My NCBISign In
The human phylome
Jaime Huerta-Cepas, Hernán Dopazo, Joaquín Dopazo, Toni Gabaldón
Genome Biol. 2007; 8(6): R109. Published online 2007 June 13. doi: 10.1186/gb-2007-8-6-r109
PMCID:
PMC2394744
Abstract Full Text PDF–491K Supplementary Material

Is Cited by the Following 35 Articles in this Archive:

Unified modeling of gene duplication, loss, and coalescence using a locus tree
Matthew D. Rasmussen, Manolis Kellis
Genome Res. 2012 April; 22(4): 755–765. doi: 10.1101/gr.123901.111
PMCID:
PMC3317157
Abstract Full Text PDF–1.2M
Comparison of Gene Repertoires and Patterns of Evolutionary Rates in Eight Aphid Species That Differ by Reproductive Mode
M. Ollivier, T. Gabaldón, J. Poulain, F. Gavory, N. Leterme, J.-P. Gauthier, F. Legeai, D. Tagu, J. C. Simon, C. Rispe
Genome Biol Evol. 2012; 4(2): 155–167. Published online 2012 January 2. doi: 10.1093/gbe/evr140
PMCID:
PMC3319000
Abstract Full Text PDF–375K
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
Global Analysis of Serine-Threonine Protein Kinase Genes in Neurospora crassa
Gyungsoon Park, Jacqueline A. Servin, Gloria E. Turner, Lorena Altamirano, Hildur V. Colot, Patrick Collopy, Liubov Litvinkova, Liande Li, Carol A. Jones, Fitz-Gerald Diala, Jay C. Dunlap, Katherine A. Borkovich
Eukaryot Cell. 2011 November; 10(11): 1553–1564. doi: 10.1128/EC.05140-11
PMCID:
PMC3209061
Abstract Full Text PDF–1.1M Supplementary Material
Statistics and Truth in Phylogenomics
Sudhir Kumar, Alan J. Filipski, Fabia U. Battistuzzi, Sergei L. Kosakovsky Pond, Koichiro Tamura
Mol Biol Evol. 2012 February; 29(2): 457–472. Published online 2011 August 26. doi: 10.1093/molbev/msr202
PMCID:
PMC3258035
Free in PMC on 2013/02/01
Phylogenomics-Based Reconstruction of Protozoan Species Tree
Kary A.C.S. Ocaña, Alberto M.R. Dávila
Evol Bioinform Online. 2011; 7: 107–121. Published online 2011 July 31. doi: 10.4137/EBO.S6861
PMCID:
PMC3153122
Abstract Full Text PDF–1.0M 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
Genomic revelations of a mutualism: the pea aphid and its obligate bacterial symbiont
Shuji Shigenobu, Alex C. C. Wilson
Cell Mol Life Sci. 2011 April; 68(8): 1297–1309. Published online 2011 March 10. doi: 10.1007/s00018-011-0645-2
PMCID:
PMC3064905
Abstract Full Text PDF–590K Supplementary Material
Considerations for the inclusion of 2x mammalian genomes in phylogenetic analyses
Albert J Vilella, Ewan Birney, Paul Flicek, Javier Herrero
Genome Biol. 2011; 12(2): 401. Published online 2011 February 21. doi: 10.1186/gb-2011-12-2-401
PMCID:
PMC3188792
Abstract Full Text PDF–355K
B2G-FAR, a species-centered GO annotation repository
Stefan Götz, Roland Arnold, Patricia Sebastián-León, Samuel Martín-Rodríguez, Patrick Tischler, Marc-André Jehl, Joaquín Dopazo, Thomas Rattei, Ana Conesa
Bioinformatics. 2011 April 1; 27(7): 919–924. Published online 2011 February 18. doi: 10.1093/bioinformatics/btr059
PMCID:
PMC3065692
Abstract Full Text PDF–369K Supplementary Material
Horizontal gene transfer between bacteria and animals
Julie C. Dunning Hotopp
Trends Genet. Author manuscript; available in PMC 2012 April 1.
Published in final edited form as: Trends Genet. 2011 April; 27(4): 157–163. Published online 2011 February 18. doi: 10.1016/j.tig.2011.01.005
PMCID:
PMC3068243
Abstract Full Text PDF–340K
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
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
Molecular characterization of the evolution of phagosomes
Jonathan Boulais, Matthias Trost, Christian R Landry, Régis Dieckmann, Emmanuel D Levy, Thierry Soldati, Stephen W Michnick, Pierre Thibault, Michel Desjardins
Mol Syst Biol. 2010; 6: 423. Published online 2010 October 19. doi: 10.1038/msb.2010.80
PMCID:
PMC2990642
Abstract Full Text PDF–4.1M Supplementary Material
A Bayesian Approach for Fast and Accurate Gene Tree Reconstruction
Matthew D. Rasmussen, Manolis Kellis
Mol Biol Evol. 2011 January; 28(1): 273–290. Published online 2010 July 25. doi: 10.1093/molbev/msq189
PMCID:
PMC3002250
Abstract Full Text PDF–756K 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
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
Whole-genome phylogeny of mammals: Evolutionary information in genic and nongenic regions
Gregory E. Sims, Se-Ran Jun, Guohong Albert Wu, Sung-Hou Kim
Proc Natl Acad Sci U S A. 2009 October 6; 106(40): 17077–17082. doi: 10.1073/pnas.0909377106
PMCID:
PMC2761373
Abstract Full Text PDF–880K Supplementary Material
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
Salvador Capella-Gutiérrez, José M. Silla-Martínez, Toni Gabaldón
Bioinformatics. 2009 August 1; 25(15): 1972–1973. Published online 2009 June 8. doi: 10.1093/bioinformatics/btp348
PMCID:
PMC2712344
Abstract Full Text PDF–57K
Breakpoint graphs and ancestral genome reconstructions
Max A. Alekseyev, Pavel A. Pevzner
Genome Res. 2009 May; 19(5): 943–957. doi: 10.1101/gr.082784.108
PMCID:
PMC2675983
Abstract Full Text PDF–1.8M
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
ComPhy: prokaryotic composite distance phylogenies inferred from whole-genome gene sets
Guan Ning Lin, Zhipeng Cai, Guohui Lin, Sounak Chakraborty, Dong Xu
BMC Bioinformatics. 2009; 10(Suppl 1): S5. Published online 2009 January 30. doi: 10.1186/1471-2105-10-S1-S5
PMCID:
PMC2648732
Abstract Full Text PDF–1.2M
metaTIGER: a metabolic evolution resource
John W. Whitaker, Ivica Letunic, Glenn A. McConkey, David R. Westhead
Nucleic Acids Res. 2009 January; 37(Database issue): D531–D538. Published online 2009 January. doi: 10.1093/nar/gkn826
PMCID:
PMC2686446
Abstract Full Text PDF–3.0M
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
Protein co-evolution, co-adaptation and interactions
Florencio Pazos, Alfonso Valencia
EMBO J. 2008 October 22; 27(20): 2648–2655. Published online 2008 September 25. doi: 10.1038/emboj.2008.189
PMCID:
PMC2556093
Abstract Full Text PDF–280K
GPCR Genes Are Preferentially Retained after Whole Genome Duplication
Jenia Semyonov, Jae-Il Park, Chia Lin Chang, Sheau Yu Teddy Hsu
PLoS ONE. 2008; 3(4): e1903. Published online 2008 April 2. doi: 10.1371/journal.pone.0001903
PMCID:
PMC2270905
Abstract Full Text PDF–341K Supplementary Material
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