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Andrew Roger

Research Profile

Concepts & Ideas

Phenomena

Evolution, Molecular

Anatomy

Eukaryotic Cells

Genes & Molecular Sequences

Physiology

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Publications

TOP 3
Tommy Harding; Jong Soo Park; Andrey Plotnikov; Andrew J Roger; Elena Selivanova; Jeffrey D Silberman; Manuela Baumgartner; Matthew W Brown; John H Gunderson; Alastair G B Simpson
Amoeba stages in the deepest branching heteroloboseans, including Pharyngomonas: evolutionary and systematic implications.
Edward Susko; Andrew J Roger
Problems with estimation of ancestral frequencies under stationary models.
Edward Susko; Andrew J Roger
The probability of correctly resolving a split as an experimental design criterion in phylogenetics.

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All Publications

2013: Tommy Harding; Jong Soo Park; Andrey Plotnikov; Andrew J Roger; Elena Selivanova; Jeffrey D Silberman; Manuela Baumgartner; Matthew W Brown; John H Gunderson; Alastair G B Simpson
Amoeba stages in the deepest branching heteroloboseans, including Pharyngomonas: evolutionary and systematic implications.
Protist 2013;164(2):272-86.
2013: Edward Susko; Andrew J Roger
Problems with estimation of ancestral frequencies under stationary models.
Systematic biology 2013;62(2):330-8.
2012: Edward Susko; Andrew J Roger
The probability of correctly resolving a split as an experimental design criterion in phylogenetics.
Systematic biology 2012;61(5):811-21.
2012: Anastasios Tsaousis; Daniel Vinella; Julius Lukes; Alexandra Stechmann; Frédéric Barras; Marc Fontecave; Daniel Gaston; Eleni Gentekaki; Shaojun Long; Sandrine Ollagnier-de Choudens; Béatrice Py; Andrew J Roger
Evolution of Fe/S cluster biogenesis in the anaerobic parasite Blastocystis.
Proceedings of the National Academy of Sciences of the United States of America 2012;109(26):10426-31.
2012: Matthew W Brown; Martin Kolisko; Jeffrey D Silberman; Andrew J Roger
Aggregative multicellularity evolved independently in the eukaryotic supergroup Rhizaria.
Current biology : CB 2012;22(12):1123-7.
2012: Guifré Torruella; Kamran Shalchian-Tabrizi; Romain Derelle; B Franz Lang; Jordi Paps; Andrew J Roger; Iñaki Ruiz-Trillo
Phylogenetic relationships within the Opisthokonta based on phylogenomic analyses of conserved single-copy protein domains.
Molecular biology and evolution 2012;29(2):531-44.
2011: Daniel Gaston; Edward Susko; Andrew J Roger
A phylogenetic mixture model for the identification of functionally divergent protein residues.
Bioinformatics (Oxford, England) 2011;27(19):2655-63.
2011: Shaojun Long; Piya Changmai; Andrew J Roger; Tomáš Skalický; Anastasios Tsaousis; Zdeněk Verner; Yan-Zi Wen; Julius Lukeš
Stage-specific requirement for Isa1 and Isa2 proteins in the mitochondrion of Trypanosoma brucei and heterologous rescue by human and Blastocystis orthologues.
Molecular microbiology 2011;81(6):1403-18.
2011: Huai-Chun Wang; Edward Susko; Andrew J Roger
Fast statistical tests for detecting heterotachy in protein evolution.
Molecular biology and evolution 2011;28(8):2305-15.
2011: Ryoma Kamikawa; Andrew J Roger; Yuji Inagaki; Tetsuo Hashimoto
Splintrons in Giardia intestinalis: Spliceosomal introns in a split form.
Communicative & integrative biology 2011;4(4):454-6.
2011: Courtney W Stairs; Andrew J Roger; Vladimír Hampl
Eukaryotic pyruvate formate lyase and its activating enzyme were acquired laterally from a Firmicute.
Molecular biology and evolution 2011;28(7):2087-99.
2011: Ryoma Kamikawa; Yuji Inagaki; Masaharu Tokoro; Andrew J Roger; Tetsuo Hashimoto
Split introns in the genome of Giardia intestinalis are excised by spliceosome-mediated trans-splicing.
Current biology : CB 2011;21(4):311-5.
2011: Anastasios Tsaousis; Daniel Gaston; Alexandra Stechmann; Peter B Walker; Trevor Lithgow; Andrew J Roger
A functional Tom70 in the human parasite Blastocystis sp.: implications for the evolution of the mitochondrial import apparatus.
Molecular biology and evolution 2011;28(1):781-91.
2010: Maria José Barberà; Iñaki Ruiz-Trillo; Julia Y A Tufts; Amandine Bery; Jeffrey D Silberman; Andrew J Roger
Sawyeria marylandensis (Heterolobosea) has a hydrogenosome with novel metabolic properties.
Eukaryotic cell 2010;9(12):1913-24.
2010: Martin Kolisko; Jeffrey D Silberman; Ivan Cepicka; Naoji Yubuki; Kiyotaka Takishita; Akinori Yabuki; Brian S Leander; Isao Inouye; Yuji Inagaki; Andrew J Roger; Alastair G B Simpson
A wide diversity of previously undetected free-living relatives of diplomonads isolated from marine/saline habitats.
Environmental microbiology 2010;12(10):2700-10.
2010: Denis BAURAIN; Henner Brinkmann; Jörn Petersen; Naiara Rodriguez-Ezpeleta; Alexandra Stechmann; Vincent Demoulin; Andrew J Roger; Gertraud Burger; B Franz Lang; Hervé Philippe
Phylogenomic evidence for separate acquisition of plastids in cryptophytes, haptophytes, and stramenopiles.
Molecular biology and evolution 2010;27(7):1698-709.
2010: Arnau Sebé-Pedrós; Andrew J Roger; Franz B Lang; Nicole King; Iñaki Ruiz-Trillo
Ancient origin of the integrin-mediated adhesion and signaling machinery.
Proceedings of the National Academy of Sciences of the United States of America 2010;107(22):10142-7.
2010: Laura A Hug; Alexandra Stechmann; Andrew J Roger
Phylogenetic distributions and histories of proteins involved in anaerobic pyruvate metabolism in eukaryotes.
Molecular biology and evolution 2010;27(2):311-24.
2009: Christian Blouin; Scott Perry; Allan Lavell; Edward Susko; Andrew J Roger
Reproducing the manual annotation of multiple sequence alignments using a SVM classifier.
Bioinformatics (Oxford, England) 2009;25(23):3093-8.
2009: Vladimír Hampl; Laura Hug; Jessica W Leigh; Joel B Dacks; B Franz Lang; Alastair G B Simpson; Andrew J Roger
Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic "supergroups".
Proceedings of the National Academy of Sciences of the United States of America 2009;106(10):3859-64.
2009: Huai-Chun Wang; Edward Susko; Andrew J Roger
PROCOV: maximum likelihood estimation of protein phylogeny under covarion models and site-specific covarion pattern analysis.
BMC evolutionary biology 2009;9():225.
2009: Edward Susko; Andrew J Roger
Statistical analysis of expressed sequence tags.
Methods in molecular biology (Clifton, N.J.) 2009;533():277-87.
2008: Gabino Sanchez-Perez; Vladimír Hampl; Alastair G B Simpson; Andrew J Roger
A new divergent type of eukaryotic methionine adenosyltransferase is present in multiple distantly related secondary algal lineages.
The Journal of eukaryotic microbiology 2008;55(5):374-81.
2008: Karleigh Hamblin; Daron M Standley; Matthew Rogers; Alexandra Stechmann; Andrew J Roger; Robin Maytum; Mark van der Giezen
Localization and nucleotide specificity of Blastocystis succinyl-CoA synthetase.
Molecular microbiology 2008;68(6):1395-405.
2008: Alexandra Stechmann; Karleigh Hamblin; Vicente Pérez-Brocal; Daniel Gaston; Gregory S Richmond; Mark van der Giezen; C Graham Clark; Andrew J Roger
Organelles in Blastocystis that blur the distinction between mitochondria and hydrogenosomes.
Current biology : CB 2008;18(8):580-5.
2008: Iñaki Ruiz-Trillo; Andrew J Roger; Gertraud Burger; Michael W Gray; B Franz Lang
A phylogenomic investigation into the origin of metazoa.
Molecular biology and evolution 2008;25(4):664-72.
2008: Jessica W Leigh; Edward Susko; Manuela Baumgartner; Andrew J Roger
Testing congruence in phylogenomic analysis.
Systematic biology 2008;57(1):104-15.
2008: Jihua Wu; Edward Susko; Andrew J Roger
An independent heterotachy model and its implications for phylogeny and divergence time estimation.
Molecular phylogenetics and evolution 2008;46(2):801-6.
2008: Huai-Chun Wang; Karen Li; Edward Susko; Andrew J Roger
A class frequency mixture model that adjusts for site-specific amino acid frequencies and improves inference of protein phylogeny.
BMC evolutionary biology 2008;8():331.
2008: Martin Kolisko; Ivan Cepicka; Vladimír Hampl; Jessica Leigh; Andrew J Roger; Jaroslav Kulda; Alastair G B Simpson; Jaroslav Flegr
Molecular phylogeny of diplomonads and enteromonads based on SSU rRNA, alpha-tubulin and HSP90 genes: implications for the evolutionary history of the double karyomastigont of diplomonads.
BMC evolutionary biology 2008;8():205.
2008: Vladimír Hampl; Jeffrey D Silberman; Alexandra Stechmann; Sara Diaz-Triviño; Patricia J Johnson; Andrew J Roger
Genetic evidence for a mitochondriate ancestry in the 'amitochondriate' flagellate Trimastix pyriformis.
PloS one 2008;3(1):e1383.
2008: Huai-Chun Wang; Edward Susko; Matthew Spencer; Andrew J Roger
Topological estimation biases with covarion evolution.
Journal of molecular evolution 2008;66(1):50-60.
2007: Erin E Gill; Sara Diaz-Triviño; Maria José Barberà; Jeffrey D Silberman; Alexandra Stechmann; Daniel Gaston; Ivica Tamas; Andrew J Roger
Novel mitochondrion-related organelles in the anaerobic amoeba Mastigamoeba balamuthi.
Molecular microbiology 2007;66(6):1306-20.
2007: Edward Susko; Andrew J Roger
On reduced amino acid alphabets for phylogenetic inference.
Molecular biology and evolution 2007;24(9):2139-50.
2007: Laura A Hug; Andrew J Roger
The impact of fossils and taxon sampling on ancient molecular dating analyses.
Molecular biology and evolution 2007;24(8):1889-97.
2007: Iñaki Ruiz-Trillo; Gertraud Burger; Peter W H Holland; Nicole King; B Franz Lang; Andrew J Roger; Michael W Gray
The origins of multicellularity: a multi-taxon genome initiative.
Trends in genetics : TIG 2007;23(3):113-8.
2007: Jan O Andersson; Asa M Sjögren; David S Horner; Colleen A Murphy; Patricia L Dyal; Staffan G Svärd; John M Logsdon; Mark A Ragan; Robert Hirt; Andrew J Roger
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 2007;8():51.
2007: Shirley L Pepke; Davin Butt; Isabelle Nadeau; Andrew J Roger; Christian Blouin
Using confidence set heuristics during topology search improves the robustness of phylogenetic inference.
Journal of molecular evolution 2007;64(1):80-9.
2007: Huai-Chun Wang; Matthew Spencer; Edward Susko; Andrew J Roger
Testing for covarion-like evolution in protein sequences.
Molecular biology and evolution 2007;24(1):294-305.
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: Andrew J Roger; Laura A Hug
The origin and diversification of eukaryotes: problems with molecular phylogenetics and molecular clock estimation.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2006;361(1470):1039-54.
2006: Huai-Chun Wang; Edward Susko; Andrew J Roger
On the correlation between genomic G+C content and optimal growth temperature in prokaryotes: data quality and confounding factors.
Biochemical and biophysical research communications 2006;342(3):681-4.
2006: Yuji Inagaki; Edward Susko; Andrew J Roger
Recombination between elongation factor 1alpha genes from distantly related archaeal lineages.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(12):4528-33.
2006: Alastair G B Simpson; Yuji Inagaki; Andrew J Roger
Comprehensive multigene phylogenies of excavate protists reveal the evolutionary positions of "primitive" eukaryotes.
Molecular biology and evolution 2006;23(3):615-25.
2006: Matthew Spencer; Edward Susko; Andrew J Roger
Modelling prokaryote gene content.
Evolutionary bioinformatics online 2006;2():157-78.
2006: Alexandra Stechmann; Manuela Baumgartner; Jeffrey D Silberman; Andrew J Roger
The glycolytic pathway of Trimastix pyriformis is an evolutionary mosaic.
BMC evolutionary biology 2006;6():101.
2006: Jan O Andersson; Robert Hirt; Peter G Foster; Andrew J Roger
Evolution of four gene families with patchy phylogenetic distributions: influx of genes into protist genomes.
BMC evolutionary biology 2006;6():27.
2005: Edward Susko; Matthew Spencer; Andrew J Roger
Biases in phylogenetic estimation can be caused by random sequence segments.
Journal of molecular evolution 2005;61(3):351-9.
2005: Matthew Spencer; Edward Susko; Andrew J Roger
Likelihood, parsimony, and heterogeneous evolution.
Molecular biology and evolution 2005;22(5):1161-4.
2005: Christian Blouin; Davin Butt; Andrew J Roger
Impact of taxon sampling on the estimation of rates of evolution at sites.
Molecular biology and evolution 2005;22(3):784-91.
2005: Davin Butt; Andrew J Roger; Christian Blouin
libcov: a C++ bioinformatic library to manipulate protein structures, sequence alignments and phylogeny.
BMC bioinformatics 2005;6():138.
2005: Jan O Andersson; Stewart W Sarchfield; Andrew J Roger
Gene transfers from nanoarchaeota to an ancestor of diplomonads and parabasalids.
Molecular biology and evolution 2005;22(1):85-90.
2004: Alastair G B Simpson; Erin E Gill; Heather A Callahan; R Wayne Litaker; Andrew J Roger
Early evolution within kinetoplastids (euglenozoa), and the late emergence of trypanosomatids.
Protist 2004;155(4):407-22.
2004: Iñaki Ruiz-Trillo; Yuji Inagaki; Lesley A M Davis; Sigmund Sperstad; Bjarne Landfald; Andrew J Roger
Capsaspora owczarzaki is an independent opisthokont lineage.
Current biology : CB 2004;14(22):R946-7.
2004: Edward Susko; Andrew J Roger
Estimating and comparing the rates of gene discovery and expressed sequence tag (EST) frequencies in EST surveys.
Bioinformatics (Oxford, England) 2004;20(14):2279-87.
2004: Alastair G B Simpson; Andrew J Roger
The real 'kingdoms' of eukaryotes.
Current biology : CB 2004;14(17):R693-6.
2004: Edward Susko; Yuji Inagaki; Andrew J Roger
On inconsistency of the neighbor-joining, least squares, and minimum evolution estimation when substitution processes are incorrectly modeled.
Molecular biology and evolution 2004;21(9):1629-42.
2004: Yuji Inagaki; Edward Susko; Naomi M Fast; Andrew J Roger
Covarion shifts cause a long-branch attraction artifact that unites microsporidia and archaebacteria in EF-1alpha phylogenies.
Molecular biology and evolution 2004;21(7):1340-9.
2004: Jeffrey D Silberman; Allen G Collins; Lisa-Ann Gershwin; Patricia J Johnson; Andrew J Roger
Ellobiopsids of the genus Thalassomyces are alveolates.
The Journal of eukaryotic microbiology 2004;51(2):246-52.
2004: Christian Blouin; Davin Butt; Andrew J Roger
Rapid evolution in conformational space: a study of loop regions in a ubiquitous GTP binding domain.
Protein science : a publication of the Protein Society 2004;13(3):608-16.
2004: Alastair G B Simpson; Andrew J Roger
Protein phylogenies robustly resolve the deep-level relationships within Euglenozoa.
Molecular phylogenetics and evolution 2004;30(1):201-12.
2003: Joel B Dacks; Lesley A M Davis; Asa M Sjögren; Jan O Andersson; Andrew J Roger; W Ford Doolittle
Evidence for Golgi bodies in proposed 'Golgi-lacking' lineages.
Proceedings. Biological sciences / The Royal Society 2003;270 Suppl 2():S168-71.
2003: Edward Susko; Chris Field; Christian Blouin; Andrew J Roger
Estimation of rates-across-sites distributions in phylogenetic substitution models.
Systematic biology 2003;52(5):594-603.
2003: Yuji Inagaki; Christian Blouin; Edward Susko; Andrew J Roger
Assessing functional divergence in EF-1alpha and its paralogs in eukaryotes and archaebacteria.
Nucleic acids research 2003;31(14):4227-37.
2003: Jan O Andersson; Andrew J Roger
Evolution of glutamate dehydrogenase genes: evidence for lateral gene transfer within and between prokaryotes and eukaryotes.
BMC evolutionary biology 2003;3():14.
2003: W Ford Doolittle; Yan Boucher; Camilla L Nesbø; Christophe J Douady; Jan O Andersson; Andrew J Roger
How big is the iceberg of which organellar genes in nuclear genomes are but the tip?
Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2003;358(1429):39-57; discussion 57-8.
2003: Jan O Andersson; Asa M Sjögren; Lesley A M Davis; T Martin Embley; Andrew J Roger
Phylogenetic analyses of diplomonad genes reveal frequent lateral gene transfers affecting eukaryotes.
Current biology : CB 2003;13(2):94-104.
2003: Christian Blouin; Yan Boucher; Andrew J Roger
Inferring functional constraints and divergence in protein families using 3D mapping of phylogenetic information.
Nucleic acids research 2003;31(2):790-7.
2002: Alastair G B Simpson; Julius Lukes; Andrew J Roger
The evolutionary history of kinetoplastids and their kinetoplasts.
Molecular biology and evolution 2002;19(12):2071-83.
2002: Alastair G B Simpson; Andrew J Roger
Eukaryotic evolution: getting to the root of the problem.
Current biology : CB 2002;12(20):R691-3.
2002: Alastair G B Simpson; Andrew J Roger; Jeffrey D Silberman; Detlef D Leipe; Virginia P Edgcomb; Lars S Jermiin; David J Patterson; Mitchell L Sogin
Evolutionary history of "early-diverging" eukaryotes: the excavate taxon Carpediemonas is a close relative of Giardia.
Molecular biology and evolution 2002;19(10):1782-91.
2002: Alastair G B Simpson; Erin K MacQuarrie; Andrew J Roger
Eukaryotic evolution: early origin of canonical introns.
Nature 2002;419(6904):270.
2002: Edward Susko; Yuji Inagaki; Chris Field; Michael E Holder; Andrew J Roger
Testing for differences in rates-across-sites distributions in phylogenetic subtrees.
Molecular biology and evolution 2002;19(9):1514-23.
2002: Andrew J Roger; Jeffrey D Silberman
Cell evolution: mitochondria in hiding.
Nature 2002;418(6900):827-9.
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: Jeffrey D Silberman; Alastair G B Simpson; Jaroslav Kulda; Ivan Cepicka; Vladimír Hampl; Patricia J Johnson; Andrew J Roger
Retortamonad flagellates are closely related to diplomonads--implications for the history of mitochondrial function in eukaryote evolution.
Molecular biology and evolution 2002;19(5):777-86.
2002: Yuji Inagaki; W Ford Doolittle; Sandra L Baldauf; Andrew J Roger
Lateral transfer of an EF-1alpha gene: origin and evolution of the large subunit of ATP sulfurylase in eubacteria.
Current biology : CB 2002;12(9):772-6.
2002: Jan O Andersson; Andrew J Roger
Evolutionary analyses of the small subunit of glutamate synthase: gene order conservation, gene fusions, and prokaryote-to-eukaryote lateral gene transfers.
Eukaryotic cell 2002;1(2):304-10.
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.
2002: Jan O Andersson; Andrew J Roger
A cyanobacterial gene in nonphotosynthetic protists--an early chloroplast acquisition in eukaryotes?
Current biology : CB 2002;12(2):115-9.
2002: Yuji Inagaki; Christian Blouin; W Ford Doolittle; Andrew J Roger
Convergence and constraint in eukaryotic release factor 1 (eRF1) domain 1: the evolution of stop codon specificity.
Nucleic acids research 2002;30(2):532-44.
2001: Hilary G Morrison; Andrew J Roger; T G Nystul; Frances D Gillin; Mitchell L Sogin
Giardia lamblia expresses a proteobacterial-like DnaK homolog.
Molecular biology and evolution 2001;18(4):530-41.
2001: Virginia P Edgcomb; Andrew J Roger; Alastair G B Simpson; David Kysela; Mitchell L Sogin
Evolutionary relationships among "jakobid" flagellates as indicated by alpha- and beta-tubulin phylogenies.
Molecular biology and evolution 2001;18(4):514-22.
2000: Sandra L Baldauf; Andrew J Roger; I Wenk-Siefert; W Ford Doolittle
A kingdom-level phylogeny of eukaryotes based on combined protein data.
Science (New York, N.Y.) 2000;290(5493):972-7.
1999: Andrew J Roger; Hilary G Morrison; Mitchell L Sogin
Primary structure and phylogenetic relationships of a malate dehydrogenase gene from Giardia lamblia.
Journal of molecular evolution 1999;48(6):750-5.
1999: Andrew J Roger; O Sandblom; W Ford Doolittle; H Philippe
An evaluation of elongation factor 1 alpha as a phylogenetic marker for eukaryotes.
Molecular biology and evolution 1999;16(2):218-33.
1998: Naomi M Fast; Andrew J Roger; C A Richardson; W Ford Doolittle
U2 and U6 snRNA genes in the microsporidian Nosema locustae: evidence for a functional spliceosome.
Nucleic acids research 1998;26(13):3202-7.
1998: Andrew J Roger; Staffan G Svärd; J Tovar; C G Clark; M W Smith; Frances D Gillin; Mitchell L Sogin
A mitochondrial-like chaperonin 60 gene in Giardia lamblia: evidence that diplomonads once harbored an endosymbiont related to the progenitor of mitochondria.
Proceedings of the National Academy of Sciences of the United States of America 1998;95(1):229-34.
1996: Andrew J Roger; C G Clark; W Ford Doolittle
A possible mitochondrial gene in the early-branching amitochondriate protist Trichomonas vaginalis.
Proceedings of the National Academy of Sciences of the United States of America 1996;93(25):14618-22.
1996: Andrew J Roger; M W Smith; R F Doolittle; W Ford Doolittle
Evidence for the Heterolobosea from phylogenetic analysis of genes encoding glyceraldehyde-3-phosphate dehydrogenase.
The Journal of eukaryotic microbiology 1996;43(6):475-85.
1995: P J Keeling; Andrew J Roger
The selfish pursuit of sex.
Nature 1995;375(6529):283.
1994: Andrew J Roger; P J Keeling; W Ford Doolittle
Introns, the broken transposons.
Society of General Physiologists series 1994;49():27-37.