Feng, Y., Louyakis, A., Makkay, A.M., Guerrero, R., Papke, R.T. and Gogarten, J.P. (2019) Complete genome of Halorubrum ezzemoulense strain Fb21. Microbiology Resource Announcements.
Fullmer, M.S., Ouellette, M., Papke, R.T., and Gogarten, J.P. (2019). The patchy distribution of Restriction-Modification system genes in Haloarchaea. Genes.
Corral, P., de la Haba, R.R., Infante-Domínguez, C., Sánchez -Porro, C., Amoozegar, M.A., Papke, R.T., and Ventosa, A. (2018) Halorubrum chaoviator Mancinelli et al., 2009 is a later, heterotypic synonym of Halorubrum ezzemoulense Kharroub et al. 2006. IJSEM.
Méheust, R., Watson, A., Lapointe, F.-J., Papke, R.T., Lopez, P., and Bapteste, E. (2018) Hundreds of novel composite genes and chimeric genes with bacterial origins contributed to haloarchaeal evolution. Genome Biology
de la Haba, R.R., Corral, P., Sánchez-Porro, C., Infante-Domínguez, C. Makkay, A.M., Amoozegar, M.A., Ventosa, A., and Papke, R.T. (2018). Genotypic and lipid analyses of strains from the archaeal genus Halorubrum reveal insights into their taxonomy, divergence and population structure. Frontiers in Microbiology.
Ouellette, M., Gogarten, J.P., Lajoie, J., Makkay, A.M., and Papke, R.T. (2018) Characterizing the DNA methyltransferases of Haloferax volcanii via bioinformatics, gene deletion and SMRT sequencing. Genes.
Shalev, Y., Soucy, S.M., Papke, R.T., Gogarten, J.P., Eichler, J., and Gophna, U. (2018) Comparative analysis of surface layer glycoproteins and genes involved in protein glycosylation in the genus Haloferax. Genes
Lopez-Hermosa, C., De la Haba, R.R., Sánchez-Porro, C., Papke, R.T. and Ventosa, A. (2017) Assessment of multilocus sequence analysis as a valuable tool for the classification of the genus Salinivibrio. Frontiers in Microbiology
Prunetti, L. Graf, M. Blaby, I.K., Peil, L., Makkay, A.M., Starosta, A.L., Papke, R.T., Oshima, T., Wilson, D.N. and de Crécy-Lagard, V. (2016) Deciphering the Translation Initiation Factor 5A Modification Pathway in Halophilic Archaea. Archaea
Ram-Mohan, N., Oren, A., and Papke, R.T. (2016) Analysis of the bacteriorhodopsin-producing haloarchaea reveals a core community that is stable over time in the salt crystallizer pond in Eilat, Israel. Extremophiles
Corral, P., De la Haba, R.R., Sánchez-Porro, C. Amoozegar, M.A., Papke, R.T., and Ventosa, A. (2015) Halorubrum halodurans sp. nov., an extremely halophilic archaeon insolated from a hypersaline lake. IJSEM
Papke, R.T., Corral, P., Ram-Mohan, N., de la Haba, R.R., Sánchez-Porro, C., Makkay, A. and Ventosa, A. (2015) Horizontal gene transfer, dispersal and haloarchaeal speciation. Life 5:1405-1426
Papke, R.T. Preface to the proceedings of Halophiles 2013 (2015) Frontiers in Microbiology 6:341
Articles in refereed journals PubMed
Ventosa, A., De la Haba, R.R., Sánchez-Porro, C. and Papke, R.T. (2015) Microbial diversity of hypersaline environments: a metagenomic approach. Current Opinions in Microbiology.25:80-87
Papke, R.T., Corral, P., Ram-Mohan, N., de la Haba, R.R., Sánchez-Porro, C., Makkay, A. and Ventosa, A. (2015) Horizontal gene transfer, dispersal and haloarchaeal speciation. Life 5:1405-1426
Chimileski S and Papke RT (2015) Getting a hold on archaeal type IV pili: an expanding repertoire of cellular appendages implicates complex regulation and diverse functions. Front. Microbiol. 6:362. doi: 10.3389/fmicb.2015.00362
Zerulla K, Chimileski S, Näther D, Gophna U, Papke RT, Soppa J (2014) DNA as a phosphate storage polymer and the alternative advantages of polyploidy for growth or survival.PLoS ONE 9(4): e94819. doi:10.1371/journal.pone.0094819
Fullmer MS, Soucy SM, Swithers KS, Makkay AM, Wheeler R, Ventosa A, Gogarten JP, Papke RT (2014)
Population and genomic analysis of the genus Halorubrum. Frontiers in Microbiology 2014, 5: 140. doi: 10.3389/fmicb.2014.00140
Ram Mohan N, Fullmer MS, Makkay AM, Wheeler R, Ventosa A, Naor A, Gogarten JP and Papke RT (2014) Evidence from phylogenetic and genome fingerprinting analyses suggests rapidly changing variation in Halorubrum and Haloarcula populations. Front. Microbiol. 5:143. doi: 10.3389/fmicb.2014.00143
Ouellette, M., Jackson, L., Chimileski, S. and Papke, R.T. (2015) Genome-wide DNA methylation analysis of Haloferax volcanii H26 and identification of DNA methyltransferase related PD-(D/E)XK nuclease family protein HVO_A0006. Frontiers in Microbiology doi: 10.3389/fmicb.2015.00251
Corral, P., de la Haba, R.R., Sánchez-Porro, C., Amoozegar, M.A., Papke, R.T., and Ventosa, A. (2015) Halorubrum persicum sp. nov., an extremely halophilc archeaon isolated from sediment of a hypersaline lake. IJSEM doi:10.1099/ijs.0.000175
Luk AWS, Williams TJ, Erdman S, Papke RT and Cavicchioli R. (2014) Viruses of Haloarchaea. Life. doi:10.3390/life4040681
Chimileski S, Franklin MJ and Papke RT (2014) Biofilms formed by the archaeon Haloferax volcanii exhibit cellular differentiation and social motility, and facilitate horizontal gene transfer. BMC Biology 12:65. doi:10.1186/s12915-014-0065-5
Soucy S, Fullmer M, Papke RT and Gogarten JP (2014) Inteins as indicators of gene flow in the halobacteria. Frontiers in Microbiology 5: 299, 25
Zerulla K, Chimileski S, Näther D, Gophna U, Papke RT, Soppa J (2014) DNA as a phosphate storage polymer and the alternative advantages of polyploidy for growth or survival.PLoS ONE 9(4): e94819. doi:10.1371/journal.pone.0094819
Fullmer MS, Soucy SM, Swithers KS, Makkay AM, Wheeler R, Ventosa A, Gogarten JP, Papke RT (2014)
Population and genomic analysis of the genus Halorubrum. Frontiers in Microbiology 2014, 5: 140. doi: 10.3389/fmicb.2014.00140
Ram Mohan N, Fullmer MS, Makkay AM, Wheeler R, Ventosa A, Naor A, Gogarten JP and Papke RT (2014) Evidence from phylogenetic and genome fingerprinting analyses suggests rapidly changing variation in Halorubrum and Haloarcula populations. Front. Microbiol. 5:143. doi: 10.3389/fmicb.2014.00143
Chimileski S, Dolas K, Naor A, Gophna U and Papke RT (2014) Extracellular DNA metabolism in Haloferax volcanii. Front. Microbiol. 5:57. doi: 10.3389/fmicb.2014.00057
Ouellette M, Makkay AM and Papke RT (2013) Dihydroxyacetone metabolism in Haloferax volcanii. Front. Microbiol. 4:376. doi: 10.3389/fmicb.2013.00376
de al Haba, R.R., Sánchez-Porro, C., León, M.J., Papke, R.T., . and Ventosa, A. (2013) Draft genome of the moderately halophilic bacterium Pseudoalteromonas ruthenica strain CP76. Genome Announcements. 1:e00268-13
Papke, R.T., de al Haba, R.R., Infante, C., Perez, D., Sánchez-Porro, C., Lapierre, P, and Ventosa, A. (2013) Draft genome of the moderately halophilic bacterium Marinobacter lipolyticus strain SM19. Genome Announcements 1:e00379-13.
Olga Zhaxybayeva, Ramunas Stepanauskas, Nikhil Ram Mohan, R. Thane Papke (2013) Cell Sorting Analysis of Geographically Separated Hypersaline Environments. Extremophiles,doi:10.1007/s00792-013-0514-z
Williams, D., Gogarten, J.P., and Papke, R.T. (2012) Quantifying homologous replacement of loci between haloarchaeal species. Genome Biology and Evolution 4:1223-1244
Andam, C.P., Harlow, T.J., Papke, R.T., and Gogarten, J.P. (2012)
Ancient origin of the divergent forms of leucyl-tRNA synthetases in the Halobacteriales. BMC Evol. Biol.
Noar, A., Mevarech, M., Lapierre, P., Papke, R.T., and Gophna U. (2012)
Efficient Interspecies recombination in halophilic Archaea and the formation
of recombinant hybrids. Current Biology.
Rohit Ghai, Lejla Pašić, Ana Beatriz Fernández, Ana-Belen Martin-Cuadrado, Carolina Megumi Mizuno , Katherine D. McMahon, R. Thane Papke, Ramunas Stepanauskas, Beltran Rodriguez-Brito, Forest Rohwer, Cristina Sánchez-Porro, Antonio Ventosa, & Francisco Rodríguez-Valera (2011) New Abundant Microbial Groups in Aquatic Hypersaline Environments. Scientific Reports. 1:135
de la Haba, R.R., Marquez, M.C. Papke, R.T. and Ventosa, A. (2011)
Multilocus sequence analysis (MLSA) of the family Halomonadaceae.
International Journal of Systematic and Evolutionary Microbiology.
Papke RT, White E, Reddy P, Weigel G, Kamekura M, Minegishi H, Usami R, Ventosa A. (2011) A Multilocus Sequence Analysis (MLSA) Approach to Halobacteriales Phylogeny and Taxonomy. Int J Syst Evol Microbiol. 2011 Feb 4.
Bahl, J., M. C. Y. Lau, G. J. D. Smith, D. Vijaykrishna, S. C. Cary, D. C. Lacap, C. K. Lee, R. T. Papke, K. A. Warren-Rhodes, F. K. Y. Wong, et al. (2011) Ancient origins determine global biogeography of hot and cold desert Cyanobacteria. Nature Communications 2, 163: doi:10.1038/ncomms1167.
Zhaxybayeva O, Doolittle WF, Papke RT, Gogarten JP (2009) Intertwined Evolutionary Histories of Marine Synechococcus and Prochlorococcus marinus. Genome Biology and Evolution.
Papke RT (2009) A critique of prokaryotic species concepts. Methods Mol Biol 532:379-95.
Sharma, A.K., Zhaxybayeva, O., Papke, R.T., & Doolittle, W.F. (2008) Actinorhodopsins: relatives of proteorhodopsin found predominantly in nonmarine environments. Environmental Microbiology. 10: 1039–1056
Papke, R.T., Zhaxybayeva, O., Feil, E., Sommerfeld, K., Muise, D. and Doolittle, W.F. (2007) Searching for species in haloarchaea. PNAS. 104:14092-14097.
Cuadros-Orellana, S., Legault, B., Martin-Cuadorado, A.-B., D’Auria, G., Zhaxybayeva, O., Papke, R.T. and Rodriguez-Valera, F. (2007) Genomic plasticity in Prokaryotes; the case of the square haloarchaeon. ISME Journal. 1:235-245.
Sharma, A.K., Walsh, D.A., Bapteste, E., Rodriguez-Valera, F., Doolittle, W.F. and Papke, R.T. (2007) Evolution of rhodopsin ion pumps in haloarchaea. BMC Evolutionary Biology. 7:79.
Doolittle, W.F. and Papke, R.T. (2006). Genomics and the bacterial species problem. Genome Biology. 7:116. Sharma, A.K., Walsh, D.A., Bapteste, E., Rodriguez-Valera, F., Doolittle, W.F. and Papke, R.T. (2007) Evolution of rhodopsin ion pumps in haloarchaea. BMC Evolutionary Biology. 7:79.
Zhaxybayeva, O., Gogarten, J.P., Charlebois, R.L., Doolittle, W.F. and Papke, R.T. (2006). Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events. Genome Research. 16:1099-1108.
Legault, B., López-López A., Alba-Casado, J.C., Doolittle, W.F., Bolhuis, H., Rodríguez-Valera F. and Papke, R.T. (2006) Environmental genomics of Haloquadratum walsbyiin a saltern crystallizer indicates a large pool of accessory genes in an otherwise coherent species. BMC Genomics. 7:171
Mongodin, E.F., Legault, B., Walsh, D.A., Daugherty, S., Nesbø, C.L., Papke, R.T. Shanchez-Perez, G., Sharma, A.K., Charlebois, R.L., Bapteste, E., Nelson, K.E., Doolittle, W.F., and Rodríguez-Valera, F. (2005). The genome of Salinibacter ruber: convergence and gene exchange among hyperhalophilic bacteria and archaea. Proc. Natl. Acad. Sci. U.S.A. 102:18147-18152.
Walsh, D.A., Papke, R.T. and Doolittle, W.F. (2005) Archaeal diversity along a soil salinity gradient prone to disturbance. Environ. Microbiol. 7:1655-1666.
Papke, R.T., Koenig, J.E., Rodríguez-Valera, F. and Doolittle, W.F. (2004) Frequent recombination in a saltern population of Halorubrum. Science. 306: 1928-1929.
Papke, R.T. and Ward, D.M. (2004) Minireview: The importance of physical isolation to microbial diversification. FEMS Microbiol. Ecol. 48:293-303. Also published in the Virtual Journal of Geobiology: 3(6) (2004). http://earth.elsevier.com/geobiology
Papke, R.T., Ramsing, N.B., Bateson, M.M. and Ward, D.M. (2003) Geographic isolation in thermophilic cyanobacteria. Environ. Microbiol. 5:650-659. This manuscript was highlighted in Science Perspectives [Fenchel, T., (2003) Biogeography for Bacteria. Science 311:925-926] and The New York Times (August 26th, 2003), received a “Must Read” recommendation from Faculty of 1000 (www.facultyof1000.com) and is the 4th most cited article in Environmental Microbiology.
Papke, R.T., Douady, C.J., Doolittle, W.F. and Rodríguez-Valera, F. (2003) Diversity of bacteriorhodopsins in different hypersaline waters from a single Spanish saltern. Environ. Microbiol. 5:1039-1045.
Papke, R.T. and Doolittle, W.F. (2003) Phage evolution: new worlds of genomic diversity. Curr. Biol. 13:R606-R607.
Boucher, Y., Douady, C.J., Papke, R.T., Walsh, D.A., Boudreau, M.E.R., Nesbø, C.L., Case, R.J. and Doolittle, W.F. (2003) Lateral gene transfer, adaptation and the origins of prokaryotic groups. Annu. Rev. Genet. 37:283-328.
Books/Book Chapters:
Papke, RT and Oren, A (editors). (2014) Halophiles: Genetics and Genomes. Caister Academic Press. ISBN 978-1908230423. Amazon
Papke, R.T. and Chimileski, S. (2013) Gene Transfer Mechanisms,
Population Genetics/Genomics and the Evolution of Haloarchaea, in Advances
in understanding the Biology of Halophilc Bacteria and Archaea (Vreeland,
R., ed). Springer. ISBN-13: 978-9400755383. Amazon
Oren, A and Papke, RT (editors). (2010) Molecular Phylogeny of Microorganisms. Caister Academic Press. ISBN 978-1-904455-67-7. Amazon
Maria B. Gogarten, Johann Peter Gogarten, Lorraine C. Olendzenski (Editors). (2009) Horizontal Gene Transfer: Genomes in Flux. Humana Press – Springer; ISBN-13: 978-1603278522. Amazon
Ward, D.M., Papke, R.T., Nübel, U. and McKitrick, M.C. (2001) Natural history of microorganisms inhabiting hot spring microbial mat communities: clues to the origin of microbial diversity and implication for microbiology and macrobiology, pp. 25-48 in Biodiversity of Microbial Life: Foundation of Earth’s Biosphere (Staley, J.T. and Reysenbach, A.-L., eds.) John Wiley and Sons, NY. Amazon