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Authors whose works are in public domain in at least one jurisdiction

List of works by Andrew J. Roger

A Eukaryote without a Mitochondrial Organelle.

scientific article

A Functional Tom70 in the Human Parasite Blastocystis sp.: Implications for the Evolution of the Mitochondrial Import Apparatus

scientific article published on 22 September 2010

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

scientific article published on 01 September 2008

A SUF Fe-S cluster biogenesis system in the mitochondrion-related organelles of the anaerobic protist Pygsuia

scientific article published on 22 May 2014

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

scientific article published in 2018

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

scientific article

A cyanobacterial gene in nonphotosynthetic protists--an early chloroplast acquisition in eukaryotes?

scientific article (publication date: 22 January 2002)

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

2007 thesis

A large number of nuclear genes in the human parasite blastocystis require mRNA polyadenylation to create functional termination codons

scientific article published on 10 July 2014

A natural toroidal microswimmer with a rotary eukaryotic flagellum

scientific article published on 10 June 2019

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

scientific article published on 11 August 2011

A phylogenomic investigation into the origin of metazoa.

scientific article

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

scientific article

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

scientific article published on 01 May 2018

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

scientific article

Aggregative multicellularity evolved independently in the eukaryotic supergroup Rhizaria

scientific article

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

scientific article published on 28 September 2012

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

scientific article published on 16 January 2014

An ancestral bacterial division system is widespread in eukaryotic mitochondria.

scientific article

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

scientific article published on 12 July 2007

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

scientific article published on 25 February 2019

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

scientific article published in December 2021

Ancient origin of the integrin-mediated adhesion and signaling machinery

scientific article

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

scientific article

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

scientific article

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

scientific article published on 15 May 2017

Biases in phylogenetic estimation can be caused by random sequence segments

scientific article published on 21 July 2005

Can commercial protection be good for research?

scientific article published on 12 September 2002

Capsaspora owczarzaki is an independent opisthokont lineage.

scientific article published in November 2004

Cell evolution: mitochondria in hiding

scientific article

Characterization of <i>Skoliomonas</i> gen. nov., a haloalkaliphilic anaerobe related to barthelonids (Metamonada)

scientific article published on 3 September 2024

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

scientific article

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

scientific article

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

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

scientific article published on January 2002

Corrigendum Correction to "Novel hydrogenosomes in the microaerophilic jakobid Stygiella incarcerata".

scientific article published on 2 February 2017

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

scientific article published on 19 March 2004

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

article

Diversity and origins of anaerobic metabolism in mitochondria and related organelles

scientific article

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

scientific article published in December 2004

Ellobiopsids of the genus Thalassomyces are alveolates

scientific article published in March 2004

Environmental Breviatea harbour mutualistic Arcobacter epibionts

scientific article

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

scientific article published on 12 September 2016

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

scientific article published in April 2004

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

scientific article published in October 2003

Eukaryotic Evolution: Getting to the Root of the Problem

scientific article published on 01 October 2002

Eukaryotic evolution: early origin of canonical introns.

scientific article published in September 2002

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

scientific article published on 3 February 2011

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

scientific article published in November 2003

Evidence for a hydrogenosomal-type anaerobic ATP generation pathway in Acanthamoeba castellanii

scientific article

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

scientific article

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

scientific article published on 21 March 2006

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

scientific article

Evolution of the cytosolic iron-sulfur cluster assembly machinery in Blastocystis species and other microbial eukaryotes

scientific article published on 15 November 2013

Evolution: revisiting the root of the eukaryote tree

scientific article (publication date: 24 February 2009)

Evolutionary analyses of the small subunit of glutamate synthase: gene order conservation, gene fusions, and prokaryote-to-eukaryote lateral gene transfers

scientific article

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

scientific article

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

scientific article published on 03 July 2009

Extreme genome diversity in the hyper-prevalent parasitic eukaryote Blastocystis.

scientific article published on 11 September 2017

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

scientific article published in 2024

Fast Statistical Tests for Detecting Heterotachy in Protein Evolution ⬇️

scientific article published on February 22, 2011

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

scientific article published on 27 January 2016

Fitting Nonstationary General-Time-Reversible Models to Obtain Edge-Lengths and Frequencies for the Barry–Hartigan Model ⬇️

scientific article published on April 16, 2012

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

scientific article published on July 30, 2013

Gene content evolution in Discobid mitochondria deduced from the phylogenetic position and complete mitochondrial genome of Tsukubamonas globosa.

scientific article published on February 2014

Gene conversion and the evolution of euryarchaeal chaperonins: a maximum likelihood-based method for detecting conflicting phylogenetic signals

scientific article published on 01 August 2002

Gene duplication and gene conversion shape the evolution of archaeal chaperonins

scientific article published in March 2002

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

article

Gene transfers from nanoarchaeota to an ancestor of diplomonads and parabasalids

scientific article published on 8 September 2004

Genetic evidence for a mitochondriate ancestry in the 'amitochondriate' flagellate Trimastix pyriformis

scientific article published in 2008

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

scientific article

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

scientific article published in Nature

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

scientific article

Insights into the evolutionary origin and genome architecture of the unicellular opisthokonts Capsaspora owczarzaki and Sphaeroforma arctica

scientific article

Invasion and persistence of a selfish gene in the Cnidaria

scientific article (publication date: 20 December 2006)

Lateral Gene Transfer Mechanisms and Pan-genomes in Eukaryotes

scientific article published on 19 August 2020

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

scientific article

Lateral Transfer of an EF-1α Gene

article

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

scientific article

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

scientific article (publication date: February 2012)

Leaving negative ancestors behind.

scientific article

Likelihood, parsimony, and heterogeneous evolution

scientific article published on 02 March 2005

Localization and nucleotide specificity of Blastocystis succinyl-CoA synthetase

scientific article published on 29 April 2008

Microbial Eukaryotes that Lack Sterols

scientific article

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

scientific article published on 26 April 2018

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

scientific article published in September 2016

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

scientific article

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

scientific article

Modelling prokaryote gene content

scientific article published on January 2006

Molecular clocks provide little information to date methanogenic Archaea

scientific article published on 01 November 2018

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

scientific article

Multigene Phylogenies of Diverse Carpediemonas-like Organisms Identify the Closest Relatives of ‘Amitochondriate’ Diplomonads and Retortamonads

scientific article published on 23 February 2012

Novel Hydrogenosomes in the Microaerophilic Jakobid Stygiella incarcerata

scientific article published on 08 June 2016

Novel mitochondrion-related organelles in the anaerobic amoeba Mastigamoeba balamuthi

scientific article

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

scientific article

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

scientific article published on 28 November 2018

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

scientific article

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

scientific article published on 21 May 2004

On reduced amino acid alphabets for phylogenetic inference

scientific article published on 25 July 2007

On the Use of Information Criteria for Model Selection in Phylogenetics

scientific article published on 01 February 2020

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

scientific article

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

scientific article

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

scientific article

Organelles in Blastocystis that blur the distinction between mitochondria and hydrogenosomes

scientific article

Organelles that illuminate the origins of Trichomonas hydrogenosomes and Giardia mitosomes

scientific article

Osmoadaptative Strategy and Its Molecular Signature in Obligately Halophilic Heterotrophic Protists

scientific article published on 12 July 2016

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

scientific article

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

scientific article

PhyloFisher: A phylogenomic package for resolving eukaryotic relationships ⬇️

scientific article published on 06 August 2021

Phylogenetic analyses of diplomonad genes reveal frequent lateral gene transfers affecting eukaryotes.

scientific article

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

scientific article published in August 2004

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

scientific article published on 5 October 2009

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

scientific article published on 02 May 2006

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

scientific article

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

scientific article

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

scientific article

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

scientific article published on 19 January 2018

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

scientific article

Phylogenomics demonstrates that breviate flagellates are related to opisthokonts and apusomonads

scientific article published in 2013

Phylogenomics places orphan protistan lineages in a novel eukaryotic super-group

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

scientific article

Problems With Estimation of Ancestral Frequencies Under Stationary Models ⬇️

scientific article published on September 4, 2012

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

scientific article published in January 2004

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

scholarly article

Reply to 'Eukaryote lateral gene transfer is Lamarckian'

scientific article published on 01 May 2018

Reproducing the manual annotation of multiple sequence alignments using a SVM classifier

scientific article published on 21 September 2009

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

scientific article

Sawyeria marylandensis (Heterolobosea) has a hydrogenosome with novel metabolic properties

scientific article published on 29 October 2010

Splintrons in Giardia intestinalis: Spliceosomal introns in a split form ⬇️

scientific article published on July 1, 2011

Split introns in the genome of Giardia intestinalis are excised by spliceosome-mediated trans-splicing.

scientific article published in February 2011

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

scientific article

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

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

scientific article published in 2011

Statistical analysis of expressed sequence tags

scientific article

Testing congruence in phylogenomic analysis

scientific article

Testing for covarion-like evolution in protein sequences

scientific article

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

scientific article published in September 2002

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

The Capsaspora genome reveals a complex unicellular prehistory of animals

scientific article

The Diversity of Mitochondrion-Related Organelles Amongst Eukaryotic Microbes

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

scientific article

The New Tree of Eukaryotes

scientific article published on 09 October 2019

The Origin and Diversification of Mitochondria

scientific article published in November 2017

The Origin of Mitochondrial Cristae from Alphaproteobacteria

scientific article

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

scientific article published on 01 October 2019

The Parameters of the Barry and Hartigan General Markov Model Are Statistically NonIdentifiable ⬇️

scientific article published on April 6, 2011

The Probability of Correctly Resolving a Split as an Experimental Design Criterion in Phylogenetics ⬇️

scientific article published on February 15, 2012

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

scientific article published on 01 November 2019

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

scientific article published on April 18, 2013

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

scientific article

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

scientific article published on 02 March 2020

The evolutionary history of kinetoplastids and their kinetoplasts

scientific article published on December 2002

The glycolytic pathway of Trimastix pyriformis is an evolutionary mosaic

scientific article

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

scientific article

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

scientific article (publication date: 29 June 2006)

The origins of multicellularity: a multi-taxon genome initiative

scientific article published in February 2007

The other eukaryotes in light of evolutionary protistology

article by Maureen A. O’Malley et al published 22 December 2012 in Biology and Philosophy

The real 'kingdoms' of eukaryotes

scientific article

The tangled past of eukaryotic enzymes involved in anaerobic metabolism

scientific article published on May 2011

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

Topological estimation biases with covarion evolution

scientific article published on 14 December 2007

Toward resolving the eukaryotic tree: the phylogenetic positions of jakobids and cercozoans.

scientific article

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

scientific article published on 27 August 2021

Using confidence set heuristics during topology search improves the robustness of phylogenetic inference

scientific article published on 9 December 2006

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

scientific article

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