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Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution
Matthew W Hahn
Genome Biol. 2007; 8(7): R141. Published online 2007 July 16. doi: 10.1186/gb-2007-8-7-r141
PMCID:
PMC2323230
Abstract Full Text PDF–296K Supplementary Material
 Is Cited by the Following 12 Articles in this Archive:
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
The Potential for pathogenicity was present in the ancestor of the Ascomycete subphylum Pezizomycotina
Aminael Sánchez-Rodríguez, Cindy Martens, Kristof Engelen, Yves Van de Peer, Kathleen Marchal
BMC Evol Biol. 2010; 10: 318. Published online 2010 October 21. doi: 10.1186/1471-2148-10-318
PMCID:
PMC3087541
Abstract Full Text PDF–1.7M 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
Nonallelic Gene Conversion in the Genus Drosophila
Claudio Casola, Carrie L. Ganote, Matthew W. Hahn
Genetics. 2010 May; 185(1): 95–103. doi: 10.1534/genetics.110.115444
PMCID:
PMC2870979
Abstract Full Text PDF–1.2M
Gene duplication and the origins of morphological complexity in pancrustacean eyes, a genomic approach
Ajna S Rivera, M Sabrina Pankey, David C Plachetzki, Carlos Villacorta, Anna E Syme, Jeanne M Serb, Angela R Omilian, Todd H Oakley
BMC Evol Biol. 2010; 10: 123. Published online 2010 April 30. doi: 10.1186/1471-2148-10-123
PMCID:
PMC2888819
Abstract Full Text PDF–815K Supplementary Material
PLAZA: A Comparative Genomics Resource to Study Gene and Genome Evolution in Plants
Sebastian Proost, Michiel Van Bel, Lieven Sterck, Kenny Billiau, Thomas Van Parys, Yves Van de Peer, Klaas Vandepoele
Plant Cell. 2009 December; 21(12): 3718–3731. doi: 10.1105/tpc.109.071506
PMCID:
PMC2814516
Abstract Full Text PDF–1.2M Supplementary Material
Consequences of Lineage-Specific Gene Loss on Functional Evolution of Surviving Paralogs: ALDH1A and Retinoic Acid Signaling in Vertebrate Genomes
Cristian Cañestro, Julian M. Catchen, Adriana Rodríguez-Marí, Hayato Yokoi, John H. Postlethwait
PLoS Genet. 2009 May; 5(5): e1000496. Published online 2009 May 29. doi: 10.1371/journal.pgen.1000496
PMCID:
PMC2682703
Abstract Full Text PDF–2.8M Supplementary Material
Phylogenomics: Gene Duplication, Unrecognized Paralogy and Outgroup Choice
Scott William Roy
PLoS ONE. 2009; 4(2): e4568. Published online 2009 February 23. doi: 10.1371/journal.pone.0004568
PMCID:
PMC2640465
Abstract Full Text PDF–519K
Reconciliation with Non-Binary Species Trees
Benjamin Vernot, Maureen Stolzer, Aiton Goldman, Dannie Durand
J Comput Biol. 2008 October; 15(8): 981–1006. doi: 10.1089/cmb.2008.0092
PMCID:
PMC3205801
Abstract Full Text PDF–448K
Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes
Matthew D. Rasmussen, Manolis Kellis
Genome Res. 2007 December; 17(12): 1932–1942. doi: 10.1101/gr.7105007
PMCID:
PMC2099600
Abstract Full Text PDF–1.1M
Gene Family Evolution across 12 Drosophila Genomes
Matthew W Hahn, Mira V Han, Sang-Gook Han
PLoS Genet. 2007 November; 3(11): e197. Published online 2007 November 9. doi: 10.1371/journal.pgen.0030197
PMCID:
PMC2065885
Abstract Full Text PDF–271K Supplementary Material
Accelerated Rate of Gene Gain and Loss in Primates
Matthew W. Hahn, Jeffery P. Demuth, Sang-Gook Han
Genetics. 2007 November; 177(3): 1941–1949. doi: 10.1534/genetics.107.080077
PMCID:
PMC2147951
Abstract Full Text PDF–939K
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