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Convergent evolution of hydrogenosomes from mitochondria by gene transfer and loss.

Lewis WH, Lind AE, Sendra KM, Onsbring H, Williams TA, Esteban GF, Hirt RP, Ettema TJG, Embley TM.

Mol Biol Evol. 2019 Oct 24. pii: msz239. doi: 10.1093/molbev/msz239. [Epub ahead of print]


A new family of cell surface located purine transporters in Microsporidia and related fungal endoparasites.

Major P, Sendra KM, Dean P, Williams TA, Watson AK, Thwaites DT, Embley TM, Hirt RP.

Elife. 2019 Jul 29;8. pii: e47037. doi: 10.7554/eLife.47037.


Genomes of two archaeal endosymbionts show convergent adaptations to an intracellular lifestyle.

Lind AE, Lewis WH, Spang A, Guy L, Embley TM, Ettema TJG.

ISME J. 2018 Nov;12(11):2655-2667. doi: 10.1038/s41396-018-0207-9. Epub 2018 Jul 10.


Transporter gene acquisition and innovation in the evolution of Microsporidia intracellular parasites.

Dean P, Sendra KM, Williams TA, Watson AK, Major P, Nakjang S, Kozhevnikova E, Goldberg AV, Kunji ERS, Hirt RP, Embley TM.

Nat Commun. 2018 Apr 27;9(1):1709. doi: 10.1038/s41467-018-03923-4.


Morphology and Phylogeny of a New Species of Anaerobic Ciliate, Trimyema finlayi n. sp., with Endosymbiotic Methanogens.

Lewis WH, Sendra KM, Embley TM, Esteban GF.

Front Microbiol. 2018 Feb 19;9:140. doi: 10.3389/fmicb.2018.00140. eCollection 2018.


The Effect of Nonreversibility on Inferring Rooted Phylogenies.

Cherlin S, Heaps SE, Nye TMW, Boys RJ, Williams TA, Embley TM.

Mol Biol Evol. 2018 Apr 1;35(4):984-1002. doi: 10.1093/molbev/msx294. Erratum in: Mol Biol Evol. 2018 Jul 1;35(7):1821.


Resculpting the binding pocket of APC superfamily LeuT-fold amino acid transporters.

Edwards N, Anderson CMH, Conlon NJ, Watson AK, Hall RJ, Cheek TR, Embley TM, Thwaites DT.

Cell Mol Life Sci. 2018 Mar;75(5):921-938. doi: 10.1007/s00018-017-2677-8. Epub 2017 Oct 23.


Integrative modeling of gene and genome evolution roots the archaeal tree of life.

Williams TA, Szöllősi GJ, Spang A, Foster PG, Heaps SE, Boussau B, Ettema TJG, Embley TM.

Proc Natl Acad Sci U S A. 2017 Jun 6;114(23):E4602-E4611. doi: 10.1073/pnas.1618463114. Epub 2017 May 22.


Phylogenetic Diversity of NTT Nucleotide Transport Proteins in Free-Living and Parasitic Bacteria and Eukaryotes.

Major P, Embley TM, Williams TA.

Genome Biol Evol. 2017 Feb 1;9(2):480-487. doi: 10.1093/gbe/evx015.


Evolutionary conservation and in vitro reconstitution of microsporidian iron-sulfur cluster biosynthesis.

Freibert SA, Goldberg AV, Hacker C, Molik S, Dean P, Williams TA, Nakjang S, Long S, Sendra K, Bill E, Heinz E, Hirt RP, Lucocq JM, Embley TM, Lill R.

Nat Commun. 2017 Jan 4;8:13932. doi: 10.1038/ncomms13932.


Microsporidia: Why Make Nucleotides if You Can Steal Them?

Dean P, Hirt RP, Embley TM.

PLoS Pathog. 2016 Nov 17;12(11):e1005870. doi: 10.1371/journal.ppat.1005870. eCollection 2016 Nov. Review.


A Recent Whole-Genome Duplication Divides Populations of a Globally Distributed Microsporidian.

Williams TA, Nakjang S, Campbell SE, Freeman MA, Eydal M, Moore K, Hirt RP, Embley TM, Williams BA.

Mol Biol Evol. 2016 Aug;33(8):2002-15. doi: 10.1093/molbev/msw083. Epub 2016 Apr 27.


Differential remodelling of peroxisome function underpins the environmental and metabolic adaptability of diplonemids and kinetoplastids.

Morales J, Hashimoto M, Williams TA, Hirawake-Mogi H, Makiuchi T, Tsubouchi A, Kaga N, Taka H, Fujimura T, Koike M, Mita T, Bringaud F, Concepción JL, Hashimoto T, Embley TM, Nara T.

Proc Biol Sci. 2016 May 11;283(1830). pii: 20160520. doi: 10.1098/rspb.2016.0520.


Transcriptomic profiling of host-parasite interactions in the microsporidian Trachipleistophora hominis.

Watson AK, Williams TA, Williams BA, Moore KA, Hirt RP, Embley TM.

BMC Genomics. 2015 Nov 21;16:983. doi: 10.1186/s12864-015-1989-z.


New substitution models for rooting phylogenetic trees.

Williams TA, Heaps SE, Cherlin S, Nye TM, Boys RJ, Embley TM.

Philos Trans R Soc Lond B Biol Sci. 2015 Sep 26;370(1678):20140336. doi: 10.1098/rstb.2014.0336.


Changing ideas about eukaryotic origins.

Williams TA, Embley TM.

Philos Trans R Soc Lond B Biol Sci. 2015 Sep 26;370(1678):20140318. doi: 10.1098/rstb.2014.0318.


Coupling of diversification and pH adaptation during the evolution of terrestrial Thaumarchaeota.

Gubry-Rangin C, Kratsch C, Williams TA, McHardy AC, Embley TM, Prosser JI, Macqueen DJ.

Proc Natl Acad Sci U S A. 2015 Jul 28;112(30):9370-5. doi: 10.1073/pnas.1419329112. Epub 2015 Jul 13.


Evolution: Steps on the road to eukaryotes.

Embley TM, Williams TA.

Nature. 2015 May 14;521(7551):169-70. doi: 10.1038/nature14522. Epub 2015 May 6. No abstract available.


Plastid establishment did not require a chlamydial partner.

Domman D, Horn M, Embley TM, Williams TA.

Nat Commun. 2015 Mar 11;6:6421. doi: 10.1038/ncomms7421.


Lateral gene transfers and the origins of the eukaryote proteome: a view from microbial parasites.

Hirt RP, Alsmark C, Embley TM.

Curr Opin Microbiol. 2015 Feb;23:155-62. doi: 10.1016/j.mib.2014.11.018. Epub 2014 Dec 5. Review.


Plasma membrane-located purine nucleotide transport proteins are key components for host exploitation by microsporidian intracellular parasites.

Heinz E, Hacker C, Dean P, Mifsud J, Goldberg AV, Williams TA, Nakjang S, Gregory A, Hirt RP, Lucocq JM, Kunji ER, Embley TM.

PLoS Pathog. 2014 Dec 4;10(12):e1004547. doi: 10.1371/journal.ppat.1004547. eCollection 2014 Dec.


Bayesian modelling of compositional heterogeneity in molecular phylogenetics.

Heaps SE, Nye TM, Boys RJ, Williams TA, Embley TM.

Stat Appl Genet Mol Biol. 2014 Oct;13(5):589-609. doi: 10.1515/sagmb-2013-0077.


Transport proteins of parasitic protists and their role in nutrient salvage.

Dean P, Major P, Nakjang S, Hirt RP, Embley TM.

Front Plant Sci. 2014 Apr 29;5:153. doi: 10.3389/fpls.2014.00153. eCollection 2014. Review.


Compositional biases among synonymous substitutions cause conflict between gene and protein trees for plastid origins.

Li B, Lopes JS, Foster PG, Embley TM, Cox CJ.

Mol Biol Evol. 2014 Jul;31(7):1697-709. doi: 10.1093/molbev/msu105. Epub 2014 May 2.


Archaeal "dark matter" and the origin of eukaryotes.

Williams TA, Embley TM.

Genome Biol Evol. 2014 Mar;6(3):474-81. doi: 10.1093/gbe/evu031.


Conflicting phylogenies for early land plants are caused by composition biases among synonymous substitutions.

Cox CJ, Li B, Foster PG, Embley TM, Civán P.

Syst Biol. 2014 Mar;63(2):272-9. doi: 10.1093/sysbio/syt109. Epub 2014 Jan 6. No abstract available.


An archaeal origin of eukaryotes supports only two primary domains of life.

Williams TA, Foster PG, Cox CJ, Embley TM.

Nature. 2013 Dec 12;504(7479):231-6. doi: 10.1038/nature12779. Review.


The genome of the obligate intracellular parasite Trachipleistophora hominis: new insights into microsporidian genome dynamics and reductive evolution.

Heinz E, Williams TA, Nakjang S, Noël CJ, Swan DC, Goldberg AV, Harris SR, Weinmaier T, Markert S, Becher D, Bernhardt J, Dagan T, Hacker C, Lucocq JM, Schweder T, Rattei T, Hall N, Hirt RP, Embley TM.

PLoS Pathog. 2012;8(10):e1002979. doi: 10.1371/journal.ppat.1002979. Epub 2012 Oct 25.


A congruent phylogenomic signal places eukaryotes within the Archaea.

Williams TA, Foster PG, Nye TM, Cox CJ, Embley TM.

Proc Biol Sci. 2012 Dec 22;279(1749):4870-9. doi: 10.1098/rspb.2012.1795. Epub 2012 Oct 24.


The SAR11 group of alpha-proteobacteria is not related to the origin of mitochondria.

Rodríguez-Ezpeleta N, Embley TM.

PLoS One. 2012;7(1):e30520. doi: 10.1371/journal.pone.0030520. Epub 2012 Jan 23.


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.


Informational gene phylogenies do not support a fourth domain of life for nucleocytoplasmic large DNA viruses.

Williams TA, Embley TM, Heinz E.

PLoS One. 2011;6(6):e21080. doi: 10.1371/journal.pone.0021080. Epub 2011 Jun 16.


Diversity and reductive evolution of mitochondria among microbial eukaryotes.

Hjort K, Goldberg AV, Tsaousis AD, Hirt RP, Embley TM.

Philos Trans R Soc Lond B Biol Sci. 2010 Mar 12;365(1541):713-27. doi: 10.1098/rstb.2009.0224. Review.


The primary divisions of life: a phylogenomic approach employing composition-heterogeneous methods.

Foster PG, Cox CJ, Embley TM.

Philos Trans R Soc Lond B Biol Sci. 2009 Aug 12;364(1527):2197-207. doi: 10.1098/rstb.2009.0034.


Horizontal gene transfer in eukaryotic parasites: a case study of Entamoeba histolytica and Trichomonas vaginalis.

Alsmark UC, Sicheritz-Ponten T, Foster PG, Hirt RP, Embley TM.

Methods Mol Biol. 2009;532:489-500. doi: 10.1007/978-1-60327-853-9_28.


Reductive evolution of the mitochondrial processing peptidases of the unicellular parasites trichomonas vaginalis and giardia intestinalis.

Smíd O, Matusková A, Harris SR, Kucera T, Novotný M, Horváthová L, Hrdý I, Kutejová E, Hirt RP, Embley TM, Janata J, Tachezy J.

PLoS Pathog. 2008 Dec;4(12):e1000243. doi: 10.1371/journal.ppat.1000243. Epub 2008 Dec 19.


The archaebacterial origin of eukaryotes.

Cox CJ, Foster PG, Hirt RP, Harris SR, Embley TM.

Proc Natl Acad Sci U S A. 2008 Dec 23;105(51):20356-61. doi: 10.1073/pnas.0810647105. Epub 2008 Dec 10.


A novel route for ATP acquisition by the remnant mitochondria of Encephalitozoon cuniculi.

Tsaousis AD, Kunji ER, Goldberg AV, Lucocq JM, Hirt RP, Embley TM.

Nature. 2008 May 22;453(7194):553-6. doi: 10.1038/nature06903. Epub 2008 Apr 30.


Localization and functionality of microsporidian iron-sulphur cluster assembly proteins.

Goldberg AV, Molik S, Tsaousis AD, Neumann K, Kuhnke G, Delbac F, Vivares CP, Hirt RP, Lill R, Embley TM.

Nature. 2008 Apr 3;452(7187):624-8. doi: 10.1038/nature06606. Epub 2008 Mar 2.


Structure and content of the Entamoeba histolytica genome.

Clark CG, Alsmark UC, Tazreiter M, Saito-Nakano Y, Ali V, Marion S, Weber C, Mukherjee C, Bruchhaus I, Tannich E, Leippe M, Sicheritz-Ponten T, Foster PG, Samuelson J, Noël CJ, Hirt RP, Embley TM, Gilchrist CA, Mann BJ, Singh U, Ackers JP, Bhattacharya S, Bhattacharya A, Lohia A, Guillén N, Duchêne M, Nozaki T, Hall N.

Adv Parasitol. 2007;65:51-190.


Frataxin, a conserved mitochondrial protein, in the hydrogenosome of Trichomonas vaginalis.

Dolezal P, Dancis A, Lesuisse E, Sutak R, Hrdý I, Embley TM, Tachezy J.

Eukaryot Cell. 2007 Aug;6(8):1431-8. Epub 2007 Jun 15.


Of clades and clans: terms for phylogenetic relationships in unrooted trees.

Wilkinson M, McInerney JO, Hirt RP, Foster PG, Embley TM.

Trends Ecol Evol. 2007 Mar;22(3):114-5. Epub 2007 Jan 18. No abstract available.


Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis.

Carlton JM, Hirt RP, Silva JC, Delcher AL, Schatz M, Zhao Q, Wortman JR, Bidwell SL, Alsmark UC, Besteiro S, Sicheritz-Ponten T, Noel CJ, Dacks JB, Foster PG, Simillion C, Van de Peer Y, Miranda-Saavedra D, Barton GJ, Westrop GD, Müller S, Dessi D, Fiori PL, Ren Q, Paulsen I, Zhang H, Bastida-Corcuera FD, Simoes-Barbosa A, Brown MT, Hayes RD, Mukherjee M, Okumura CY, Schneider R, Smith AJ, Vanacova S, Villalvazo M, Haas BJ, Pertea M, Feldblyum TV, Utterback TR, Shu CL, Osoegawa K, de Jong PJ, Hrdy I, Horvathova L, Zubacova Z, Dolezal P, Malik SB, Logsdon JM Jr, Henze K, Gupta A, Wang CC, Dunne RL, Upcroft JA, Upcroft P, White O, Salzberg SL, Tang P, Chiu CH, Lee YS, Embley TM, Coombs GH, Mottram JC, Tachezy J, Fraser-Liggett CM, Johnson PJ.

Science. 2007 Jan 12;315(5809):207-12.


Multiple secondary origins of the anaerobic lifestyle in eukaryotes.

Embley TM.

Philos Trans R Soc Lond B Biol Sci. 2006 Jun 29;361(1470):1055-67. Review.


Introduction: How and when did microbes change the world?

Cavalier-Smith T, Brasier M, Embley TM.

Philos Trans R Soc Lond B Biol Sci. 2006 Jun 29;361(1470):845-50. Review. No abstract available.


Eukaryotic evolution, changes and challenges.

Embley TM, Martin W.

Nature. 2006 Mar 30;440(7084):623-30. Review.


Inference of the phylogenetic position of oxymonads based on nine genes: support for metamonada and excavata.

Hampl V, Horner DS, Dyal P, Kulda J, Flegr J, Foster PG, Embley TM.

Mol Biol Evol. 2005 Dec;22(12):2508-18. Epub 2005 Aug 24.


The genome of the African trypanosome Trypanosoma brucei.

Berriman M, Ghedin E, Hertz-Fowler C, Blandin G, Renauld H, Bartholomeu DC, Lennard NJ, Caler E, Hamlin NE, Haas B, Böhme U, Hannick L, Aslett MA, Shallom J, Marcello L, Hou L, Wickstead B, Alsmark UC, Arrowsmith C, Atkin RJ, Barron AJ, Bringaud F, Brooks K, Carrington M, Cherevach I, Chillingworth TJ, Churcher C, Clark LN, Corton CH, Cronin A, Davies RM, Doggett J, Djikeng A, Feldblyum T, Field MC, Fraser A, Goodhead I, Hance Z, Harper D, Harris BR, Hauser H, Hostetler J, Ivens A, Jagels K, Johnson D, Johnson J, Jones K, Kerhornou AX, Koo H, Larke N, Landfear S, Larkin C, Leech V, Line A, Lord A, Macleod A, Mooney PJ, Moule S, Martin DM, Morgan GW, Mungall K, Norbertczak H, Ormond D, Pai G, Peacock CS, Peterson J, Quail MA, Rabbinowitsch E, Rajandream MA, Reitter C, Salzberg SL, Sanders M, Schobel S, Sharp S, Simmonds M, Simpson AJ, Tallon L, Turner CM, Tait A, Tivey AR, Van Aken S, Walker D, Wanless D, Wang S, White B, White O, Whitehead S, Woodward J, Wortman J, Adams MD, Embley TM, Gull K, Ullu E, Barry JD, Fairlamb AH, Opperdoes F, Barrell BG, Donelson JE, Hall N, Fraser CM, Melville SE, El-Sayed NM.

Science. 2005 Jul 15;309(5733):416-22.


Comparative genomics of trypanosomatid parasitic protozoa.

El-Sayed NM, Myler PJ, Blandin G, Berriman M, Crabtree J, Aggarwal G, Caler E, Renauld H, Worthey EA, Hertz-Fowler C, Ghedin E, Peacock C, Bartholomeu DC, Haas BJ, Tran AN, Wortman JR, Alsmark UC, Angiuoli S, Anupama A, Badger J, Bringaud F, Cadag E, Carlton JM, Cerqueira GC, Creasy T, Delcher AL, Djikeng A, Embley TM, Hauser C, Ivens AC, Kummerfeld SK, Pereira-Leal JB, Nilsson D, Peterson J, Salzberg SL, Shallom J, Silva JC, Sundaram J, Westenberger S, White O, Melville SE, Donelson JE, Andersson B, Stuart KD, Hall N.

Science. 2005 Jul 15;309(5733):404-9.

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