Select List of Publications (last 5 years only). See full list of publications (2008-2017) here.

2017 (Jan.- present)

Archibald, J.M., Simpson, A.G.B. and Slamovits, C. 2017. Editors of Handbook of the Protists (2nd Edition of the Handbook of Protoctista by Margulis et al.), Springer.

Chan, C.X., Beiko, R.G. and Ragan, M.A. 2017. Scaling up the phylogenetic detection of lateral gene transfer events. Methods Mol. Biol. 1525: 421-432.

Comeau, A.M., Douglas, G.M. and Langille, M.G. 2017. Microbiome Helper: a custom and streamlined workflow for microbiome research. mSystems 2: e00127-16.

de Vries, J. and Archibald, J.M. 2017. Endosymbiosis: Did plastids evolve from a freshwater cyanobacterium? Curr. Biol. 27: R103-R105.

de Vries, J., de Vries, S., Slamovits, C.H., Rose, L.E. and Archibald, J.M. 2017. How embryophytic is the biosynthesis of phenylpropanoids and their derivatives in streptophyte algae? Plant Cell Physiol., online 13 Mar.

Doolittle, W.F. 2017. Darwinizing Gaia. J. Theoret. Biol., online 22 Feb.

Doolittle, W.F. 2017. Making the most of clade selection. Phil. Sci. 84: 275-295.

Eme, L., Gentekaki, E., Curtis, B., Archibald, J.M. and Roger, A.J. 2017. Lateral gene transfer in the adaptation of the anaerobic parasite Blastocystis to the gut. Curr. Biol. 27: 807-820.

Jones, C.T., Youssef, N., Susko, E. and Bielawski, J.P. 2017. Shifting balance on a static mutation-selection landscape: a novel scenario of positive selection. Mol. Biol. Evol. 34: 391-407.

Leger, M.M. et al. (17 authors, incl. Roger, A.J.) 2017. Organelles that illuminate the origins of Trichomonas hydrogenosomes and Giardia mitosomes. Nature Ecol. Evol. 1: 0092.

Munoz-Gomez, S.A., Wideman, J.G., Roger, A.J. and Slamovits, C.H. 2017. The origin of mitochondrial cristae from alphaproteobacteria. Mol. Biol. Evol. 34: 943-956.

Panek, T., Zihala, D., Sokol, M., Derelle, R., Klimes, V., Hradilova, M., Zadrobilkova, E., Susko, E., Roger, A.J., Cepicka, I. and Elias, M. 2017. Nuclear genetic codes with a different meaning of the UAG and the UAA codon. BMC Biol. 15: 8.

Robicheau, B.M., Susko, E., Harrigan, A.M. and Snyder, M. 2017. Ribosomal RNA genes contribute to the formation of pseudogenes and junk DNA in the human genome. Genome Biol. Evol., online 15 Feb.

Sibbald, S.J. and Archibald, J.M. 2017. More protist genomes needed. Nature Ecol. Evol., in press.

Zhan, L., Paterson, I.G., Fraser, B.A., Watson, B., Bradbury, I.R., Nadukkalam Ravindran, P., Reznick, D., Beiko, R.G. and Bentzen, P. 2017. Megasat: automated inference of microsatellite genotypes from sequence data. Mol. Evol. Resourc. 17: 247-256.


Baker, J.L., Dunn, K., Mingrone, J., Wood, B.A., Karpinski, B.A., Sherwood, C.C., Wildman, D.E., Maynard, T.M. and Bielawski, J.P. 2016. Functional divergence of the nuclear receptor NR2C1 as a modulator of pluripotentiality during hominid evolution. Genetics 203: 905-922.

Bielawski, J.P., Baker, J.L. and Mingrone, J. 2016. Inference of episodic changes in natural selection acting on protein coding sequences via CODEML. Curr. Protoc. Bioinformatics 54: 6.

Booth, A., Mariscal, C. and Doolittle, W.F. 2016. The modern synthesis in the light of microbial genomics. Ann. Rev. Microbiol. 70: 279-297.

Cenci, U., Moog, D., Curtis, B.A., Tanifuji, G., Eme, L., Lukes, J. and Archibald, J.M. 2016. Heme pathway evolution in kinetoplastid protists. BMC Evol. Biol. 16: 109.

de Vries, J., Stanton, A., Archibald, J.M. and Gould, S.B. 2016. Streptophyte terrestrialization in light of plastid evolution. Trends Plant Sci. 21: 467-476.

Doolittle, W.F. and Brunet, T.D. 2016. What is the Tree of Life? PLoS Genet. 12: e1005912.

Eme, L. and Doolittle, W.F. 2016. Microbial evolution: xenology (apparently) trumps paralogy. Curr. Biol. 22: R1181-1183.

Castro, S.I., Hleap, J.S., Cardenas, H. and Blouin, C. 2016. Molecular organization of the 5S rDNA gene type II in elasmobranchs. RNA Biol. 13: 391-399.

Hleap, J.S. and Blouin, C. 2016. The semantics of the modular architecture of protein structures. Curr. Prot. Peptide Sci. 17: 62-71.

Kamikawa, R., Shiratori, T., Ishida, K., Miyashita, H. and Roger, A.J. 2016. Group II intron-mediated trans-splicing in the gene-rich mitochondrial genome of an enigmatic eukaryote, Diphylleia rotans. Genome Biol. Evol. 8: 458-466.

Karnkowska, A. (plus 18 co-authors incl. A.J. Roger). 2016. A eukaryote without a mitochondrial organelle. Curr. Biol. 26: 1274-1284.

Mingrone, J., Susko, E. and Bielawski, J. 2016. Smoothed bootstrap aggregtion for assessing selection pressure at amino acid sites. Mol. Biol. Evol. 33: 2976-2989.

Moore-Connors, J.M., Dunn, K.A., Bielawski, J.P. and Van Limbergen, J. 2016. Novel strategies for applied metagenomics. Inflamm. Bowel Dis. 22: 709-718.

Park, J.S. and Simpson, A.G. 2016. Characterization of a deep-branching heterolobosean isolated from a non-hypersaline habitat, and ultrastructural comparison of cysts and amoebae among pharyngomonas strains. J. Eukaryot. Microbiol. 63: 100-111.

Sierra, R. (with 12 co-authors incl. Slamovits, C.H.) 2016. Evolutionary origins of rhizarian parasites. Mol. Biol. Evol. 33: 980-983.

Tanifuji, G., Archibald, J.M. and Hashimoto, T. 2016. Comparative genomics of mitochondria in chlorarachniophyte algae: endosymbiotic gene transfer and organellar genome dynamics. Sci. Rep. 6: 21016.

Wang, H., Susko, E. and Roger, A.J. 2016. Split-specific bootstrap measures for quantifying phylogenetic stability and the influence of taxon selection. Mol. Phyloget. Evol. 105: 114-125.

Zhang, Q., Taborsky, P., Silberman, J.D., Panek, T., Cepicka, I. and Simpson, A.G. 2016. Marine isolates of Trimastix marina form a Plesiomorphic deep-branching lineage within Preaxostyla, separate from other known Trimastigids. Protist 166: 468-491.


Archibald, J.M. 2015. Endosymbiosis and eukaryotic cell evolution. Curr. Biol. 25: R911-21.

Bertrand, E.M. (& 12 co-authors). 2015. Phytoplankton-bacterial interactions mediate micronutrient colimitation at the coastal Antarctic sea ice edge. PNAS 112: 9938-9943.

Booth, A. and Doolittle, W.F. 2015. Eukaryogenesis, how special really? PNAS 112: 10278-10285.

David, V., Flegontov, P., Gerasimov, E., Tanifuji, G., Hashimi, H., Logacheva, M.D., Maruyama, S., Onodera, N.T., Gray, M.W., Archibald, J.M. and Lukes, J. 2015. Gene loss and error-prone RNA editing in the mitochondrion of Perkinsela, an endosymbiont kinetoplastid. MBio 6: pii: e01498-15.

Eme, L. and Doolittle, W.F. 2015. Microbial diversity: a bonanza of phyla. Curr. Biol. 25: R227-230.

Garvin, M.R., Bielawski, J.P., Sazanov, L.A. and Gharrett, A.J. 2015. Review and meta-analysis of natural selection in mitochondrial complex I in metazoans. J. Zool. Syst. Evol. Res. 53: 1-17.

Gawryluk, R., Eme, L. and Roger, A.J. 2015. Gene fusion, fission, lateral transfer, and loss: not-so-rare events in the evolution of eukaryotic ATP citrate lyase. Mol. Phylogenet. Evol. 91: 12-16.

Gile, G.H., Moog, D., Slamovits, C.H., Maier, U.G. and Archibald, J.M. 2015. Dual organellar targeting of aminoacyl-tRNA synthetases in Diatoms and Cryptophytes. Genome Biol. 7: 1728-1742.

Gray, M.W. 2015. Mosaic nature of the mitochondrial proteome: implications for the origin and evolution of mitochondria. PNAS 112: 10133-38.

Kirby, W.A., Tikhonenkov, D.V., Mylnikov, A.P., Janouskovec, J., Lax, G. and Simpson, A.G.B. 2015. Characterization of T. bucina n. sp., an extremely halotolerant amoeboflagellate heterolobosean belonging to the Tulamoeba-Pleurostomum clade. J. Euk. Microbiol. 62: 227-238.

Laird, M.R., Langille, M.G.I. and Brinkman, F.S.L. 2015. GenomeD3Plot: A library for rich, interactive visualizations of genomic data in web applications. Bioinformatics 31: 3348-3349.

Leger, M.M., Petru, M., Zarsky,V., Eme, L., Vlcek, C., Harding, T., Lang, B.F., Elias, M., Dolezal, P. and Roger, A.J. 2015. An ancestral bacterial division system is widespread in eukaryotic mitochondria. PNAS 112: 10239-10246.

Meehan, C.J., Langille, M.G. and Beiko, R.G. 2015. Frailty and the microbiome. Interdiscip. Top Gerontol. Geriatr. 41: 54-65.

Munoz-Gomez, S.A., Slamovits, C.H., Dacks, J.B., Baier, K.A., Spencer, K.D., Wideman, J.G. 2015. Ancient homology of the mitochondrial contact site and cristae organizing system points to an endosymbiont origin of mitochondrial cristae. Curr. Biol. 25: 1489-1495.

Park, J.S. and Simpson, A.G. 2015. Diversity of heterotrophic protists from extremely hypersaline habitats. Protist 166: 422-37.

Safatli, A. and Blouin, C. 2015. Pylogeny: an open-source Python framework for phylogenetic tree reconstruction and search space heuristics. PeerJ Comput. Sci. 1: e9.

Shafiei, M., Dunn, K.A., Boon, E., MacDonald, S.M., Walsh, D.A., Gu, H. and Bielawski, J.P. 2015. BioMiCo: a supervised Bayesian model for inference of microbial community structure. Microbiome 3: 8.

Susko, E. 2015. Bayesian long branch attraction bias and corrections. Syst. Biol. 64: 243-255.

Whidden, C., Beiko, R.G. and Zeh, N. 2015. Fixed-parameter and approximation algorithms for maximum agreement forests of multifurcating trees. Algorithmica, 1-36.

Wong, D.H.J. and Beiko, R.G. 2015. Transfer of energy pathway genes in microbial enhanced biological phosphorus removal communities. BMC Genomics 16: 526.


Boon, E., Meehan, C.J., Whidden, C., Wong, D.H., Langille, M.G. and Beiko, R.G. 2014. Interactions in the microbiome: communities of organisms and communities of genes. FEMS Microbiol. Rev. 38: 90-118.

Brunet, T.D. and Doolittle, W.F. 2014. Getting "function" right. PNAS 111: E3365.

Doolittle, W.F. 2014. The trouble with (group II) introns. PNAS 111: 6536-6537.

Doolittle, W.F., Brunet, T.D., Linquist, S. and Gregory, T.R. 2014. Distinguishing between "function" and "effect" in genome biology. Genome Biol. Evol. 6: 1234-7.

El-Swais, H., Dunn, K.A., Bielawski, J.P., Li, W.K. and Walsh, D.A. 2014. Seasonal assemblages and short-lived blooms in coastal northwest Atlantic Ocean bacterioplankton. Environ. Microbiol.; Sept. 22 - epub ahead of print.

Eme, L., Sharpe, S.C., Brown, M.W. and Roger, A.J. 2014. On the age of eukaryotes: Evaluating evidence from fossils and molecular clocks. Cold Spring Harb Perspect Biol. 6(8): a016139.

Gile, G.H. and Slamovits, C.H. 2014. Transcriptomic analysis reveals evidence for a cryptic plastid in the colpodellid Voromonas pontica, a close relative of chromerids and apicomplexan parasites. PLoS One 9: e96258.

Gray, M.W. 2014. The pre-endosymbiont hypothesis: a new perspective on the origin and evolution of mitochondria. Cold Spring Harb. Perspect. Biol. 6(3); epub ahead of print.

Gray, M.W. 2014. Organelle evolution, fragmented ribosomal RNAs, and Carl. RNA Biol. 11: 213-216.

Hahn, M., Schmidt, J., Taipale, S.J., Doolittle, W.F. and Koll, U. 2014. Rhodoluna lacicola gen. nov., sp. nov., a planktonic freshwater bacterium with stream-lined genome. Int. J. Syst. Evol. Microbiol. 64(Pt 9): 3254-63.

Hleap, J.S. and Blouin, C. 2014. Inferring meaningful communities from topology-constrained correlation networks. PLoS One 9: e113438.

Kirby, W.A., Tikhonenkov, D.V., Mylnikov, A.P., Janouskovec,J., Lax, G. and Simpson, A.G. 2014. Characterization of T. bucina n. sp., an extremely halotolerant amoeboflagellate heterolobosean belonging to the Tulamoeba-Pleurostomum clade. J. Euk. Microbiol.; Sept. 17 - epub ahead of print.

Klimes, V., Gentekaki, E., Roger, A.J. and Elias, M. 2014. A large number of nuclear genes in the human parasite blastocystis require mRNA polyadenylation to create functional termination codons. Genome Biol Evol. 6(8): 1956-61.

Langille, M.G., Meehan, C.J., Koenig, J.E., Dhanani, A.S., Rose, R.A., Howlett, S.E. and Beiko, R.G. 2014. Microbial shifts in the aging mouse gut. Microbiome 2: 50.

Lee, R., Lai, H., Malik, S.B., Saldarriaga, J.F., Keeling, P.J. and Slamovits, C.H. 2014. Analysis of EST data of the marine protist Oxyrrhis marina, an emerging model for alveolate biology and evolution. BMC Genomics 15: 122.

Nakayama, T., Kamikawa, R., Tanifuji, G., Kashiyama, Y., Ohkouchi, N., Archibald, J.M. and Inagaki, Y. 2014. Complete genome of a nonphotosynthetic cyanobacterium in a diatom reveals recent adaptations to an intracellular lifestyle. PNAS 111: 11407-412.

Panek, T., Simpson, A.G., Hampl, V. and Cepicka, I. 2014. Creneis carolina gen. et sp. nov. (Heterolobosea), a novel marine anaerobic protist with strikingly derived morphology and life cycle. Protist 165: 542-67.

Parks, D.H., Tyson, G.W., Hugenholtz, P. and Beiko, R.G. 2014. STAMP: statistical analysis of taxonomic and functional profiles. Bioinformatics 30: 3123-24.

Shafiei, M., Dunn, K.A., Chipman, H., Gu, H. and Bielawski, J.P. 2014. BiomeNet: A Bayesian model for inference of metabolic divergence among microbial communities. PLoS Comput. Biol. 10: e1003918.

Stairs, C.W., Eme, L., Brown, M.W., Mutsaers, C., Susko, E., Dellaire, G., Soanes, D.M., van der Giezen, M. and Roger, A.J. 2014. A SUF Fe-S cluster biogenesis system in the mitochondrion-related organelles of the anaerobic protist Pygsuia. Curr. Biol. 24: 1176-86.

Tanifuji, G., Onodera, N.T., Moore, C.E. and Archibald, J.M. 2014. Reduced nuclear genomes maintain high gene transcription levels. Mol. Biol. Evol. 31: 625-35.

Tanifuji, G., Onodera, N.T., Brown, M.W., Curtis, B.A., Roger, A.J., Ka-Shu Wong, G., Melkonian, M. and Archibald, J.M. 2014. Nucleomorph and plastid genome sequences of the chlorarachniophyte L. oceanica: convergent reductive evolution and frequent recombination in nucleomorph-bearing algae. BMC Genomics 15: 374.

Wang, H.C., Susko, E. and Roger, A.J. 2014. An amino acid substitution-selection model adjusts residue fitness to improve phylogenetic estimation. Mol Biol Evol. 31(4): 779-92.

Xu, Z., Malmer, D., Langille, M.G., Way, S.F. and Knight, R. 2014. Which is more important for classifying microbial communities: who's there or what they can do? ISME J. 8: 2357-59.


Bay, R.A. and Bielawski, J.P. 2013. Inference of functional divergence among proteins when the evolutionary process is non-stationary. J. Mol. Evol. 76: 205-15.

Bielawski, J.P. 2013. Detecting the signatures of adaptive evolution in protein coding genes. In Curr Protoc Mol. Biol. Jan; Chapter 19: Unit 19.1.

Brown, M.W., Sharpe, S.C., Silberman, J.D., Heiss, A.A., Lang, B.F., Simpson, A.G. and Roger, A.J. 2013. Phylogenomics demonstrates that breviate flagellates are related to opisthokonts and apusomonads. Proc. Biol. Sci. 280: 20131755.

Doolittle, W.F. 2013. Is junk DNA bunk? A critique of ENCODE. PNAS 110: 5294-300.

Doolittle, W.F. 2013. The spliceosomal catalytic core arose in the RNA world...or did it? Genome Biol. 14: 141.

Dunn, K.A., Jiang, W., Field, C. and Bielawski, J.P. 2013. Improving evolutionary models for mitochondrial protein data with site-class specific amino acid exchangeability matrices. PLoS One 8: e55816.

Eveleigh, R.J., Meehan, C.J., Archibald, J.M. and Beiko, R.G. 2013. Being Aquifex aeolicus: Untangling a hyperthermophile's checkered past. Genome Biol. Evol. 5: 2478-97.

Harding, T., Brown, M.W., Plotnikov, A., Selivanova, E., Park, J., Gunderson, J.H., Baumgartner, M., Silberman, J.D., Roger, A.J. and Simpson, A.G.B. 2013. Amoeba stages in the deepest branching heteroloboseans, including Pharyngomonas: Evolutionary and systematic implications. Protist 164: 272-86.

Hleap, J.S., Susko, E. and Blouin, C. 2013. Defining structural and evolutionary modules in proteins: a community detection approach to explore sub-domain architecture. BMC Struct. Biol. 13: 20.

Kamikawa, R., Brown, M.W., Nishimura, Y., Sako, Y., Heiss, A.A., Yubuki, N., Gawryluk, R., Simpson, A.G., Roger, A.J., Hashimoto, T. and Inagaki, Y. Parallel re-modeling of EF-1a function: divergent EF-1a genes co-occur with EFL genes in diverse distantly related eukaryotes. BMC Evol. Biol. 13: 131.

Kim, E. and Archibald, J.M. 2013. Ultrastructure and molecular phylogeny of the cryptomonad Goniomonas avonlea sp. nov. Protist 164: 160-82.

Langille, M.G., Zaneveld, J., Caporaso, J.G., McDonald, D., Knights, D., Reyes, J.A., Clemente, J.C., Burkepile, D.E., Vega Thurber, R.L., Knight, R., Beiko, R.G. and Huttenhower, C. 2013. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat. Biotechnol. 31: 814-21.

Leger, M.M., Gawryluk, R.M., Gray, M.W. and Roger, A.J. 2013. Evidence for a hydrogenosomal-type anaerobic ATP generation pathway in Acanthamoeba castellanii. PLoS One 8: e69532.

Maruyama, S., Eveleigh, R.J. and Archibald, J.M. 2013. Treetrimmer: a method for phylogenetic dataset size reduction. BMC Res. Notes 6: 145.

Parks, D.H., Mankowski, T., Zangooei, S., Porter, M.S., Armanini, D.G., Baird, D.J., Langille, M.G. and Beiko, R.G. 2013. GenGIS 2: geospatial analysis of traditional and genetic biodiversity, with new gradient algorithms and an extensible plugin framework. PLoS One 8: e69885.

Susko, E. and Roger, A.J. 2013. Problems with estimation of ancestral frequencies under stationary models. Syst. Biol. 62: 330-338.

Wang, H.C., Susko, E. and Roger, A.J. 2013. The site-wise log-likelihood score is a good predictor of genes under positive selection. J. Mol. Evol. 76(5): 280-94.


Adl, S.M., et al. [with A.G. Simpson]. 2012. The revised classification of eukaryotes. J. Euk. Microbiol. 59: 429-93.

Archibald, J.M. 2012. Plastid origins. In: Organelle Genetics: Evolution of organelle genomes and gene expression, C. Bullerwell (Ed.), pp. 19-38, Springer-Verlag.

Curtis, B.A., et al. [with R. Beiko, C.H. Slamovits, M.W. Gray and J.M. Archibald]. 2012. Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs. Nature 492: 59-65.

Doolittle, W.F. 2012. Evolutionary biology: a ratchet for protein complexity. Nature 481: 270-271.

Doolittle, W.F. 2012. Population genomics: how bacterial species form and why they don't exist. Curr. Biol. 22: R451-453.

Gile, G.H. and Slamovits, C.H. 2012. Phylogenetic position of Lophomonas striata Butschli (Parabasalia) from the hindgut of the cockroach Periplaneta americana. Protist 163: 274-283.

Gray, M.W. 2012. Evolutionary origin of RNA editing. Biochemistry 51: 5235-42.

Hopkins, J.F., Spencer, D.F., Laboissiere, S.., Neilson, J.A., Eveleigh, R.J.,Durnford, D.G., Gray, M.W. and Archibald, J.M. 2012. Proteomics reveals plastid- and periplastid-targeted proteins in the chlorarachniophyte alga Bigelowiella natans. Genome Biol. Evol. 4: 1391-406.

Jackman, J.E., Gott, J.M. and Gray, M.W. 2012. Doing it in reverse: 3' to-5' polymerization by the Thg1 superfamily. RNA 18: 886-899.

Langille, M.G., Meehan, C.J. and Beiko, R.G. 2012. Human microbiome: a genetic bazaar for microbes? Curr. Biol. 22: R20-22.

Nakayama, T. and Archibald, J.M. 2012. Evolving a photosynthetic organelle. BMC Biology 10: 35.

Nesbo, C.L., Bradnan, D.M., Adebusuyi, A., Dlutek, M., Petrus, A.K., Foght, J., Doolittle, W.F. and Noll, K.M. 2012. Mesotoga prima gen. nov., sp. nov., the first described mesophilic species of the Thermotogales. Extremophiles 16: 387-93.

Park, J.S., De Jonckheere, J.F. and Simpson, A.G. 2012. Characterization of Selenaion koniopes n. gen., n. sp., an amoeba that represents a new major lineage within herterolobosea, isolated from the Wieliczka salt mine. J. Euk. Microbiol. 59: 601-13.

Parks, D.H. and Beiko, R.G. 2012. Measuring community similarity with phylogenetic networks. Mol. Biol. Evol. 29: 3947-58.

Susko, E. and Roger, A.J. 2012. The probability of correctly resolving a split as an experimental design criterion in phylogenetics. Syst. Biol. 61: 811-821.

Takishita, K., Kolisko, M., Komatsuzaki, H., Yabuki, A., Inagaki, Y., Cepicka, I., Smejkalova, P., Silberman, J.D., Hashimoto, T., Roger, A.J. and Simpson, A.G. 2012. Multigene phylogenies of diverse Carpediemonas-like organisms identify the closest relatives of 'amitochondriate' diplomonads and retortamonads. Protist 163: 344-355.

Zou, L., Susko, E., Field, C. and Roger, A.J. 2012. Fitting nonstationary general-time-reversible models to obtain edge-lengths and frequencies for the Barry-Hartigan model. Syst. Biol. 61: 927-40.


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Last updated: April 2017