a tool to assess fungal metabolic pathways predicted by orthology
Sandrine Grossetête, Bernard Labedan, Olivier Lespinet
BMC Genomics. 2010; 11: 81. Published online 2010 February 1. doi: 10.1186/1471-2164-11-81
PMCID:
PMC2829015
Abstract Full Text PDF–1.6M Supplementary Material
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
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