Bay Paul Center Publication Co-authorship Network

Top 25 Journals

Proc Natl Acad Sci U S A (51), PLoS One (27), Appl Environ Microbiol (24), ISME J (23), Mol Biol Evol (21), J Bacteriol (18), Environ Microbiol (18), Nucleic Acids Res (17), J Biol Chem (16), Biol Bull (15), J Mol Biol (14), Science (13), European Journal of Protistology (12), Nature (11), Front Microbiol (11), J Eukaryot Microbiol (10), BMC Genomics (9), Microbiome (8), Hydrobiologia (8), Genetics (8), PLoS Biol (7), Mol Microbiol (7), Gene (7), Protist (6), Limnology and Oceanography (6)


2015 (36) | 2014 (68) | 2013 (39) | 2012 (45) | 2011 (40) | 2010 (32) | 2009 (42) | 2008 (37) | 2007 (41) | 2006 (35) | 2005 (45) | 2004 (26) | 2003 (42) | 2002 (43) | 2001 (34) | 2000 (39) | 1999 (26) | 1998 (30) | 1997 (22) | 1996 (22)



Amata, E., Bland, N. D., Campbell, R. K., and Pollastri, M. P. (2015). “Evaluation of pyrrolidine and pyrazolone derivatives as inhibitors of trypanosomal phosphodiesterase B1 (TbrPDEB1).Tetrahedron Lett, 56(21), 2832-2835.

Anderson, R. E., Sogin, M. L., and Baross, J. A. (2015). “Biogeography and ecology of the rare and abundant microbial lineages in deep-sea hydrothermal vents.FEMS Microbiol Ecol, 91(1), 1-11.

Angermeyer, A., Crosby, S. C., and Huber, J. A. (2015). “Decoupled distance-decay patterns between dsrA and 16S rRNA genes among salt marsh sulfate-reducing bacteria.Environ Microbiol, 10.1111/1462-2920.12821, n/a-n/a.

Berni Canani, R., Gilbert, J. A., and Nagler, C. R. (2015). “The role of the commensal microbiota in the regulation of tolerance to dietary allergens.Curr Opin Allergy Clin Immunol, 15(3), 243-249.

Bertrand, E. M., McCrow, J. P., Moustafa, A., Zheng, H., McQuaid, J. B., Delmont, T. O., Post, A. F., Sipler, R. E., Spackeen, J. L., Xu, K., Bronk, D. A., Hutchins, D. A., and Allen, A. E. (2015). “Phytoplankton–bacterial interactions mediate micronutrient colimitation at the coastal Antarctic sea ice edge.Proc Natl Acad Sci U S A, 10.1073/pnas.1501615112.

Bowen, J. L., Weisman, D., Yasuda, M., Jayakumar, A., Morrison, H. G., and Ward, B. B. (2015). “Marine Oxygen-Deficient Zones Harbor Depauperate Denitrifying Communities Compared to Novel Genetic Diversity in Coastal Sediments.Microb Ecol, 70(2), 311-21.

Delmont, T. O., Eren, A. M., Maccario, L., Prestat, E., Esen, O. C., Pelletier, E., Le Paslier, D., Simonet, P., and Vogel, T. M. (2015). “Reconstructing rare soil microbial genomes using in situ enrichments and metagenomics.Frontiers in Microbiology, 6.

Ducklow, H. W., Wilson, S. E., Post, A. F., Stammerjohn, S. E., Erickson, M., Lee, S., Lowry, K. E., Sherrell, R. M., and Yager, P. L. (2015). “Particle flux on the continental shelf in the Amundsen Sea Polynya and Western Antarctic Peninsula.Elementa: Science of the Anthropocene, 3(46), 000046.

Eren, A. M., Morrison, H. G., Lescault, P. J., Reveillaud, J., Vineis, J. H., and Sogin, M. L. (2015). “Minimum entropy decomposition: unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences.ISME J, 9(4), 968-79.

Eren, A. M., Sogin, M. L., Morrison, H. G., Vineis, J. H., Fisher, J. C., Newton, R. J., and McLellan, S. L. (2015). “A single genus in the gut microbiome reflects host preference and specificity.ISME J, 9(1), 90-100.

Gibbons, S. M., Schwartz, T., Fouquier, J., Mitchell, M., Sangwan, N., Gilbert, J. A., and Kelley, S. T. (2015). “Ecological succession and viability of human-associated microbiota on restroom surfaces.Appl Environ Microbiol, 81(2), 765-73.

Gilbert, J. A., and Henry, C. (2015). “Predicting ecosystem emergent properties at multiple scales.Environ Microbiol Rep, 7(1), 20-2.

Hoen, A. G., Li, J., Moulton, L. A., O’Toole, G. A., Housman, M. L., Koestler, D. C., Guill, M. F., Moore, J. H., Hibberd, P. L., Morrison, H. G., Sogin, M. L., Karagas, M. R., and Madan, J. C. (2015). “Associations between Gut Microbial Colonization in Early Life and Respiratory Outcomes in Cystic Fibrosis.J Pediatr, 167(1), 138-147 e3.

Huang, E. Y., Inoue, T., Leone, V. A., Dalal, S., Touw, K., Wang, Y., Musch, M. W., Theriault, B., Higuchi, K., Donovan, S., Gilbert, J., and Chang, E. B. (2015). “Using corticosteroids to reshape the gut microbiome: implications for inflammatory bowel diseases.Inflamm Bowel Dis, 21(5), 963-72.

Hunter-Cevera, K. R., Post, A. F., and Sosik, H. M. (2015). “Diversity of Synechococcus at the Martha’s Vineyard Coastal Observatory: Insights from culture isolations, clone libraries and flow cytometry.Microbial Ecol., in press.

Huo, Y. Y., Cheng, H., Post, A. F., Wang, C. S., Jiang, X. W., Pan, J., Wu, M., and Xu, X. W. (2015). “Ecological functions of uncultured microorganisms in the cobalt-rich ferromanganese crust of a seamount in the central Pacific are elucidated by fosmid sequencing.Acta Oceanologica Sinica, 34(4), 92-113.

Kopf, A., Bicak, M., Kottmann, R., Schnetzer, J., Kostadinov, I., Lehmann, K., Fernandez-Guerra, A., Jeanthon, C., Rahav, E., Ullrich, M., Wichels, A., Gerdts, G., Polymenakou, P., Kotoulas, G., Siam, R., Abdallah, R. Z., Sonnenschein, E. C., Cariou, T., O’Gara, F., Jackson, S., Orlic, S., Steinke, M., Busch, J., Duarte, B., Cacador, I., Canning-Clode, J., Bobrova, O., Marteinsson, V., Reynisson, E., Loureiro, C. M., Luna, G. M., Quero, G. M., Loscher, C. R., Kremp, A., DeLorenzo, M. E., Ovreas, L., Tolman, J., LaRoche, J., Penna, A., Frischer, M., Davis, T., Katherine, B., Meyer, C. P., Ramos, S., Magalhaes, C., Jude-Lemeilleur, F., Aguirre-Macedo, M. L., Wang, S., Poulton, N., Jones, S., Collin, R., Fuhrman, J. A., Conan, P., Alonso, C., Stambler, N., Goodwin, K., Yakimov, M. M., Baltar, F., Bodrossy, L., Van De Kamp, J., Frampton, D. M., Ostrowski, M., Van Ruth, P., Malthouse, P., Claus, S., Deneudt, K., Mortelmans, J., Pitois, S., Wallom, D., Salter, I., Costa, R., Schroeder, D. C., Kandil, M. M., Amaral, V., Biancalana, F., Santana, R., Pedrotti, M. L., Yoshida, T., Ogata, H., Ingleton, T., Munnik, K., Rodriguez-Ezpeleta, N., Berteaux-Lecellier, V., Wecker, P., Cancio, I., Vaulot, D., Bienhold, C., Ghazal, H., Chaouni, B., Essayeh, S., Ettamimi, S., Zaid el, H., Boukhatem, N., Bouali, A., Chahboune, R., Barrijal, S., Timinouni, M., El Otmani, F., Bennani, M., Mea, M., et al. (2015). “The ocean sampling day consortium.Gigascience, 4, 27.

Larsen, P. E., Scott, N., Post, A. F., Field, D., Knight, R., Hamada, Y., and Gilbert, J. A. (2015). “Satellite remote sensing data can be used to model marine microbial metabolite turnover.ISME J, 9(1), 166-79.

Lax, S., and Gilbert, J. A. (2015). “Hospital-associated microbiota and implications for nosocomial infections.Trends Mol Med, 21(7), 427-32.

Lax, S., Hampton-Marcell, J. T., Gibbons, S. M., Colares, G. B., Smith, D., Eisen, J. A., and Gilbert, J. A. (2015). “Forensic analysis of the microbiome of phones and shoes.Microbiome, 3, 21.

Lax, S., Nagler, C. R., and Gilbert, J. A. (2015). “Our interface with the built environment: immunity and the indoor microbiota.Trends Immunol, 36(3), 121-3.

Liebeskind, B. J., Hillis, D. M., and Zakon, H. H. (2015). “Convergence of ion channel genome content in early animal evolution.Proc Natl Acad Sci U S A, 112(8), E846-51.

Martinez, I., Stegen, J. C., Maldonado-Gomez, M. X., Eren, A. M., Siba, P. M., Greenhill, A. R., and Walter, J. (2015). “The gut microbiota of rural papua new guineans: composition, diversity patterns, and ecological processes.Cell Rep, 11(4), 527-38.

Moczek, A. P., Sears, K. E., Stollewerk, A., Wittkopp, P. J., Diggle, P., Dworkin, I., Ledon-Rettig, C., Matus, D. Q., Roth, S., Abouheif, E., Brown, F. D., Chiu, C. H., Cohen, C. S., Tomaso, A. W., Gilbert, S. F., Hall, B., Love, A. C., Lyons, D. C., Sanger, T. J., Smith, J., Specht, C., Vallejo-Marin, M., and Extavour, C. G. (2015). “The significance and scope of evolutionary developmental biology: a vision for the 21st century.Evol Dev, 17(3), 198-219.

Moran, Y., Barzilai, M. G., Liebeskind, B. J., and Zakon, H. H. (2015). “Evolution of voltage-gated ion channels at the emergence of Metazoa.J Exp Biol, 218(Pt 4), 515-25.

Newton, R. J., McLellan, S. L., Dila, D. K., Vineis, J. H., Morrison, H. G., Eren, A. M., and Sogin, M. L. (2015). “Sewage reflects the microbiomes of human populations.MBio, 6(2), e02574.

Ochiana, S. O., Bland, N. D., Settimo, L., Campbell, R. K., and Pollastri, M. P. (2015). “Repurposing human PDE4 inhibitors for neglected tropical diseases. Evaluation of analogs of the human PDE4 inhibitor GSK-256066 as inhibitors of PDEB1 of Trypanosoma brucei.Chem Biol Drug Des, 85(5), 549-64.

Saito, M. A., Dorsk, A., Post, A. F., McIlvin, M., Rappe, M. S., DiTullio, G., and Moran, D. (2015). “Needles in the Blue Sea: Sub-Species Specificity in Targeted Protein Biomarker Analyses Within the Vast Oceanic Microbial Metaproteome.Proteomics, 10.1002/pmic.201400630, n/a-n/a.

Saulnier Sholler, G. L., Bond, J. P., Bergendahl, G., Dutta, A., Dragon, J., Neville, K., Ferguson, W., Roberts, W., Eslin, D., Kraveka, J., Kaplan, J., Mitchell, D., Parikh, N., Merchant, M., Ashikaga, T., Hanna, G., Lescault, P. J., Siniard, A., Corneveaux, J., Huentelman, M., and Trent, J. (2015). “Feasibility of implementing molecular-guided therapy for the treatment of patients with relapsed or refractory neuroblastoma.Cancer Med, 4(6), 871-86.

Schmidt, V. T., Smith, K. F., Melvin, D. W., and Amaral-Zettler, L. A. (2015). “Community assembly of a euryhaline fish microbiome during salinity acclimation.Mol Ecol, 24(10), 2537-50.

Shade, A., and Gilbert, J. A. (2015). “Temporal patterns of rarity provide a more complete view of microbial diversity.Trends Microbiol, 23(6), 335-340.

Snell, T. W., Johnston, R. K., Gribble, K. E., and Mark Welch, D. B. (2015). “Rotifers as experimental tools for investigating aging.Invertebr Reprod Dev, 59(1), 5-10.

Traeger, L. L., Volkening, J. D., Moffett, H., Gallant, J. R., Chen, P. H., Novina, C. D., Phillips, G. N. Jr., Anand, R., Wells, G. B., Pinch, M., Guth, R., Unguez, G. A., Albert, J. S., Zakon, H., Sussman, M. R., and Samanta, M. P. (2015). “Unique patterns of transcript and miRNA expression in the South American strong voltage electric eel (Electrophorus electricus).BMC Genomics, 16, 243.

Walsh, E. A., Smith, D. C., Sogin, M. L., and D’Hondt, S. (2015). “Bacterial and archaeal biogeography of the deep chlorophyll maximum in the South Pacific Gyre.Aquatic Microbial Ecology, 75(1), 1-13.

Wood, M., Gibbons, S. M., Lax, S., Eshoo-Anton, T. W., Owens, S. M., Kennedy, S., Gilbert, J. A., and Hampton-Marcell, J. T. (2015). “Athletic equipment microbiota are shaped by interactions with human skin.Microbiome, 3, 25.

Zarraonaindia, I., Owens, S. M., Weisenhorn, P., West, K., Hampton-Marcell, J., Lax, S., Bokulich, N. A., Mills, D. A., Martin, G., Taghavi, S., van der Lelie, D., and Gilbert, J. A. (2015). “The soil microbiome influences grapevine-associated microbiota.MBio, 6(2).



Amata, E., Bland, N. D., Hoyt, C. T., Settimo, L., Campbell, R. K., and Pollastri, M. P. (2014). “Repurposing human PDE4 inhibitors for neglected tropical diseases: design, synthesis and evaluation of cilomilast analogues as Trypanosoma brucei PDEB1 inhibitors.Bioorg Med Chem Lett, 24(17), 4084-9.

Anderson, R. E., Sogin, M. L., and Baross, J. A. (2014). “Evolutionary strategies of viruses, bacteria and archaea in hydrothermal vent ecosystems revealed through metagenomics.PLoS One, 9(10), e109696.

Apprill, A., Robbins, J., Eren, A. M., Pack, A. A., Reveillaud, J., Mattila, D., Moore, M., Niemeyer, M., Moore, K. M., and Mincer, T. J. (2014). “Humpback whale populations share a core skin bacterial community: towards a health index for marine mammals?PLoS One, 9(3), e90785.

Beliaev, A. S., Romine, M. F., Serres, M. H., Bernstein, H. C., Linggi, B. E., Markillie, L. M., Isern, N. G., Chrisler, W. B., Kucek, L. A., Hill, E. A., Pinchuk, G. E., Bryant, D. A., Wiley, H. S., Fredrickson, J. K., and Konopka, A. (2014). “Inference of interactions in cyanobacterial-heterotrophic co-cultures via transcriptome sequencing.ISME J, 8(11), 2243-55.

Bullerjahn, G. S., and Post, A. F. (2014). “Physiology and molecular biology of aquatic cyanobacteria.Front Microbiol, 5, 359.

Celaj, S., Gleeson, M. W., Deng, J., O’Toole, G. A., Hampton, T. H., Toft, M. F., Morrison, H. G., Sogin, M. L., Putra, J., Suriawinata, A. A., and Gorham, J. D. (2014). “The microbiota regulates susceptibility to Fas-mediated acute hepatic injury.Lab Invest, 94(9), 938-49.

Chafee, M., Maignien, L., and Simmons, S. L. (2014). “The effects of variable sample biomass on comparative metagenomics.Environ Microbiol, 10.1111/1462-2920.12668.

Chernikova, D. A., Koestler, D. C., Hoen, A. G., Housman, M. L., Hibberd, P. L., Moore, J. H., Morrison, H. G., Sogin, M. L., Zain-Ul-Abideen, M., and Madan, J. C. (2014). “Fetal exposures and perinatal influences on the stool microbiota of premature infants.J Matern Fetal Neonatal Med, 10.3109/14767058.2014.987748, 1-7.

Cusack, D. F., Axsen, J., Shwom, R., Hartzell-Nichols, L., White, S., and Mackey, K. R. M. (2014). “An interdisciplinary assessment of climate engineering strategies.Frontiers in Ecology and the Environment, 12(5), 280-287.

Davies, N., Field, D., Amaral-Zettler, L. A., Bicak, M., Bourlat, S., Coddington, J., Deck, J., Drummond, A., Gilbert, J. A., Glöckner, F. O., Kottmann, R., Meyer, C., Morrison, N., Obst, M., Robbins, R., Schriml, L., Sterk, P., and Stones-Havas, S. (2014). “Report of the 14th Genomic Standards Consortium Meeting, Oxford, UK, September 17-21, 2012.Standards in Genomic Sciences; Vol 9, No 3 (2014): Standards in Genomic Sciences.

Davies, N., Field, D., Amaral-Zettler, L. A., Clark, M. S., Deck, J., Drummond, A., Faith, D. P., Geller, J., Gilbert, J., Glockner, F. O., Hirsch, P. R., Leong, J. A., Meyer, C., Obst, M., Planes, S., Scholin, C., Vogler, A. P., Gates, R. D., Toonen, R., Berteaux-Lecellier, V., Barbier, M., Barker, K., Bertilsson, S., Bicak, M., Bietz, M. J., Bobe, J., Bodrossy, L., Borja, A., Coddington, J., Fuhrman, J., Gerdts, G., Gillespie, R., Goodwin, K., Hanson, P. C., Hero, J. M., Hoekman, D., Jansson, J., Jeanthon, C., Kao, R., Klindworth, A., Knight, R., Kottmann, R., Koo, M. S., Kotoulas, G., Lowe, A. J., Marteinsson, V. T., Meyer, F., Morrison, N., Myrold, D. D., Pafilis, E., Parker, S., Parnell, J. J., Polymenakou, P. N., Ratnasingham, S., Roderick, G. K., Rodriguez-Ezpeleta, N., Schonrogge, K., Simon, N., Valette-Silver, N. J., Springer, Y. P., Stone, G. N., Stones-Havas, S., Sansone, S. A., Thibault, K. M., Wecker, P., Wichels, A., Wooley, J. C., Yahara, T., Zingone, A., and COS, G. O. (2014). “The founding charter of the Genomic Observatories Network.Gigascience, 3(1), 2.

Dejea, C. M., Wick, E. C., Hechenbleikner, E. M., White, J. R., Mark Welch, J. L., Rossetti, B. J., Peterson, S. N., Snesrud, E. C., Borisy, G. G., Lazarev, M., Stein, E., Vadivelu, J., Roslani, A. C., Malik, A. A., Wanyiri, J. W., Goh, K. L., Thevambiga, I., Fu, K., Wan, F., Llosa, N., Housseau, F., Romans, K., Wu, X., McAllister, F. M., Wu, S., Vogelstein, B., Kinzler, K. W., Pardoll, D. M., and Sears, C. L. (2014). “Microbiota organization is a distinct feature of proximal colorectal cancers.Proc Natl Acad Sci U S A, 111(51), 18321-6.

Delmont, T. O., Francioli, D., Jacquesson, S., Laoudi, S., Mathieu, A., Nesme, J., Ceccherini, M. T., Nannipieri, P., Simonet, P., and Vogel, T. M. (2014). “Microbial community development and unseen diversity recovery in inoculated sterile soil.Biology and Fertility of Soils, 50(7), 1069-1076.

Delmont, T. O., Hammar, K. M., Ducklow, H. W., Yager, P. L., and Post, A. F. (2014). “Phaeocystis antarctica blooms strongly influence bacterial community structures in the Amundsen Sea polynya.Front Microbiol, 5, 646.

Durham, B. P., Grote, J., Whittaker, K. A., Bender, S. J., Luo, H., Grim, S. L., Brown, J. M., Casey, J. R., Dron, A., Florez-Leiva, L., Krupke, A., Luria, C. M., Mine, A. H., Nigro, O. D., Pather, S., Talarmin, A., Wear, E. K., Weber, T. S., Wilson, J. M., Church, M. J., DeLong, E. F., Karl, D. M., Steward, G. F., Eppley, J. M., Kyrpides, N. C., Schuster, S., and Rappe, M. S. (2014). “Draft genome sequence of marine alphaproteobacterial strain HIMB11, the first cultivated representative of a unique lineage within the Roseobacter clade possessing an unusually small genome.Stand Genomic Sci, 9(3), 632-45.

Eren, A. M., Borisy, G. G., Huse, S. M., and Mark Welch, J. L. (2014). “Oligotyping analysis of the human oral microbiome.Proc Natl Acad Sci U S A, 111(28), E2875-84.

Eren, A. M., Morrison, H. G., Huse, S. M., and Sogin, M. L. (2014). “DRISEE overestimates errors in metagenomic sequencing data.Brief Bioinform, 15(5), 783-7.

Ferreira, A. J., Siam, R., Setubal, J. C., Moustafa, A., Sayed, A., Chambergo, F. S., Dawe, A. S., Ghazy, M. A., Sharaf, H., Ouf, A., Alam, I., Abdel-Haleem, A. M., Lehvaslaiho, H., Ramadan, E., Antunes, A., Stingl, U., Archer, J. A., Jankovic, B. R., Sogin, M., Bajic, V. B., and El-Dorry, H. (2014). “Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses.PLoS One, 9(6), e97338.

Field, D., Sterk, P., Kottmann, R., De Smet, J. W., Amaral-Zettler, L. A., Cochrane, G., Cole, J. R., Davies, N., Dawyndt, P., Garrity, G. M., Gilbert, J. A., Glockner, F. O., Hirschman, L., Klenk, H. P., Knight, R., Kyrpides, N., Meyer, F., Karsch-Mizrachi, I., Morrison, N., Robbins, R., San Gil, I., Sansone, S., Schriml, L., Tatusova, T., Ussery, D., Yilmaz, P., White, O., Wooley, J., and Caporaso, G. (2014). “Genomic standards consortium projects.Stand Genomic Sci, 9(3), 599-601.

Fischer, A. H., Mozzherin, D., Eren, A. M., Lans, K. D., Wilson, N., Cosentino, C., and Smith, J. (2014). “SeaBase: a multispecies transcriptomic resource and platform for gene network inference.Integr Comp Biol, 54(2), 250-63.

Gallant, J. R., Traeger, L. L., Volkening, J. D., Moffett, H., Chen, P. H., Novina, C. D., Phillips, G. N. Jr., Anand, R., Wells, G. B., Pinch, M., Guth, R., Unguez, G. A., Albert, J. S., Zakon, H. H., Samanta, M. P., and Sussman, M. R. (2014). “Nonhuman genetics. Genomic basis for the convergent evolution of electric organs.Science, 344(6191), 1522-5.

Ghezzi, A., Liebeskind, B. J., Thompson, A., Atkinson, N. S., and Zakon, H. H. (2014). “Ancient association between cation leak channels and Mid1 proteins is conserved in fungi and animals.Front Mol Neurosci, 7, 15.

Gifford, A. H., Alexandru, D. M., Li, Z., Dorman, D. B., Moulton, L. A., Price, K. E., Hampton, T. H., Sogin, M. L., Zuckerman, J. B., Parker, H. W., Stanton, B. A., and O’Toole, G. A. (2014). “Iron supplementation does not worsen respiratory health or alter the sputum microbiome in cystic fibrosis.J Cyst Fibros, 13(3), 311-8.

Gilbert, J. A., Dick, G. J., Jenkins, B., Heidelberg, J., Allen, E., Mackey, K. R., and DeLong, E. F. (2014). “Meeting report: Ocean ‘omics science, technology and cyberinfrastructure: current challenges and future requirements (August 20-23, 2013).Stand Genomic Sci, 9(3), 1252-8.

Gilbert, J. A., and Neufeld, J. D. (2014). “Life in a World without Microbes.PLoS Biol, 12(12), e1002020.

Glass, E. M., Dribinsky, Y., Yilmaz, P., Levin, H., Van Pelt, R., Wendel, D., Wilke, A., Eisen, J. A., Huse, S. M., Shipanova, A., Sogin, M., Stajich, J., Knight, R., Meyer, F., and Schriml, L. M. (2014). “MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment.ISME J, 8(1), 1-3.

Gribble, K. E., Jarvis, G., Bock, M., and Mark Welch, D. B. (2014). “Maternal caloric restriction partially rescues the deleterious effects of advanced maternal age on offspring.Aging Cell, 13(4), 623-30.

Gribble, K. E., Kaido, O., Jarvis, G., and Mark Welch, D. B. (2014). “Patterns of intraspecific variability in the response to caloric restriction.Exp Gerontol, 51, 28-37.

Halliday, E., McLellan, S. L., Amaral-Zettler, L. A., Sogin, M. L., and Gast, R. J. (2014). “Comparison of bacterial communities in sands and water at beaches with bacterial water quality violations.PLoS One, 9(3), e90815.

Hampton, T. H., Green, D. M., Cutting, G. R., Morrison, H. G., Sogin, M. L., Gifford, A. H., Stanton, B. A., and O’Toole, G. A. (2014). “The microbiome in pediatric cystic fibrosis patients: the role of shared environment suggests a window of intervention.Microbiome, 2, 14.

Huo, Y. Y., Li, Z. Y., You, H., Wang, C. S., Post, A. F., Oren, A., and Xu, X. W. (2014). “Oceanicola antarcticus sp. nov. and Oceanicola flagellatus sp. nov., moderately halophilic bacteria isolated from seawater.Int J Syst Evol Microbiol, 64(Pt 9), 2975-9.

Huse, S. M., Mark Welch, D. B., Voorhis, A., Shipunova, A., Morrison, H. G., Eren, A. M., and Sogin, M. L. (2014). “VAMPS: a website for visualization and analysis of microbial population structures.BMC Bioinformatics, 15(1), 41.

Huse, S. M., Young, V. B., Morrison, H. G., Antonopoulos, D. A., Kwon, J., Dalal, S., Arrieta, R., Hubert, N. A., Shen, L., Vineis, J. H., Koval, J. C., Sogin, M. L., Chang, E. B., and Raffals, L. E. (2014). “Comparison of brush and biopsy sampling methods of the ileal pouch for assessment of mucosa-associated microbiota of human subjects.Microbiome, 2(1), 5.

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Bowen, J. L., Morrison, H. G., Hobbie, J. E., and Sogin, M. L. (2012). “Salt marsh sediment diversity: a test of the variability of the rare biosphere among environmental replicates.ISME J, 6(11), 2014-23.

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Duyzend, M. H., Clark, C. T., Simmons, S. L., Johnson, W. B., Larson, A. M., Leconte, A. M., Wills, A. W., Ginder-Vogel, M., Wilhelm, A. K., Czechowicz, J. A., and Alberg, D. G. (2012). “Synthesis and evaluation of substrate analogue inhibitors of trypanothione reductase.J Enzyme Inhib Med Chem, 27(6), 784-94.

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Finkel, O. M., Burch, A. Y., Elad, T., Huse, S. M., Lindow, S. E., Post, A. F., and Belkin, S. (2012). “Distance-decay relationships partially determine diversity patterns of phyllosphere bacteria on Tamarix trees across the Sonoran Desert [corrected].Appl Environ Microbiol, 78(17), 6187-93.

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Gilbert, J. A., Steele, J. A., Caporaso, J. G., Steinbruck, L., Reeder, J., Temperton, B., Huse, S. M., McHardy, A. C., Knight, R., Joint, I., Somerfield, P., Fuhrman, J. A., and Field, D. (2012). “Defining seasonal marine microbial community dynamics.ISME J, 6(2), 298-308.

Gobet, A., Boer, S. I., Huse, S. M., van Beusekom, J. E., Quince, C., Sogin, M. L., Boetius, A., and Ramette, A. (2012). “Diversity and dynamics of rare and of resident bacterial populations in coastal sands.ISME J, 6(3), 542-53.

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Mackey, K. R. M., Roberts, K., Lomas, M. W., Saito, M. A., Post, A. F., and Paytan, A. (2012). “Enhanced solubility and ecological impact of atmospheric phosphorus deposition upon extended seawater exposure.Environ Sci Technol, 46(19), 10438-46.

Madan, J. C., Koestler, D. C., Stanton, B. A., Davidson, L., Moulton, L. A., Housman, M. L., Moore, J. H., Guill, M. F., Morrison, H. G., Sogin, M. L., Hampton, T. H., Karagas, M. R., Palumbo, P. E., Foster, J. A., Hibberd, P. L., and O’Toole, G. A. (2012). “Serial analysis of the gut and respiratory microbiome in cystic fibrosis in infancy: interaction between intestinal and respiratory tracts and impact of nutritional exposures.MBio, 3(4).

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McCliment, E. A., Nelson, C. E., Carlson, C. A., Alldredge, A. L., Witting, J., and Amaral-Zettler, L. A. (2012). “An all-taxon microbial inventory of the Moorea coral reef ecosystem.ISME J, 6(2), 309-19.

Meeder, E., Mackey, K. R. M., Paytan, A., Shaked, Y., Iluz, D., Stambler, N., Rivlin, T., Post, A. F., and Lazar, B. (2012). “Nitrite dynamics in the open ocean—clues from seasonal and diurnal variations.Marine Ecology Progress Series, 453, 11-26.

Ochiana, S. O., Gustafson, A., Bland, N. D., Wang, C., Russo, M. J., Campbell, R. K., and Pollastri, M. P. (2012). “Synthesis and evaluation of human phosphodiesterases (PDE) 5 inhibitor analogs as trypanosomal PDE inhibitors. Part 2. Tadalafil analogs.Bioorg Med Chem Lett, 22(7), 2582-4.

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Siam, R., Mustafa, G. A., Sharaf, H., Moustafa, A., Ramadan, A. R., Antunes, A., Bajic, V. B., Stingl, U., Marsis, N. G., Coolen, M. J., Sogin, M., Ferreira, A. J., and Dorry, H. E. (2012). “Unique prokaryotic consortia in geochemically distinct sediments from Red Sea Atlantis II and discovery deep brine pools.PLoS One, 7(8), e42872.

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Sukenik, A., Kaplan-Levy, R. N., Mark Welch, J. L., and Post, A. F. (2012). “Massive multiplication of genome and ribosomes in dormant cells (akinetes) of Aphanizomenon ovalisporum (Cyanobacteria).ISME J, 6(3), 670-9.

Sun, Y., Cai, Y., Huse, S. M., Knight, R., Farmerie, W. G., Wang, X., and Mai, V. (2012). “A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis.Brief Bioinform, 13(1), 107-21.

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Finkel, O. M., Burch, A. Y., Lindow, S. E., Post, A. F., and Belkin, S. (2011). “Geographical location determines the population structure in phyllosphere microbial communities of a salt-excreting desert tree.Appl Environ Microbiol, 77(21), 7647-55.

Garbuz, D. G., Astakhova, L. N., Zatsepina, O. G., Arkhipova, I. R., Nudler, E., and Evgen’ev, M. B. (2011). “Functional organization of hsp70 cluster in camel (Camelus dromedarius) and other mammals.PLoS One, 6(11), e27205.

Garbuz, D. G., Yushenova, I. A., Zatsepina, O. G., Przhiboro, A. A., Bettencourt, B. R., and Evgen’ev, M. B. (2011). “Organization and evolution of hsp70 clusters strikingly differ in two species of Stratiomyidae (Diptera) inhabiting thermally contrasting environments.BMC Evol Biol, 11, 74.

Gast, R. J., Moran, D. M., Dennett, M. R., Wurtsbaugh, W. A., and Amaral-Zettler, L. A. (2011). “Amoebae and Legionella pneumophila in saline environments.J Water Health, 9(1), 37-52.

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Kamennaya, N. A., and Post, A. F. (2011). “Characterization of cyanate metabolism in marine Synechococcus and Prochlorococcus spp.Appl Environ Microbiol, 77(1), 291-301.

Mackey, K. R. M., Bristow, L., Parks, D. R., Altabet, M. A., Post, A. F., and Paytan, A. (2011). “The influence of light on nitrogen cycling and the primary nitrite maximum in a seasonally stratified sea.Progress in Oceanography, 91(4), 545-560.

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Smith, H. A., Snell, T. W., Serra, M., Hecox-Lea, B., and Mark Welch, D. (2011). “Molecular evolution of the membrane associated progesterone receptor within the Brachionus plicatilis (Rotifera) cryptic species complex.Hydrobiolgia (662), 99-106.

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Valm, A. M., Mark Welch, J. L., Rieken, C. W., Hasegawa, Y., Sogin, M. L., Oldenbourg, R., Dewhirst, F. E., and Borisy, G. G. (2011). “Systems-level analysis of microbial community organization through combinatorial labeling and spectral imaging.Proc Natl Acad Sci U S A, 108(10), 4152-7.

White, J., Gilbert, J., Hill, G., Hill, E., Huse, S. M., Weightman, A. J., and Mahenthiralingam, E. (2011). “Culture-independent analysis of bacterial fuel contamination provides insight into the level of concordance with the standard industry practice of aerobic cultivation.Appl Environ Microbiol, 77(13), 4527-38.

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Edgcomb, V. P., Kysela, D. T., Teske, A., de Vera Gomez, A., and Sogin, M. L. (2002). “Benthic eukaryotic diversity in the Guaymas Basin hydrothermal vent environment.Proc Natl Acad Sci U S A, 99(11), 7658-62.

Edgcomb, V. P., Simpson, A. G., Zettler, L. A., Nerad, T. A., Patterson, D. J., Holder, M. E., and Sogin, M. L. (2002). “Pelobionts are degenerate protists: insights from molecules and morphology.Mol Biol Evol, 19(6), 978-82.

Gerbod, D., Noel, C., Dolan, M. F., Edgcomb, V. P., Kitade, O., Noda, S., Dufernez, F., Ohkuma, M., Kudo, T., Capron, M., Sogin, M. L., and Viscogliosi, E. (2002). “Molecular phylogeny of parabasalids inferred from small subunit rRNA sequences, with emphasis on the Devescovinidae and Calonymphidae (Trichomonadea).Mol Phylogenet Evol, 25(3), 545-56.

Gillor, O., Hadas, O., Post, A. F., and Belkin, S. (2002). “Phosphorus bioavailability monitoring by a bioluminescent cyanobacterial sensor strain.Journal of Phycology, 38, 107-105.

Holtzendorff, J., Marie, D., Post, A. F., Partensky, F., Rivlin, A., and Hess, W. R. (2002). “Synchronized expression of ftsZ in natural Prochlorococcus populations of the Red Sea.Environ Microbiol, 4(11), 644-53.

Huber, J. A., Butterfield, D. A., and Baross, J. A. (2002). “Temporal changes in archaeal diversity and chemistry in a mid-ocean ridge subseafloor habitat.Appl Environ Microbiol, 68(4), 1585-94.

Ichiyanagi, K., Beauregard, A., Lawrence, S., Smith, D., Cousineau, B., and Belfort, M. (2002). “Retrotransposition of the Ll.LtrB group II intron proceeds predominantly via reverse splicing into DNA targets.Mol Microbiol, 46(5), 1259-72.

Langford, T. D., Silberman, J. D., Weiland, M. E., Svard, S. G., McCaffery, J. M., Sogin, M. L., and Gillin, F. D. (2002). “Giardia lamblia: identification and characterization of Rab and GDI proteins in a genome survey of the ER to Golgi endomembrane system.Exp Parasitol, 101(1), 13-24.

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Lee, W. J., and Patterson, D. J. (2002). “Abundance and biomass of heterotrophic flagellates, and factors controlling their abundance and distribution in sediments of Botany Bay.Microb Ecol, 43(4), 467-81.

Lindell, D., Erdner, D., Marie, D., Claustre, H., Prasil, O., Le Gall, F., Rippka, R., Partensky, F., Scanlan, D. J., and Post, A. F. (2002). “Contrasting expression of ntcA and amt in Prochlorococcus sp. strain PCC 9511.Journal of Phycology, 38(6), 1113-1124.

Lovell, S., Goryshin, I. Y., Reznikoff, W. R., and Rayment, I. (2002). “Two-metal active site binding of a Tn5 transposase synaptic complex.Nat Struct Biol, 9(4), 278-81.

Moore, L. R., Post, A. F., Rocap, G., and Chisholm, S. W. (2002). “Differential nitrogen utilization of the marine cyanobacteria Prochlorococcus and Synechococcus.Limnology and Oceanography, 47(4), 989-996.

Morrison, H. G., Zamora, G., Campbell, R. K., and Sogin, M. L. (2002). “Inferring protein function from genomic sequence: Giardia lamblia expresses a phosphatidylinositol kinase-related kinase similar to yeast and mammalian TOR.Comp Biochem Physiol B Biochem Mol Biol, 133(4), 477-91.

Murray, S., and Patterson, D. J. (2002). “The benthic dinoflagellate genus Amphidinium in south-eastern Australian waters, including three new species.European Journal of Phycology, 37(2), 279-298.

Murray, S., and Patterson, D. J. (2002). “Amphidiniopsis korewalensis sp. nov., a new heterotrophic benthic dinoflagellates.Phycologica, 41, 382-88.

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Nixon, J. E., Wang, A., Field, J., Morrison, H. G., McArthur, A. G., Sogin, M. L., Loftus, B. J., and Samuelson, J. (2002). “Evidence for lateral transfer of genes encoding ferredoxins, nitroreductases, NADH oxidase, and alcohol dehydrogenase 3 from anaerobic prokaryotes to Giardia lamblia and Entamoeba histolytica.Eukaryot Cell, 1(2), 181-90.

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Power, J., Mayer-Pröschel, M., Smith, J., and Noble, M. (2002). “Oligodendrocyte precursor cells from different brain regions express divergent properties consistent with the differing time courses of myelination in these regions.Developmental Biology, 245(2), 362-375.

Simpson, A. G., Roger, A. J., Silberman, J. D., Leipe, D. D., Edgcomb, V. P., Jermiin, L. S., Patterson, D. J., and Sogin, M. L. (2002). “Evolutionary history of “early-diverging” eukaryotes: the excavate taxon Carpediemonas is a close relative of Giardia.Mol Biol Evol, 19(10), 1782-91.

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Teske, A., Hinrichs, K. U., Edgcomb, V., de Vera Gomez, A., Kysela, D., Sylva, S. P., Sogin, M. L., and Jannasch, H. W. (2002). “Microbial diversity of hydrothermal sediments in the Guaymas Basin: evidence for anaerobic methanotrophic communities.Appl Environ Microbiol, 68(4), 1994-2007.

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Gerbod, D., Edgcomb, V. P., Noel, C., Zenner, L., Wintjens, R., Delgado-Viscogliosi, P., Holder, M. E., Sogin, M. L., and Viscogliosi, E. (2001). “Phylogenetic position of the trichomonad parasite of turkeys, Histomonas meleagridis (Smith) Tyzzer, inferred from small subunit rRNA sequence.J Eukaryot Microbiol, 48(4), 498-504.

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Mark Welch, D. B., and Meselson, M. S. (2001). “Rates of nucleotide substitution in sexual and anciently asexual rotifers.Proc Natl Acad Sci U S A, 98(12), 6720-4.

McArthur, A. G., Knodler, L. A., Silberman, J. D., Davids, B. J., Gillin, F. D., and Sogin, M. L. (2001). “The evolutionary origins of eukaryotic protein disulfide isomerase domains: new evidence from the Amitochondriate protist Giardia lamblia.Mol Biol Evol, 18(8), 1455-63.

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Mikrjukov, K. A., and Patterson, D. J. (2001). “Taxonomy and phylogeny of heliozoa. III. Actinophryids.Acta Protozoologica, 40(1), 3-25.

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Schreiter, P., Gillor, O., Post, A. F., Belkin, S., Schmid, R. D., and Bachmann, T. T. (2001). “Monitoring of phosphorus availability in water by an immobilized lumniscent cyanobacterial reporter strain.Biosensors and Bioelectronics, 16, 811-818.

Serres, M. H., Gopal, S., Nahum, L. A., Liang, P., Gaasterland, T., and Riley, M. (2001). “A functional update of the Escherichia coli K-12 genome.Genome Biol, 2(9), RESEARCH0035.

Simpson, A. G., and Patterson, D. J. (2001). “On core jakobids and excavate taxa: the ultrastructure of Jakoba incarcerata.J Eukaryot Microbiol, 48(4), 480-92.

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Stihl, A., Sommer, U., and Post, A. F. (2001). “Alkaline phosphatase activities among populations of the colony-forming diazotrophic cyanobacterium Trichodesmium spp. (cyanobacteria) in the Red Sea.Journal of Phycology, 37(2), 310-317.

Torino, J. L., Burger, M. S., Reznikoff, C. A., and Swaminathan, S. (2001). “Role of TP53 in repair of N-(deoxyguanosin-8-yl)-4-aminobiphenyl adducts in human transitional cell carcinoma of the urinary bladder.Carcinogenesis, 22(1), 147-54.

Twining, S. S., Goryshin, I. Y., Bhasin, A., and Reznikoff, W. S. (2001). “Functional characterization of arginine 30, lysine 40, and arginine 62 in Tn5 transposase.J Biol Chem, 276(25), 23135-43.

Van Roey, P., Waddling, C. A., Fox, K. M., Belfort, M., and Derbyshire, V. (2001). “Intertwined structure of the DNA-binding domain of intron endonuclease I-TevI with its substrate.EMBO J, 20(14), 3631-7.

Walker, G., Simpson, A. G. B., Edgcomb, V. P., Sogin, M. L., and Patterson, D. J. (2001). “Ultrastructural identities of Mastigamoeba Protozoologica punctachora, Mastigamoeba simplex and Mastigella commutans and assessment of hypotheses of relatedness of the pelobionts (Protista).Europ. J. Protistol, 37, 25-49.

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West, N. J., Schoenhuber, W. A., Fuller, N. J., Walsby, A. E., Amann, R. I., Rippka, R., Post, A. F., and Scanlan, D. J. (2001). “Identification and enumeration of Prochlorococcus sp. in natural communities by in situ hybridization using 16S rRNA-targeted oligonucleotides and tyramide signal amplification.Microbiology, 147, 1731-1744.

Wu, C. H., Madabusi, L., Nishioka, H., Emanuel, P., Sypes, M., Arkhipova, I. R., and Gilmour, D. S. (2001). “Analysis of core promoter sequences located downstream from the TATA element in the hsp70 promoter from Drosophila melanogaster.Mol Cell Biol, 21(5), 1593-602.



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Bordenstein, S. R., Drapeau, M. D., and Werren, J. H. (2000). “Intraspecific variation in sexual isolation in the jewel wasp Nasonia.Evolution, 54(2), 567-73.

Bouzat, J. L., McNeil, L. K., Robertson, H. M., Solter, L. F., Nixon, J. E., Beever, J. E., Gaskins, H. R., Olsen, G., Subramaniam, S., Sogin, M. L., and Lewin, H. A. (2000). “Phylogenomic analysis of the alpha proteasome gene family from early-diverging eukaryotes.J Mol Evol, 51(6), 532-43.

Clark, M. A., Moran, N. A., Baumann, P., and Wernegreen, J. J. (2000). “Cospeciation between bacterial endosymbionts (Buchnera) and a recent radiation of aphids (Uroleucon) and pitfalls of testing for phylogenetic congruence.Evolution, 54(2), 517-25.

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Delgado-Viscogliosi, P., Viscogliosi, E., Gerbod, D., Kulda, J., Sogin, M. L., and Edgcomb, V. P. (2000). “Molecular phylogeny of parabasalids based on small subunit rRNA sequences, with emphasis on the Trichomonadinae subfamily.J Eukaryot Microbiol, 47(1), 70-5.

Edgell, D. R., Belfort, M., and Shub, D. A. (2000). “Barriers to intron promiscuity in bacteria.J Bacteriol, 182(19), 5281-9.

Funk, D. J., Helbling, L., Wernegreen, J. J., and Moran, N. A. (2000). “Intraspecific phylogenetic congruence among multiple symbiont genomes.Proc Biol Sci, 267(1461), 2517-21.

Goryshin, I. Y., Jendrisak, J., Hoffman, L. M., Meis, R., and Reznikoff, W. S. (2000). “Insertional transposon mutagenesis by electroporation of released Tn5 transposition complexes.Nat Biotechnol, 18(1), 97-100.

Gould, R. M., Freund, C. M., Engler, J., and Morrison, H. G. (2000). “Optimization of homogenization conditions used to isolate mRNAs in processes of myelinating oligodendrocytes.Biol Bull, 199(2), 215-7.

Hoffman, L. M., Jendrisak, J. J., Meis, R. J., Goryshin, I. Y., and Reznikoff, W. S. (2000). “Transposome insertional mutagenesis and direct sequencing of microbial genomics.Genetica, 108, 19-24.

Lease, R. A., and Belfort, M. (2000). “A trans-acting RNA as a control switch in Escherichia coli: DsrA modulates function by forming alternative structures.Proc Natl Acad Sci U S A, 97(18), 9919-24.

Lease, R. A., and Belfort, M. (2000). “Riboregulation by DsrA RNA: trans-actions for global economy.Mol Microbiol, 38(4), 667-72.

Lee, W. J., and Patterson, D. J. (2000). “Heterotrophic flagellates (Protista) from marine sediments of Botany Bay, Australia.Journal of Natural History, 34(4), 483-562.

Mark Welch, D. B. (2000). “Evidence from a protein-coding gene that acanthocephalans are rotifers.Invertebrate Biology, 119(1), 17-26.

Mark Welch, D. B., and Meselson, M. (2000). “Evidence for the Evolution of Bdelloid Rotifers Without Sexual Reproduction or Genetic Exchange.Science, 288(5469), 1211-1215.

McArthur, A. G., Morrison, H. G., Nixon, J. E., Passamaneck, N. Q., Kim, U., Hinkle, G., Crocker, M. K., Holder, M. E., Farr, R., Reich, C. I., Olsen, G. E., Aley, S. B., Adam, R. D., Gillin, F. D., and Sogin, M. L. (2000). “The Giardia genome project database.FEMS Microbiol Lett, 189(2), 271-3.

Mohr, G., Smith, D., Belfort, M., and Lambowitz, A. M. (2000). “Rules for DNA target-site recognition by a lactococcal group II intron enable retargeting of the intron to specific DNA sequences.Genes Dev, 14(5), 559-73.

Moran, N. A., and Wernegreen, J. J. (2000). “Lifestyle evolution in symbiotic bacteria: insights from genomics.Trends Ecol Evol, 15(8), 321-326.

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Noel, R. J. Jr., and Reznikoff, W. S. (2000). “Structural studies of lacUV5-RNA polymerase interactions in vitro. Ethylation interference and missing nucleoside analysis.J Biol Chem, 275(11), 7708-12.

Riley, M., and Serres, M. H. (2000). “Interim report on genomics of Escherichia coli.Annu Rev Microbiol, 54, 341-411.

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Serres, M. H., and Riley, M. (2000). “MultiFun, a multifunctional classification scheme for Escherichia coli K-12 gene products.Microb Comp Genomics, 5(4), 205-22.

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Smith, J., Ladi, E., Mayer-Proschel, M., and Noble, M. (2000). “Redox state is a central modulator of the balance between self-renewal and differentiation in a dividing glial precursor cell.Proc Natl Acad Sci U S A, 97(18), 10032-7.

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Wernegreen, J. J., and Moran, N. A. (2000). “Decay of mutualistic potential in aphid endosymbionts through silencing of biosynthetic loci: Buchnera of Diuraphis.Proc Biol Sci, 267(1451), 1423-31.

Wernegreen, J. J., Ochman, H., Jones, I. B., and Moran, N. A. (2000). “Decoupling of genome size and sequence divergence in a symbiotic bacterium.J Bacteriol, 182(13), 3867-9.

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Anderson, O. R., Gastrich, M. D., and Amaral-Zettler, L. A. (1999). “Fine structure of the colonial radiolarian Collozoum serpentinum (Polycystinea: Spumellarida) with consideration of its taxonomic status and the recommendation for the reestablishment of the genus Collophidium (Haeckel).Marine Micropaleontology, 36(81-9).

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Doehmer, J., Buters, J. T., Luch, A., Soballa, V., Baird, W. M., Morisson, H., Stegeman, J. J., Townsend, A. J., Greenlee, W. F., Glatt, H. R., Seidel, A., Jacob, J., and Greim, H. (1999). “Molecular studies on the toxifying effects by genetically engineered cytochromes P450.Drug Metab Rev, 31(2), 423-35.

Gould, R., Freund, C., Palmer, F., Knapp, P. E., Huang, J., Morrison, H., and Feinstein, D. L. (1999). “Messenger RNAs for kinesins and dynein are located in neural processes.Biol Bull, 197(2), 259-60.

Kohler, A., Jostarndt-Fogen, K., Rottner, K., Alliegro, M. C., and Draeger, A. (1999). “Intima-like smooth muscle cells: developmental link between endothelium and media?Anat Embryol (Berl), 200(3), 313-23.

Lee, W. J., Blackmore, R., and Patterson, D. J. (1999). “Australian records of two lesser known genera of heterotrophic euglenids – Chasmostoma Massart 1920 and Jenningsia Schaeffer 1918.Protistology, 1, 10-16.

Mahnke Braam, L. A., Goryshin, I. Y., and Reznikoff, W. S. (1999). “A mechanism for Tn5 inhibition. carboxyl-terminal dimerization.J Biol Chem, 274(1), 86-92.

Meselson, M. (1999). “The challenge of biological and chemical weapons.Bull World Health Organ, 77(2), 102-3.

Orgel, L., Hearn, M. A., Bada, J., Barros, J., Chapman, C., Drake, M., Kerridge, J., Race, M., Sogin, M. L., and Squyres, S. (1999). “Sample return from small solar system bodies.Adv. Space Res., 25, 239-48.

Patterson, D. J. (1999). “The Diversity of Eukaryotes.Am Nat, 154(S4), S96-S124.

Patterson, D. J., Simpson, A. G., and Weerakoon, N. (1999). “Free-living flagellates from anoxic habitats and the assembly of the eukaryotic cell.Biol Bull, 196(3), 381-3; discussion 383-4.

Reznikoff, W. S., Bhasin, A., Davies, D. R., Goryshin, I. Y., Mahnke, L. A., Naumann, T., Rayment, I., Steiniger-White, M., and Twining, S. S. (1999). “Tn5: A molecular window on transposition.Biochem Biophys Res Commun, 266(3), 729-34.

Roger, A. J., Morrison, H. G., and Sogin, M. L. (1999). “Primary structure and phylogenetic relationships of a malate dehydrogenase gene from Giardia lamblia.J Mol Evol, 48(6), 750-5.

Sanchez, L. B., Morrison, H. G., Sogin, M. L., and Muller, M. (1999). “Cloning and sequencing of an acetyl-CoA synthetase (ADP-forming) gene from the amitochondriate protist, Giardia lamblia.Gene, 233(1-2), 225-31.

Silberman, J. D., Clark, C. G., Diamond, L. S., and Sogin, M. L. (1999). “Phylogeny of the genera Entamoeba and Endolimax as deduced from small-subunit ribosomal RNA sequences.Mol Biol Evol, 16(12), 1740-51.

Simpson, A. G. B., and Patterson, D. J. (1999). “The ultrastructure of Carpediemonas membranifera (Eukaryota) with reference to the “Excavate hypothesis”.European Journal of Protistology, 35(4), 353-370.

Sogin, M. L. (1999). “A molecular point of view (introductory and concluding remarks.Biol. Bull, 196, 415-16.

Teske, A., Sogin, M. L., Nielsen, L. P., and Jannasch, H. W. (1999). “Phylogenetic relationships of a large marine Beggiatoa.Syst Appl Microbiol, 22(1), 39-44.

Weerakoon, N. D., Harper, J. D. I., Simpson, A. G. B., and Patterson, D. J. (1999). “Centrin in the groove: immunolocalisation of centrin and microtubules in the putatively primitive protist Chilomastix cuspidata (Retortamonadida).Protoplasma, 210(1-2), 75-84.

Wernegreen, J. J., and Moran, N. A. (1999). “Evidence for genetic drift in endosymbionts (Buchnera): analyses of protein-coding genes.Mol Biol Evol, 16(1), 83-97.

Wernegreen, J. J., and Riley, M. A. (1999). “Comparison of the evolutionary dynamics of symbiotic and housekeeping loci: a case for the genetic coherence of rhizobial lineages.Mol Biol Evol, 16(1), 98-113.

Yigit, H., and Reznikoff, W. S. (1999). “Escherichia coli DNA topoisomerase I copurifies with Tn5 transposase, and Tn5 transposase inhibits topoisomerase I.J Bacteriol, 181(10), 3185-92.

Zaman, V., Zaki, M., Howe, J., Ng, M., Leipe, D. D., Sogin, M. L., and Silberman, J. D. (1999). “Hyperamoeba isolated from human feces: Description and phylogenetic affinity.European Journal of Protistology, 35(2), 197-207.



Alliegro, M. C. (1998). “Myosin-carbohydrate interactions.Cell Motil Cytoskeleton, 39(3), 191-4.

Alliegro, M. C., and Alliegro, M. A. (1998). “Protein heterogeneity in the coiled body compartment.Exp Cell Res, 239(1), 60-8.

Amaral-Zettler, L. A., Anderson, O. R., and Caron, D. A. (1998). “Insights on the diversity within a “species” of Thalassicolla (Spumellarida) based on 16S-like ribosomal RNA gene sequencing.J Eukaryot Microbiol, 45(5), 488-96.

Bordenstein, S. R., and Werren, J. H. (1998). “Effects of A and B Wolbachia and host genotype on interspecies cytoplasmic incompatibility in Nasonia.Genetics, 148(4), 1833-44.

Cousineau, B., Smith, D., Lawrence-Cavanagh, S., Mueller, J. E., Yang, J., Mills, D., Manias, D., Dunny, G., Lambowitz, A. M., and Belfort, M. (1998). “Retrohoming of a bacterial group II intron: mobility via complete reverse splicing, independent of homologous DNA recombination.Cell, 94(4), 451-62.

Derbyshire, V., and Belfort, M. (1998). “Lightning strikes twice: intron-intein coincidence.Proc Natl Acad Sci U S A, 95(4), 1356-7.

Edgcomb, V., Viscogliosi, E., Simpson, A. G. B., Delgado-Viscogliosi, P., Roger, A. J., and Sogin, M. L. (1998). “New insights into the phylogeny of trichomonads inferred from small subunit rRNA sequences.Protist, 149(4), 359-366.

Fladmark, K. E., Serres, M. H., Larsen, N. L., Yasumoto, T., Aune, T., and Doskeland, S. O. (1998). “Sensitive detection of apoptogenic toxins in suspension cultures of rat and salmon hepatocytes.Toxicon, 36(8), 1101-14.

Goryshin, I. Y., Miller, J. A., Kil, Y. V., Lanzov, V. A., and Reznikoff, W. S. (1998). “Tn5/IS50 target recognition.Proc Natl Acad Sci U S A, 95(18), 10716-21.

Goryshin, I. Y., and Reznikoff, W. S. (1998). “Tn5 in vitro transposition.J Biol Chem, 273(13), 7367-74.

Heep, T., Rohozinski, J., Simpson, A. G. B., and Patterson, D. J. (1998). “Stentor amethystinus (Ciliophora, Heterotrichida), a common member of fresh-water plankton in Australia.Records of the Australian Museum, 50, 211-16.

Henze, K., Morrison, H. G., Sogin, M. L., and MullerM. (1998). “Sequence and phylogenetic position of a class II aldolase gene in the amitochondriate protist, Giardia lamblia.Gene, 222(2), 163-8.

Lee, W. J., and Patterson, D. J. (1998). “Diversity and geographic distribution of free-living heterotrophic flagellates – Analysis by PRIMER.Protist, 149(3), 229-244.

Li, H., Veldhuis, M. J. W., and Post, A. F. (1998). “Alkaline phosphatase activities among planktonic communities in the northern Red Sea.Marine Ecology Progress Series, 173, 107-115.

Lindell, D., Padan, E., and Post, A. F. (1998). “Regulation of ntcA expression and nitrite uptake in the marine Synechococcus sp. strain WH 7803.J Bacteriol, 180(7), 1878-86.

Mahnke Braam, L. A., and Reznikoff, W. S. (1998). “Functional characterization of the Tn5 transposase by limited proteolysis.J Biol Chem, 273(18), 10908-13.

Mark Welch, D. B., and Meselson, M. (1998). “Measurements of the genome size of the monogonont rotifer Brachionus plicatilis and of the bdelloid rotifers Philodina roseola and Habrotrocha constricta.Hydrobiologia, 387/388, 395-402.

Mark Welch, D. B., and Meselson, M. (1998). “Karyotypes of bdelloid rotifers from three families.Hydrobiologia, 387/388, 403-07.

Meselson, M. S., and Stahl, F. W. (1998). “Young Jan.Genetics, 148(4), 1413-4.

Morrison, H. G., Weil, E. J., Karchner, S. I., Sogin, M. L., and Stegeman, J. J. (1998). “Molecular cloning of CYP1A from the estuarine fish Fundulus heteroclitus and phylogenetic analysis of CYP1 genes: update with new sequences.Comp Biochem Physiol C Pharmacol Toxicol Endocrinol, 121(1-3), 231-40.

Noel, R. J. Jr., and Reznikoff, W. S. (1998). “CAP, the -45 region, and RNA polymerase: three partners in transcription initiation at lacP1 in Escherichia coli.J Mol Biol, 282(3), 495-504.

Roger, A. J., Svard, S. G., Tovar, J., Clark, C. G., Smith, M. W., Gillin, F. D., and Sogin, M. L. (1998). “A mitochondrial-like chaperonin 60 gene in Giardia lamblia: evidence that diplomonads once harbored an endosymbiont related to the progenitor of mitochondria.Proc Natl Acad Sci U S A, 95(1), 229-34.

Smith, M. W., Aley, S. B., Sogin, M. L., Gillin, F. D., and Evans, G. A. (1998). “Sequence survey of the Giardia lamblia genome.Mol Biochem Parasitol, 95(2), 267-80.

Sogin, M. L., and Silberman, J. D. (1998). “Evolution of the protists and protistan parasites from the perspective of molecular systematics.Int J Parasitol, 28(1), 11-20.

Stegeman, J. J., Soballa, V., Morrison, H. G., Jacob, J., and Doehmer, J. (1998). “Catalytic Properties of Scup Cytochrome P4501A Expressed in Chinese Hamster V79 Cells.Marine Environmental Research, 46, 395-395.

Tong, S. M., Nygaard, K., Bernard, C., Vors, N., and Patterson, D. J. (1998). “Heterotrophic flagellates from the water column in Port Jackson, Sydney, Australia.European Journal of Protistology, 34(2), 162-194.

Yahel, G., Post, A. F., Fabricius, K., Marie, D., Vaulot, D., and Genin, A. (1998). “Phytoplankton distribution and grazing near coral reefs.Limnology and Oceanography, 43(4), 551-563.

Yigit, H., and Reznikoff, W. S. (1998). “Escherichia coli DNA topoisomerase I and suppression of killing by Tn5 transposase overproduction: topoisomerase I modulates Tn5 transposition.J Bacteriol, 180(22), 5866-74.

York, D., Welch, K., Goryshin, I. Y., and Reznikoff, W. S. (1998). “Simple and efficient generation in vitro of nested deletions and inversions: Tn5 intramolecular transposition.Nucleic Acids Res, 26(8), 1927-33.

Zhou, M., Bhasin, A., and Reznikoff, W. S. (1998). “Molecular genetic analysis of transposase-end DNA sequence recognition: cooperativity of three adjacent base-pairs in specific interaction with a mutant Tn5 transposase.J Mol Biol, 276(5), 913-25.



Alliegro, M. C., and Alliegro, M. A. (1997). “Identification of a new coiled body component.Exp Cell Res, 231(2), 386-90.

Alliegro, M. C., and Linz, L. A. (1997). “Novel characteristics of a myosin isolated from mammalian retinal pigment epithelial and endothelial cells.J Biol Chem, 272(13), 8759-63.

Amaral-Zettler, L. A., Sogin, M. L., and Caron, D. A. (1997). “Phylogenetic relationships between the Acantharea and the Polycystinea: a molecular perspective on Haeckel’s Radiolaria.Proc Natl Acad Sci U S A, 94(21), 11411-6.

Arkhipova, I. R., Li, J., and Meselson, M. (1997). “On the mode of gene-dosage compensation in Drosophila.Genetics, 145(3), 729-36.

Bernard, C., Simpson, A. G., and Patterson, D. J. (1997). “An ultrastructural study of a free-living retortamonad, Chilomastix cuspidata (Larsen & Patterson 1990) n. comb. (Retortamonadida, Protista).European Journal of Protistology, 33, 254-65.

Brugerolle, G., and Patterson, D. J. (1997). “Ultrastructure of Trimastix convexa Hollande, an amitochondriate anaerobic flagellate with a previously undescribed organization.European Journal of Protistology, 33(2), 121-130.

Czarniecki, D., Noel, R. J. Jr., and Reznikoff, W. S. (1997). “The -45 region of the Escherichia coli lac promoter: CAP-dependent and CAP-independent transcription.J Bacteriol, 179(2), 423-9.

Danilevskaya, O. N., Arkhipova, I. R., Traverse, K. L., and Pardue, M. L. (1997). “Promoting in tandem: the promoter for telomere transposon HeT-A and implications for the evolution of retroviral LTRs.Cell, 88(5), 647-55.

Ekelund, F., and Patterson, D. J. (1997). “Some heterotrophic flagellates from a cultivated garden soil in Australia.Archiv Fur Protistenkunde, 148(4), 461-478.

Hinkle, G., Morrison, H. G., and Sogin, M. L. (1997). “Genes coding for reverse transcriptase, DNA-directed RNA polymerase, and chitin synthase from the microsporidian Spraguea lophii.Biol Bull, 193(2), 250-1.

Post, A. F., and Arieli, B. (1997). “Photosynthesis of Prochlorothrix hollandica under Sulfide-Rich Anoxic Conditions.Appl Environ Microbiol, 63(9), 3507-11.

Simpson, A. G., Bernard, C., Fenchel, T., and Patterson, D. J. (1997). “The organisation of Mastigamoeba schizophrenia n. sp.: More evidence of ultrastructural idiosyncrasy and simplicity in pelobiont protests.European Journal of Protistology, 33, 87-98.

Simpson, A. G., van den Hoff, J., Bernard, C., Burton, H., and Patterson, D. J. (1997). “The ultrastructure and systematic position of the euglenozoan Postgaardi mariagerensis, Fenchel et al.Arch. Protistenk, 147, 213-25.

Sogin, M. L. (1997). “History assignment: when was the mitochondrion founded?Current Opinions in Genetics & Development, 7, 792-99.

Sogin, M. L. (1997). “Organelle origins: energy-producing symbionts in early eukaryotes?Curr Biol, 7(5), R315-7.

Tong, S., Vors, N., and Patterson, D. J. (1997). “Heterotrophic flagellates, centrohelid heliozoa and filose amoebae from marine and freshwater sites in the Antarctic.Polar Biology, 18(2), 91-106.

Wernegreen, J. J., Harding, E. E., and Riley, M. A. (1997). “Rhizobium gone native: unexpected plasmid stability of indigenous Rhizobium leguminosarum.Proc Natl Acad Sci U S A, 94(10), 5483-8.

Yigit, H., and Reznikoff, W. S. (1997). “Examination of the Tn5 transposase overproduction phenotype in Escherichia coli and localization of a suppressor of transposase overproduction killing that is an allele of rpoH.J Bacteriol, 179(5), 1704-13.

York, D., and Reznikoff, W. S. (1997). “DNA binding and phasing analyses of Tn5 transposase and a monomeric variant.Nucleic Acids Res, 25(11), 2153-60.

Zettler, L. A., Sogin, M. L., and Caron, D. A. (1997). “Phylogenetic relationships between the Acantharea and the Polycystinea: a molecular perspective on Haeckel’s Radiolaria.Proc Natl Acad Sci U S A, 94(21), 11411-6.

Zhou, M., and Reznikoff, W. S. (1997). “Tn5 transposase mutants that alter DNA binding specificity.J Mol Biol, 271(3), 362-73.

Zhou, Q., Hinkle, G., Sogin, M. L., and Dionne, V. E. (1997). “Phylogenetic analysis of olfactory receptor genes from mudpuppy (Necturus maculosus).Biol Bull, 193(2), 248-50.



Agamalian, N. S., Arkhipova, I. R., Surkov, S. A., and Il’in Iu, V. (1996). “[Regulating polyadenylation of jockey mobile genetic element transcripts belonging to the LINE class, in Drosophila cell culture].Mol Biol (Mosk), 30(4), 818-28.

Alliegro, M. C., and Alliegro, M. A. (1996). “A nuclear protein regulated during the transition from active to quiescent phenotype in cultured endothelial cells.Dev Biol, 174(2), 288-97.

Alliegro, M. C., and Alliegro, M. A. (1996). “Identification of a new coiled body component.Exp Cell Res, 227(2), 386-90.

Bahr, M., Hobbie, J. E., and Sogin, M. L. (1996). “Bacterial diversity in an arctic lake: A freshwater SAR11 cluster.Aquatic Microbial Ecology, 11(3), 271-277.

Dwivedi, K., Post, A. F., and Bullerjahn, G. S. (1996). “Cloning and functional analysis of the pmmA gene encoding phosphomannomutase from the photosynthetic prokaryote Prochlorothrix hollandica.Biochim Biophys Acta, 1290(3), 210-4.

Ekebom, J., Patterson, D. J., and Vors, N. (1996). “Heterotrophic flagellates from coral reef sediments (Great Barrier Reef, Australia).Archiv Fur Protistenkunde, 146(3-4), 251-272.

Hammerschmidt, B., Schlegel, M., Lynn, D. H., Leipe, D. D., Sogin, M. L., and Raikov, I. B. (1996). “Insights into the evolution of nuclear dualism in the ciliates revealed by phylogenetic analysis of rRNA sequences.J Eukaryot Microbiol, 43(3), 225-30.

Jilk, R. A., York, D., and Reznikoff, W. S. (1996). “The organization of the outside end of transposon Tn5.J Bacteriol, 178(6), 1671-9.

Leipe, D. D., Tong, S. M., Goggin, C. L., Slemenda, S. B., Pieniazek, N. J., and Sogin, M. L. (1996). “16S-like rDNA sequences from Developayella elegans, Labyrinthuloides haliotidis, and Proteromonas lacertae confirm that the stramenopiles are a primarily heterotrophic group.European Journal of Protistology, 32(4), 449-458.

O’Kelly, C. J., and Patterson, D. J. (1996). “The flagellar apparatus of Cafeteria roenbergensis Fenchel & Patterson 1988 (Bicosoecales = Bicosoecida).European Journal of Protistology, 32, 216-26.

Patterson, D. J., and Simpson, A. G. B. (1996). “Heterotrophic flagellates from coastal marine and hypersaline sediments in Western Australia.European Journal of Protistology, 32(4), 423-448.

Relman, D. A., Schmidt, T. M., Gajadhar, A., Sogin, M. L., Cross, J., Yoder, K., Sethabutr, O., and Echeverria, P. (1996). “Molecular phylogenetic analysis of Cyclospora, the human intestinal pathogen, suggests that it is closely related to Eimeria species.Journal of Infectious Diseases, 173(2), 440-445.

Santamaria-Fries, M., Fajardo, L. F., Sogin, M. L., Olson, P. D., and Relman, D. A. (1996). “Lethal infection by a previously unrecognised metazoan parasite.Lancet, 347(9018), 1797-801.

Schlegel, M., Lom, J., Stechmann, A., Bernhard, D., Leipe, D., Dykova, I., and Sogin, M. L. (1996). “Phylogenetic analysis of complete small subunit ribosomal RNA coding region of Myxidium lieberkuehni: Evidence that Myxozoa are Metazoa and related to the Bilateria.Archiv Fur Protistenkunde, 147(1), 1-9.

Serres, M. H., and Ensign, J. C. (1996). “Endogenous ADP-ribosylation of proteins in Mycobacterium smegmatis.J Bacteriol, 178(20), 6074-7.

Silberman, J. D., Clark, C. G., and Sogin, M. L. (1996). “Dientamoeba fragilis shares a recent common evolutionary history with the trichomonads.Mol Biochem Parasitol, 76(1-2), 311-4.

Silberman, J. D., Sogin, M. L., Leipe, D. D., and Clark, C. G. (1996). “Human parasite finds taxonomic home.Nature, 380(6573), 398.

Simpson, A. G. B., and Patterson, D. J. (1996). “Ultrastructure and identification of the predatory flagellate Colpodella pugnax Cienkowski (Apicomplexa) with a description of Colpodella turpis n sp and a review of the genus.Systematic Parasitology, 33(3), 187-198.

Sogin, M. L., Morrison, H. G., Hinkle, G., and Silberman, J. D. (1996). “Ancestral relationships of the major eukaryotic lineages.Microbiologia, 12(1), 17-28.

Tavormina, P. L., Reznikoff, W. S., and Gross, C. A. (1996). “Identifying interacting regions in the beta subunit of Escherichia coli RNA polymerase.J Mol Biol, 258(2), 213-23.

Udomkit, A., Forbes, S., McClean, C., Arkhipova, I. R., and Finnegan, D. J. (1996). “Control of expression of the I factor, a LINE-like transposable element in Drosophila melanogaster.EMBO J, 15(12), 3174-81.

York, D., and Reznikoff, W. S. (1996). “Purification and biochemical analyses of a monomeric form of Tn5 transposase.Nucleic Acids Res, 24(19), 3790-6.

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