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"Every Gene Is Everywhere but the Environment Selects": Global Geolocalization of Gene Sharing in Environmental Samples through Network Analysis.

Fondi M, Karkman A, Tamminen MV, Bosi E, Virta M, Fani R, Alm E, McInerney JO.

Genome Biol Evol. 2016 May 13;8(5):1388-400. doi: 10.1093/gbe/evw077.


Horizontal gene flow from Eubacteria to Archaebacteria and what it means for our understanding of eukaryogenesis.

Akanni WA, Siu-Ting K, Creevey CJ, McInerney JO, Wilkinson M, Foster PG, Pisani D.

Philos Trans R Soc Lond B Biol Sci. 2015 Sep 26;370(1678):20140337. doi: 10.1098/rstb.2014.0337.


Endosymbiotic origin and differential loss of eukaryotic genes.

Ku C, Nelson-Sathi S, Roettger M, Sousa FL, Lockhart PJ, Bryant D, Hazkani-Covo E, McInerney JO, Landan G, Martin WF.

Nature. 2015 Aug 27;524(7566):427-32. doi: 10.1038/nature14963. Epub 2015 Aug 19.


Evolutionary developmental biology: Ghost locus appears.

McInerney JO, O'Connell MJ.

Nature. 2014 Oct 30;514(7524):570-1. doi: 10.1038/514570a. No abstract available.


Origins of major archaeal clades correspond to gene acquisitions from bacteria.

Nelson-Sathi S, Sousa FL, Roettger M, Lozada-Chávez N, Thiergart T, Janssen A, Bryant D, Landan G, Schönheit P, Siebers B, McInerney JO, Martin WF.

Nature. 2015 Jan 1;517(7532):77-80. doi: 10.1038/nature13805. Epub 2014 Oct 15.


SMBE Satellite meeting on reticulated microbial evolution 2014--meeting report.

Dagan T, Bapteste E, McInerney JO, Martin WF.

Genome Biol Evol. 2014 Aug 12;6(9):2206-9. doi: 10.1093/gbe/evu173. No abstract available.


The hybrid nature of the Eukaryota and a consilient view of life on Earth.

McInerney JO, O'Connell MJ, Pisani D.

Nat Rev Microbiol. 2014 Jun;12(6):449-55. doi: 10.1038/nrmicro3271. Epub 2014 May 12.


Population genomics reveal recent speciation and rapid evolutionary adaptation in polar bears.

Liu S, Lorenzen ED, Fumagalli M, Li B, Harris K, Xiong Z, Zhou L, Korneliussen TS, Somel M, Babbitt C, Wray G, Li J, He W, Wang Z, Fu W, Xiang X, Morgan CC, Doherty A, O'Connell MJ, McInerney JO, Born EW, Dalén L, Dietz R, Orlando L, Sonne C, Zhang G, Nielsen R, Willerslev E, Wang J.

Cell. 2014 May 8;157(4):785-94. doi: 10.1016/j.cell.2014.03.054.


A pluralistic account of homology: adapting the models to the data.

Haggerty LS, Jachiet PA, Hanage WP, Fitzpatrick DA, Lopez P, O'Connell MJ, Pisani D, Wilkinson M, Bapteste E, McInerney JO.

Mol Biol Evol. 2014 Mar;31(3):501-16. doi: 10.1093/molbev/mst228. Epub 2013 Nov 22. Review.


Integration of two ancestral chaperone systems into one: the evolution of eukaryotic molecular chaperones in light of eukaryogenesis.

Bogumil D, Alvarez-Ponce D, Landan G, McInerney JO, Dagan T.

Mol Biol Evol. 2014 Feb;31(2):410-8. doi: 10.1093/molbev/mst212. Epub 2013 Nov 4.


More than tree dimensions: inter-lineage evolution's ecological importance.

McInerney JO.

Trends Ecol Evol. 2013 Nov;28(11):624-5. doi: 10.1016/j.tree.2013.09.002. Epub 2013 Sep 12.


Translational selection frequently overcomes genetic drift in shaping synonymous codon usage patterns in vertebrates.

Doherty A, McInerney JO.

Mol Biol Evol. 2013 Oct;30(10):2263-7. doi: 10.1093/molbev/mst128. Epub 2013 Jul 24.


EGN: a wizard for construction of gene and genome similarity networks.

Halary S, McInerney JO, Lopez P, Bapteste E.

BMC Evol Biol. 2013 Jul 11;13:146. doi: 10.1186/1471-2148-13-146.


Heterogeneous models place the root of the placental mammal phylogeny.

Morgan CC, Foster PG, Webb AE, Pisani D, McInerney JO, O'Connell MJ.

Mol Biol Evol. 2013 Sep;30(9):2145-56. doi: 10.1093/molbev/mst117. Epub 2013 Jun 29.


Networks: expanding evolutionary thinking.

Bapteste E, van Iersel L, Janke A, Kelchner S, Kelk S, McInerney JO, Morrison DA, Nakhleh L, Steel M, Stougie L, Whitfield J.

Trends Genet. 2013 Aug;29(8):439-41. doi: 10.1016/j.tig.2013.05.007. Epub 2013 Jun 11.


Gene similarity networks provide tools for understanding eukaryote origins and evolution.

Alvarez-Ponce D, Lopez P, Bapteste E, McInerney JO.

Proc Natl Acad Sci U S A. 2013 Apr 23;110(17):E1594-603. doi: 10.1073/pnas.1211371110. Epub 2013 Apr 1.


New approaches for unravelling reassortment pathways.

Svinti V, Cotton JA, McInerney JO.

BMC Evol Biol. 2013 Jan 1;13:1. doi: 10.1186/1471-2148-13-1.


Acquisition of 1,000 eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea.

Nelson-Sathi S, Dagan T, Landan G, Janssen A, Steel M, McInerney JO, Deppenmeier U, Martin WF.

Proc Natl Acad Sci U S A. 2012 Dec 11;109(50):20537-42. doi: 10.1073/pnas.1209119109. Epub 2012 Nov 26.


Metazoan opsin evolution reveals a simple route to animal vision.

Feuda R, Hamilton SC, McInerney JO, Pisani D.

Proc Natl Acad Sci U S A. 2012 Nov 13;109(46):18868-72. doi: 10.1073/pnas.1204609109. Epub 2012 Oct 29.


Evolutionary analyses of non-genealogical bonds produced by introgressive descent.

Bapteste E, Lopez P, Bouchard F, Baquero F, McInerney JO, Burian RM.

Proc Natl Acad Sci U S A. 2012 Nov 6;109(45):18266-72. doi: 10.1073/pnas.1206541109. Epub 2012 Oct 22.

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