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Items: 1 to 50 of 259

1.

Neutral evolution of cellular phenotypes.

Wideman JG, Novick A, Muñoz-Gómez SA, Doolittle WF.

Curr Opin Genet Dev. 2019 Sep 28;58-59:87-94. doi: 10.1016/j.gde.2019.09.004. [Epub ahead of print] Review.

PMID:
31574422
2.

Making Evolutionary Sense of Gaia.

Doolittle WF.

Trends Ecol Evol. 2019 Oct;34(10):889-894. doi: 10.1016/j.tree.2019.05.001. Epub 2019 May 30. Review.

PMID:
31155421
3.

How microbes "jeopardize" the modern synthesis.

Novick A, Doolittle WF.

PLoS Genet. 2019 May 15;15(5):e1008166. doi: 10.1371/journal.pgen.1008166. eCollection 2019 May. No abstract available.

4.

We simply cannot go on being so vague about 'function'.

Doolittle WF.

Genome Biol. 2018 Dec 18;19(1):223. doi: 10.1186/s13059-018-1600-4.

5.

Processes and patterns of interaction as units of selection: An introduction to ITSNTS thinking.

Doolittle WF, Inkpen SA.

Proc Natl Acad Sci U S A. 2018 Apr 17;115(16):4006-4014. doi: 10.1073/pnas.1722232115. Epub 2018 Mar 26.

6.

On causal roles and selected effects: our genome is mostly junk.

Doolittle WF, Brunet TDP.

BMC Biol. 2017 Dec 5;15(1):116. doi: 10.1186/s12915-017-0460-9.

7.

Darwinizing Gaia.

Doolittle WF.

J Theor Biol. 2017 Dec 7;434:11-19. doi: 10.1016/j.jtbi.2017.02.015. Epub 2017 Feb 22.

PMID:
28237396
8.

Microbial Evolution: Xenology (Apparently) Trumps Paralogy.

Eme L, Doolittle WF.

Curr Biol. 2016 Nov 21;26(22):R1181-R1183. doi: 10.1016/j.cub.2016.09.049.

9.

Molecular Phylogenetics and the Perennial Problem of Homology.

Inkpen SA, Doolittle WF.

J Mol Evol. 2016 Dec;83(5-6):184-192. Epub 2016 Nov 21. Review.

PMID:
27872952
10.

The Modern Synthesis in the Light of Microbial Genomics.

Booth A, Mariscal C, Doolittle WF.

Annu Rev Microbiol. 2016 Sep 8;70:279-97. doi: 10.1146/annurev-micro-102215-095456. Epub 2016 Jul 6. Review.

PMID:
27482743
11.

What Is the Tree of Life?

Doolittle WF, Brunet TD.

PLoS Genet. 2016 Apr 14;12(4):e1005912. doi: 10.1371/journal.pgen.1005912. eCollection 2016 Apr. Review.

12.

Archaea.

Eme L, Doolittle WF.

Curr Biol. 2015 Oct 5;25(19):R851-5. doi: 10.1016/j.cub.2015.05.025.

13.

Eukaryotes first: how could that be?

Mariscal C, Doolittle WF.

Philos Trans R Soc Lond B Biol Sci. 2015 Sep 26;370(1678):20140322. doi: 10.1098/rstb.2014.0322. Review.

14.

Reply to Lane and Martin: Being and becoming eukaryotes.

Booth A, Doolittle WF.

Proc Natl Acad Sci U S A. 2015 Sep 1;112(35):E4824. doi: 10.1073/pnas.1513285112. Epub 2015 Aug 17. No abstract available.

15.

Symbiosis becoming permanent: Survival of the luckiest.

Keeling PJ, McCutcheon JP, Doolittle WF.

Proc Natl Acad Sci U S A. 2015 Aug 18;112(33):10101-3. doi: 10.1073/pnas.1513346112. No abstract available.

16.

Multilevel Selection Theory and the Evolutionary Functions of Transposable Elements.

Brunet TD, Doolittle WF.

Genome Biol Evol. 2015 Aug 6;7(8):2445-57. doi: 10.1093/gbe/evv152.

17.

Eukaryogenesis, how special really?

Booth A, Doolittle WF.

Proc Natl Acad Sci U S A. 2015 Aug 18;112(33):10278-85. doi: 10.1073/pnas.1421376112. Epub 2015 Apr 16. Review.

18.

Microbial diversity: a bonanza of phyla.

Eme L, Doolittle WF.

Curr Biol. 2015 Mar 16;25(6):R227-R230. doi: 10.1016/j.cub.2014.12.044.

19.

Getting "function" right.

Brunet TD, Doolittle WF.

Proc Natl Acad Sci U S A. 2014 Aug 19;111(33):E3365. doi: 10.1073/pnas.1409762111. Epub 2014 Aug 8. No abstract available.

20.

Rhodoluna lacicola gen. nov., sp. nov., a planktonic freshwater bacterium with stream-lined genome.

Hahn MW, Schmidt J, Taipale SJ, Doolittle WF, Koll U.

Int J Syst Evol Microbiol. 2014 Sep;64(Pt 9):3254-63. doi: 10.1099/ijs.0.065292-0. Epub 2014 Jul 1.

21.

How natural a kind is "eukaryote?".

Doolittle WF.

Cold Spring Harb Perspect Biol. 2014 Jun 2;6(6). pii: a015974. doi: 10.1101/cshperspect.a015974.

22.

Distinguishing between "function" and "effect" in genome biology.

Doolittle WF, Brunet TD, Linquist S, Gregory TR.

Genome Biol Evol. 2014 May 9;6(5):1234-7. doi: 10.1093/gbe/evu098.

23.

The trouble with (group II) introns.

Doolittle WF.

Proc Natl Acad Sci U S A. 2014 May 6;111(18):6536-7. doi: 10.1073/pnas.1405174111. Epub 2014 Apr 22. No abstract available.

24.

The spliceosomal catalytic core arose in the RNA world… or did it?

Doolittle WF.

Genome Biol. 2013 Dec 13;14(12):141. doi: 10.1186/gb4145.

25.

Sixty years of genome biology.

Doolittle WF, Fraser P, Gerstein MB, Graveley BR, Henikoff S, Huttenhower C, Oshlack A, Ponting CP, Rinn JL, Schatz MC, Ule J, Weigel D, Weinstock GM.

Genome Biol. 2013 Apr 25;14(4):113. doi: 10.1186/gb-2013-14-4-113.

26.

Carl R. Woese (1928–2012).

Doolittle WF.

Curr Biol. 2013 Mar 4;23(5):R183-5. No abstract available.

27.

Is junk DNA bunk? A critique of ENCODE.

Doolittle WF.

Proc Natl Acad Sci U S A. 2013 Apr 2;110(14):5294-300. doi: 10.1073/pnas.1221376110. Epub 2013 Mar 11.

28.

Genome sequence of the mesophilic Thermotogales bacterium Mesotoga prima MesG1.Ag.4.2 reveals the largest Thermotogales genome to date.

Zhaxybayeva O, Swithers KS, Foght J, Green AG, Bruce D, Detter C, Han S, Teshima H, Han J, Woyke T, Pitluck S, Nolan M, Ivanova N, Pati A, Land ML, Dlutek M, Doolittle WF, Noll KM, Nesbø CL.

Genome Biol Evol. 2012;4(8):700-8. doi: 10.1093/gbe/evs059. Epub 2012 Jul 12.

29.

Population genomics: how bacterial species form and why they don't exist.

Doolittle WF.

Curr Biol. 2012 Jun 5;22(11):R451-3. doi: 10.1016/j.cub.2012.04.034.

30.

Mesotoga prima gen. nov., sp. nov., the first described mesophilic species of the Thermotogales.

Nesbø CL, Bradnan DM, Adebusuyi A, Dlutek M, Petrus AK, Foght J, Doolittle WF, Noll KM.

Extremophiles. 2012 May;16(3):387-93. doi: 10.1007/s00792-012-0437-0. Epub 2012 Mar 13.

PMID:
22411358
31.

Evolutionary biology: A ratchet for protein complexity.

Doolittle WF.

Nature. 2012 Jan 8;481(7381):270-1. doi: 10.1038/nature10816. No abstract available.

PMID:
22230958
32.

How a neutral evolutionary ratchet can build cellular complexity.

Lukeš J, Archibald JM, Keeling PJ, Doolittle WF, Gray MW.

IUBMB Life. 2011 Jul;63(7):528-37. doi: 10.1002/iub.489. Review.

33.

Comment on "Does constructive neutral evolution play an important role in the origin of cellular complexity?" DOI 10.1002/bies.201100010.

Doolittle WF, Lukeš J, Archibald JM, Keeling PJ, Gray MW.

Bioessays. 2011 Jun;33(6):427-9. doi: 10.1002/bies.201100039. Epub 2011 Apr 29. No abstract available.

PMID:
21538416
34.

Lateral gene transfer.

Zhaxybayeva O, Doolittle WF.

Curr Biol. 2011 Apr 12;21(7):R242-6. doi: 10.1016/j.cub.2011.01.045. No abstract available.

35.

Coral-mucus-associated Vibrio integrons in the Great Barrier Reef: genomic hotspots for environmental adaptation.

Koenig JE, Bourne DG, Curtis B, Dlutek M, Stokes HW, Doolittle WF, Boucher Y.

ISME J. 2011 Jun;5(6):962-72. doi: 10.1038/ismej.2010.193. Epub 2011 Jan 27.

36.

Cell biology. Irremediable complexity?

Gray MW, Lukes J, Archibald JM, Keeling PJ, Doolittle WF.

Science. 2010 Nov 12;330(6006):920-1. doi: 10.1126/science.1198594. No abstract available.

PMID:
21071654
37.

Searching for mesophilic Thermotogales bacteria: "mesotogas" in the wild.

Nesbø CL, Kumaraswamy R, Dlutek M, Doolittle WF, Foght J.

Appl Environ Microbiol. 2010 Jul;76(14):4896-900. doi: 10.1128/AEM.02846-09. Epub 2010 May 21.

38.

Eradicating typological thinking in prokaryotic systematics and evolution.

Doolittle WF.

Cold Spring Harb Symp Quant Biol. 2009;74:197-204. doi: 10.1101/sqb.2009.74.002. Epub 2009 Aug 10. Review.

PMID:
19667014
39.

Kosmotoga olearia gen. nov., sp. nov., a thermophilic, anaerobic heterotroph isolated from an oil production fluid.

Dipippo JL, Nesbø CL, Dahle H, Doolittle WF, Birkland NK, Noll KM.

Int J Syst Evol Microbiol. 2009 Dec;59(Pt 12):2991-3000. doi: 10.1099/ijs.0.008045-0. Epub 2009 Jul 30.

PMID:
19643902
40.

'Candidatus Planktophila limnetica', an actinobacterium representing one of the most numerically important taxa in freshwater bacterioplankton.

Jezbera J, Sharma AK, Brandt U, Doolittle WF, Hahn MW.

Int J Syst Evol Microbiol. 2009 Nov;59(Pt 11):2864-9. doi: 10.1099/ijs.0.010199-0. Epub 2009 Jul 23.

PMID:
19628588
41.

The practice of classification and the theory of evolution, and what the demise of Charles Darwin's tree of life hypothesis means for both of them.

Doolittle WF.

Philos Trans R Soc Lond B Biol Sci. 2009 Aug 12;364(1527):2221-8. doi: 10.1098/rstb.2009.0032.

42.

On the origin of prokaryotic species.

Doolittle WF, Zhaxybayeva O.

Genome Res. 2009 May;19(5):744-56. doi: 10.1101/gr.086645.108. Review.

43.

Integron gene cassettes and degradation of compounds associated with industrial waste: the case of the Sydney tar ponds.

Koenig JE, Sharp C, Dlutek M, Curtis B, Joss M, Boucher Y, Doolittle WF.

PLoS One. 2009;4(4):e5276. doi: 10.1371/journal.pone.0005276. Epub 2009 Apr 23.

44.

ACID: annotation of cassette and integron data.

Joss MJ, Koenig JE, Labbate M, Polz MF, Gillings MR, Stokes HW, Doolittle WF, Boucher Y.

BMC Bioinformatics. 2009 Apr 21;10:118. doi: 10.1186/1471-2105-10-118.

45.

On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales.

Zhaxybayeva O, Swithers KS, Lapierre P, Fournier GP, Bickhart DM, DeBoy RT, Nelson KE, Nesbø CL, Doolittle WF, Gogarten JP, Noll KM.

Proc Natl Acad Sci U S A. 2009 Apr 7;106(14):5865-70. doi: 10.1073/pnas.0901260106. Epub 2009 Mar 23.

46.

Actinorhodopsin genes discovered in diverse freshwater habitats and among cultivated freshwater Actinobacteria.

Sharma AK, Sommerfeld K, Bullerjahn GS, Matteson AR, Wilhelm SW, Jezbera J, Brandt U, Doolittle WF, Hahn MW.

ISME J. 2009 Jun;3(6):726-37. doi: 10.1038/ismej.2009.13. Epub 2009 Feb 26.

PMID:
19242530
47.

The genome of Thermosipho africanus TCF52B: lateral genetic connections to the Firmicutes and Archaea.

Nesbø CL, Bapteste E, Curtis B, Dahle H, Lopez P, Macleod D, Dlutek M, Bowman S, Zhaxybayeva O, Birkeland NK, Doolittle WF.

J Bacteriol. 2009 Mar;191(6):1974-8. doi: 10.1128/JB.01448-08. Epub 2009 Jan 5.

48.

Intertwined evolutionary histories of marine Synechococcus and Prochlorococcus marinus.

Zhaxybayeva O, Doolittle WF, Papke RT, Gogarten JP.

Genome Biol Evol. 2009 Sep 2;1:325-39. doi: 10.1093/gbe/evp032.

49.

The impact of reticulate evolution on genome phylogeny.

Beiko RG, Doolittle WF, Charlebois RL.

Syst Biol. 2008 Dec;57(6):844-56. doi: 10.1080/10635150802559265.

PMID:
19085328
50.

Microbial evolution: stalking the wild bacterial species.

Doolittle WF.

Curr Biol. 2008 Jul 8;18(13):R565-7. doi: 10.1016/j.cub.2008.05.029.

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