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Phylogenomics provides robust support for a two-domains tree of life.

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

Nat Ecol Evol. 2020 Jan;4(1):138-147. doi: 10.1038/s41559-019-1040-x. Epub 2019 Dec 9.


First record of translocation in Culicidae (Diptera) mitogenomes: evidence from the tribe Sabethini.

Lorenz C, Alves JMP, Foster PG, Sallum MAM, Suesdek L.

BMC Genomics. 2019 Sep 27;20(1):721. doi: 10.1186/s12864-019-6069-3.


Phylogenomics suggests oxygen availability as a driving force in Thaumarchaeota evolution.

Ren M, Feng X, Huang Y, Wang H, Hu Z, Clingenpeel S, Swan BK, Fonseca MM, Posada D, Stepanauskas R, Hollibaugh JT, Foster PG, Woyke T, Luo H.

ISME J. 2019 Sep;13(9):2150-2161. doi: 10.1038/s41396-019-0418-8. Epub 2019 Apr 25.


Environment-dependent fitness gains can be driven by horizontal gene transfer of transporter-encoding genes.

Milner DS, Attah V, Cook E, Maguire F, Savory FR, Morrison M, Müller CA, Foster PG, Talbot NJ, Leonard G, Richards TA.

Proc Natl Acad Sci U S A. 2019 Mar 19;116(12):5613-5622. doi: 10.1073/pnas.1815994116. Epub 2019 Mar 6.


Nuclear protein phylogenies support the monophyly of the three bryophyte groups (Bryophyta Schimp.).

de Sousa F, Foster PG, Donoghue PCJ, Schneider H, Cox CJ.

New Phytol. 2019 Apr;222(1):565-575. doi: 10.1111/nph.15587. Epub 2018 Dec 7.


Atezolizumab Plus nab-Paclitaxel in the Treatment of Metastatic Triple-Negative Breast Cancer With 2-Year Survival Follow-up: A Phase 1b Clinical Trial.

Adams S, Diamond JR, Hamilton E, Pohlmann PR, Tolaney SM, Chang CW, Zhang W, Iizuka K, Foster PG, Molinero L, Funke R, Powderly J.

JAMA Oncol. 2019 Mar 1;5(3):334-342. doi: 10.1001/jamaoncol.2018.5152.


Phylogeny of Anophelinae using mitochondrial protein coding genes.

Foster PG, de Oliveira TMP, Bergo ES, Conn JE, Sant'Ana DC, Nagaki SS, Nihei S, Lamas CE, González C, Moreira CC, Sallum MAM.

R Soc Open Sci. 2017 Nov 8;4(11):170758. doi: 10.1098/rsos.170758. eCollection 2017 Nov.


Can quartet analyses combining maximum likelihood estimation and Hennigian logic overcome long branch attraction in phylogenomic sequence data?

Kück P, Wilkinson M, Groß C, Foster PG, Wägele JW.

PLoS One. 2017 Aug 25;12(8):e0183393. doi: 10.1371/journal.pone.0183393. eCollection 2017. Erratum in: PLoS One. 2017 Oct 12;12 (10 ):e0186617.


A phase 2 randomised discontinuation trial of cabozantinib in patients with ovarian carcinoma.

Vergote IB, Smith DC, Berger R, Kurzrock R, Vogelzang NJ, Sella A, Wheler J, Lee Y, Foster PG, Weitzman R, Buckanovich RJ.

Eur J Cancer. 2017 Sep;83:229-236. doi: 10.1016/j.ejca.2017.06.018. Epub 2017 Jul 26.


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.


Curious bivalves: Systematic utility and unusual properties of anomalodesmatan mitochondrial genomes.

Williams ST, Foster PG, Hughes C, Harper EM, Taylor JD, Littlewood DTJ, Dyal P, Hopkins KP, Briscoe AG.

Mol Phylogenet Evol. 2017 May;110:60-72. doi: 10.1016/j.ympev.2017.03.004. Epub 2017 Mar 6.


Next-Generation Mitogenomics: A Comparison of Approaches Applied to Caecilian Amphibian Phylogeny.

Maddock ST, Briscoe AG, Wilkinson M, Waeschenbach A, San Mauro D, Day JJ, Littlewood DT, Foster PG, Nussbaum RA, Gower DJ.

PLoS One. 2016 Jun 9;11(6):e0156757. doi: 10.1371/journal.pone.0156757. eCollection 2016.


Mitochondrial Genomes of Anopheles (Kerteszia) (Diptera: Culicidae) From the Atlantic Forest, Brazil.

Oliveira TM, Foster PG, Bergo ES, Nagaki SS, Sanabani SS, Marinotti O, Marinotti PN, Sallum MA.

J Med Entomol. 2016 Jul;53(4):790-797. Epub 2016 May 4.


Family-Level Sampling of Mitochondrial Genomes in Coleoptera: Compositional Heterogeneity and Phylogenetics.

Timmermans MJ, Barton C, Haran J, Ahrens D, Culverwell CL, Ollikainen A, Dodsworth S, Foster PG, Bocak L, Vogler AP.

Genome Biol Evol. 2015 Dec 8;8(1):161-75. doi: 10.1093/gbe/evv241.


Mitochondrial genomes and comparative analyses of Culex camposi, Culex coronator, Culex usquatus and Culex usquatissimus (Diptera:Culicidae), members of the coronator group.

Demari-Silva B, Foster PG, de Oliveira TM, Bergo ES, Sanabani SS, Pessôa R, Sallum MA.

BMC Genomics. 2015 Oct 21;16:831. doi: 10.1186/s12864-015-1951-0.


Implementing and testing Bayesian and maximum-likelihood supertree methods in phylogenetics.

Akanni WA, Wilkinson M, Creevey CJ, Foster PG, Pisani D.

R Soc Open Sci. 2015 Aug 5;2(8):140436. doi: 10.1098/rsos.140436. eCollection 2015 Aug.


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.


The mitochondrial genome of Parascaris univalens--implications for a "forgotten" parasite.

Jabbar A, Littlewood DT, Mohandas N, Briscoe AG, Foster PG, Müller F, von Samson-Himmelstjerna G, Jex AR, Gasser RB.

Parasit Vectors. 2014 Sep 4;7:428. doi: 10.1186/1756-3305-7-428.


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.


Analyses of charophyte chloroplast genomes help characterize the ancestral chloroplast genome of land plants.

Civaň P, Foster PG, Embley MT, Séneca A, Cox CJ.

Genome Biol Evol. 2014 Apr;6(4):897-911. doi: 10.1093/gbe/evu061.


The complete mitochondrial genome of Limnoria quadripunctata Holthuis (Isopoda: Limnoriidae).

Lloyd RE, Streeter SD, Foster PG, Littlewood DT, Huntley J, Beckham GT, Himmel ME, Cragg SM.

Mitochondrial DNA. 2015;26(6):825-6. doi: 10.3109/19401736.2013.855912. Epub 2014 Jan 10.


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.


Reduction and expansion in microsporidian genome evolution: new insights from comparative genomics.

Nakjang S, Williams TA, Heinz E, Watson AK, Foster PG, Sendra KM, Heaps SE, Hirt RP, Martin Embley T.

Genome Biol Evol. 2013;5(12):2285-303. doi: 10.1093/gbe/evt184.


The complete mitochondrial genome of a turbinid vetigastropod from MiSeq Illumina sequencing of genomic DNA and steps towards a resolved gastropod phylogeny.

Williams ST, Foster PG, Littlewood DT.

Gene. 2014 Jan 1;533(1):38-47. doi: 10.1016/j.gene.2013.10.005. Epub 2013 Oct 11.


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.


Whole-community DNA barcoding reveals a spatio-temporal continuum of biodiversity at species and genetic levels.

Baselga A, Fujisawa T, Crampton-Platt A, Bergsten J, Foster PG, Monaghan MT, Vogler AP.

Nat Commun. 2013;4:1892. doi: 10.1038/ncomms2881.


A 20-state empirical amino-acid substitution model for green plant chloroplasts.

Cox CJ, Foster PG.

Mol Phylogenet Evol. 2013 Aug;68(2):218-20. doi: 10.1016/j.ympev.2013.03.030. Epub 2013 Apr 6.


Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes.

Alsmark C, Foster PG, Sicheritz-Ponten T, Nakjang S, Martin Embley T, Hirt RP.

Genome Biol. 2013 Feb 25;14(2):R19. doi: 10.1186/gb-2013-14-2-r19.


Phylogenetic analysis and DNA-based species confirmation in Anopheles (Nyssorhynchus).

Foster PG, Bergo ES, Bourke BP, Oliveira TM, Nagaki SS, Sant'Ana DC, Sallum MA.

PLoS One. 2013;8(2):e54063. doi: 10.1371/journal.pone.0054063. Epub 2013 Feb 4.


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.


Next generation sequencing and comparative analyses of Xenopus mitogenomes.

Lloyd RE, Foster PG, Guille M, Littlewood DT.

BMC Genomics. 2012 Sep 19;13:496. doi: 10.1186/1471-2164-13-496.


Horizontal gene transfer facilitated the evolution of plant parasitic mechanisms in the oomycetes.

Richards TA, Soanes DM, Jones MD, Vasieva O, Leonard G, Paszkiewicz K, Foster PG, Hall N, Talbot NJ.

Proc Natl Acad Sci U S A. 2011 Sep 13;108(37):15258-63. doi: 10.1073/pnas.1105100108. Epub 2011 Aug 30.


Phylogenetic relationships among species of Anopheles (Nyssorhynchus) (Diptera, Culicidae) based on nuclear and mitochondrial gene sequences.

Bourke BP, Foster PG, Bergo ES, Calado DC, Sallum MA.

Acta Trop. 2010 May;114(2):88-96. doi: 10.1016/j.actatropica.2010.01.009. Epub 2010 Feb 1.


Detection of a new yellow fever virus lineage within the South American genotype I in Brazil.

de Souza RP, Foster PG, Sallum MA, Coimbra TL, Maeda AY, Silveira VR, Moreno ES, da Silva FG, Rocco IM, Ferreira IB, Suzuki A, Oshiro FM, Petrella SM, Pereira LE, Katz G, Tengan CH, Siciliano MM, Dos Santos CL.

J Med Virol. 2010 Jan;82(1):175-85. doi: 10.1002/jmv.21606.


Phylogenomic analysis demonstrates a pattern of rare and ancient horizontal gene transfer between plants and fungi.

Richards TA, Soanes DM, Foster PG, Leonard G, Thornton CR, Talbot NJ.

Plant Cell. 2009 Jul;21(7):1897-911. doi: 10.1105/tpc.109.065805. Epub 2009 Jul 7.


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.


Resurrection of Anopheles goeldii from synonymy with Anopheles nuneztovari (Diptera, Culicidae) and a new record for Anopheles dunhami in the Brazilian Amazon.

Calado DC, Foster PG, Bergo ES, Santos CL, Galardo AK, Sallum MA.

Mem Inst Oswaldo Cruz. 2008 Dec;103(8):791-9.


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.


Detection of a new mumps virus genotype during parotitis epidemic of 2006-2007 in the state of São Paulo, Brazil.

Santos CL, Ishida MA, Foster PG, Sallum MA, Benega MA, Borges DB, Corrêa KO, Constantino CR, Afzal MA, Paiva TM.

J Med Virol. 2008 Feb;80(2):323-9.


Molecular Phylogeny of Neotropical Anopheles (Nyssorhynchus) Albitarsis Species Complex (Diptera: Culicidae).

Wilkerson RC, Foster PG, Li C, Sallum MA.

Ann Entomol Soc Am. 2005 Nov;98(6):918-925.


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.


VNTR analysis of selected outbreaks of Burkholderia pseudomallei in Australia.

Pearson T, U'Ren JM, Schupp JM, Allan GJ, Foster PG, Mayo MJ, Gal D, Choy JL, Daugherty RL, Kachur S, Friedman CL, Leadem B, Georgia S, Hornstra H, Vogler AJ, Wagner DM, Keim P, Currie BJ.

Infect Genet Evol. 2007 Jul;7(4):416-23. Epub 2006 Dec 20.


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.


Evolutionary origins of the eukaryotic shikimate pathway: gene fusions, horizontal gene transfer, and endosymbiotic replacements.

Richards TA, Dacks JB, Campbell SA, Blanchard JL, Foster PG, McLeod R, Roberts CW.

Eukaryot Cell. 2006 Sep;5(9):1517-31.


Dense taxonomic EST sampling and its applications for molecular systematics of the Coleoptera (beetles).

Hughes J, Longhorn SJ, Papadopoulou A, Theodorides K, de Riva A, Mejia-Chang M, Foster PG, Vogler AP.

Mol Biol Evol. 2006 Feb;23(2):268-78. Epub 2005 Oct 19.


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