List of publications by members of our team.

2014

Cox CJ, Li B, Foster PG, Embley TM, Civan P. Conflicting Phylogenies for Early Land Plants are Caused by Composition Biases among Synonymous Substitutions.. Syst Biol. (2014). pubmed

2013

Alsmark C, Foster PG, Sicheritz-Ponten T, Nakjang S, Embley TM, Hirt RP. Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes. Genome Biol. vol 14 (2013). pubmed
Campbell SE, Williams TA, Yousuf A, Soanes DM, Paszkiewicz KH, Williams BA. The genome of Spraguea lophii and the basis of host-microsporidian interactions.. PLoS Genet. vol 9 p. e1003676 (2013). pubmed
Dagan T, Roettger M, Stucken K, Landan G, Koch R, Major P, Gould SB, Goremykin VV, Rippka R, Tandeau de Marsac N, Gugger M, Lockhart PJ, Allen JF, Brune I, Maus I, Puhler A, Martin WF. Genomes of stigonematalean cyanobacteria (subsection V) and the evolution of oxygenic photosynthesis from prokaryotes to plastids. Genome Biol Evol. vol 5 p. 31-44 (2013). pubmed
Dean P, Kenny B. A bacterial encoded protein induces extreme multinucleation and cell-cell internalization in intestinal cells. Tissue Barriers. vol 1 (2013).
Dean P, Young L, Quitard S, Kenny B. Insights into the Pathogenesis of Enteropathogenic E. coli Using an Improved Intestinal Enterocyte. PLos One. vol 8 (2013). pubmed
Heaps SE, Boys RJ, Farrow M. Computation of marginal likelihoods with data-dependent support for latent variables. Computational Statistics & Data Analysis. (2013).
Hirt RP. Trichomonas vaginalis virulence factors: an integrative overview. Sex Transm Infect. (2013). pubmed
Major P, Zimorski V, Hoffmann K, Pereira Bras X, Martin WF, Gould SB. The N-terminal sequences of four major hydrogenosomal proteins are not essential for import into hydrogenosomes of Trichomonas vaginalis. J Euk Microbiol. vol 60 p. 89?97 (2013). pubmed
Nakjang S, Williams TA, Heinz E, Watson AK, Foster PG, Sendra KM, Heaps SE, Hirt RP, Embley TM. Reduction and expansion in microsporidian genome evolution: new insights from comparative genomics. Genome Biol Evol. vol 5 p. 2285-303 (2013). pubmed
Williams TA, Foster PG, Cox CJ, Embley TM. An archaeal origin of eukaryotes supports only two primary domains of life.. Nature. vol 504 p. 231-236 (2013). pubmed

2012

Bulmer DM, Kharraz L, Grant AJ, Dean P, Morgan FJ, Karavolos MH, Doble AC, McGhie EJ, Koronakis V, Daniel RA, Mastroeni P, Khan CM. The bacterial cytoskeleton modulates motility, type 3 secretion, and colonization in Salmonella. PLoS Pathog. vol 8 p. doi:10.1371/ (2012). pubmed
Burstein D, Gould SB, Zimorski V, Kloesges T, Kiosse F, Major P, Martin WF, Pupko T, Dagan T. A machine-learning approach to identify hydrogenosomal proteins in Trichomonas vaginalis. Euk Cell. vol 11 p. 217-228 (2012). pubmed
Caffrey BE, Williams TA, Jiang X, Toft C, Hokamp K, Fares MA. Proteome-wide analysis of functional divergence in bacteria: exploring a host of ecological adaptations. PLoS One. vol 7 p. e35659 (2012). pubmed
Collison M, Hirt RP, Wipat A, Nakjang S, Sanseau P, Brown JR. Data mining the human gut microbiota for therapeutic targets. Brief Bioinform. epub (2012). pubmed
Flanagan K, Nakjang S, Hallinan J, Harwood C, Hirt RP, Pocock MR, Wipat A. Microbase2.0: a generic framework for computationally intensive bioinformatics workflows in the cloud . J Integr Bioinform. vol 9 p. doi: 10.2390 (2012). pubmed
Heinz E, Williams TA, Nakjang S, Noel 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. The Genome of the Obligate Intracellular Parasite Trachipleistophora hominis: New Insights into Microsporidian Genome Dynamics and Reductive Evolution. PLoS Pathog. vol 8 p. e1002979 (2012). pubmed
Nakjang S, Ndeh AN, Wipat A, Bolam DN, Hirt RP. A Novel Extracellular Metallopeptidase Domain Shared by Animal Host-Associated Mutualistic and Pathogenic Microbes. PLoS ONE. vol 7 p. doi: 10.1371 (2012). pubmed
Rytkonen KT, Akbarzadeh A, Miandare HK, Kamei H, Duan C, Leder EH, Williams TA, Nikinmaa M. Subfunctionalization of cyprinid hypoxia inducible factors for roles in development and oxygen sensing. Evolution. p. DOI: 10.1111 (2012).
Williams TA, Foster PG, Nye TM, Cox CJ, Embley TM. A congruent phylogenomic signal places eukaryotes within the Archaea . Proc Biol Sci. (2012). pubmed
Zimorski V, Major P, Yu R-Y, Hoffmann K, Pereira Brás X, Tucci S, Mentel M, Gould SB, Henze K, Martin WF. Evolutionary significance of anaerobic energy metabolism in eukaryotes. Endocyt Cell Res. vol 23 p. 64-68 (2012).

2011

Collingro A, Tischler P, Weinmaier T, Penz T, Heinz E, Brunham RC, Read TD, Bavoil PM, Sachse K, Kahane S, Friedman MG, Rattei T, Myers GSA, Horn M. Unity in Variety - the Pan-Genome of the Chlamydiae. Molecular Biology and Evolution. epub (2011). pubmed
Dean P. Functional domains and motifs of bacterial type three effector proteins and their roles in infection. FEMS Microbiology Reviews. epub (2011). pubmed
Dean P, Kenny B. Cell-surface nucleolin is sequestered into EPEC microcolonies and may play a role during infection. Microbiology. vol 157 p. 1761-7 (2011). pubmed
Emelyanov VV, Goldberg AV. Fermentation enzymes of Giardia lamblia, pyruvate:ferredoxin oxidoreductase and hydrogenase, do not localize to its mitosomes. Microbiology. vol 157 p. 1602-11 (2011). pubmed
Hirt RP, de Miguel N, Nakjang S, Dessi D, Liu YC, Diaz N, Rappelli P, Acosta-Serrano A, Fiori PL, Mottram JC. Trichomonas vaginalis Pathobiology New Insights from the Genome Sequence. Adv Parasitol. vol 77 p. 87-140 (2011). pubmed
Kolluru B, Nakjang S, Hirt RP, Wipat A, Ananiadou S. Automatic extraction of microorganisms and their habitats from free text using mining workflows. J Integr Bioinform. vol 8 p. 184 (2011). pubmed
McInerney JO, Martin WF, Koonin EV, Allen JF, Galperin MY, Lane N, Archibald JM, Embley TM. Planctomycetes and eukaryotes: A case of analogy not homology. Bioessays. epub (2011). pubmed
Ruchaud-Sparagano M-H , Muhlen S , Dean P , Kenny B. The Enteropathogenic E. coli (EPEC) Tir Effector Inhibits NF-?B Activity by Targeting TNF? Receptor-Associated Factors. PLoS Pathog. vol 7 p. doi:10.1371/ (2011). pubmed
Rytkoenen KT, Williams TA, Renshaw GM, Primmer CR, Nikinmaa M. Molecular Evolution of the Metazoan PHD-HIF Oxygen-Sensing System. Mol Biol Evol. vol 28 p. 1913-26 (2011). pubmed
Sixt BS, HeinzC, Pichler P, Heinz E, Montanaro J, op den Camp HJM, Ammerer G, Mechtler K, Wagner M, Horn M. Proteomic analysis reveals a virtually complete set of proteins for translation and energy generation in elementary bodies of the amoeba symbiont Protochlamydia amoebophila. Proteomics. vol 11 p. 1868-92 (2011). pubmed
Williams TA, Embley TM, Heinz E. Informational Gene Phylogenies Do Not Support a Fourth Domain of Life for Nucleocytoplasmic Large DNA Viruses. PLoS ONE. vol 6 p. doi:10.1371/ (2011). pubmed

2010

Carlton JM, Malik SB, Sullivan SA, Sicheritz-Ponten T, Tang P, Hirt RP. Trichomonas vaginalis genome. In: Anaerobic Parasitic Protozoa: Genomics and Molecular Biology. Horizon Press. p. 45-80 (2010).
Dean P, Muehlen S, Quitard S, Kenny B. The bacterial effectors EspG and EspG2 induce a destructive calpain activity that is kept in check by the co-delivered Tir effector. Cell Microbiol. vol 12 p. 1308-21 (2010). pubmed
Dean P, Scott JA, Knox AA, Quitard S, Watkins NJ, Kenny B. The enteropathogenic E. coli effector EspF targets and disrupts the nucleolus by a process regulated by mitochondrial dysfunction. PLoS Pathog. vol 24 p. e1000961 (2010). pubmed
Heinz E, Pichler P, Heinz C, op den Camp HJM, Toenshoff ER, Ammerer G, Mechtler K, Wagner M, Horn M. Proteomic analysis of the outer membrane of Protochlamydia amoebophila elementary bodies. Proteomics. vol 10 p. 4363-76 (2010). pubmed
Heinz E, Rockey DD, Montanaro J, Aistleitner K, Wagner M, Horn M. Inclusion membrane proteins of Protochlamydia amoebophila UWE25 reveal a conserved mechanism for host cell interaction among the Chlamydiae. Journal of Bacteriology. vol 192 p. 5093-102 (2010). pubmed
Hjort K, Goldberg AV, Tsaousis AD, Hirt RP, Embley TM. Diversity and reductive evolution of mitochondria among microbial eukaryotes. Philos Trans R Soc Lond B Biol Sci. vol 365 p. 713-27 (2010). pubmed
Holmes A, Muehlen S, Roe AJ, Dean P. The EspF effector, a bacterial pathogen's Swiss army knife. Infect Immun. vol 78 p. 4445-53 (2010). pubmed
Noel CJ, Diaz N, Sicheritz-Ponten T, Safarikova L, Tachezy J, Tang P, Fiori P-L, Hirt RP. Trichomonas vaginalis vast BspA-like gene family: evidence for functional diversity from structural organisation and transcriptomics. BMC Genomics. vol 8 (2010). pubmed
Simoes-Barbosa A, Hirt RP, Johnson PJ. A metazoan/plant-like capping enzyme and cap modified nucleotides in the protist Trichomonas vaginalis. PLoS Pathogens. vol 6 p. e1000999 (2010). pubmed
Tyc J, Long S, Jirku M, Lukes J. The YCF45 protein, usually associated with plastids, is targeted to the mitochondrion of Trypanosoma brucei. Mol. Biochem. Parasitol. vol 173 p. 43-47 (2010). pubmed
Williams TA, Codoner FM, Toft C, Fares MA. Two chaperonin systems in bacterial genomes with distinct ecological roles. Trends Genet. vol 26 p. 47-51 (2010). pubmed
Williams TA, Fares MA. The effect of chaperonin buffering on protein evolution. Genome Biol. Evol. vol 2 p. 609-19 (2010). pubmed

2009

Alsmark UC, Sicheritz-Ponten T, Foster PG, Hirt RP, Embley TM. Horizontal gene transfer in eukaryotic parasites: a case study of Entamoeba histolytica and Trichomonas vaginalis. Methods in Molecular Biology. vol 532 p. 489-500 (2009). pubmed
Arnold R, Brandmaier S, Kleine F, Tischler P, Heinz E, Behrens S, Niinikoski A, Mewes H-W, Horn M, Rattei T. Sequence-based prediction of Type III secreted proteins. PLoS Pathog. vol 5 p. e1000376 (2009). pubmed
Dean P, Kenny B. The effector repertoire of enteropathogenic E. coli: ganging up on the host cell. Curr Opin Microbiol. vol 12 p. 101-9 (2009). pubmed
Emelyanov VV. Mitochondrial porin VDAC1 seems to be functional in rickettsial cells. Ann. NY Acad. Sci.. vol 1166 p. 38-48 (2009). pubmed
Foster PG, Cox CJ, Embley TM. The primary divisions of Life: a phylogenomic approach employing composition-heterogeneous methods. Philos Trans Roy Soc. vol 00 p. doi:10.1095/ (2009).
Green DM, Gregory A, Munro LA. Small- and large-scale network structure of live fish movements in Scotland. Preventiative Veterinary Medicine. vol 91 p. 261-9 (2009). pubmed
Heinz E, Tischler P, Rattei T, Myers G, Wagner M, Horn M. Comprehensive in silico prediction and analysis of chlamydial outer membrane proteins reflects evolution and life style of the Chlamydiae. BMC Genomics. vol 10 p. 634 (2009). pubmed
Iguchi A, Thomson NR, Ogura Y, Saunders D, Ooka T, Henderson IR, Harris D, Asadulghani M, Kurokawa K, Dean P, Kenny B, Quail MA, Thurston S, Dougan G, Hayashi T, Parkhill J, Frankel G. Complete genome sequence and comparative genome analysis of enteropathogenic Escherichia coli O127:H6 strain E2348/69. J Bacteriol. vol 191 p. 347-54 (2009). pubmed
Munro LA, Gregory A. Application of network analysis to farmed salmonid movement data from Scotland. Journal of Fish Disease. vol 32 p. 641-4 (2009). pubmed
Toft C, Williams TA, Fares MA. Genome-wide functional divergence after the symbiosis of proteobacteria with insects unraveled through a novel computational approach. PLoS Comput. Biol. vol 5 p. e1000344 (2009). pubmed
Williams TA, Wolfe KH, Fares MA. No rosetta stone for a sense-antisense origin of aminoacyl tRNA synthetase classes. Mol. Biol. Evol. vol 26 p. 445-50 (2009). pubmed
Wohlgamuth-Benedum JM, Rubio MAT, Paris Z, Long S, Poliak P, Lukes J, Alfonzo JD. Thiolation controls cytoplasmic tRNA stability and acts as a negative determinant for tRNA editing in mitochondria. J. Biol. Chem. vol 284 p. 23947-23953 (2009). pubmed

2008

Bain N, Gregory A, Raynard RS. Genetic analysis of infectious pancreatic necrosis virus from Scotland. Journal of Fish Disease. vol 31 p. 37-47 (2008). pubmed
Cox CJ, Foster PG, Hirt RP, Harris SR, Embley TM. The archaebacterial origin of eukaryotes. Proc Natl Acad Sci USA. vol 105 p. 20356-61 (2008). pubmed
Goldberg AV, Molik S, Tsaousis AD, Neumann K, Kuhnke G, Delbac F, Vivares CP, Hirt RP, Lill R and Embley TM. Localization and functionality of microsporidian iron-sulphur cluster assembly proteins. Nature. vol 452 p. 624-8 (2008). pubmed
Gregory A, Munro LA, Snow M, Urquhart KL, Murray AG, Raynard RS. An experimental investigation on aspects of infectious salmon anaemia virus (ISAV) infection dynamics in seawater Atlantic salmon, Salmo salar L. Journal of Fish Disease. vol 32 p. 481-9 (2008). pubmed
Long S, Jirku M, Ayala FJ, Lukes J. Mitochondrial localization of human frataxin is necessary but processing is not, for rescuing frataxin deficiency in Trypanosoma brucei. Proc Natl Acad Sci USA. vol 105 p. 13468-13473 (2008). pubmed
Long S, Jirku M, Mach J, Ginger ML, Sutak R, Richardson D, Tachezy J, Lukes J. Ancestral roles of eukaryotic frataxin: mitochondrial frataxin function and heterologous expression of hydrogenosomal Trichomonas homologues in trypanosomes. Mol. Microbiol.. vol 69 p. 94-109 (2008). pubmed
Long S, Vavrova Z, Lukes J. The import and function of diatom and plant frataxins in the mitochondrion of Trypanosoma brucei. Mol. Biochem. Parasitol.. vol 162 p. 100-104 (2008). pubmed
Schmitz-Esser S, Toenshoff ER, Haider S, Heinz E, Hoenninger VM, Wagner M, Horn M. Diversity of bacterial endosymbionts of environmental Acanthamoeba isolates. Appl Environ Microbiol. vol 74 p. 5822-31 (2008). pubmed
Simillion C, Janssens K, Sterck L and Van de Peer Y. i-ADHoRe 2.0: an improved tool to detect degenerated genomic homology using genomic profiles. Bioinformatics. vol 24 p. 127-8 (2008). pubmed
Smid O, Matuskova A, Harris SR, Kucera T, Novotny M, Horvathova L, Hrdy I, Kutejova E, Hirt RP, Embley TM, Janata J, Tacheyy J. Reductive evolution of the mitochondrial processing peptidases of the unicellular parasites trichomonas vaginalis and giardia intestinalis.. PLoS Pathog.. vol 4 p. e1000243 (2008). pubmed
Tsaousis AD, Kunji ER, Goldberg AV, Lucocq JM, Hirt RP and Embley TM. A novel route for ATP acquisition by the remnant mitochondria of Encephalitozoon cuniculi. Nature. vol 453 p. 553-6 (2008). pubmed
Urquhart KL, Murray AG, Gregory A, O'Dea M, Munro LA, Smail DS, Shanks AM, Raynard RS. Estimation of infectious dose and viral shedding rates for infectious pancreatic necrosis virus in Atlantic salmon, Salmo salar L., post-smolts. Journal of Fish Disease. vol 31 p. 879-887 (2008). pubmed
Wallace IS, Gregory A, Murray AG, Munro ES, Raynard RS. Distribution of infectious pancreatic necrosis virus (IPNV) in wild marine fish from Scottish waters with respect to clinically infected aquaculture sites producing Atlantic salmon, Salmo salar L. Journal of Fish Disease. vol 31 p. 177-186 (2008). pubmed

2007

Andersson JO, Sjogren AM, Horner DS, Murphy CA, Dyal PL, Svard SG, Logsdon JM Jr, Ragan MA, Hirt RP and Roger AJ. A genomic survey of the fish parasite Spironucleus salmonicida indicates genomic plasticity among diplomonads and significant lateral gene transfer in eukaryote genome evolution. BMC Genomics. vol 8 (2007). pubmed
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, Muller 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 and Johnson PJ. Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis. Science. vol 315 p. 207-12 (2007). pubmed
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, Noel 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 and Hall N. Structure and content of the Entamoeba histolytica genome. Adv Parasitol.. vol 67 p. 51-190 (2007). pubmed
Dolezal P, Dancis A, Lesuisse E, Sutak R, Hrdy I, Embley TM and Tachezy J. Frataxin, a conserved mitochondrial protein, in hydrogenosomes of Trichomonas vaginalis. Eukaryot Cell. (2007). pubmed
Dufernez F, Walker RL, Noel C, Caby S, Mantini C, Delgado-Viscogliosi P, Ohkuma M, Kudo T, Capron M, Pierce RJ, Villanueva MR and Viscogliosi E. Morphological and molecular identification of non-Tritrichomonas foetus trichomonad protozoa from the bovine preputial cavity. J Eukaryot Microbiol.. vol 54 p. 161-8 (2007). pubmed
Emelyanov VV. Constantin Merezhkowsky and the endokaryotic hypothesis. In: Origins of Mitochondria and Hydrogenosomes. Springer-Verlag, Berlin, Heidelberg. p. 201-237 (2007).
Gregory A, Munro LA, Ostergard PS, Raynard RS. The importance of applying confirmatory tests to diagnose the presence of infectious salmon anaemia virus (ISAV) in environmental samples by RT-PCR. Bulletin of the European Association of Fish Patho. vol 27 (2007).
Gregory A, Munro LA, Wallace IS, Bain N, Raynard RS. Detection of infectious pancreatic necrosis virus (IPNV) from the environment in the vicinity of IPN-infected Atlantic salmon farms in Scotland. Journal of Fish Diseases. vol 30 p. 621-630 (2007). pubmed
Harris SR, Pisani D, Gower DG and Wilkinson M. Investigating stagnation in morphological phylogenetics using consensus data. Systematic Biology. vol 56 p. 125-9 (2007). pubmed
Heinz E, Kolarov I, Kaestner C, Toenshoff ER, Wagner M, Horn M. An Acanthamoeba sp. containing two phylogenetically different bacterial endosymbionts. Environ. Microbiol.. vol 9 p. 1604-9 (2007). pubmed
Hirt RP, Noel CJ, Sicheritz-Ponten T, Tachezy J and Fiori PL. Trichomonas vaginalis surface proteins: a view from the genome. Trends Parasitol.. (2007). pubmed
Lefevre E, Bardot C, Noel C, Carrias JF, Viscogliosi E, Amblard C and Sime-Ngando T. Unveiling fungal zooflagellates as members of freshwater picoeukaryotes: evidence from a molecular diversity study in a deep meromictic lake. Environ Microbiol. vol 9 p. 61-71 (2007). pubmed
Noel C, Noda S, Mantini C, Dolan MF, Moriya S, Delgado-Viscogliosi P, Kudo T, Capron M, Pierce RJ, Ohkuma M and Viscogliosi E. Molecular Phylogenetic Position of the Genera Stephanonympha and Caduceia (Parabasalia) Inferred from Nuclear Small Subunit rRNA Gene Sequences. J Eukaryot Microbiol. vol 54 p. 93-9 (2007). pubmed
Rodriguez-Ezpeleta N, Brinkmann H, Burger G, Roger AJ, Gray MW, Philippe H and Lang BF. Toward the resolution of the eukaryotic tree: the phylogenetic positions of jakobids and cercozoans. Curr Biol. vol 17 p. 1420-5 (2007). pubmed
Rodriguez-Ezpeleta N, Brinkmann H, Roure B, Lartillot N, Lang BF and Philippe H. Detecting and overcoming systematic errors in genome-scale phylogenies. Syst Biol. vol 56 p. 389-99 (2007). pubmed
Rodriguez-Ezpeleta N, Philippe H, Brinkmann H, Becker B and Melkonian M. Phylogenetic analyses of nuclear, mitochondrial, and plastid multigene data sets support the placement of Mesostigma in the Streptophyta. Mol Biol Evol. vol 24 p. 723-31 (2007). pubmed
Roure B, Rodriguez-Ezpeleta N and Philippe H. SCaFoS: a tool for selection, concatenation and fusion of sequences for phylogenomics. BMC Evol Biol. vol 7 (2007). pubmed
Wilkinson M, McInerney JO, Hirt RP, Foster PG and Embley TM. Of clades and clans: terms for phylogenetic relationships in unrooted trees. Trends Ecol Evol. vol 22 p. 114-5 (2007). pubmed

2006

Andersson JO, Hirt RP, Foster PG and Roger AJ. Evolution of four gene families with patchy phylogenetic distributions: influx of genes into protist genomes. BMC Evol Biol. vol 6 p. 27 (2006). pubmed
Bahia D, Avelar L, Mortara RA, Khayath N, Yan Y, Noel C, Capron M, Dissous C, Pierce RJ and Oliveira G. SmPKC1, a new protein kinase C identified in the platyhelminth parasite Schistosoma mansoni. Biochem Biophys Res Commun. vol 345 p. 1138-48 (2006). pubmed
Bertin B, Oger F, Cornette J, Caby S, Noel C, Capron M, Fantappie MR, Rumjanek FD and Pierce RJ. Schistosoma mansoni CBP/p300 has a conserved domain structure and interacts functionally with the nuclear receptor SmFtz-F1. Mol Biochem Parasitol. vol 146 p. 180-91 (2006). pubmed
Blomme T, Vandepoele K, De Bodt S, Simillion C, Maere S and Van de Peer Y. The gain and loss of genes during 600 million years of vertebrate evolution. Genome Biol. vol 7 p. R43 (2006). pubmed
Dacks JB, Dyal PL, Embley TM and van der Giezen M. Hydrogenosomal succinyl-CoA synthetase from the rumen-dwelling fungus Neocallimastix patriciarum; an energy-producing enzyme of mitochondrial origin. Gene. vol 373 p. 75-82 (2006). pubmed
Dean P, Maresca M, Schueller S, Phillips AD, Kenny B. Potent diarrheagenic mechanism mediated by the cooperative action of three enteropathogenic Escherichia coli-injected effector proteins. Proc Natl Acad Sci USA. vol 103 p. 1876-81 (2006). pubmed
Dei-Cas E, Chabe M, Moukhlis R, Durand-Joly I, Aliouat el M, Stringer JR, Cushion M, Noel C, de Hoog GS, Guillot J and Viscogliosi E. Pneumocystis oryctolagi sp. nov., an uncultured fungus causing pneumonia in rabbits at weaning: review of current knowledge, and description of a new taxon on genotypic, phylogenetic and phenotypic bases. FEMS Microbiol Rev. vol 30 p. 853-71 (2006). pubmed
Dufernez F, Yernaux C, Gerbod D, Noel C, Chauvenet M, Wintjens R, Edgcomb VP, Capron M, Opperdoes FR and Viscogliosi E. The presence of four iron-containing superoxide dismutase isozymes in trypanosomatidae: characterization, subcellular localization, and phylogenetic origin in Trypanosoma brucei. Free Radic Biol Med. vol 40 p. 210-25 (2006). pubmed
Embley TM and Martin W. Eukaryotic evolution, changes and challenges. Nature. vol 440 p. 623-30 (2006). pubmed
Emelyanov VV, Vyssokikh MYu. On the nature of obligate intracellular symbiosis of rickettsiae ? Rickettsia prowazekii cells import mitochondrial porin. Biochemistry (Moscow). vol 71 p. 730-735 (2006). pubmed
Frealle E, Noel C, Nolard N, Symoens F, Felipe MS, Dei-Cas E, Camus D, Viscogliosi E and Delhaes L. Manganese superoxide dismutase based phylogeny of pathogenic fungi. Mol Phylogenet Evol. vol 41 p. 28-39 (2006). pubmed
Hjort K, Lembke A, Speksnijder A, Smalla K and Jansson JK. Community Structure of Actively Growing Bacterial Populations in Plant Pathogen Suppressive Soil. Microb Ecol. (2006). pubmed
Lal K, Noel CJ, Field MC, Goulding D and Hirt RP. Dramatic reorganisation of Trichomonas endomembranes during amoebal transformation: A possible role for G-proteins. Mol Biochem Parasitol. vol 148 p. 99-102 (2006). pubmed
Pisani D, Mohun SM, Harris SR, McInerney JO and Wilkinson M. Molecular evidence for dim-light vision in the last common ancestor of the vertebrates. Current Biology. vol 16 p. R318-9 (2006). pubmed
Quitard S, Dean P, Maresca M, Kenny B. The enteropathogenic Escherichia coli EspF effector molecule inhibits PI-3 kinase-mediated uptake independently of mitochondrial targeting. Cell Microbiol. vol 8 p. 972-81 (2006). pubmed
Rodriguez-Ezpeleta N and Philippe H. Plastid origin: replaying the tape. Curr Biol. vol 16 p. R53-6 (2006). pubmed

2005

Berriman M, Ghedin E, Hertz-Fowler C, Blandin G, Renauld H, Bartholomeu DC, Lennard NJ, Caler E, Hamlin NE, Haas B, Bohme 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 and El-Sayed NM. The genome of the African trypanosome Trypanosoma brucei. Science. vol 309 p. 416-22 (2005). pubmed
Bouton D, Escriva H, de Mendonca RL, Glineur C, Bertin B, Noel C, Robinson-Rechavi M, de Groot A, Cornette J, Laudet V and Pierce RJ. A conserved retinoid X receptor (RXR) from the mollusk Biomphalaria glabrata transactivates transcription in the presence of retinoids. J Mol Endocrinol. vol 34 p. 567-82 (2005). pubmed
Chan KW, Slotboom DJ, Cox S, Embley TM, Fabre O, van der Giezen M, Harding M, Horner DS, Kunji ER, Leon-Avila G and Tovar J. A novel ADP/ATP transporter in the mitosome of the microaerophilic human parasite Entamoeba histolytica. Curr Biol. vol 15 p. 737-42 (2005). pubmed
Collingro A, Poppert S, Heinz E, Schmitz-Esser S, Essig A, Schweikert M, Wagner M, Horn M. Recovery of an environmental Chlamydia strain from activated sludge by co-cultivation with Acanthamoeba sp.. Microbiology. vol 151 p. 301-9 (2005). pubmed
Dean P, Maresca M, Kenny B. EPEC's weapons of mass subversion. Curr Opin Microbiol. vol 8 p. 28-34 (2005). pubmed
Duboucher C, Gerbod D, Noel C, Durand-Joly I, Delgado-Viscogliosi P, Leclerc C, Pham S, Capron M, Dei-Cas E and Viscogliosi E. Frequency of trichomonads as coinfecting agents in Pneumocystis pneumonia. Acta Cytol. vol 49 p. 273-7 (2005). pubmed
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 and Hall N. Comparative genomics of trypanosomatid parasitic protozoa. Science. vol 309 p. 404-9 (2005). pubmed
Frank AC, Alsmark CM, Thollesson M and Andersson SG. Functional Divergence and Horizontal Transfer of Type IV Secretion Systems. Mol Biol Evol. vol 22 p. 1325-36 (2005). pubmed
Frealle E, Noel C, Viscogliosi E, Camus D, Dei-Cas E and Delhaes L. Manganese superoxide dismutase in pathogenic fungi: an issue with pathophysiological and phylogenetic involvements. FEMS Immunol Med Microbiol. vol 45 p. 411-22 (2005). pubmed
Hampl V, Horner DS, Dyal P, Kulda J, Flegr J, Foster PG and Embley TM. Inference of the phylogenetic position of oxymonads based on nine genes: support for metamonada and excavata. Mol Biol Evol. vol 22 p. 2508-18 (2005). pubmed
Lal K, Field MC, Carlton JM, Warwicker J and Hirt RP. Identification of a very large Rab GTPase family in the parasitic protozoan Trichomonas vaginalis. Mol Biochem Parasitol. vol 143 p. 226-35 (2005). pubmed
Loftus B anderson I, Davies R, Alsmark UC, Samuelson J, Amedeo P, Roncaglia P, Berriman M, Hirt RP, Mann BJ, Nozaki T, Suh B, Pop M, Duchene M, Ackers J, Tannich E, Leippe M, Hofer M, Bruchhaus I, Willhoeft U, Bhattacharya A, Chillingworth T, Churcher C, Hance Z, Harris B, Harris D, Jagels K, Moule S, Mungall K, Ormond D, Squares R, Whitehead S, Quail MA, Rabbinowitsch E, Norbertczak H, Price C, Wang Z, Guillen N, Gilchrist C, Stroup SE, Bhattacharya S, Lohia A, Foster PG, Sicheritz-Ponten T, Weber C, Singh U, Mukherjee C, El-Sayed NM, Petri WA Jr, Clark CG, Embley TM, Barrell B, Fraser CM and Hall N. The genome of the protist parasite Entamoeba histolytica. Nature. vol 433 p. 865-8 (2005). pubmed
Maresca M, Miller D, Quitard S, Dean P, Kenny B. Enteropathogenic Escherichia coli (EPEC) effector-mediated suppression of antimicrobial nitric oxide production in a small intestinal epithelial model system. Cell Microbiol. vol 7 p. 1749-62 (2005). pubmed
Nicol GW, Tscherko D, Embley TM and Prosser JI. Primary succession of soil Crenarchaeota across a receding glacier foreland. Environ Microbiol. vol 7 p. 337-47 (2005). pubmed
Noel C, Dufernez F, Gerbod D, Edgcomb VP, Delgado-Viscogliosi P, Ho LC, Singh M, Wintjens R, Sogin ML, Capron M, Pierce R, Zenner L and Viscogliosi E. Molecular phylogenies of Blastocystis isolates from different hosts: implications for genetic diversity, identification of species, and zoonosis. J Clin Microbiol. vol 43 p. 348-55 (2005). pubmed
Pierce RJ, Wu W, Hirai H, Ivens A, Murphy LD, Noel C, Johnston DA, Artiguenave F, Adams M, Cornette J, Viscogliosi E, Capron M and Balavoine G. Evidence for a dispersed Hox gene cluster in the platyhelminth parasite Schistosoma mansoni. Mol Biol Evol. vol 22 p. 2491-503 (2005). pubmed
Rodriguez-Ezpeleta N, Brinkmann H, Burey SC, Roure B, Burger G, Loffelhardt W, Bohnert HJ, Philippe H and Lang BF. Monophyly of primary photosynthetic eukaryotes: green plants, red algae, and glaucophytes. Curr Biol. vol 15 p. 1325-30 (2005). pubmed
Tsaousis AD, Martin DP, Ladoukakis ED, Posada D and Zouros E. Widespread recombination in published animal mtDNA sequences. Mol Biol Evol. vol 22 p. 1-Sep (2005). pubmed
Wallace IS, Gregory A, Munro ES, Bain N, Raynard RS. Infectious pancreatic necrosis virus (IPNV) isolated from hake, Merluccius merluccius, from Scotland. Bulletin of the European Association of Fish Patho. vol 25 p. 86-90 (2005).
Webster G, Embley TM, Freitag TE, Smith Z and Prosser JI. Links between ammonia oxidizer species composition, functional diversity and nitrification kinetics in grassland soils. Environ Microbiol. vol 7 p. 676-84 (2005). pubmed
Wilkinson M, Cotton JA, Creevey C, Eulenstein O, Harris SR, Lapointe FJ, Levasseur C, McInerney JO, Pisani D and Thorley JL. The shape of supertrees to come: tree shape related properties of fourteen supertree methods. Syst Biol. vol 54 p. 419-31 (2005). pubmed

2004

Alsmark CM, Frank AC, Karlberg EO, Legault BA, Ardell DH, Canback B, Eriksson AS, Naslund AK, H Andley SA, Huvet M, La Scola B, Holmberg M and Andersson SG. The louse-borne human pathogen Bartonella quintana is a genomic derivative of the zoonotic agent Bartonella henselae. Proc Natl Acad Sci U S A. vol 101 p. 9716-21 (2004). pubmed
Au C, Dean P, Reynolds SE, ffrench-Constant RH. Effect of the insect pathogenic bacterium Photorhabdus on insect phagocytes. Cell Microbiol. vol 6 p. 89-95 (2004). pubmed
Coombs GH, Westrop GD, Suchan P, Puzova G, Hirt RP, Embley TM, Mottram JC and Muller S. The amitochondriate eukaryote Trichomonas vaginalis contains a divergent thioredoxin-linked peroxiredoxin antioxidant system. J Biol Chem. vol 279 p. 5249-56 (2004). pubmed
Dean P, Kenny B. Intestinal barrier dysfunction by enteropathogenic Escherichia coli is mediated by two effector molecules and a bacterial surface protein. Mol Microbiol. vol 54 p. 665-75 (2004). pubmed
Dean P, Potter U, Richards EH, Edwards JP, Charnley AK, Reynolds SE. Hyperphagocytic haemocytes in Manduca sexta. J Insect Physiol. vol 50 p. 1027-36 (2004). pubmed
Dean P, Richards EH, Edwards JP, Reynolds SE, Charnley K. Microbial infection causes the appearance of hemocytes with extreme spreading ability in monolayers of the tobacco hornworm Manduca sexta. Dev Comp Immunol. vol 28 p. 689-700 (2004). pubmed
Emelyanov VV, Loukianov EV. A 29.5 kDa heat-modifiable major outer membrane protein of Rickettsia prowazekii, putative virulence factor, is a peptidyl-prolyl cis/trans isomerase. IUBMB Life. vol 56 p. 215-219 (2004). pubmed
Gerbod D, Sanders E, Moriya S, Noel C, Takasu H, Fast NM, Delgado-Viscogliosi P, Ohkuma M, Kudo T, Capron M, Palmer JD, Keeling PJ and Viscogliosi E. Molecular phylogenies of Parabasalia inferred from four protein genes and comparison with rRNA trees. Mol Phylogenet Evol. vol 31 p. 572-80 (2004). pubmed
Gevers D, Vandepoele K, Simillion C and Van de Peer Y. Gene duplication and biased functional retention of paralogs in bacterial genomes. Trends Microbiol. vol 12 p. 148-54 (2004). pubmed
Hirt RP and Horner DS. Organelles, genomes and eukaryote phylogeny: an evolutionary synthesis in the age of genomics. CRC Press, New York. Pp. 400. (2004).
Horner DS and Hirt RP. An overview of eukaryote origins and evolution: the beauty of the cell and the fabulous gene phylogenies. p. 1-23 in RP Hirt and DS Horner, eds. Organelles, genomes and eukaryotic phylogeny. CRC Press, New York. (2004).
Hrdy I, Hirt RP, Dolezal P, Bardonova L, Foster PG, Tachezy J and Embley TM. Trichomonas hydrogenosomes contain the NADH dehydrogenase module of mitochondrial complex I. Nature. vol 432 p. 618-22 (2004). pubmed
Martin W and Embley TM. Evolutionary biology: Early evolution comes full circle. Nature. vol 431 p. 134-7 (2004). pubmed
Purdy KJ, Cresswell-Maynard TD, Nedwell DB, McGenity TJ, Grant WD, Timmis KN and Embley TM. Isolation of haloarchaea that grow at low salinities. Environ Microbiol. vol 6 p. 591-5 (2004). pubmed
Simillion C, Vandepoele K and Van de Peer Y. Recent developments in computational approaches for uncovering genomic homology. Bioessays. vol 26 p. 1225-35 (2004). pubmed
Simillion C, Vandepoele K, Saeys Y and Van de Peer Y. Building genomic profiles for uncovering segmental homology in the twilight zone. Genome Res. vol 14 p. 1095-106 (2004). pubmed
Vandepoele K, Simillion C and and Van de Peer Y. The quest for genomic homology. Curr. Genomics. vol 5 p. 299-308 (2004).
Williams BA and Hirt RP. RACE and RAGE cloning in parasitic microbial eukaryotes. Methods Mol Biol. vol 270 p. 151-72 (2004). pubmed
Wintjens R, Noel C, May AC, Gerbod D, Dufernez F, Capron M, Viscogliosi E and Rooman M. Specificity and phenetic relationships of iron- and manganese-containing superoxide dismutases on the basis of structure and sequence comparisons. J Biol Chem. vol 279 p. 9248-54 (2004). pubmed

2003

Andersson JO, Sjogren AM, Davis LA, Embley TM and Roger AJ. Phylogenetic analyses of diplomonad genes reveal frequent lateral gene transfers affecting eukaryotes. Curr Biol. vol 13 p. 94-104 (2003). pubmed
Bundey S, Raymond S, Dean P, Roberts SK, Dillon RJ, Charnley AK. Eicosanoid involvement in the regulation of behavioral fever in the desert locust, Schistocerca gregaria. Arch Insect Biochem Physiol. vol 52 p. 183-92 (2003). pubmed
Chose O, Sarde CO, Noel C, Gerbod D, Jimenez JC, Brenner C, Capron M, Viscogliosi E and Roseto A. Cell death in protists without mitochondria. Ann N Y Acad Sci. vol 1010 p. 121-5 (2003). pubmed
Dean P. Cell of the month: An insect blood cell engulfing bacteria. Nat Cell Biol. vol 5 p. 957 (2003). pubmed
Duboucher C, Noel C, Dur and-Joly I, Gerbod D, Delgado-Viscogliosi P, Jouveshomme S, Leclerc C, Cartolano GL, Dei-Cas E, Capron M and Viscogliosi E. Pulmonary coinfection by Trichomonas vaginalis and Pneumocystis sp. as a novel manifestation of AIDS. Hum Pathol. vol 34 p. 508-11 (2003). pubmed
Embley TM, van der Giezen M, Horner DS, Dyal PL and Foster P. Mitochondria and hydrogenosomes are two forms of the same fundamental organelle. Philos Trans R Soc Lond B Biol Sci. vol 358 p. 191-201; dis (2003). pubmed
Embley TM, van der Giezen M, Horner DS, Dyal PL, Bell S and Foster PG. Hydrogenosomes, mitochondria and early eukaryotic evolution. IUBMB Life. vol 55 p. 387-95 (2003). pubmed
Emelyanov VV. Common evolutionary origin of mitochondrial and rickettsial respiratory chains. Arch. Biochem. Biophys.. vol 420 p. 130-141 (2003). pubmed
Emelyanov VV. Phylogenetic affinity of a Giardia lamblia cysteine desulfurase conforms to canonical pattern of mitochondrial ancestry. FEMS Microbiol. Lett. vol 226 p. 257-266 (2003). pubmed
Emelyanov VV. Mitochondrial connection to the origin of the eukaryotic cell. Eur. J. Biochem.. vol 270 p. 1599-1618 (2003). pubmed
Harris SR, Gower DJ and Wilkinson M. Phylogenetic methods and aetosaur interrelationships: a rejoinder. Syst Biol. vol 52 p. 851-2 (2003). pubmed
Harris SR, Gower DJ and Wilkinson M. Intraorganismal homology, character construction, and the phylogeny of aetosaurian archosaurs (reptilia, diapsida). Syst Biol. vol 52 p. 239-52 (2003). pubmed
Harris SR, Wilkinson M and Gower DJ. Countering concerted homoplasy. Cladistics. vol 19 p. 128-30 (2003).
Hirt RP, Lal K, Pinxteren J, Warwicker J, Healy B, Coombs GH, Field MC and Embley TM. Biochemical and genetic evidence for a family of heterotrimeric G-proteins in Trichomonas vaginalis. Mol Biochem Parasitol. vol 129 p. 179-89 (2003). pubmed
Leigh J, Seif E, Rodriguez-Ezpeleta N, Jacob Y, Lang BF. Fungal evolution meets fungal genomics. In Handbook of Fungal Biotechnology, 2nd ed. (D. Arora, ed.) pp. 145-161. Marcel Dekker Inc. New York, NY. (2003).
Noel C, Gerbod D, Delgado-Viscogliosi P, Fast NM, Younes AB, Chose O, Roseto A, Capron M and Viscogliosi E. Morphogenesis during division and griseofulvin-induced changes of the microtubular cytoskeleton in the parasitic protist, Trichomonas vaginalis. Parasitol Res. vol 89 p. 487-94 (2003). pubmed
Noel C, Gerbod D, Delgado-Viscogliosi P, Fast NM, Younes AB, Chose O, Roseto A, Capron M and Viscogliosi E. Morphogenesis during division and griseofulvin-induced changes of the microtubular cytoskeleton in the parasitic protist, Trichomonas vaginalis. Parasitol. Res. vol 89 p. 487-94 (2003). pubmed
Noel C, Peyronnet C, Gerbod D, Edgcomb VP, Delgado-Viscogliosi P, Sogin ML, Capron M, Viscogliosi E and Zenner L. Phylogenetic analysis of Blastocystis isolates from different hosts based on the comparison of small-subunit rRNA gene sequences. Mol Biochem Parasitol. vol 126 p. 119-23 (2003). pubmed
Olsson JA, Nordstrom K, Hjort K and Dasgupta S. Eclipse-synchrony relationship in Escherichia coli strains with mutations affecting sequestration, initiation of replication and superhelicity of the bacterial chromosome. J Mol Biol. vol 334 p. 919-31 (2003). pubmed
Purdy KJ, Nedwell DB and Embley TM. Analysis of the sulfate-reducing bacterial and methanogenic archaeal populations in contrasting Antarctic sediments. Appl Environ Microbiol. vol 69 p. 3181-91 (2003). pubmed
Raes J, Vandepoele K, Simillion C, Saeys Y and Van de Peer Y. Investigating ancient duplication events in the Arabidopsis genome. J Struct Funct Genomics. vol 3 p. 117-29 (2003). pubmed
Richards TA, Hirt RP, Williams BA and Embley TM. Horizontal gene transfer and the evolution of parasitic protozoa. Protist. vol 154 p. 17-32 (2003). pubmed
Snow M, Raynard RS, Murray AG, Bruno DW, King JA, Grant R, Bricknell IR, Gregory A. An evaluation of current diagnostic tests for the detection of infectious salmon anaemia virus (ISAV) following experimental water-borne infection of Atlantic salmon, Salmo salar L. Journal of Fish Diseases. vol 26 p. 135-146 (2003). pubmed
van der Giezen M, Birdsey GM, Horner DS, Lucocq J, Dyal PL, Benchimol M, Danpure CJ and Embley TM. Fungal hydrogenosomes contain mitochondrial heat-shock proteins. Mol Biol Evol. vol 20 p. 1051-61 (2003). pubmed
Vandepoele K, Simillion C and Van de Peer Y. Evidence that rice and other cereals are ancient aneuploids. Plant Cell. vol 15 p. 2192-202 (2003). pubmed
Vicogne J, Pin JP, Lardans V, Capron M, Noel C and Dissous C. An unusual receptor tyrosine kinase of Schistosoma mansoni contains a Venus Flytrap module. Mol Biochem Parasitol. vol 126 p. 51-62 (2003). pubmed

2002

Amiri H, Alsmark CM and Andersson SG. Proliferation and deterioration of Rickettsia palindromic elements. Mol Biol Evol. vol 19 p. 1234-43 (2002). pubmed
Andersson SG, Alsmark C, Canback B, Davids W, Frank C, Karlberg O, Klasson L, Antoine-Legault B, Mira A and Tamas I. Comparative genomics of microbial pathogens and symbionts. Bioinformatics. vol 18 Su p. S17 (2002). pubmed
Baxter NJ, Hirt RP, Bodrossy L, Kovacs KL, Embley TM, Prosser JI and Murrell JC. The ribulose-1,5-bisphosphate carboxylase/oxygenase gene cluster of Methylococcus capsulatus (Bath). Arch Microbiol. vol 177 p. 279-89 (2002). pubmed
Chose O, Noel C, Gerbod D, Brenner C, Viscogliosi E and Roseto A. A form of cell death with some features resembling apoptosis in the amitochondrial unicellular organism Trichomonas vaginalis. Exp Cell Res. vol 276 p. 32-9 (2002). pubmed
Cunningham CO, Gregory A, Black J, Simpson I, Raynard RS. A novel variant of the infectious salmon anaemia virus (ISAV) haemagglutinin gene suggests mechanisms for virus diversity. Bulletin of the European Association of Fish Patho. vol 22 p. 366-374 (2002).
Davidson EA, van der Giezen M, Horner DS, Embley TM and Howe CJ. An [Fe] hydrogenase from the anaerobic hydrogenosome-containing fungus Neocallimastix frontalis L2. Gene. vol 296 p. 45-52 (2002). pubmed
De Mendonca RL, Bouton D, Bertin B, Escriva H, Noel C, Vanacker JM, Cornette J, Laudet V and Pierce RJ. A functionally conserved member of the FTZ-F1 nuclear receptor family from Schistosoma mansoni. Eur J Biochem. vol 269 p. 5700-11 (2002). pubmed
Dean P, Gadsden JC, Richards EH, Edwards JP, Keith Charnley A, Reynolds SE. Modulation by eicosanoid biosynthesis inhibitors of immune responses by the insect Manduca sexta to the pathogenic fungus Metarhizium anisopliae. J Invertebr Pathol. vol 79 p. 93-101 (2002). pubmed
Embley TM. Anaerobic eukaryotes and their archaebacterial endosymbionts. Environ Microbiol. vol 4 p. 15-Jun (2002). pubmed
Emelyanov VV. Phylogenetic relationships of organellar Hsp90 homologs reveal fundamental differences to organellar Hsp70 and Hsp60 evolution. Gene. vol 299 p. 125-133 (2002). pubmed
Goldberg AV, Romanowski V, Federici BA and Sciocco de Cap A. Effects of the Epap granulovirus on its host, Epinotia aporema (Lepidoptera: Tortricidae). J Invertebr Pathol. vol 80 p. 148-59 (2002). pubmed
Gregory A. Detection of infectious salmon anaemia virus (ISAV) by in situ hybridisation. Diseases of Aquatic Organisms. vol 50 p. 105-110 (2002). pubmed
Hirt RP, Harriman N, Kajava AV and Embley TM. A novel potential surface protein in Trichomonas vaginalis contains a leucine-rich repeat shared by micro-organisms from all three domains of life. Mol Biochem Parasitol. vol 125 p. 195-9 (2002). pubmed
Hirt RP, Muller S, Embley TM and Coombs GH. The diversity and evolution of thioredoxin reductase: new perspectives. Trends Parasitol. vol 18 p. 302-8 (2002). pubmed
Horner DS, Heil B, Happe T and Embley TM. Iron hydrogenases--ancient enzymes in modern eukaryotes. Trends Biochem Sci. vol 27 p. 148-53 (2002). pubmed
Noel C, Gerbod D, Dolan MF, Edgcomb VP, Kitade O, Noda S, Dufernez F, Ohkuma M, Kudo T, Capron M, Sogin ML and Viscogliosi E. Molecular phylogeny of parabasalids inferred from small subunit rRNA sequences, with emphasis on the Devescovinidae and Calonymphidae (Trichomonadea). Mol Phylogenet Evol. vol 25 p. 545-56 (2002). pubmed
Prosser JI and Embley TM. Cultivation-based and molecular approaches to characterisation of terrestrial and aquatic nitrifiers. Antonie Van Leeuwenhoek. vol 81 p. 165-79 (2002). pubmed
Purdy KJ, Embley TM and Nedwell DB. The distribution and activity of sulphate reducing bacteria in estuarine and coastal marine sediments. Antonie Van Leeuwenhoek. vol 81 p. 181-7 (2002). pubmed
Sanchez L, Horner D, Moore D, Henze K, Embley T and Muller M. Fructose-1,6-bisphosphate aldolases in amitochondriate protists constitute a single protein subfamily with eubacterial relationships. Gene. vol 295 p. 51-9 (2002). pubmed
Silva CP, Waterfield NR, Daborn PJ, Dean P, Chilver T, Au CP, Sharma S, Potter U, Reynolds SE, ffrench-Constant RH. Bacterial infection of a model insect: Photorhabdus luminescens and Manduca sexta. Cell Microbiol. vol 4 p. 329-39 (2002). pubmed
Simillion C, Vandepoele K, Van Montagu MC, Zabeau M and Van de Peer Y. The hidden duplication past of Arabidopsis thaliana. Proc Natl Acad Sci U S A. vol 99 p. 13627-32 (2002). pubmed
van der Giezen M, Slotboom DJ, Horner DS, Dyal PL, Harding M, Xue GP, Embley TM and Kunji ER. Conserved properties of hydrogenosomal and mitochondrial ADP/ATP carriers: a common origin for both organelles. Embo J. vol 21 p. 572-9 (2002). pubmed
Vandepoele K, Saeys Y, Simillion C, Raes J and Van De Peer Y. The automatic detection of homologous regions (ADHoRe) and its application to microcolinearity between Arabidopsis and rice. Genome Res. vol 12 p. 1792-801 (2002). pubmed
Vandepoele K, Simillion C and Van de Peer Y. Detecting the undetectable: uncovering duplicated segments in Arabidopsis by comparison with rice. Trends Genet. vol 18 p. 606-8 (2002). pubmed
Webster G, Embley TM and Prosser JI. Grassland management regimens reduce small-scale heterogeneity and species diversity of beta-proteobacterial ammonia pxidizer populations. Appl Environ Microbiol. vol 68 p. 20-30 (2002). pubmed
Williams BA, Hirt RP, Lucocq JM and Embley TM. A mitochondrial remnant in the microsporidian Trachipleistophora hominis. Nature. vol 418 p. 865-9 (2002). pubmed

2001

Emelyanov VV. Evolutionary Relationship of Rickettsiae and Mitochondria. FEBS Lett.. vol 501 p. 11-18 (2001). pubmed
Gerbod D, Edgcomb VP, Noel C, Vanacova S, Wintjens R, Tachezy J, Sogin ML and Viscogliosi E. Phylogenetic relationships of class II fumarase genes from trichomonad species. Mol Biol Evol. vol 18 p. 1574-84 (2001). pubmed
Gerbod D, Edgcomb VP, Noel C, Zenner L, Wintjens R, Delgado-Viscogliosi P, Holder ME, Sogin ML and Viscogliosi E. Phylogenetic position of the trichomonad parasite of turkeys, Histomonas meleagridis (Smith) Tyzzer, inferred from small subunit rRNA sequence. J Eukaryot Microbiol. vol 48 p. 498-504 (2001). pubmed
Henze K, Horner DS, Suguri S, Moore DV, Sanchez LB, Muller M and Embley TM. Unique phylogenetic relationships of glucokinase and glucosephosphate isomerase of the amitochondriate eukaryotes Giardia intestinalis, Spironucleus barkhanus and Trichomonas vaginalis. Gene. vol 281 p. 123-31 (2001). pubmed
Hjort K and Bernander R. Cell cycle regulation in the hyperthermophilic crenarchaeon Sulfolobus acidocaldarius. Mol Microbiol. vol 40 p. 225-34 (2001). pubmed
Horner DS and Embley TM. Chaperonin 60 phylogeny provides further evidence for secondary loss of mitochondria among putative early-branching eukaryotes. Mol Biol Evol. vol 18 p. 1970-5 (2001). pubmed
Noel C, Gerbod D, Fast NM, Wintjens R, Delgado-Viscogliosi P, Doolittle WF and Viscogliosi E. Tubulins in Trichomonas vaginalis: molecular characterization of alpha-tubulin genes, posttranslational modifications, and homology modeling of the tubulin dimer. J Eukaryot Microbiol. vol 48 p. 647-54 (2001). pubmed
Purdy KJ, Nedwell DB, Embley TM and Takii S. Use of 16S rRNA-targeted oligonucleotide probes to investigate the distribution of sulphate-reducing bacteria in estuarine sediments. FEMS Microbiol Ecol. vol 36 p. 165-168 (2001). pubmed
Raynard RS, Murray AS, Gregory A. Infectious salmon anaemia virus in wild fish from Scotland. Diseases of Aquatic Organisms. vol 46 p. 93-100 (2001). pubmed
Sciocco-Cap A, Parola AD, Goldberg AV, Ghiringhelli PD and Romanowski V. Characterization of a granulovirus isolated from Epinotia aporema Wals. (Lepidoptera: Tortricidae) larvae. Appl Environ Microbiol. vol 67 p. 3702-6 (2001). pubmed
Smith Z, McCaig AE, Stephen JR, Embley TM and Prosser JI. Species Diversity of Uncultured and Cultured Populations of Soil and Marine Ammonia Oxidizing Bacteria. Microb Ecol. vol 42 p. 228-237 (2001). pubmed

2000

Gerbod D, Edgcomb VP, Noel C, Delgado-Viscogliosi P and Viscogliosi E. Phylogenetic position of parabasalid symbionts from the termite Calotermes flavicollis based on small subunit rRNA sequences. Int Microbiol. vol 3 p. 165-72 (2000). pubmed
Horner DS, Foster PG and Embley TM. Iron hydrogenases and the evolution of anaerobic eukaryotes. Mol Biol Evol. vol 17 p. 1695-709 (2000). pubmed
Xia Y, Dean P, Judge AJ, Gillespie JP, Clarkson JM, Charnley AK. Acid phosphatases in the haemolymph of the desert locust, Schistocerca gregaria, infected with the entomopathogenic fungus Metarhizium anisopliae. J Insect Physiol. vol 46 p. 1249-1257 (2000). pubmed

1999

Emelyanov VV, Sinitsyn BV. A groE-based phylogenetic analysis shows the closest evolutionary relationship of mitochondria to obligate intracytoplasmic bacterium Rickettsia prowazekii. In: Rickettsiae and Rickettsial Diseases at the Turn of the Third Millennium (D. Raoult and P. Brouqui, eds). Elsevier, Paris. p. 31-37 (1999).
Hirt RP, Logsdon JM Jr, Healy B, Dorey MW, Doolittle WF and Embley TM. Microsporidia are related to Fungi: evidence from the largest subunit of RNA polymerase II and other proteins. Proc Natl Acad Sci U S A. vol 96 p. 580-5 (1999). pubmed
Hjort K and Bernander R. Changes in cell size and DNA content in Sulfolobus cultures during dilution and temperature shift experiments. J Bacteriol. vol 181 p. 5669-75 (1999). pubmed
Horner DS, Hirt RP and Embley TM. A single eubacterial origin of eukaryotic pyruvate: ferredoxin oxidoreductase genes: implications for the evolution of anaerobic eukaryotes. Mol Biol Evol. vol 16 p. 1280-91 (1999). pubmed
McCaig AE, Phillips CJ, Stephen JR, Kowalchuk GA, Harvey SM, Herbert RA, Embley TM and Prosser JI. Nitrogen cycling and community structure of proteobacterial beta-subgroup ammonia-oxidizing bacteria within polluted marine fish farm sediments. Appl Environ Microbiol. vol 65 p. 213-20 (1999). pubmed
Phillips CJ, Smith Z, Embley TM and Prosser JI. Phylogenetic differences between particle-associated and planktonic ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria in the Northwestern Mediterranean Sea. Appl Environ Microbiol. vol 65 p. 779-86 (1999). pubmed
Viscogliosi E, Edgcomb VP, Gerbod D, Noel C and Delgado-Viscogliosi P. Molecular evolution inferred from small subunit rRNA sequences: what does it tell us about phylogenetic relationships and taxonomy of the parabasalids?. Parasite. vol 6 p. 279-91 (1999). pubmed
Walton A (Gregory A) and Smith VJ. Primary culture of the hyaline haemocytes from marine decapods. Fish and Shellfish Immunology. vol 9 p. 181-184 (1999).
Walton A (Gregory A), Montanie H, Arcier JM, Smith VJ, Bonami JR. Construction of a gene probe for detection of P virus (Reoviridae) in a marine decapod. J Virol Methods. vol 81 p. 183-92 (1999). pubmed

1998

Andersson SG, Zomorodipour A andersson JO, Sicheritz-Ponten T, Alsmark UC, Podowski RM, Naslund AK, Eriksson AS, Winkler HH and Kurl and CG. The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature. vol 396 p. 133-40 (1998). pubmed
Embley TM and Hirt RP. Early branching eukaryotes?. Curr Opin Genet Dev. vol 8 p. 624-9 (1998). pubmed
Embley TM and Martin W. A hydrogen-producing mitochondrion. Nature. vol 396 p. 517-9 (1998). pubmed
Stephen JR, Kowalchuk GA, Bruns MAV, McCaig AE, Phillips CJ, Embley TM and Prosser JI. Analysis of beta-subgroup proteobacterial ammonia oxidizer populations in soil by denaturing gradient gel electrophoresis analysis and hierarchical phylogenetic probing. Appl Environ Microbiol. vol 64 p. 2958-65 (1998). pubmed

1997

Einvik C, Decatur WA, Embley TM, Vogt VM and Johansen S. Naegleria nucleolar introns contain two group I ribozymes with different functions in RNA splicing and processing. Rna. vol 3 p. 710-20 (1997). pubmed
Hirt RP, Healy B, Vossbrinck CR, Canning EU and Embley TM. A mitochondrial Hsp70 orthologue in Vairimorpha necatrix: molecular evidence that microsporidia once contained mitochondria. Curr Biol. vol 7 p. 995-8 (1997). pubmed
Kowalchuk GA, Stephen JR, De Boer W, Prosser JI, Embley TM and Woldendorp JW. Analysis of ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria in coastal sand dunes by denaturing gradient gel electrophoresis and sequencing of PCR-amplified 16S ribosomal DNA fragments. Appl Environ Microbiol. vol 63 p. 1489-97 (1997). pubmed
Munson MA, Nedwell DB and Embley TM. Phylogenetic diversity of Archaea in sediment samples from a coastal salt marsh. Appl Environ Microbiol. vol 63 p. 4729-33 (1997). pubmed
van der Giezen M, Rechinger KB, Svendsen I, Dur and R, Hirt RP, Fevre M, Embley TM and Prins RA. A mitochondrial-like targeting signal on the hydrogenosomal malic enzyme from the anaerobic fungus Neocallimastix frontalis: support for the hypothesis that hydrogenosomes are modified mitochondria. Mol Microbiol. vol 23 p. Nov-21 (1997). pubmed

1996

Horner DS, Hirt RP, Kilvington S, Lloyd D and Embley TM. Molecular data suggest an early acquisition of the mitochondrion endosymbiont. Proc R Soc Lond B Biol Sci. vol 263 p. 1053-9 (1996). pubmed
Stephen JR, McCaig AE, Smith Z, Prosser JI and Embley TM. Molecular diversity of soil and marine 16S rRNA gene sequences related to beta-subgroup ammonia-oxidizing bacteria. Appl Environ Microbiol. vol 62 p. 4147-54 (1996). pubmed

1995

Dyal PL, Hope S, Roberts DM and Embley TM. Use of the PCR and fluorescent probes to recover SSU rRNA gene sequences from single cells of the ciliate protozoon Spathidium. Mol Ecol. vol 4 p. 499-503 (1995). pubmed
Embley TM, Finlay BJ, Dyal PL, Hirt RP, Wilkinson M and Williams AG. Multiple origins of anaerobic ciliates with hydrogenosomes within the radiation of aerobic ciliates. Proc R Soc Lond B Biol Sci. vol 262 p. 87-93 (1995). pubmed
Hirt RP, Dyal PL, Wilkinson M, Finlay BJ, Roberts DM and Embley TM. Phylogenetic relationships among karyorelictids and heterotrichs inferred from small subunit rRNA sequences: resolution at the base of the ciliate tree. Mol Phylogenet Evol. vol 4 p. 77-87 (1995). pubmed
McInerney JO, Wilkinson M, Patching JW, Embley TM and Powell R. Recovery and phylogenetic analysis of novel archaeal rRNA sequences from a deep-sea deposit feeder. Appl Environ Microbiol. vol 61 p. 1646-8 (1995). pubmed
Poulain-Godefroy O, Hirt RP, Fasel N and Kraehenbuhl JP. The polymeric immunoglobulin receptor: signals for polarized expression. Adv Exp Med Biol. vol 371A p. 217-20 (1995). pubmed

1994

Embley TM and Finlay BJ. The use of small subunit rRNA sequences to unravel the relationships between anaerobic ciliates and their methanogen endosymbionts. Microbiology. vol 140 ( p. 225-35 (1994). pubmed
Embley TM and Stackebrandt E. The molecular phylogeny and systematics of the actinomycetes. Annu Rev Microbiol. vol 48 p. 257-89 (1994). pubmed
Embley TM, Hirt RP and Williams DM. Biodiversity at the molecular level: the domains, kingdoms and phyla of life. Philos Trans R Soc Lond B Biol Sci. vol 345 p. 21-33 (1994). pubmed
Finlay BJ, Esteban G, Clarke KJ, Williams AG, Embley TM and Hirt RP. Some rumen ciliates have endosymbiotic methanogens. FEMS Microbiol Lett. vol 117 p. 157-61 (1994). pubmed
Hirt RP, Fasel N and Kraehenbuhl JP. Inducible protein expression using a glucocorticoid-sensitive vector. Methods Cell Biol. vol 43 Pt p. 247-62 (1994). pubmed
Macnaughton SJ, O'Donnell AG and Embley TM. Permeabilization of mycolic-acid-containing actinomycetes for in situ hybridization with fluorescently labelled oligonucleotide probes. Microbiology. vol 140 ( p. 2859-65 (1994). pubmed
McCaig AE, Embley TM and Prosser JI. Molecular analysis of enrichment cultures of marine ammonia oxidisers. FEMS Microbiol Lett. vol 120 p. 363-7 (1994). pubmed
McVeigh HP, Munro J and Embley TM. The phylogenetic position of Pseudoamycolata halophobica (Akimov et al. 1989) and a proposal to reclassify it as Pseudonocardia halophobica. Int J Syst Bacteriol. vol 44 p. 300-2 (1994). pubmed
Warwick S, Bowen T, McVeigh H and Embley TM. A phylogenetic analysis of the family Pseudonocardiaceae and the genera Actinokineospora and Saccharothrix with 16S rRNA sequences and a proposal to combine the genera Amycolata and Pseudonocardia in an emended genus Pseudonocardia. Int J Syst Bacteriol. vol 44 p. 293-9 (1994). pubmed

1993

Embley TM and Finlay BJ. Systematic and morphological diversity of endosymbiotic methanogens in anaerobic ciliates. Antonie Van Leeuwenhoek. vol 64 p. 261-71 (1993). pubmed
Finlay BJ, Embley TM and Fenchel T. A new polymorphic methanogen, closely related to Methanocorpusculum parvum, living in stable symbiosis within the anaerobic ciliate Trimyema sp. J Gen Microbiol. vol 139 ( p. 371-8 (1993). pubmed
Head IM, Hiorns WD, Embley TM, McCarthy AJ and Saunders JR. The phylogeny of autotrophic ammonia-oxidizing bacteria as determined by analysis of 16S ribosomal RNA gene sequences. J Gen Microbiol. vol 139 ( p. 1147-53 (1993). pubmed
Hirt RP, Hughes GJ, Frutiger S, Michetti P, Perregaux C, Poulain-Godefroy O, Jeanguenat N, Neutra MR and Kraehenbuhl JP. Transcytosis of the polymeric Ig receptor requires phosphorylation of serine 664 in the absence but not the presence of dimeric IgA. Cell. vol 74 p. 245-55 (1993). pubmed
Johansen S, Embley TM and Willassen NP. A family of nuclear homing endonucleases. Nucleic Acids Res. vol 21 p. 4405 (1993). pubmed

1992

Embley TM, Dyal P and Kilvington S. A group I intron in the small subunit ribosomal RNA gene from Naegleria andersoni ssp. andersoni strain PPMFB-6. Nucleic Acids Res. vol 20 p. 6411 (1992). pubmed
Embley TM, Finlay BJ and Brown S. RNA sequence analysis shows that the symbionts in the ciliate Metopus contortus are polymorphs of a single methanogen species. FEMS Microbiol Lett. vol 76 p. 57-61 (1992). pubmed
Embley TM, Finlay BJ, Thomas RH and Dyal PL. The use of rRNA sequences and fluorescent probes to investigate the phylogenetic positions of the anaerobic ciliate Metopus palaeformis and its archaeobacterial endosymbiont. J Gen Microbiol. vol 138 ( p. 1479-87 (1992). pubmed
Hirt RP, Poulain-Godefroy O, Billotte J, Kraehenbuhl JP and Fasel N. Highly inducible synthesis of heterologous proteins in epithelial cells carrying a glucocorticoid-responsive vector. Gene. vol 111 p. 199-206 (1992). pubmed

1991

Embley TM. The linear PCR reaction: a simple and robust method for sequencing amplified rRNA genes. Lett Appl Microbiol. vol 13 p. 171-4 (1991). pubmed
Fry NK, Rowbotham TJ, Saunders NA and Embley TM. Direct amplification and sequencing of the 16S ribosomal DNA of an intracellular Legionella species recovered by amoebal enrichment from the sputum of a patient with pneumonia. FEMS Microbiol Lett. vol 67 p. 165-8 (1991). pubmed
Fry NK, Warwick S, Saunders NA and Embley TM. The use of 16S ribosomal RNA analyses to investigate the phylogeny of the family Legionellaceae. J Gen Microbiol. vol 137 ( p. 1215-22 (1991). pubmed

1988

Embley TM, Smida J and Stackebrandt E. Reverse transcriptase sequencing of 16S ribosomal RNA from Faenia rectivirgula, Pseudonocardia thermophila and Saccharopolyspora hirsuta, three wall type IV actinomycetes which lack mycolic acids. J Gen Microbiol. vol 134 ( p. 961-6 (1988). pubmed

1984

Embley TM, Goodfellow M, Minnikin DE and O'Donnell AG. Lipid and wall amino acid composition in the classification of Rothia dentocariosa. Zentralbl Bakteriol Mikrobiol Hyg [A]. vol 257 p. 285-95 (1984). pubmed