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Items: 1 to 50 of 85

1.

Eukaryote Genes Are More Likely than Prokaryote Genes to Be Composites.

Ou Y, McInerney JO.

Genes (Basel). 2019 Aug 28;10(9). pii: E648. doi: 10.3390/genes10090648.

2.

Gene Fusions Derived by Transcriptional Readthrough are Driven by Segmental Duplication in Human.

McCartney AM, Hyland EM, Cormican P, Moran RJ, Webb AE, Lee KD, Hernandez-Rodriguez J, Prado-Martinez J, Creevey CJ, Aspden JL, McInerney JO, Marques-Bonet T, O'Connell MJ.

Genome Biol Evol. 2019 Sep 1;11(9):2678-2690. doi: 10.1093/gbe/evz163.

3.

Formation of chimeric genes with essential functions at the origin of eukaryotes.

Méheust R, Bhattacharya D, Pathmanathan JS, McInerney JO, Lopez P, Bapteste E.

BMC Biol. 2018 Mar 13;16(1):30. doi: 10.1186/s12915-018-0500-0.

4.

Bipartite Network Analysis of Gene Sharings in the Microbial World.

Corel E, Méheust R, Watson AK, McInerney JO, Lopez P, Bapteste E.

Mol Biol Evol. 2018 Apr 1;35(4):899-913. doi: 10.1093/molbev/msy001. Erratum in: Mol Biol Evol. 2018 Jul 1;35(7):1821.

5.

Reply to 'The population genetics of pangenomes'.

McInerney JO, McNally A, O'Connell MJ.

Nat Microbiol. 2017 Dec;2(12):1575. doi: 10.1038/s41564-017-0068-4. No abstract available.

PMID:
29176701
6.

The role of public goods in planetary evolution.

McInerney JO, Erwin DH.

Philos Trans A Math Phys Eng Sci. 2017 Dec 28;375(2109). pii: 20160359. doi: 10.1098/rsta.2016.0359.

7.

Function-related replacement of bacterial siderophore pathways.

Bruns H, Crüsemann M, Letzel AC, Alanjary M, McInerney JO, Jensen PR, Schulz S, Moore BS, Ziemert N.

ISME J. 2018 Feb;12(2):320-329. doi: 10.1038/ismej.2017.137. Epub 2017 Aug 15.

8.

Horizontal gene transfer is less frequent in eukaryotes than prokaryotes but can be important (retrospective on DOI 10.1002/bies.201300095).

McInerney JO.

Bioessays. 2017 Jun;39(6). doi: 10.1002/bies.201700002. Epub 2017 Apr 18. No abstract available.

PMID:
28418075
9.

Why prokaryotes have pangenomes.

McInerney JO, McNally A, O'Connell MJ.

Nat Microbiol. 2017 Mar 28;2:17040. doi: 10.1038/nmicrobiol.2017.40. No abstract available.

10.

Microbiology: Mind the gaps in cellular evolution.

McInerney JO, O'Connell MJ.

Nature. 2017 Jan 19;541(7637):297-299. doi: 10.1038/nature21113. Epub 2017 Jan 11. No abstract available.

11.

Society for Molecular Biology and Evolution, Council and Business Meetings, 2016, Gold Coast Australia.

McInerney JO.

Mol Biol Evol. 2017 Jan;34(1):243-244. doi: 10.1093/molbev/msw276. Epub 2016 Dec 29. No abstract available.

PMID:
28039386
12.

Combined Analysis of Variation in Core, Accessory and Regulatory Genome Regions Provides a Super-Resolution View into the Evolution of Bacterial Populations.

McNally A, Oren Y, Kelly D, Pascoe B, Dunn S, Sreecharan T, Vehkala M, Välimäki N, Prentice MB, Ashour A, Avram O, Pupko T, Dobrindt U, Literak I, Guenther S, Schaufler K, Wieler LH, Zhiyong Z, Sheppard SK, McInerney JO, Corander J.

PLoS Genet. 2016 Sep 12;12(9):e1006280. doi: 10.1371/journal.pgen.1006280. eCollection 2016 Sep.

13.

Evolution: A four billion year old metabolism.

McInerney JO.

Nat Microbiol. 2016 Jul 25;1(9):16139. doi: 10.1038/nmicrobiol.2016.139. No abstract available.

PMID:
27562267
14.

"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.

15.

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.

16.

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.

PMID:
26287458
17.

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.

PMID:
25355355
18.

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.

19.

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.

20.

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. Review.

PMID:
24814066
21.

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.

22.

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.

23.

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.

24.

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.

PMID:
24035465
25.

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.

PMID:
23883522
26.

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.

27.

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.

28.

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.

PMID:
23764187
29.

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.

30.

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.

31.

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.

32.

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.

33.

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.

34.

Increased genome sampling reveals a dynamic relationship between gene duplicability and the structure of the primate protein-protein interaction network.

Doherty A, Alvarez-Ponce D, McInerney JO.

Mol Biol Evol. 2012 Nov;29(11):3563-73. doi: 10.1093/molbev/mss165. Epub 2012 Jun 21.

PMID:
22723304
35.

The Public Goods Hypothesis for the evolution of life on Earth.

McInerney JO, Pisani D, Bapteste E, O'Connell MJ.

Biol Direct. 2011 Aug 23;6:41. doi: 10.1186/1745-6150-6-41.

36.

Planctomycetes and eukaryotes: a case of analogy not homology.

McInerney JO, Martin WF, Koonin EV, Allen JF, Galperin MY, Lane N, Archibald JM, Embley TM.

Bioessays. 2011 Nov;33(11):810-7. doi: 10.1002/bies.201100045. Epub 2011 Aug 22.

37.
38.

The human genome retains relics of its prokaryotic ancestry: human genes of archaebacterial and eubacterial origin exhibit remarkable differences.

Alvarez-Ponce D, McInerney JO.

Genome Biol Evol. 2011;3:782-90. doi: 10.1093/gbe/evr073. Epub 2011 Jul 27.

39.

Eukaryotic genes of archaebacterial origin are more important than the more numerous eubacterial genes, irrespective of function.

Cotton JA, McInerney JO.

Proc Natl Acad Sci U S A. 2010 Oct 5;107(40):17252-5. doi: 10.1073/pnas.1000265107. Epub 2010 Sep 17.

40.

Gene and genome trees conflict at many levels.

Haggerty LS, Martin FJ, Fitzpatrick DA, McInerney JO.

Philos Trans R Soc Lond B Biol Sci. 2009 Aug 12;364(1527):2209-19. doi: 10.1098/rstb.2009.0042.

41.

The network of life: genome beginnings and evolution. Introduction.

Ragan MA, McInerney JO, Lake JA.

Philos Trans R Soc Lond B Biol Sci. 2009 Aug 12;364(1527):2169-75. doi: 10.1098/rstb.2009.0046. No abstract available.

42.

Trees from trees: construction of phylogenetic supertrees using clann.

Creevey CJ, McInerney JO.

Methods Mol Biol. 2009;537:139-61. doi: 10.1007/978-1-59745-251-9_7.

PMID:
19378143
43.

Molecular phylogeny of the Drosophila tripunctata and closely related species groups (Diptera: Drosophilidae).

Hatadani LM, McInerney JO, de Medeiros HF, Junqueira AC, de Azeredo-Espin AM, Klaczko LB.

Mol Phylogenet Evol. 2009 Jun;51(3):595-600. doi: 10.1016/j.ympev.2009.02.022. Epub 2009 Mar 11.

PMID:
19285146
44.

Recurring cluster and operon assembly for Phenylacetate degradation genes.

Martin FJ, McInerney JO.

BMC Evol Biol. 2009 Feb 10;9:36. doi: 10.1186/1471-2148-9-36.

45.

The tree of genomes: an empirical comparison of genome-phylogeny reconstruction methods.

McCann A, Cotton JA, McInerney JO.

BMC Evol Biol. 2008 Nov 12;8:312. doi: 10.1186/1471-2148-8-312.

46.

The prokaryotic tree of life: past, present... and future?

McInerney JO, Cotton JA, Pisani D.

Trends Ecol Evol. 2008 May;23(5):276-81. doi: 10.1016/j.tree.2008.01.008. Epub 2008 Mar 25. Review.

PMID:
18367290
47.

Genetics. Paradigm for life.

McInerney JO, Pisani D.

Science. 2007 Nov 30;318(5855):1390-1. No abstract available.

PMID:
18048672
48.

MultiPhyl: a high-throughput phylogenomics webserver using distributed computing.

Keane TM, Naughton TJ, McInerney JO.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W33-7. Epub 2007 Jun 6.

49.

Supertrees disentangle the chimerical origin of eukaryotic genomes.

Pisani D, Cotton JA, McInerney JO.

Mol Biol Evol. 2007 Aug;24(8):1752-60. Epub 2007 May 15.

PMID:
17504772
50.

TOPD/FMTS: a new software to compare phylogenetic trees.

Puigbò P, Garcia-Vallvé S, McInerney JO.

Bioinformatics. 2007 Jun 15;23(12):1556-8. Epub 2007 Apr 25.

PMID:
17459965

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