2008 Publications

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Aguero, F., B. Al-Lazikani, M. Aslett, M. Berriman, F. S. Buckner, R. K. Campbell, S. Carmona, I. M. Carruthers, A. W. Chan, F. Chen, G. J. Crowther, M. A. Doyle, C. Hertz-Fowler, A. L. Hopkins, G. McAllister, S. Nwaka, J. P. Overington, A. Pain, G. V. Paolini, U. Pieper, S. A. Ralph, A. Riechers, D. S. Roos, A. Sali, D. Shanmugam, T. Suzuki, W. C. Van Voorhis and C. L. Verlinde (2008). “Genomic-scale prioritization of drug targets: the TDR Targets database.” Nat Rev Drug Discov 7(11): 900-7.

Alliegro, M. C. and M. A. Alliegro (2008). “Centrosomal RNA correlates with intron-poor nuclear genes in Spisula oocytes.” Proc Natl Acad Sci USA (105): 6993-97.

Amaral-Zettler, L., J. Peplies, A. Ramette, B. Fuchs, W. Ludwig and F. O. Glockner (2008). “Proceedings of the international workshop on Ribosomal RNA technology, April 7-9, 2008, Bremen, Germany.” Syst Appl Microbiol 31(4): 258-68.

Souza-Egipsy, V., González-Toril E., Zettler, E., Amaral-Zettler, L., Aguilera, A. and Amils, R. 2008. Prokaryotic community structure in algal photosynthetic biofilms from extreme acidic streams in Río Tinto (Huelva, Spain). International Microbiology.doi: 10.2436/20.1501.01.xx.

Amaral-Zettler, L. A., J. D. Rocca, M. G. Lamontagne, M. R. Dennett and R. J. Gast (2008). “Changes in microbial community structure in the wake of Hurricanes Katrina and Rita.” Environmental Science & Technology 42(24): 9072-9078

Aurrecoechea, C., J. Brestelli, B. P. Brunk, J. M. Carlton, J. Dommer, S. Fischer, B. Gajria, X. Gao, A. Gingle, G. Grant, O. S. Harb, M. Heiges, F. Innamorato, J. Iodice, J. C. Kissinger, E. Kraemer, W. Li, J. A. Miller, H. G. Morrison, V. Nayak, C. Pennington, D. F. Pinney, D. S. Roos, C. Ross, C. J. Stoeckert, Jr., S. Sullivan, C. Treatman and H. Wang (2008). “GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis.” Nucl. Acids Res.: gkn631.

Davey, J. C., A. P. Nomikos, M. Wungjiranirun, J. R. Sherman, L. Ingram, C. Batki, J. P. Lariviere and J. W. Hamilton (2008). “Arsenic as an endocrine disruptor: arsenic disrupts retinoic acid receptor-and thyroid hormone receptor-mediated gene regulation and thyroid hormone-mediated amphibian tail metamorphosis.” Environ Health Perspect 116(2): 165-72.

Dethlefsen, L., S. Huse, M. L. Sogin and D. A. Relman (2008). “The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing.” PLoS Biology 6(11): e280.

Fredrickson, J. K., M. F. Romine, A. S. Beliaev, J. M. Auchtung, M. E. Driscoll, T. S. Gardner, K. H. Nealson, A. L. Osterman, G. Pinchuk, J. L. Reed, D. A. Rodionov, J. L. Rodrigues, D. A. Saffarini, M. H. Serres, A. M. Spormann, I. B. Zhulin and J. M. Tiedje (2008). “Towards environmental systems biology of Shewanella.” Nat Rev Microbiol 6(8): 592-603.

Gil, I. S., W. Sheldon, T. Schmidt, M. Servilla, R. Aguilar, C. Gries, T. Gray, D. Field, J. Cole, J. Y. Pan, G. Palanisamy, D. Henshaw, M. O’Brien, L. Kinkel, K. McMahon, R. Kottmann, L. Amaral-Zettler, J. Hobbie, P. Goldstein, R. P. Guralnick, J. Brunt and W. K. Michener (2008). “Defining linkages between the GSC and NSF’s LTER program: how the Ecological Metadata Language (EML) relates to GCDML and other outcomes.” OMICS 12(2): 151-6.

Gladyshev, E. and M. Meselson (2008). “Extreme resistance of bdelloid rotifers to ionizing radiation.” Proc Natl Acad Sci USA 105(13): 5139-5144.

Gladyshev, E. A., M. Meselson and I. R. Arkhipova (2008). “Massive Horizontal Gene Transfer in Bdelloid Rotifers.” Science 320(5880): 1210-1213.

Gradman, R. J., J. L. Ptacin, A. Bhasin, W. S. Reznikoff and I. Y. Goryshin (2008). “A bifunctional DNA binding region in Tn5 transposase.” Mol Microbiol 67(3): 528-40.

Gradman, R. J. and W. S. Reznikoff (2008). “Tn5 synaptic complex formation: role of transposase residue w450.” J Bacteriol 190(4): 1484-7.

Hays, A.M., Lantz, R.C., Rodgers, L.S., Sollome, J.J., Vaillancourt, R.R., Andrew, A.S., Hamilton, J.W., Camenisch, T.  “Arsenic down-regulates vascular matrix.” Toxicol Pathol 36:805-817, 2008.

Huber, J. A. and J. F. Holden (2008). Modeling the impact of diffuse vent microorganisms along mid-ocean ridges and flanks. Magma to Microbe: Modeling Hydrothermal Processes at Oceanic Spreading Ridges. R. P. Lowell, J. S. Seewald, A. Metaxas and M. R. Perfit. Washington, D.C., American Geophysical Union Press: 215-231.

Huse, S. M., L. Dethlefsen, J. A. Huber, D. M. Welch, D. A. Relman and M. L. Sogin (2008). “Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing.” PLoS Genetics 4(11): e1000255.

Jost, M. C., D. M. Hillis, Y. Lu, J. W. Kyle, H. A. Fozzard and H. H. Zakon (2008). “Toxin-resistant sodium channels: parallel adaptive evolution across a complete gene family.” Mol Biol Evol 25(6): 1016-24.

Keijser, B. J., E. Zaura, S. M. Huse, J. M. van der Vossen, F. H. Schuren, R. C. Montijn, J. M. ten Cate and W. Crielaard (2008). “Pyrosequencing analysis of the oral microflora of healthy adults.” J Dent Res 87(11): 1016-20.

Kozul, C. D., A. P. Nomikos, T. H. Hampton, L. A. Warnke, J. A. Gosse, J. C. Davey, J. E. Thorpe, B. P. Jackson, M. A. Ihnat and J. W. Hamilton (2008). “Laboratory diet profoundly alters gene expression and confounds genomic analysis in mouse liver and lung.” Chem Biol Interact 173(2): 129-40.

Lasek-Nesselquist, E., A. L. Bogomolni, R. J. Gast, D. M. Welch, J. C. Ellis, M. L. Sogin and M. J. Moore (2008). “Molecular characterization of Giardia intestinalis haplotypes in marine animals: variation and zoonotic potential.” Dis Aquat Organ 81(1): 39-51.

Mark Welch, D. B., J. L. Mark Welch and M. Meselson (2008). “Evidence for degenerate tetraploidy in bdelloid rotifers.” Proc Natl Acad Sci U S A.

Nahum, L. A. and S. L. Pereira (2008). Phylogenomics, Protein Family Evolution, and the Tree of Life: An Integrated Approach between Molecular Evolution and Computational Intelligence. Studies in Computational Intelligence (SCI). T. Smolinski, M. Milanova and A.-E. Hassanien. Berlin Heidelberg, Springer-Verlag. 122: 259-79.

Palacios, C., E. Zettler, R. Amils and L. Amaral-Zettler (2008). “Contrasting microbial community assembly hypotheses: a reconciling tale from the Rio Tinto.” PLoS ONE 3(12): e3853.

Riley, M., J. T. Staley, A. Danhin, T. Wang, T. S. Brettin, L. J. Hauser, M. L. Land and L. S. Thompson (2008). “Genomics of an extreme psychrophile, Psychromonas ingrahamii.” BMC Genomics 9(1): 210.

Rull, K., P. Hallast, L. Uuskula, J. Jackson, M. Punab, A. Salumets, R. K. Campbell and M. Laan (2008). “Fine-scale quantification of HCG beta gene transcription in human trophoblastic and non-malignant non-trophoblastic tissues.” Mol Hum Reprod 14(1): 23-31.

Santelli, C. M., B. N. Orcutt, E. Banning, W. Bach, C. L. Moyer, M. L. Sogin, H. Staudigel and K. J. Edwards (2008). “Abundance and diversity of microbial life in ocean crust.” Nature 453(7195): 653-656.

Schostak, N., K. I. Pyatkov, E. Zelentsova, I. R. Arkhipova, D. Shagin, I. Shagina, E. Mudrik, A. Blintsov, I. Clark, D. J. Finnegan and M. B. Evgen’ev (2008). “Molecular dissection of Penelope transposable element regulatory machinery.” Nucleic Acids Res. 36(8): 2522-2529.

Stewart, J. R., R. J. Gast, R. S. Fujioka, H. M. Solo-Gabriele, J. S. Meschke, L. A. Amaral-Zettler, E. Del Castillo, M. F. Polz, T. K. Collier, M. S. Strom, C. D. Sinigalliano, P. D. Moeller and A. F. Holland (2008). “The coastal environment and human health: microbial indicators, pathogens, sentinels and reservoirs.” Environ Health 7 Suppl 2: S3.

Souza-Egipsy, V., González-Toril E., Zettler, E., Amaral-Zettler, L., Aguilera, A. and Amils, R. 2008. Prokaryotic community structure in algal photosynthetic biofilms from extreme acidic streams in Río Tinto (Huelva, Spain). International Microbiology.11: 251-260

Suga, K., D. B. Mark Welch, Y. Tanaka, Y. Sakakura and A. Hagiwara (2008). “Two circular chromosomes of unequal copy number make up the mitochondrial genome of the rotifer Brachionus plicatilis.” Molecular Biology and Evolution 25(4): 1129-37.

Tamas, I., J. J. Wernegreen, B. Nystedt, S. N. Kauppinen, A. C. Darby, L. Gomez-Valero, D. Lundin, A. M. Poole and S. G. Andersson (2008). “Endosymbiont gene functions impaired and rescued by polymerase infidelity at poly(A) tracts.” Proc Natl Acad Sci U S A 105(39): 14934-9.

Turnbaugh, P. J., M. Hamady, T. Yatsunenko, B. L. Cantarel, A. Duncan, R. E. Ley, M. L. Sogin, W. J. Jones, B. A. Roe, J. P. Affourtit, M. Egholm, B. Henrissat, A. C. Heath, R. Knight and J. I. Gordon (2008). “A core gut microbiome in obese and lean twins.” Nature.

Ye, S., MacEachran, D.P., Hamilton, J.W., O’Toole, G.A, Stanton, B.A. “Surface expression of P-glycoprotein is regulated by the Pseudomonas aeruginosa toxin Cif.” Am J Physiol: Cell Physiol 295:C807-C818, 2008.

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