A. Roger

发表

Testing for differences in rates-across-sites distributions in phylogenetic subtrees.

Y. Inagaki, C. Field, M. Holder, 2002, Molecular biology and evolution.

Rapid evolution in conformational space: A study of loop regions in a ubiquitous GTP binding domain

A. Roger, C. Blouin, D. Butt, 2004, Protein science : a publication of the Protein Society.

On the correlation between genomic G+C content and optimal growth temperature in prokaryotes: data quality and confounding factors.

E. Susko, A. Roger, Huai-chun Wang, 2006, Biochemical and biophysical research communications.

The Capsaspora genome reveals a complex unicellular prehistory of animals

Matthew W. Brown, B. Haas, Zehua Chen, 2013, Nature Communications.

An independent heterotachy model and its implications for phylogeny and divergence time estimation.

Edward Susko, Jihua Wu, E. Susko, 2008, Molecular phylogenetics and evolution.

Phylogenetic relationships within the Opisthokonta based on phylogenomic analyses of conserved single-copy protein domains.

B. Lang, A. Roger, I. Ruiz-Trillo, 2012, Molecular biology and evolution.

Environmental Breviatea harbor mutualistic Arcobacter epibionts

Harald R. Gruber-Vodicka, Matthew W. Brown, M. Strous, 2016, Nature.

Gene Content Evolution in Discobid Mitochondria Deduced from the Phylogenetic Position and Complete Mitochondrial Genome of Tsukubamonas globosa

Matthew W. Brown, Sohta A. Ishikawa, Y. Inagaki, 2014, Genome biology and evolution.

Modeling Site Heterogeneity with Posterior Mean Site Frequency Profiles Accelerates Accurate Phylogenomic Estimation

E. Susko, A. Roger, Huai-chun Wang, 2018, Systematic biology.

Hemimastigophora is a novel supra-kingdom-level lineage of eukaryotes

A. Simpson, A. Roger, E. Bertrand, 2018, Nature.

Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic “supergroups”

L. Hug, B. Lang, A. Simpson, 2009, Proceedings of the National Academy of Sciences.

Aggregative Multicellularity Evolved Independently in the Eukaryotic Supergroup Rhizaria

Matthew W. Brown, A. Roger, M. Kolisko, 2012, Current Biology.

Lateral Gene Transfer Mechanisms and Pan-genomes in Eukaryotes.

A. Roger, J. Archibald, Laura Eme, 2020, Trends in parasitology.

Supplemental Data Organelles in Blastocystis That Blur the Distinction between Mitochondria and Hydrogenosomes

A. Roger, V. Pérez-Brocal, C. Clark, 2022 .

Phylogenetic distributions and histories of proteins involved in anaerobic pyruvate metabolism in eukaryotes.

L. Hug, A. Roger, A. Stechmann, 2010, Molecular biology and evolution.

Evidence for a Hydrogenosomal-Type Anaerobic ATP Generation Pathway in Acanthamoeba castellanii

M. W. Gray, A. Roger, Ryan M R Gawryluk, 2013, PloS one.

Recombination between elongation factor 1alpha genes from distantly related archaeal lineages.

Y. Inagaki, E. Susko, A. Roger, 2006, Proceedings of the National Academy of Sciences of the United States of America.

How big is the iceberg of which organellar genes in nuclear genomes are but the tip?

W. Doolittle, J. Andersson, C. Douady, 2003, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

Gene duplication and gene conversion shape the evolution of archaeal chaperonins.

A. Roger, J. Archibald, 2002, Journal of molecular biology.

The interface of protein structure, protein biophysics, and molecular evolution

Lucy J. Colwell, Johan A. Grahnen, Nimrod D. Rubinstein, 2012, Protein science : a publication of the Protein Society.

Evolution: Revisiting the Root of the Eukaryote Tree

A. Simpson, A. Roger, 2009, Current Biology.

A phylogenomic investigation into the origin of metazoa.

B Franz Lang, Gertraud Burger, B. Lang, 2008, Molecular biology and evolution.

Functional Divergence and Convergent Evolution in the Plastid-Targeted Glyceraldehyde-3-Phosphate Dehydrogenases of Diverse Eukaryotic Algae

A. Roger, D. Gaston, 2013, PloS one.

A kingdom-level phylogeny of eukaryotes based on combined protein data.

W. Doolittle, A. Roger, S. Baldauf, 2000, Science.

An amino acid substitution-selection model adjusts residue fitness to improve phylogenetic estimation.

Edward Susko, E. Susko, A. Roger, 2014, Molecular biology and evolution.

The origins of multicellularity: a multi-taxon genome initiative.

B Franz Lang, Gertraud Burger, P. Holland, 2007, Trends in genetics : TIG.

Comprehensive multigene phylogenies of excavate protists reveal the evolutionary positions of "primitive" eukaryotes.

Yuji Inagaki, Y. Inagaki, A. Simpson, 2006, Molecular biology and evolution.

Insights into the Evolutionary Origin and Genome Architecture of the Unicellular Opisthokonts Capsaspora owczarzaki and Sphaeroforma arctica

A. Roger, I. Ruiz-Trillo, J. Archibald, 2006, The Journal of eukaryotic microbiology.

The tree of eukaryotes.

B Franz Lang, Gertraud Burger, B. Lang, 2005, Trends in ecology & evolution.

Capsaspora owczarzaki is an independent opisthokont lineage

Y. Inagaki, A. Roger, I. Ruiz-Trillo, 2004, Current Biology.

Eukaryotic Evolution: Getting to the Root of the Problem

A. Simpson, A. Roger, Andrew J Roger, 2002, Current Biology.

Eukaryotic evolution: Early origin of canonical introns

A. Simpson, A. Roger, Erin MacQuarrie, 2002, Nature.

Lateral gene transfer and gene duplication played a key role in the evolution of Mastigamoeba balamuthi hydrogenosomes.

J. Pačes, A. Roger, Courtney W. Stairs, 2015, Molecular biology and evolution.

Diversity and origins of anaerobic metabolism in mitochondria and related organelles

A. Roger, Courtney W. Stairs, Michelle M. Leger, 2015, Philosophical Transactions of the Royal Society B: Biological Sciences.

Sawyeria marylandensis (Heterolobosea) Has a Hydrogenosome with Novel Metabolic Properties

A. Roger, I. Ruiz-Trillo, J. D. Silberman, 2010, Eukaryotic Cell.

A genomic survey of the fish parasite Spironucleus salmonicida indicates genomic plasticity among diplomonads and significant lateral gene transfer in eukaryote genome evolution

Mark A Ragan, Robert P Hirt, David S Horner, 2007, BMC Genomics.

Molecular clocks provide little information to date methanogenic Archaea

E. Susko, A. Roger, 2018, Nature Ecology & Evolution.

Evolution of Fe/S cluster biogenesis in the anaerobic parasite Blastocystis

Anastasios D. Tsaousis, A. Roger, M. Fontecave, 2012, Proceedings of the National Academy of Sciences.

Predicting proteomes of mitochondria and related organelles from genomic and expressed sequence tag data.

Anastasios D. Tsaousis, A. Roger, A. Tsaousis, 2009, Methods in enzymology.

The probability of correctly resolving a split as an experimental design criterion in phylogenetics.

E. Susko, A. Roger, 2012, Systematic biology.

The draft nuclear genome sequence and predicted mitochondrial proteome of Andalucia godoyi, a protist with the most gene-rich and bacteria-like mitochondrial genome

B. Lang, M. W. Gray, A. Roger, 2020, BMC Biology.

Nuclear genome sequence of the plastid-lacking cryptomonad Goniomonas avonlea provides insights into the evolution of secondary plastids

B. Henrissat, A. Roger, E. Maréchal, 2018, BMC Biology.

An ancestral bacterial division system is widespread in eukaryotic mitochondria

B. Lang, A. Roger, M. Eliáš, 2015, Proceedings of the National Academy of Sciences.

Convergence and constraint in eukaryotic release factor 1 (eRF1) domain 1: the evolution of stop codon specificity.

Y. Inagaki, W. Doolittle, A. Roger, 2002, Nucleic acids research.

The Earliest Stages of Mitochondrial Adaptation to Low Oxygen Revealed in a Novel Rhizarian

Matthew W. Brown, A. Roger, Ryan M R Gawryluk, 2016, Current Biology.

U2 and U6 snRNA genes in the microsporidian Nosema locustae: evidence for a functional spliceosome

Andrew J. Roger, W. Ford Doolittle, Naomi M. Fast, 1998, Nucleic Acids Res..

Problems with estimation of ancestral frequencies under stationary models.

E. Susko, A. Roger, 2013, Systematic biology.

Using Confidence Set Heuristics During Topology Search Improves the Robustness of Phylogenetic Inference

S. Pepke, A. Roger, C. Blouin, 2006, Journal of Molecular Evolution.

Statistical analysis of expressed sequence tags.

E. Susko, A. Roger, 2009, Methods in molecular biology.

Comparative transcriptomics reveals the molecular toolkit used by an algivorous protist for cell wall perforation

A. Simpson, A. Roger, Tommy Harding, 2022, Current Biology.

Fitting nonstationary general-time-reversible models to obtain edge-lengths and frequencies for the barry-hartigan model.

C. Field, E. Susko, A. Roger, 2012, Systematic biology.

The development of intracytoplasmic membranes in alphaproteobacteria involves the conserved mitochondrial crista-developing Mic60 protein

A. Roger, C. Slamovits, J. Beatty, 2022, bioRxiv.

Microbial eukaryotes have adapted to hypoxia by horizontal acquisitions of a gene involved in rhodoquinone biosynthesis

A. Roger, J. P. Fawcett, G. Dellaire, 2018, eLife.

Clocks On the Age of Eukaryotes : Evaluating Evidence from Fossils and Subject Collection The Origin and Evolution of Eukaryotes from Fossils and Molecular Clocks On the Age of Eukaryotes : Evaluating Evidence

Matthew W. Brown, A. Roger, Laura Eme, 2014 .

On the age of eukaryotes: evaluating evidence from fossils and molecular clocks.

Matthew W. Brown, A. Roger, Laura Eme, 2014, Cold Spring Harbor perspectives in biology.

Cell evolution: Mitochondria in hiding

A. Roger, J. D. Silberman, 2002, Nature.

Phylogenomics demonstrates that breviate flagellates are related to opisthokonts and apusomonads

Matthew W. Brown, B. Lang, A. Simpson, 2013, Proceedings of the Royal Society B: Biological Sciences.

Novel mitochondrion‐related organelles in the anaerobic amoeba Mastigamoeba balamuthi

Erin E. Gill, A. Roger, I. Tamas, 2007, Molecular microbiology.

A phylogenomically informed five-order system for the closest relatives of land plants

C. Delwiche, A. Roger, T. Darienko, 2022, Current Biology.

Split-specific bootstrap measures for quantifying phylogenetic stability and the influence of taxon selection.

E. Susko, A. Roger, Huai-chun Wang, 2016, Molecular phylogenetics and evolution.

Demystifying Eukaryote Lateral Gene Transfer (Response to Martin 2017 DOI: 10.1002/bies.201700115)

A. Roger, Courtney W. Stairs, Laura Eme, 2018, BioEssays : news and reviews in molecular, cellular and developmental biology.

The selfish pursuit of sex

A. Roger, P. Keeling, 1995, Nature.

A chimeric origin for eukaryotes re-examined.

J. R. Brown, A. Roger, 1996, Trends in biochemical sciences.

An Evaluation of Elongation Factor 1 (cid:97) as a Phylogenetic Marker for Eukaryotes

W. Doolittle, H. Philippe, A. Roger, 2022 .

Assessing functional divergence in EF-1alpha and its paralogs in eukaryotes and archaebacteria.

Y. Inagaki, E. Susko, A. Roger, 2003, Nucleic acids research.

A Single Tim Translocase in the Mitosomes of Giardia intestinalis Illustrates Convergence of Protein Import Machines in Anaerobic Eukaryotes

A. Roger, M. Kolisko, R. Fišer, 2018, Genome biology and evolution.

Lateral transfer of tetrahymanol-synthesizing genes has allowed multiple diverse eukaryote lineages to independently adapt to environments without oxygen

A. Roger, K. Takishita, Eunsoo Kim, 2012, Biology Direct.

Characterization and Comparative Analyses of Mitochondrial Genomes in Single-Celled Eukaryotes to Shed Light on the Diversity and Evolution of Linear Molecular Architecture

A. Roger, Tengteng Zhang, Chundi Wang, 2021, International journal of molecular sciences.

PML and PML-like exonucleases restrict retrotransposons in jawed vertebrates

A. Roger, I. Braasch, G. Dellaire, 2022, bioRxiv.

New Insights into the Phylogeny of Trichomonads Inferred from Small Subunit rRNA Sequences.

M. Sogin, A. Simpson, A. Roger, 1998, Protist.

The other eukaryotes in light of evolutionary protistology

Maureen A. O’Malley, A. Simpson, A. Roger, 2012, Biology & Philosophy.

The parameters of the Barry and Hartigan general Markov model are statistically nonidentifiable.

C. Field, E. Susko, A. Roger, 2011, Systematic biology.

Stage‐specific requirement for Isa1 and Isa2 proteins in the mitochondrion of Trypanosoma brucei and heterologous rescue by human and Blastocystis orthologues

Anastasios D. Tsaousis, A. Roger, J. Lukeš, 2011, Molecular microbiology.

Novel Hydrogenosomes in the Microaerophilic Jakobid Stygiella incarcerata

L. Hug, A. Roger, Laura Eme, 2016, Molecular biology and evolution.

Accelerated Estimation of Frequency Classes in Site‐Heterogeneous Profile Mixture Models

E. Susko, A. Roger, Léa Lincker, 2018, Molecular biology and evolution.

Phylogenomic evidence for separate acquisition of plastids in cryptophytes, haptophytes, and stramenopiles.

B. Lang, H. Philippe, A. Roger, 2010, Molecular biology and evolution.

Evolution of four gene families with patchy phylogenetic distributions: influx of genes into protist genomes

J. Andersson, A. Roger, P. Foster, 2006, BMC Evolutionary Biology.

The evolutionary history of kinetoplastids and their kinetoplasts.

A. Simpson, A. Roger, J. Lukeš, 2002, Molecular biology and evolution.

Covarion shifts cause a long-branch attraction artifact that unites microsporidia and archaebacteria in EF-1alpha phylogenies.

Edward Susko, Yuji Inagaki, Y. Inagaki, 2004, Molecular biology and evolution.

An evaluation of elongation factor 1 alpha as a phylogenetic marker for eukaryotes.

H Philippe, W. Doolittle, H. Philippe, 1999, Molecular biology and evolution.

The Origin and Diversification of Mitochondria

A. Roger, Sergio A. Muñoz-Gómez, Ryoma Kamikawa, 2017, Current Biology.

Evolutionary history of "early-diverging" eukaryotes: the excavate taxon Carpediemonas is a close relative of Giardia.

Detlef D. Leipe, Lars S Jermiin, M. Sogin, 2002, Molecular biology and evolution.

Multiple Lateral Transfers of Dissimilatory Sulfite Reductase Genes between Major Lineages of Sulfate-Reducing Prokaryotes

Linda L. Blackall, Michael Wagner, Philip Hugenholtz, 2001, Journal of bacteriology.

Phylogeny of Dissimilatory Sulfite Reductases Supports an Early Origin of Sulfate Respiration

Michael Wagner, Andrew J. Roger, David A. Stahl, 1998, Journal of bacteriology.

Adaptations to High Salt in a Halophilic Protist: Differential Expression and Gene Acquisitions through Duplications and Gene Transfers

A. Simpson, A. Roger, Tommy Harding, 2017, Front. Microbiol..

Localization and nucleotide specificity of Blastocystis succinyl-CoA synthetase

Daron M Standley, D. Standley, A. Roger, 2008, Molecular microbiology.

A Eukaryote without a Mitochondrial Organelle

Andrew J. Roger, Miluše Hroudová, Laura Eme, 2016, Current Biology.

Eukaryotic pyruvate formate lyase and its activating enzyme were acquired laterally from a Firmicute.

A. Roger, V. Hampl, Courtney W. Stairs, 2011, Molecular biology and evolution.

Phylogenetic Analyses of Diplomonad Genes Reveal Frequent Lateral Gene Transfers Affecting Eukaryotes

J. Andersson, A. Roger, T. Embley, 2003, Current Biology.

Evolutionary Analyses of the Small Subunit of Glutamate Synthase: Gene Order Conservation, Gene Fusions, and Prokaryote-to- Eukaryote Lateral Gene Transfers

J. Andersson, A. Roger, 2002, Eukaryotic Cell.

Transfers Prokaryote-to-Eukaryote Lateral Gene Conservation , Gene Fusions , and of Glutamate Synthase : Gene Order Evolutionary Analyses of the Small Subunit

J. Andersson, A. Roger, 2002 .

Parallel re-modeling of EF-1α function: divergent EF-1α genes co-occur with EFL genes in diverse distantly related eukaryotes

Matthew W. Brown, Y. Inagaki, A. Simpson, 2013, BMC Evolutionary Biology.

On the Use of Information Criteria for Model Selection in Phylogenetics.

E. Susko, A. Roger, 2020, Molecular biology and evolution.

On reduced amino acid alphabets for phylogenetic inference.

Edward Susko, E. Susko, A. Roger, 2007, Molecular biology and evolution.

Topological Estimation Biases with Covarion Evolution

M. Spencer, E. Susko, A. Roger, 2007, Journal of Molecular Evolution.

Biases in Phylogenetic Estimation Can Be Caused by Random Sequence Segments

Andrew J. Roger, Edward Susko, E. Susko, 2005, Journal of Molecular Evolution.

Ancient origin of the integrin-mediated adhesion and signaling machinery

A. Roger, N. King, A. Sebé-Pedrós, 2010, Proceedings of the National Academy of Sciences.

Phylogenetic estimation under codon models can be biased by codon usage heterogeneity.

Y. Inagaki, A. Roger, 2006, Molecular phylogenetics and evolution.

A class frequency mixture model that adjusts for site-specific amino acid frequencies and improves inference of protein phylogeny

E. Susko, A. Roger, Huai-chun Wang, 2008, BMC Evolutionary Biology.

Lateral Gene Transfer in the Adaptation of the Anaerobic Parasite Blastocystis to the Gut

A. Roger, B. Curtis, J. Archibald, 2017, Current Biology.

Introns, the broken transposons.

W. Doolittle, A. Roger, P. Keeling, 1994, Society of General Physiologists series.

The impact of fossils and taxon sampling on ancient molecular dating analyses.

L. Hug, A. Roger, 2007, Molecular biology and evolution.

Modelling prokaryote gene content

Andrew J. Roger, Edward Susko, Matthew Spencer, 2006, Evolutionary bioinformatics online.

Genomic analysis finds no evidence of canonical eukaryotic DNA processing complexes in a free-living protist

A. Simpson, A. Roger, B. Curtis, 2021, Nature Communications.

Invasion and Persistence of a Selfish Gene in the Cnidaria

A. Roger, J. Leigh, M. Goddard, 2006, PloS one.

Evolution of Amino Acid Propensities under Stability-Mediated Epistasis

E. Susko, A. Roger, J. Bielawski, 2022, Molecular biology and evolution.

The ups and downs of amino acid co-evolution: evolutionary Stokes and anti-Stokes shifts

E. Susko, A. Roger, J. Bielawski, 2020, bioRxiv.

Sequence Analysis of the Mitochondrial Genome of Sarcophyton glaucum: Conserved Gene Order Among Octocorals

T. Cavalier-smith, A. Roger, M. Beaton, 1998, Journal of Molecular Evolution.

Genetic Evidence for a Mitochondriate Ancestry in the ‘Amitochondriate’ Flagellate Trimastix pyriformis

A. Roger, V. Hampl, Patricia J. Johnson, 2008, PloS one.

The Site-Wise Log-Likelihood Score is a Good Predictor of Genes under Positive Selection

E. Susko, A. Roger, Huai-chun Wang, 2013, Journal of Molecular Evolution.

libcov: A C++ bioinformatic library to manipulate protein structures, sequence alignments and phylogeny

Christian Blouin, Andrew J. Roger, Davin Butt, 2005, BMC Bioinformatics.

Estimation of rates-across-sites distributions in phylogenetic substitution models.

Chris Field, Christian Blouin, Edward Susko, 2003, Systematic biology.

Extreme genome diversity in the hyper-prevalent parasitic eukaryote Blastocystis

Anastasios D. Tsaousis, B. Henrissat, A. Roger, 2017, PLoS biology.

Mitochondrial Genome Evolution and a Novel RNA Editing System in Deep-Branching Heteroloboseids

A. Simpson, A. Roger, Tommy Harding, 2017, Genome biology and evolution.

Estimating and comparing the rates of gene discovery and expressed sequence tag (EST) frequencies in EST surveys

Andrew J. Roger, Edward Susko, E. Susko, 2004, Bioinform..

PROCOV: maximum likelihood estimation of protein phylogeny under covarion models and site-specific covarion pattern analysis

Edward Susko, E. Susko, A. Roger, 2009, BMC Evolutionary Biology.

Testing for covarion-like evolution in protein sequences.

Edward Susko, Matthew Spencer, M. Spencer, 2007, Molecular biology and evolution.

The Diversity of Mitochondrion-Related Organelles Amongst Eukaryotic Microbes

L. Hug, A. Roger, J. Leigh, 2007 .

Phylogenomics Reveals Convergent Evolution of Lifestyles in Close Relatives of Animals and Fungi

A. Roger, I. Ruiz-Trillo, G. Torruella, 2015, Current Biology.

First multigene analysis of Archamoebae (Amoebozoa: Conosa) robustly reveals its phylogeny and shows that Entamoebidae represents a deep lineage of the group.

Matthew W. Brown, A. Roger, I. Čepička, 2016, Molecular phylogenetics and evolution.

Multigene phylogenies of diverse Carpediemonas-like organisms identify the closest relatives of 'amitochondriate' diplomonads and retortamonads.

Y. Inagaki, A. Simpson, A. Roger, 2012, Protist.

A mitochondrial-like chaperonin 60 gene in Giardia lamblia: evidence that diplomonads once harbored an endosymbiont related to the progenitor of mitochondria.

M. Sogin, F. Gillin, A. Roger, 1998, Proceedings of the National Academy of Sciences of the United States of America.

Direct evidence for secondary loss of mitochondria in Entamoeba histolytica.

A. Roger, C. Clark, A J Roger, 1995, Proceedings of the National Academy of Sciences of the United States of America.

Between a Pod and a Hard Test: The Deep Evolution of Amoebae

Matthew W. Brown, A. Roger, A. Smirnov, 2017, Molecular biology and evolution.

Primary Structure and Phylogenetic Relationships of Glyceraldehyde‐3‐Phosphate Dehydrogenase Genes of Free‐Living and Parasitic Diplomonad Flagellates

A. Roger, M. Müller, L. Morin, 1996, The Journal of eukaryotic microbiology.

Unexpected organellar locations of ESCRT machinery in Giardia intestinalis and complex evolutionary dynamics spanning the transition to parasitism in the lineage Fornicata

A. Hehl, A. Roger, J. Dacks, 2021, BMC Biology.

The Oxymonad Genome Displays Canonical Eukaryotic Complexity in the Absence of a Mitochondrion

A. Roger, M. Eliáš, V. Hampl, 2019, Molecular biology and evolution.

Shifts in amino acid preferences as proteins evolve: A synthesis of experimental and theoretical work

E. Susko, A. Roger, J. Bielawski, 2021, Protein science : a publication of the Protein Society.

The Relative Importance of Modeling Site Pattern Heterogeneity Versus Partition-Wise Heterotachy in Phylogenomic Inference.

E. Susko, A. Roger, Huai-chun Wang, 2019, Systematic biology.

The other eukaryotes in light of evolutionary protistology

Maureen A. O’Malley, A. Simpson, A. Roger, 2013 .

The New Tree of Eukaryotes.

Matthew W. Brown, A. Simpson, A. Roger, 2019, Trends in ecology & evolution.

Fast statistical tests for detecting heterotachy in protein evolution.

E. Susko, A. Roger, Huai-chun Wang, 2011, Molecular biology and evolution.

Likelihood, parsimony, and heterogeneous evolution.

Edward Susko, Matthew Spencer, M. Spencer, 2005, Molecular biology and evolution.

Comparative transcriptomics reveals the molecular toolkit used by an algivorous protist for cell wall perforation

A. Simpson, A. Roger, Tommy Harding, 2021, Current Biology.

Inferring functional constraints and divergence in protein families using 3D mapping of phylogenetic information.

Yan Boucher, Christian Blouin, Y. Boucher, 2003, Nucleic acids research.

A phylogenetic mixture model for the identification of functionally divergent protein residues

Andrew J. Roger, Edward Susko, Daniel Gaston, 2011, Bioinform..

Impact of taxon sampling on the estimation of rates of evolution at sites.

A. Roger, C. Blouin, D. Butt, 2005, Molecular biology and evolution.

Primary Structure and Phylogenetic Relationships of a Malate Dehydrogenase Gene from Giardia lamblia

M. Sogin, H. Morrison, A. Roger, 1999, Journal of Molecular Evolution.

Site-and-branch-heterogeneous analyses of an expanded dataset favour mitochondria as sister to known Alphaproteobacteria

E. Susko, A. Roger, C. Slamovits, 2022, Nature Ecology & Evolution.

A free-living protist that lacks canonical eukaryotic DNA replication and segregation systems

A. Simpson, A. Roger, B. Curtis, 2021, bioRxiv.

Toward Resolving the Eukaryotic Tree: The Phylogenetic Positions of Jakobids and Cercozoans

B. Lang, H. Philippe, A. Roger, 2007, Current Biology.

PhyloFisher: A phylogenomic package for resolving eukaryotic relationships

Matthew W. Brown, A. Rokas, A. Roger, 2021, PLoS biology.

On the reversibility of parasitism: adaptation to a free-living lifestyle via gene acquisitions in the diplomonad Trepomonas sp. PC1

J. Andersson, A. Simpson, A. Roger, 2016, BMC Biology.

An updated phylogeny of the Alphaproteobacteria reveals that the parasitic Rickettsiales and Holosporales have independent origins

B. Lang, E. Susko, A. Roger, 2019, eLife.

A functional Tom70 in the human parasite Blastocystis sp.: implications for the evolution of the mitochondrial import apparatus.

Anastasios D. Tsaousis, T. Lithgow, A. Roger, 2011, Molecular biology and evolution.

Giardia lamblia expresses a proteobacterial-like DnaK homolog.

M. Sogin, H. Morrison, F. Gillin, 2001, Molecular biology and evolution.

Why introns-in-pieces?

W. Doolittle, A. Roger, 1993, Nature.

Timing the Origins of Multicellular Eukaryotes Through Phylogenomics and Relaxed Molecular Clock Analyses

Matthew W. Brown, A. Roger, Laura Eme, 2015 .

The glycolytic pathway of Trimastix pyriformis is an evolutionary mosaic

A. Roger, M. Baumgartner, J. D. Silberman, 2006, BMC Evolutionary Biology.

Arginine deiminase pathway enzymes: evolutionary history in metamonads and other eukaryotes

A. Simpson, A. Roger, P. Keeling, 2016, BMC Evolutionary Biology.

Anaeramoebae are a divergent lineage of eukaryotes that shed light on the transition from anaerobic mitochondria to hydrogenosomes

A. Roger, I. Čepička, M. Kolisko, 2021, Current Biology.

Osmoadaptative Strategy and Its Molecular Signature in Obligately Halophilic Heterotrophic Protists

Matthew W. Brown, A. Simpson, A. Roger, 2016, Genome biology and evolution.

The real ‘kingdoms’ of eukaryotes

A. Simpson, A. Roger, 2004, Current Biology.

Is Over-parameterization a Problem for Profile Mixture Models?

E. Susko, A. Roger, H. Baños, 2022, bioRxiv.

The Origin of Mitochondrial Cristae from Alphaproteobacteria

Jeremy G. Wideman, A. Roger, C. Slamovits, 2017, Molecular biology and evolution.

A Large Number of Nuclear Genes in the Human Parasite Blastocystis Require mRNA Polyadenylation to Create Functional Termination Codons

A. Roger, M. Eliáš, V. Klimeš, 2014, Genome biology and evolution.

The changing view of eukaryogenesis – fossils, cells, lineages and how they all come together

Mark C. Field, D. Devos, A. Roger, 2016, Journal of Cell Science.

Lateral Transfer of an EF-1α Gene Origin and Evolution of the Large Subunit of ATP Sulfurylase in Eubacteria

Y. Inagaki, W. Doolittle, A. Roger, 2002, Current Biology.

Evolution of glutamate dehydrogenase genes: evidence for lateral gene transfer within and between prokaryotes and eukaryotes

J. Andersson, A. Roger, 2003, BMC Evolutionary Biology.

Reconstructing Early Events in Eukaryotic Evolution

Andrew J. Roger, A. Roger, 1999, The American Naturalist.

A possible mitochondrial gene in the early-branching amitochondriate protist Trichomonas vaginalis.

W. Doolittle, A. Roger, C. Clark, 1996, Proceedings of the National Academy of Sciences of the United States of America.

The origin and diversification of eukaryotes: problems with molecular phylogenetics and molecular clock estimation

L. Hug, A. Roger, 2006, Philosophical Transactions of the Royal Society B: Biological Sciences.

Evidence for the Heterolobosea from Phylogenetic Analysis of Genes Encoding Glyceraldehyde‐3‐Phosphate Dehydrogenase

Michael W. Smith, R. Doolittle, W. Doolittle, 1996, The Journal of eukaryotic microbiology.

Amoeba stages in the deepest branching heteroloboseans, including Pharyngomonas: evolutionary and systematic implications.

Matthew W. Brown, A. Simpson, A. Roger, 2013, Protist.

Phylogenomics Places Orphan Protistan Lineages in a Novel Eukaryotic Super-Group

Matthew W. Brown, Y. Inagaki, A. Simpson, 2017, bioRxiv.

The Mastigamoeba balamuthi Genome and the Nature of the Free-Living Ancestor of Entamoeba

V. Beneš, N. Hall, J. Pačes, 2021, Molecular biology and evolution.

The First Sexual Lineage and the Relevance of Facultative Sex

A. Roger, J. Dacks, 1999, Journal of Molecular Evolution.

Testing congruence in phylogenomic analysis.

Edward Susko, E. Susko, A. Roger, 2008, Systematic biology.

Gene Conversion and the Evolution of Euryarchaeal Chaperonins: A Maximum Likelihood-Based Method for Detecting Conflicting Phylogenetic Signals

Andrew J. Roger, A. Roger, J. Archibald, 2002, Journal of Molecular Evolution.

A unique symbiosome in an anaerobic single-celled eukaryote

A. Roger, B. Curtis, J. Archibald, 2023, bioRxiv.

A SUF Fe-S Cluster Biogenesis System in the Mitochondrion-Related Organelles of the Anaerobic Protist Pygsuia

Matthew W. Brown, E. Susko, A. Roger, 2014, Current Biology.

Early evolution within kinetoplastids (euglenozoa), and the late emergence of trypanosomatids.

Erin E. Gill, A. Simpson, A. Roger, 2004, Protist.

On inconsistency of the neighbor-joining, least squares, and minimum evolution estimation when substitution processes are incorrectly modeled.

Edward Susko, Yuji Inagaki, Y. Inagaki, 2004, Molecular biology and evolution.

The Biochemical Adaptations of Mitochondrion-Related Organelles of Parasitic and Free-Living Microbial Eukaryotes to Low Oxygen Environments

A. Roger, Courtney W. Stairs, A. Tsaousis, 2012 .

Ellobiopsids of the Genus Thalassomyces are Alveolates

A. Collins, A. Roger, Patricia J. Johnson, 2004, The Journal of eukaryotic microbiology.

Nuclear genetic codes with a different meaning of the UAG and the UAA codon

E. Susko, A. Roger, M. Eliáš, 2017, BMC Biology.

On the reversibility of parasitism: adaptation to a free-living lifestyle via gene acquisitions in the diplomonad Trepomonas sp. PC1

J. Andersson, A. Simpson, A. Roger, 2016, BMC Biology.

lnferring the Deep Phylogeny of Eukaryotes with Multiple Gene Data Sets : Panacean or Panglossian ?

A. Roger, 2016 .

Nucleomorph and plastid genome sequences of the chlorarachniophyte Lotharella oceanica: convergent reductive evolution and frequent recombination in nucleomorph-bearing algae

Matthew W. Brown, M. Melkonian, A. Roger, 2014, BMC Genomics.

A wide diversity of previously undetected free-living relatives of diplomonads isolated from marine/saline habitats.

Y. Inagaki, A. Simpson, A. Roger, 2010, Environmental microbiology.

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

A. Simpson, A. Roger, J. Flegr, 2008, BMC Evolutionary Biology.

Gene transfers from nanoarchaeota to an ancestor of diplomonads and parabasalids.

J. Andersson, A. Roger, Stewart W. Sarchfield, 2004, Molecular biology and evolution.

Submitted to Molecular Biology and Evolution as a Research Article

J. Andersson, A. Roger, Stewart W. Sarchfield, 2004 .

Evidence for Golgi bodies in proposed 'Golgi-lacking' lineages

W. Doolittle, J. Andersson, A. Roger, 2003, Proceedings of the Royal Society of London. Series B: Biological Sciences.

Retortamonad flagellates are closely related to diplomonads--implications for the history of mitochondrial function in eukaryote evolution.

A. Simpson, A. Roger, I. Čepička, 2002, Molecular biology and evolution.

A Cyanobacterial Gene in Nonphotosynthetic Protists—An Early Chloroplast Acquisition in Eukaryotes?

Andrew J. Roger, J. Andersson, A. Roger, 2002, Current Biology.

Evolutionary relationships among "jakobid" flagellates as indicated by alpha- and beta-tubulin phylogenies.

M. Sogin, A. Simpson, A. Roger, 2001, Molecular biology and evolution.

Phylogenetic artifacts can be caused by leucine, serine, and arginine codon usage heterogeneity: dinoflagellate plastid origins as a case study.

Y. Inagaki, A. Simpson, A. Roger, 2004, Systematic biology.

A New Divergent Type of Eukaryotic Methionine Adenosyltransferase is Present in Multiple Distantly Related Secondary Algal Lineages

A. Simpson, A. Roger, Gabino Sanchez-Perez, 2008, The Journal of eukaryotic microbiology.

Protein phylogenies robustly resolve the deep-level relationships within Euglenozoa.

A. Simpson, A. Roger, 2004, Molecular phylogenetics and evolution.

Studies on the phylogeny and gene structure of early-branching eukaryotes.

A. Roger, 1997 .

Organelles that illuminate the origins of Trichomonas hydrogenosomes and Giardia mitosomes

Y. Inagaki, J. Andersson, A. Simpson, 2017, Nature Ecology &Evolution.

Hemimastigophora is a novel supra-kingdom-level lineage of eukaryotes

A. Simpson, A. Roger, E. Bertrand, 2018, Nature.

Large-scale phylogenomic analysis reveals the phylogenetic position of the problematic taxon Protocruzia and unravels the deep phylogenetic affinities of the ciliate lineages.

F. Dini, A. Roger, D. Lynn, 2014, Molecular phylogenetics and evolution.

Long Branch Attraction Biases in Phylogenetics.

E. Susko, A. Roger, 2021, Systematic biology.

Extreme mitochondrial reduction in a novel group of free-living metamonads

A. Simpson, A. Roger, B. Curtis, 2023, bioRxiv.

Draft genomes of Blastocystis subtypes from human samples of Colombia

A. Roger, B. Curtis, M. Muñoz, 2023, Parasites & Vectors.

Group II Intron-Mediated Trans-Splicing in the Gene-Rich Mitochondrial Genome of an Enigmatic Eukaryote, Diphylleia rotans

A. Roger, H. Miyashita, K. Ishida, 2016, Genome biology and evolution.

The Site-Wise Log-Likelihood Score is a Good Predictor of Genes under Positive Selection

E. Susko, A. Roger, Huai-chun Wang, 2013, Journal of Molecular Evolution.

The development of intracytoplasmic membranes in alphaproteobacteria involves the conserved mitochondrial crista-developing protein Mic60

A. Roger, C. Slamovits, J. Beatty, 2022, bioRxiv.

Microbial Eukaryotes that Lack Sterols

A. Roger, K. Takishita, T. Hashimoto, 2017, The Journal of eukaryotic microbiology.

Lateral transfer of tetrahymanol-synthesizing genes has allowed multiple diverse eukaryote lineages to independently adapt to environments without oxygen

A. Roger, K. Takishita, Eunsoo Kim, 2012, Biology Direct.

A natural toroidal microswimmer with a rotary eukaryotic flagellum

A. Simpson, A. Roger, Laura Eme, 2019, Nature Microbiology.

Evolution of the Cytosolic Iron-Sulfur Cluster Assembly Machinery in Blastocystis Species and Other Microbial Eukaryotes

Anastasios D. Tsaousis, A. Roger, E. Gentekaki, 2013, Eukaryotic Cell.

Eukaryotes Blastocystis Species and Other Microbial Cluster Assembly Machinery in Evolution of the Cytosolic Iron-Sulfur

A. Roger, E. Gentekaki, Laura Eme, 2013 .

Reply to 'Eukaryote lateral gene transfer is Lamarckian'

A. Roger, 2018, Nature Ecology & Evolution.

Leaving negative ancestors behind

A. Roger, Sergio A. Muñoz-Gómez, 2016, eLife.

Nucleomorph and plastid genome sequences of the chlorarachniophyte Lotharella oceanica: convergent reductive evolution and frequent recombination in nucleomorph-bearing algae

Matthew W. Brown, M. Melkonian, A. Roger, 2014, BMC Genomics.

Several independent adaptations of archaea to hypersaline environments

J. Huerta-Cepas, E. Susko, A. Roger, 2023, bioRxiv.

Gene fusion, fission, lateral transfer, and loss: Not-so-rare events in the evolution of eukaryotic ATP citrate lyase.

A. Roger, Laura Eme, Ryan M. R. Gawryluk, 2015, Molecular phylogenetics and evolution.

Intracytoplasmic-membrane development in alphaproteobacteria involves the homolog of the mitochondrial crista-developing protein Mic60

A. Roger, C. Slamovits, J. Beatty, 2023, Current Biology.

A site-and-branch-heterogeneous model on an expanded dataset favor mitochondria as sister to known Alphaproteobacteria

E. Susko, A. Roger, C. Slamovits, 2021 .

Combined morphological and phylogenomic re-examination of malawimonads, a critical taxon for inferring the evolutionary history of eukaryotes

Matthew W. Brown, A. Simpson, A. Roger, 2018, Royal Society Open Science.

Evolution of the Cytosolic Iron / Sulfur cluster Assembly machinery in Blastocystis 1 sp . and other microbial eukaryotes 2

A. Roger, E. Gentekaki, Laura Eme, 2013 .

Expanded phylogenies of canonical and non-canonical types of methionine adenosyltransferase reveal a complex history of these gene families in eukaryotes.

Y. Inagaki, A. Roger, Gabino Sanchez-Perez, 2009, Molecular phylogenetics and evolution.

Meteora sporadica, a protist with incredible cell architecture, is related to Hemimastigophora

A. Simpson, A. Roger, Y. Eglit, 2023, Current Biology.

Conditions under which distributions of edge length ratios on phylogenetic trees can be used to order evolutionary events.

M. Steel, E. Susko, A. Roger, 2021, Journal of theoretical biology.

Evolution: Reconstructing the Timeline of Eukaryogenesis

E. Susko, A. Roger, Michelle M. Leger, 2021, Current Biology.

The tangled past of eukaryotic enzymes involved in anaerobic metabolism

A. Roger, V. Hampl, Courtney W. Stairs, 2011, Mobile genetic elements.

Minimal cytosolic iron‐sulfur cluster assembly machinery of Giardia intestinalis is partially associated with mitosomes

A. Roger, J. Lukeš, M. Kolisko, 2016, Molecular microbiology.