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Up to date list of publications on google scholar: link

Vonaesch P, Morien E, Andrianonimiadana L, Sanke H, Mbecko J-R, Huus KE, Naharimanananirina T, Godje BP, Nigatoloum SN, Vondo SS, Kandou K, Randremanana R, Rakotondrainipiana M, Mazel F, Djorie SG, Gody JC, Finlay BB*, Rubbo PA*, Parfrey LW*, Collard JM, Sansonetti PJ for the Afribiota investigators. 2018. Stunted childhood growth is associated with decompartmentalization of the gastrointestinal tract and overgrowth of oropharyngeal taxa. PNAS. doi:
*these authors contributed equally.

Lin JL, Lemay MA, Parfrey LW. 2018. Diverse bacteria utilize alginate within the microbiome of the giant kelp Macrocystis pyrifera. Frontiers in Microbiology. 9:1914

Růžková J, Květoňová D, Jirků M, Lhotská Z, Stensvold CR, Parfrey LW, Jirků Pomajbíková K. 2018. Evaluating rodent experimental models for studies of Blastocystis ST1. Experimental Parasitology. 191 (2018) 55–61

Louca S, Shih PM, Pennell MW, Fischer WW, Parfrey LW, Doebeli M. 2018. Bacterial diversification through geological time. Nature Ecology and Evolution. 2: 1458–1467.

Nieves-Ramírez M, Partida-Rodríguez O, Laforest-Lapointe I, Reynolds L, Brown E, Valdez-Salazar A, Morán-Silva P, Rojas L, Morien E, Parfrey LW, Minglian J, Walter J, Torres J, Arrieta MC, Ximénez-García C, Finlay BB. 2018. Asymptomatic intestinal colonization with protist Blastocystis is strongly associated with distinct microbiome ecological patterns. mSystems. 3(3): e00007-18

Lemay MA, Martone PT, Hind KR, Lindstrom SC, Parfrey LW. 2018. Alternate life history phases of a marine macroalgal genus have distinct microbial surface communitiesMolecular Ecology. 27(17): 3555-3568

Parfrey LW, Moreau CS, Russell JA. 2018. The host-associated microbiome: pattern, process, and function. Molecular Ecology. 27 (8), 1749-1765

Jirků Pomajbíková K, Jirků M, Levá J, Sobotková K, Morien E, Parfrey LW. 2018. The benign helminth Hymenolepis diminuta ameliorates chemically induced colitis in a rat model system. Parasitology. 145, 1324-1335

Lemay MA, Martone PT, Keeling PJ, Burt J, Krumhansl K, Smith R, Parfrey LW. 2018. Sympatric kelp species share a large portion of their surface bacterial communities. Environmental Microbiology. 20:658-670

Chen MY and Parfrey LW. 2018. Incubation with macroalgae induces large shifts in water column microbiota, but minor changes to the epibiota of co-occurring macroalgae. Molecular Ecology. 27(8):1966-1979

Louca S, Doebeli M, Parfrey LW. 2018. Correcting for 16S rRNA gene copy numbers in microbiome surveys remains a lost battle. Microbiome. 6:41

Louca S, Polz MF, Mazel F, Albright MBN, Huber JA, O’Connor MI, Ackermann M, Hahn AS, Crowe SA, Srivastava D, Doebeli M, Parfrey LW. 2018. Function and functional redundancy in microbial systems. Nature Ecology and Evolution.

Arrieta MC, Arévalo A, Stiemsma L, Dimitriu P, Chico ME, Loor S, Vaca M, Boutin RCT, Morien E, Jin M, Turvey S, Walter J, Parfrey LW, Cooper P, and Finlay BB. 2017. Associations between infant fungal and bacterial dysbiosis and childhood atopy and wheeze in a developing country. Journal of Allergy and Clinical Immunology.

Parfrey LW, Jirků M, Šíma R, Jalovecká M, Sak B, Grigore K, Jirků Pomajbíková K. 2017. A benign helminth alters the host immune system and the gut microbiota in a rat model system. PLoS ONE 12(8): e0182205.

Louca S, Jacques SMS, Pires APF, Leal JS, Srivastava DS, Parfrey LW, Farjalla VF, Doebeli M. 2016. High taxonomic variability despite stable functional structure across microbial communities. Nat. Ecol. Evol. doi: 10.1038/s41559-016-0015 

Louca S, Parfrey LW, Doebeli M. 2016. Decoupling function and taxonomy in the global ocean microbiome. Science. 353(6305): 1272-1277.

Lukes J, Stensvold CR, Jirků-Pomajbíková K, Parfrey LW. 2015. Are human intestinal eukaryotes beneficial, or commensals? PLoS Pathogens. 11(8): e1005039.

Parfrey LW. 2015. Mock communities highlight the diversity of host-associated eukaryotes. Molecular Ecology. 24: 4337-4339.

Korajkic A, Parfrey LW, McMinn BR, Baeza YV, VanTeuren W, Knight R, Shanks OC. 2015. Changes in bacterial and eukaryotic communities during sewage decomposition in Mississippi river water. Water Research 69, 30-39.

Parfrey LW, Walters WA, Lauber CL, Clemente JC, Berg-Lyons D, Teiling C, Kodira CD, Mohiuddin M, Brunelle J, Driscoll M, Fierer N, Gilbert JA, Knight R. 2014. Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity. Frontiers in Microbiology. 5, 298.

Yilmaz P, Parfrey LW, Yarza P, Gerken J, Prüsse E, Quast C, Schweer T, Peplies J, Ludwig W, Glöckner FO. 2014. The SILVA and “The All Species Living Tree (LTP)” Taxonomic Frameworks. Nucleic Acids Research. 42 (D1): D643-D648.

Loudon AH, Woodhams DC, Parfrey LW, Archer H, Knight, R, McKenzie, VJ, Harris, RN. 2014. Microbial community dynamics and effect of environmental microbial reservoirs on red-backed salamanders (Plethodon cinereus). ISME Journal. 8(4):830-840.

Kueneman J, Parfrey LW, Woodhams DC, Archer H, Knight R, McKenzie VJ. 2013. The amphibian skin-associated microbiome across species, space and life history stages. Molecular Ecology. 23(6): 1238-1250.

Delsuc F, Metcalf JL, Parfrey LW, Song SJ, Gonzalez A, Knight R. 2014. Convergence of gut microbiomes in myrmecophagous mammals. Molecular Ecology. 23(6): 1301-1317.

Metcalf JL, Parfrey LW, Gonzalez A, Lauber CL, Knights D, Ackermann G, Humphrey GC, Gebert MJ, Van Treuren W, Berg-Lyons D, Keepers K, Guo Y, Fierer N, Carter DO, Knight R. 2013. A microbial clock provides an accurate estimate of the postmortem interval in a mouse model system. eLife. doi: 10.7554/eLife.01104

Parfrey LW and Lahr DJG. 2013. Multicellularity arose several times in the evolution of eukaryotes. BioEssays. 35(4):339-47.

Adl SM, Simpson AGB, Lane CE, Lukeš J, Bass D, Bowser SS, Brown MW, Burki F, Dunthorn M, Hampl V, Heiss A, Hoppenrath M, Lara E, le Gall L, Lynn DH, McManus H, Mitchell EAD, Mozley-Stanridge SE, Parfrey LW, Pawlowski J, Rueckert S, Shadwick L, Schoch CL, Smirnov A, Spiegel FW. 2012. The revised classification of eukaryotes. J Euk Microbiol. 59:429-514.

Parfrey LW and Knight R. 2012. Spatial and temporal variability in the human microbiota. Clin Microbiol Infec. 18(Suppl. 4): 5–7.

Parfrey LW, Grant J, Katz LA. 2012. Ribosomal DNA is differentially amplified across life cycle stages in the foraminifer Allogromia laticollaris strain CSH. J Foram Res. 42:151-155

Katz LA, Grant J, Parfrey LW, Burleigh JG. 2012. Turning the Crown Upside Down: Gene Tree Parsimony Roots the Eukaryotic Tree of Life. Syst Biol. 61(4):653-60.

Clemente JC, Ursell LK, Parfrey LW, Knight R. 2012. The impact of the gut microbiota on human health: An integrative view. Cell. 148(6):1258-70.

Knights D, Parfrey LW, Zaneveld JRR, Lozupone CA, Knight, R. 2011. Human-associated microbial signatures: examining their predictive value. Cell Host Microbe. 10(4):292-6.

Zaneveld JR, Parfrey LW, Van Treuren W, Lozupone C, Clemente JC, Knights D, Stombaugh J, Kuczynski J, Knight R. 2011. Combined phylogenetic and genomic approaches for the high-throughput study of microbial habitat adaptation. Trends Microbiol. 19(10):472-82.

Parfrey LW, Walters WA, Knight R. 2011. Microbial eukaryotes in the human microbiome: ecology, evolution, and future directions. Frontiers Cell Infection Microbiol. 2:153.

Parfrey LW, Lahr DJG, Knoll AH, Katz LA. 2011. Estimating the timing of early eukaryotic diversification with multigene molecular clocks. Proc Nat Acad Sci USA. 108(33):13624-13629.

Katz LA, Grant J, Parfrey LW, Gant AL, O’Kelly CJ, Anderson OR, Molestina RE, Nerad T. 2011. Subulatomonas tetraspora nov. gen. nov. sp. is a member of a previously unrecognized major clade of eukaryotes. Protist. 162:762–773.

Lahr DJG, Parfrey LW, Mitchell E, Katz LA, Lara E. 2011. The chastity of amoebae: re-evaluating evidence for sex in amoeboid organisms. Proc Roy Soc B. 278:2081- 2090.

Parfrey LW and Katz LA. 2010. Genome dynamics are influenced by food source in Allogromia laticollaris strain CSH (Foraminifera). Genome Bio. Evol. 2:678-685.

Parfrey LW, Grant J, Tekle YI, Lasek-Nesselquist E, Morrison H, Sogin ML, Patterson DJ, Katz LA. 2010. Broadly sampled multigene analyses yield a well-resolved eukaryotic tree of life. Syst Biol. 59(5):518-533.

Tekle YI, Parfrey LW, Katz LA. 2009. Molecular data are transforming hypotheses on the origin and diversification of eukaryotes. BioScience 59:471–481.

Parfrey LW, Lahr DJG, Katz LA. 2008. The dynamic nature of eukaryotic genomes. Mol Biol Evol. 25(4): 787-794.

Yarragudi A, Parfrey LW, Morse RH. 2007. Genome-wide analysis of transcriptional dependence and probable target sites for Abf1 and Rap1 in Saccharomyces cerevisiae. Nucleic Acids Res. 35(1):193-202.

Parfrey LW, Barbero E, Lasser E, Dunthorn MS, Patterson DJ, Bhattacharya D, Katz LA. 2006. Evaluating support for the current classification of eukaryotic diversity. PLoS Genetics 2: 2062-2073.

Habura A, Goldstein ST, Parfrey LW, Bowser SS. 2006. Phylogeny and ultrastructure of Miliammina fusca: Evidence for secondary loss of calcification in a miliolid foraminifer. J. of Euk. Microbiol. 53(3) :204-10.

Habura A, Wegener L, Travis JL, Bowser SS. 2005. Structural and functional implications of an unusual foraminiferal beta-tubulin. Mol Biol Evol. 22(10):2000-2009.