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John Archibald

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TOP 3
Eunsoo Kim; John M Archibald
Ultrastructure and molecular phylogeny of the cryptomonad Goniomonas avonlea sp. nov.
Shinichiro Maruyama; Robert Jm Eveleigh; John M Archibald
Treetrimmer: a method for phylogenetic dataset size reduction.
Naoko T Onodera; John M Archibald; Tanja Durbic; Corey Nislow; Julie Ryu; John R Rohde
Genome sequence of Shigella flexneri serotype 5a strain M90T Sm.

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All Publications

2013: Eunsoo Kim; John M Archibald
Ultrastructure and molecular phylogeny of the cryptomonad Goniomonas avonlea sp. nov.
Protist 2013;164(2):160-82.
2013: Shinichiro Maruyama; Robert Jm Eveleigh; John M Archibald
Treetrimmer: a method for phylogenetic dataset size reduction.
BMC research notes 2013;6():145.
2012: Naoko T Onodera; John M Archibald; Tanja Durbic; Corey Nislow; Julie Ryu; John R Rohde
Genome sequence of Shigella flexneri serotype 5a strain M90T Sm.
Journal of bacteriology 2012;194(11):3022.
2012: Takuro Nakayama; Ken-ichiro Ishida; John M Archibald
Broad distribution of TPI-GAPDH fusion proteins among eukaryotes: evidence for glycolytic reactions in the mitochondrion?
PloS one 2012;7(12):e52340.
2012: Julia F Hopkins; Sylvie Laboissiere; Jonathan A D Neilson; David F Spencer; Dion G Durnford; Robert J M Eveleigh; Michael W Gray; John M Archibald
Proteomics reveals plastid- and periplastid-targeted proteins in the chlorarachniophyte alga Bigelowiella natans.
Genome biology and evolution 2012;4(12):1391-406.
2012: Christa E Moore; Goro Tanifuji; Bruce Curtis; Tyler Mills; John M Archibald
Nucleomorph genome sequence of the cryptophyte alga Chroomonas mesostigmatica CCMP1168 reveals lineage-specific gene loss and genome complexity.
Genome biology and evolution 2012;4(11):1162-75.
2012: Takuro Nakayama; John M Archibald
Evolving a photosynthetic organelle.
BMC biology 2012;10():35.
2011: Goro Tanifuji; Richard J Cawthorn; Marlena Dlutek; Ivan Fiala; Rebecca Gibeault; Spencer J Greenwood; Eunsoo Kim; Julius Lukes; Naoko T Onodera; John M Archibald
Genomic characterization of Neoparamoeba pemaquidensis (Amoebozoa) and its kinetoplastid endosymbiont.
Eukaryotic cell 2011;10(8):1143-6.
2011: W Ford Doolittle; Julius Lukeš; John M Archibald; Patrick J Keeling; Michael W Gray
Comment on "Does constructive neutral evolution play an important role in the origin of cellular complexity?" DOI 10.1002/bies.201100010.
BioEssays : news and reviews in molecular, cellular and developmental biology 2011;33(6):427-9.
2011: Eunsoo Kim; James W Harrison; Sebastian Sudek; Meredith D M Jones; Heather M Wilcox; Thomas A Richards; Alexandra Z Worden; John M Archibald
Newly identified and diverse plastid-bearing branch on the eukaryotic tree of life.
Proceedings of the National Academy of Sciences of the United States of America 2011;108(4):1496-500.
2011: Goro Tanifuji; Naoko T Onodera; Travis J Wheeler; Marlena Dlutek; Natalie Donaher; John M Archibald
Complete nucleomorph genome sequence of the nonphotosynthetic alga Cryptomonas paramecium reveals a core nucleomorph gene set.
Genome biology and evolution 2011;3():44-54.
2010: Michael W Gray; Julius Lukes; John M Archibald; Patrick J Keeling; W Ford Doolittle
Cell biology. Irremediable complexity?
Science (New York, N.Y.) 2010;330(6006):920-1.
2010: Bruce A Curtis; John M Archibald
A spliceosomal intron of mitochondrial DNA origin.
Current biology : CB 2010;20(21):R919-20.
2010: Tia D Silver; Christa E Moore; John M Archibald
Nucleomorph ribosomal DNA and telomere dynamics in chlorarachniophyte algae.
The Journal of eukaryotic microbiology 2010;57(6):453-9.
2010: Goro Tanifuji; John M Archibald
Actin gene family dynamics in cryptomonads and red algae.
Journal of molecular evolution 2010;71(3):169-79.
2010: Eunsoo Kim; Jong Soo Park; Alastair G B Simpson; Shigeru Matsunaga; Masakatsu Watanabe; Akio Murakami; Katrin Sommerfeld; Naoko T Onodera; John M Archibald
Complex array of endobionts in Petalomonas sphagnophila, a large heterotrophic euglenid protist from Sphagnum-dominated peatlands.
The ISME journal 2010;4(9):1108-20.
2010: John M Archibald; Thomas A Richards
Gene transfer: anything goes in plant mitochondria.
BMC biology 2010;8():147.
2010: Eunsoo Kim; John M Archibald
Plastid evolution: gene transfer and the maintenance of 'stolen' organelles.
BMC biology 2010;8():73.
2009: John M Archibald; Christopher E Lane
Going, going, not quite gone: nucleomorphs as a case study in nuclear genome reduction.
The Journal of heredity 2009;100(5):582-90.
2009: John M Archibald
Genomics. Green evolution, green revolution.
Science (New York, N.Y.) 2009;324(5924):191-2.
2009: John M Archibald
The puzzle of plastid evolution.
Current biology : CB 2009;19(2):R81-8.
2009: Natalie Donaher; Goro Tanifuji; Naoko T Onodera; Stephanie A Malfatti; Patrick S G Chain; Yoshiaki Hara; John M Archibald
The complete plastid genome sequence of the secondarily nonphotosynthetic alga Cryptomonas paramecium: reduction, compaction, and accelerated evolutionary rate.
Genome biology and evolution 2009;1():439-48.
2009: Fabien Burki; Yuji Inagaki; Jon Bråte; John M Archibald; Patrick J Keeling; Thomas Cavalier-Smith; Miako Sakaguchi; Tetsuo Hashimoto; Ales Horak; Surendra Kumar; Dag Klaveness; Kjetill S Jakobsen; Jan Pawlowski; Kamran Shalchian-Tabrizi
Large-scale phylogenomic analyses reveal that two enigmatic protist lineages, telonemia and centroheliozoa, are related to photosynthetic chromalveolates.
Genome biology and evolution 2009;1():231-8.
2009: Christa E Moore; John M Archibald
Nucleomorph genomes.
Annual review of genetics 2009;43():251-64.
2008: John M Archibald
Plastid evolution: remnant algal genes in ciliates.
Current biology : CB 2008;18(15):R663-R665.
2008: Hameed Khan; John M Archibald
Lateral transfer of introns in the cryptophyte plastid genome.
Nucleic acids research 2008;36(9):3043-53.
2008: Christopher E Lane; John M Archibald
The eukaryotic tree of life: endosymbiosis takes its TOL.
Trends in ecology & evolution 2008;23(5):268-75.
2008: Patrick J Keeling; John M Archibald
Organelle evolution: what's in a name?
Current biology : CB 2008;18(8):R345-7.
2008: Anna Fong; John M Archibald
Evolutionary dynamics of light-independent protochlorophyllide oxidoreductase genes in the secondary plastids of cryptophyte algae.
Eukaryotic cell 2008;7(3):550-3.
2008: Eunsoo Kim; Christopher E Lane; Bruce A Curtis; Catherine Kozera; Sharen Bowman; John M Archibald
Complete sequence and analysis of the mitochondrial genome of Hemiselmis andersenii CCMP644 (Cryptophyceae).
BMC genomics 2008;9():215.
2007: Christopher E Lane; Krystal van den Heuvel; Catherine Kozera; Bruce A Curtis; Byron J Parsons; Sharen Bowman; John M Archibald
Nucleomorph genome of Hemiselmis andersenii reveals complete intron loss and compaction as a driver of protein structure and function.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(50):19908-13.
2007: Tia D Silver; Sayaka Koike; Akinori Yabuki; Rumiko Kofuji; John M Archibald; Ken-Ichiro Ishida
Phylogeny and nucleomorph karyotype diversity of chlorarachniophyte algae.
The Journal of eukaryotic microbiology 2007;54(5):403-10.
2007: Sina M Adl; Brian S Leander; Alastair G B Simpson; John M Archibald; O Roger Anderson; David Bass; Samuel S Bowser; Guy Brugerolle; Mark Farmer; Serguei A Karpov; Martin Kolisko; Christopher E Lane; Deborah J Lodge; David G Mann; Ralf Meisterfeld; Leonel Mendoza; Øjvind Moestrup; Sharon E Mozley-Standridge; Alexey V Smirnov; Frederick Spiegel
Diversity, nomenclature, and taxonomy of protists.
Systematic biology 2007;56(4):684-9.
2007: Hameed Khan; Natalie Parks; Catherine Kozera; Bruce A Curtis; Byron J Parsons; Sharen Bowman; John M Archibald
Plastid genome sequence of the cryptophyte alga Rhodomonas salina CCMP1319: lateral transfer of putative DNA replication machinery and a test of chromist plastid phylogeny.
Molecular biology and evolution 2007;24(8):1832-42.
2007: John M Archibald
Nucleomorph genomes: structure, function, origin and evolution.
BioEssays : news and reviews in molecular, cellular and developmental biology 2007;29(4):392-402.
2007: Hameed Khan; Catherine Kozera; Bruce A Curtis; Jillian Tarrant Bussey; Stan Theophilou; Sharen Bowman; John M Archibald
Retrotransposons and tandem repeat sequences in the nuclear genomes of cryptomonad algae.
Journal of molecular evolution 2007;64(2):223-36.
2006: John M Archibald
Algal genomics: exploring the imprint of endosymbiosis.
Current biology : CB 2006;16(24):R1033-5.
2006: Christopher E Lane; John M Archibald
Novel nucleomorph genome architecture in the cryptomonad genus hemiselmis.
The Journal of eukaryotic microbiology 2006;53(6):515-21.
2006: John M Archibald
Endosymbiosis: double-take on plastid origins.
Current biology : CB 2006;16(17):R690-2.
2006: Iñaki Ruiz-Trillo; Christopher E Lane; John M Archibald; Andrew J Roger
Insights into the evolutionary origin and genome architecture of the unicellular opisthokonts Capsaspora owczarzaki and Sphaeroforma arctica.
The Journal of eukaryotic microbiology 2006;53(5):379-84.
2006: John M Archibald
Genome complexity in a lean, mean photosynthetic machine.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(31):11433-4.
2006: Christopher E Lane; Hameed Khan; Melissa MacKinnon; Anna Fong; Stan Theophilou; John M Archibald
Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Insight into the diversity and evolution of the cryptomonad nucleomorph genome.
Molecular biology and evolution 2006;23(5):856-65.
2005: John M Archibald
Jumping genes and shrinking genomes--probing the evolution of eukaryotic photosynthesis with genomics.
IUBMB life 2005;57(8):539-47.
2005: patron nicola; Ross F Waller; John M Archibald; Patrick J Keeling
Complex protein targeting to dinoflagellate plastids.
Journal of molecular biology 2005;348(4):1015-24.
2004: Patrick J Keeling; John M Archibald; Naomi M Fast; Jeffrey D Palmer
Comment on "The evolution of modern eukaryotic phytoplankton".
Science (New York, N.Y.) 2004;306(5705):2191; author reply 2191.
2004: Matthew Rogers; John M Archibald; Matthew A Field; Catherine Li; Boris Striepen; Patrick J Keeling
Plastid-targeting peptides from the chlorarachniophyte Bigelowiella natans.
The Journal of eukaryotic microbiology 2004;51(5):529-35.
2004: John M Archibald; Patrick J Keeling
Actin and ubiquitin protein sequences support a cercozoan/foraminiferan ancestry for the plasmodiophorid plant pathogens.
The Journal of eukaryotic microbiology 2004;51(1):113-8.
2003: David Longet; John M Archibald; Patrick J Keeling; Jan Pawlowski
Foraminifera and Cercozoa share a common origin according to RNA polymerase II phylogenies.
International journal of systematic and evolutionary microbiology 2003;53(Pt 6):1735-9.
2003: John M Archibald; Matthew Rogers; Michael Toop; Ken-Ichiro Ishida; Patrick J Keeling
Lateral gene transfer and the evolution of plastid-targeted proteins in the secondary plastid-containing alga Bigelowiella natans.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(13):7678-83.
2003: John M Archibald; Evelyn M Teh; Patrick J Keeling
Novel ubiquitin fusion proteins: ribosomal protein P1 and actin.
Journal of molecular biology 2003;328(4):771-8.
2003: John M Archibald; David Longet; Jan Pawlowski; Patrick J Keeling
A novel polyubiquitin structure in Cercozoa and Foraminifera: evidence for a new eukaryotic supergroup.
Molecular biology and evolution 2003;20(1):62-6.
2002: John M Archibald; Patrick J Keeling
Recycled plastids: a 'green movement' in eukaryotic evolution.
Trends in genetics : TIG 2002;18(11):577-84.
2002: John M Archibald; Andrew J Roger
Gene conversion and the evolution of euryarchaeal chaperonins: a maximum likelihood-based method for detecting conflicting phylogenetic signals.
Journal of molecular evolution 2002;55(2):232-45.
2002: John M Archibald; Charles J O'Kelly; W Ford Doolittle
The chaperonin genes of jakobid and jakobid-like flagellates: implications for eukaryotic evolution.
Molecular biology and evolution 2002;19(4):422-31.
2002: John M Archibald; Andrew J Roger
Gene duplication and gene conversion shape the evolution of archaeal chaperonins.
Journal of molecular biology 2002;316(5):1041-50.
2001: John M Archibald; Christian Blouin; W Ford Doolittle
Gene duplication and the evolution of group II chaperonins: implications for structure and function.
Journal of structural biology 2001;135(2):157-69.
2001: John M Archibald; T Cavalier-Smith; U Maier; Sue Douglas
Molecular chaperones encoded by a reduced nucleus: the cryptomonad nucleomorph.
Journal of molecular evolution 2001;52(6):490-501.
2000: John M Archibald; JM Logsdon; W Ford Doolittle
Origin and evolution of eukaryotic chaperonins: phylogenetic evidence for ancient duplications in CCT genes.
Molecular biology and evolution 2000;17(10):1456-66.
1999: John M Archibald; JM Logsdon; W Ford Doolittle
Recurrent paralogy in the evolution of archaeal chaperonins.
Current biology : CB 1999;9(18):1053-6.