2010 (34) | 2009 (46) | 2008 (41) | 2007 (54) | 2006 (36) | 2005 (48) | 2004 (27) | 2003 (44) | 2002 (56) | 2001 (41) | 2000 (44)
2010
Adam, R. D., Nigam, A., Seshadri, V., Martens, C. A., Farneth, G. A., Morrison, H. G., Nash, T. E., Porcella, S. F., & Patel, R. (2010). “The Giardia lamblia vsp gene repertoire: characteristics, genomic organization, and evolution.” BMC Genomics, 11(1), 424. doi:10.1186/1471-2164-11-42.
Adey, A., Morrison, H. G., Asan, Xun, X., Kitzman, J. O., Turner, E. H., Stackhouse, B., MacKenzie, A. P., Caruccio, N. C., Zhang, X., & Shendure, J. (2010). “Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition.” Genome Biol, 11(12), R119. doi:10.1186/gb-2010-11-12-r11.
Alliegro, M. A., Henry, J. J., & Alliegro, M. C. (2010). “Rediscovery of the nucleolinus, a dynamic RNA-rich organelle associated with the nucleolus, spindle, and centrosomes.” Proc Natl Acad Sci U S A, 107(31), 13718-13723. doi:10.1073/pnas.100846910.
Amaral-Zettler, L. A., Artigas, L. F., Baross, J., Bharathi, L., Boetius, A., Chandramohan, D., Herndl, G., Kogure, K., Neal, P., Pedros-Alio, C., Ramette, A., Schouten, S., Stal, L., Thessen, A., de Leeuw, J., & Sogin, M. L. (2010). “A global census of marine microbes Life in the World’s Oceans: Diversity, Distribution and Abundance (Vol.” 1, pp. 223-245). Oxford: Blackwell Publishing Ltd.
Bodaker, I., Sharon, I., Suzuki, M. T., Feingersch, R., Shmoish, M., Andreishcheva, E., Sogin, M. L., Rosenberg, M., Maguire, M. E., Belkin, S., Oren, A., & Beja, O. (2010). “Comparative community genomics in the Dead Sea: an increasingly extreme environment.” ISME J, 4(3), 399-407. doi:10.1038/ismej.2009.14.
Bordenstein, S. R., Brothers, C., Wolfe, G., Bahr, M., Minckley, R. L., Clark, M. E., Wernegreen, J. J., Bordenstein, S. R., Reznikoff, W. S., & Werren, J. H. (2010). “Using the Wolbachia Bacterial Symbiont to Teach Inquiry-Based Science: A High School Laboratory Series.” American Biology Teacher, 72(8), 478-483. doi:DOI 10.1525/abt.2010.72.8..
Brazelton, W. J., Ludwig, K. A., Sogin, M. L., Andreishcheva, E. N., Kelley, D. S., Shen, C. C., Edwards, R. L., & Baross, J. A. (2010). “Archaea and bacteria with surprising microdiversity show shifts in dominance over 1,000-year time scales in hydrothermal chimneys.” Proc Natl Acad Sci U S A, 107(4), 1612-1617. doi:10.1073/pnas.090536910.
Chafee, M. E., Funk, D. J., Harrison, R. G., & Bordenstein, S. R. (2010). “Lateral phage transfer in obligate intracellular bacteria (wolbachia): verification from natural populations.” Mol Biol Evol, 27(3), 501-505. doi:10.1093/molbev/msp27.
Fei, D. L., Li, H., Kozul, C. D., Black, K. E., Singh, S., Gosse, J. A., DiRenzo, J., Martin, K. A., Wang, B., Hamilton, J. W., Karagas, M. R., & Robbins, D. J. (2010). “Activation of Hedgehog signaling by the environmental toxicant arsenic may contribute to the etiology of arsenic-induced tumors.” Cancer Res, 70(5), 1981-1988. doi:10.1158/0008-5472.CAN-09-289.
German, C. R., Bowen, A., Coleman, M. L., Honig, D. L., Huber, J. A., Jakuba, M. V., Kinsey, J. C., Kurz, M. D., Leroy, S., McDermott, J. M., de Lepinay, B. M., Nakamura, K., Seewald, J. S., Smith, J. L., Sylva, S. P., Van Dover, C. L., Whitcomb, L. L., & Yoerger, D. R. (2010). “Diverse styles of submarine venting on the ultraslow spreading Mid-Cayman Rise.” Proc Natl Acad Sci U S A, 107(32), 14020-14025. doi:10.1073/pnas.100920510.
Gilg, I. C., Amaral-Zettler, L. A., Countway, P. D., Moorthi, S., Schnetzer, A., & Caron, D. A. (2010). “Phylogenetic affiliations of mesopelagic acantharia and acantharian-like environmental 18S rRNA genes off the southern California coast.” Protist, 161(2), 197-211. doi:10.1016/j.protis.2009.09.00.
Gillor, O., Hadas, O. R. A., Post, A. F., & Belkin, S. (2010). “Phosphorus and nitrogen in a monomictic freshwater lake: employing cyanobacterial bioreporters to gain new insights into nutrient bioavailability.” Freshwater Biology, 55(6), 1182-1190. doi:DOI 10.1111/j.1365-2427.2009.02342..
Gladyshev, E. A., & Arkhipova, I. R. (2010). “Bdelloid rotifers McGraw Hill 2010 Yearbook of Science and Technology (pp.” 37-39). New York, NY: McGraw Hill Inc. .
Gladyshev, E. A., & Arkhipova, I. R. (2010). “A subtelomeric non-LTR retrotransposon Hebe in the bdelloid rotifer Adineta vaga is subject to inactivation by deletions but not 5′ truncations.” Mob DNA, 1(1), 12. doi:10.1186/1759-8753-1-1.
Gladyshev, E. A., & Arkhipova, I. R. (2010). “Genome structure of bdelloid rotifers: shaped by asexuality or desiccation?” J Hered, 101 Suppl 1, S85-93. doi:10.1093/jhered/esq00.
Hasegawa, Y., Welch, J. L. M., Valm, A. M., Rieken, C., Sogin, M. L., & Borisy, G. G. (2010). “Imaging Marine Bacteria with Unique 16S rRNA V6 Sequences by Fluorescence in situ Hybridization and Spectral Analysis.” Geomicrobiology Journal, 27(3), 251-260. doi:Pii 922060090 10.1080/0149045090345680.
Huber, J. A., Cantin, H. V., Huse, S. M., Mark Welch, D. B., Sogin, M. L., & Butterfield, D. A. (2010). “Isolated communities of Epsilonproteobacteria in hydrothermal vent fluids of the Mariana Arc seamounts.” FEMS Microbiol Ecol, 73(3), 538-549. doi:10.1111/j.1574-6941.2010.00910..
Huse, S. M., Welch, D. M., Morrison, H. G., & Sogin, M. L. (2010). “Ironing out the wrinkles in the rare biosphere through improved OTU clustering.” Environ Microbiol, 12(7), 1889-1898. doi:10.1111/j.1462-2920.2010.02193..
Karpinets, T. V., Obraztsova, A. Y., Wang, Y., Schmoyer, D. D., Kora, G. H., Park, B. H., Serres, M. H., Romine, M. F., Land, M. L., Kothe, T. B., Fredrickson, J. K., Nealson, K. H., & Uberbacher, E. C. (2010). “Conserved synteny at the protein family level reveals genes underlying Shewanella species’ cold tolerance and predicts their novel phenotypes.” Funct Integr Genomics, 10(1), 97-110. doi:10.1007/s10142-009-0142-.
Karpinets, T. V., Romine, M. F., Schmoyer, D. D., Kora, G. H., Syed, M. H., Leuze, M. R., Serres, M. H., Park, B. H., Samatova, N. F., & Uberbacher, E. C. (2010). “Shewanella knowledgebase: integration of the experimental data and computational predictions suggests a biological role for transcription of intergenic regions.” Database (Oxford), 2010, baq012. doi:10.1093/database/baq01.
Keeling, P. J., Corradi, N., Morrison, H. G., Haag, K. L., Ebert, D., Weiss, L. M., Akiyoshi, D. E., & Tzipori, S. (2010). “The reduced genome of the parasitic microsporidian Enterocytozoon bieneusi lacks genes for core carbon metabolism.” Genome Biol Evol, 2, 304-309. doi:10.1093/gbe/evq02.
Lasek-Nesselquist, E., Welch, D. M., & Sogin, M. L. (2010). “The identification of a new Giardia duodenalis assemblage in marine vertebrates and a preliminary analysis of G.” duodenalis population biology in marine systems. Int J Parasitol, 40(9), 1063-1074. doi:10.1016/j.ijpara.2010.02.01.
Lee, H. S., Komarova, Y. A., Nadezhdina, E. S., Anjum, R., Peloquin, J. G., Schober, J. M., Danciu, O., van Haren, J., Galjart, N., Gygi, S. P., Akhmanova, A., & Borisy, G. G. (2010). “Phosphorylation controls autoinhibition of cytoplasmic linker protein-170.” Mol Biol Cell, 21(15), 2661-2673. doi:10.1091/mbc.E09-12-103.
Mark Welch, D. B. (2010). “Monogononta McGraw-Hill Encyclopedia of Science and Technology, 11th Edition (11th Edition ed., Vol.” 1, pp. 1-1): McGraw-Hill.
McLellan, S. L., Huse, S. M., Mueller-Spitz, S. R., Andreishcheva, E. N., & Sogin, M. L. (2010). “Diversity and population structure of sewage-derived microorganisms in wastewater treatment plant influent.” Environ Microbiol, 12(2), 378-392. doi:10.1111/j.1462-2920.2009.02075..
Morf, L., Spycher, C., Rehrauer, H., Fournier, C. A., Morrison, H. G., & Hehl, A. B. (2010). “The transcriptional response to encystation stimuli in Giardia lamblia is restricted to a small set of genes.” Eukaryot Cell, 9(10), 1566-1576. doi:10.1128/EC.00100-1.
Olins, A. L., Rhodes, G., Mark Welch, D. B., Zwerger, M., & Olins, D. E. (2010). “Lamin B receptor Multi-tasking at the nuclear envelope.” Nucleus-Austin, 1, 53-70. doi:DOI 10.4161/nucl.1.1.1051.
Parfrey, L. W., Grant, J., Tekle, Y. I., Lasek-Nesselquist, E., Morrison, H. G., Sogin, M. L., Patterson, D. J., & Katz, L. A. (2010). “Broadly sampled multigene analyses yield a well-resolved eukaryotic tree of life.” Syst Biol, 59(5), 518-533. doi:10.1093/sysbio/syq03.
Schrenk, M. O., Huber, J. A., & Edwards, K. J. (2010). “Microbial provinces in the subseafloor.” Ann Rev Mar Sci, 2(1), 279-304. doi:10.1146/annurev-marine-120308-08100.
Smith, J. L., Barrett, J. E., Tusnady, G., Rejto, L., & Cary, S. C. (2010). “Resolving environmental drivers of microbial community structure in Antarctic soils.” Antarctic Science, 22(6), 673-680. doi:Doi 10.1017/S095410201000076.
Theroux, S. M., D’Andrea, W. D., Toney, J., Amaral-Zettler, L. A., & Huang, Y. (2010). “Phylogenetic diversity and evolutionary relatedness of alkenone-producing haptophyte algae in lakes: Implications for continental paleotemperature reconstructions.” Earth and Planetary Science Letters, 300(3-4), 311-320. doi:DOI 10.1016/j.epsl.2010.10.00.
Wankel, S. D., Chen, Y., Kendall, C., Post, A. F., & Paytan, A. (2010). “Sources of aerosol nitrate to the Gulf of Aqaba: Evidence from δ15N and δ18O of nitrate and trace metal chemistry.” Marine Chemistry, 120 (1-4), 90-99. doi:10.1016/j.marchem.2009.01.01.
Wernegreen, J. J., Kauppinen, S. N., & Degnan, P. H. (2010). “Slip into something more functional: selection maintains ancient frameshifts in homopolymeric sequences.” Mol Biol Evol, 27(4), 833-839. doi:10.1093/molbev/msp29.
2009
Aberle, N., Hansen, T., Boettger-Schnack, R., Burmeister, A., Post, A. F., & Sommer, U. (2009). “Differential routing of ‘new’ nitrogen toward higher trophic levels within the marine food web of the Gulf of Aqaba, Northern Red Sea.” Marine Biology, 157(1), 157-169. doi:10.1007/s00227-009-1306-.
Akiyoshi, D. E., Morrison, H. G., Lei, S., Feng, X., Zhang, Q., Corradi, N., Mayanja, H., Tumwine, J. K., Keeling, P. J., Weiss, L. M., & Tzipori, S. (2009). “Genomic survey of the non-cultivatable opportunistic human pathogen, Enterocytozoon bieneusi.” PLoS Pathog, 5(1), e1000261. doi:10.1371/journal.ppat.100026.
Alliegro, M. C., & Satir, P. (2009). “Origin of the cilium: novel approaches to examine a centriolar evolution hypothesis.” Methods Cell Biol, 94, 53-64. doi:10.1016/S0091-679X(08)94002-.
Amaral-Zettler, L. A., McCliment, E. A., Ducklow, H. W., & Huse, S. M. (2009). “A method for studying protistan diversity using massively parallel sequencing of V9 hypervariable regions of small-subunit ribosomal RNA genes.” PLoS One, 4(7), e6372. doi:10.1371/journal.pone.000637.
Antonopoulos, D. A., Huse, S. M., Morrison, H. G., Schmidt, T. M., Sogin, M. L., & Young, V. B. (2009). “Reproducible community dynamics of the gastrointestinal microbiota following antibiotic perturbation.” Infect Immun, 77(6), 2367-2375. doi:10.1128/IAI.01520-0.
Aurrecoechea, C., Brestelli, J., Brunk, B. P., Carlton, J. M., Dommer, J., Fischer, S., Gajria, B., Gao, X., Gingle, A., Grant, G., Harb, O. S., Heiges, M., Innamorato, F., Iodice, J., Kissinger, J. C., Kraemer, E., Li, W., Miller, J. A., Morrison, H. G., Nayak, V., Pennington, C., Pinney, D. F., Roos, D. S., Ross, C., Stoeckert, C. J. Jr., Sullivan, S., Treatman, C., & Wang, H. (2009). “GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis.” Nucleic Acids Res, 37(Database issue), D526-530. doi:10.1093/nar/gkn63.
Barr, F. D., Krohmer, L. J., Hamilton, J. W., & Sheldon, L. A. (2009). “Disruption of histone modification and CARM1 recruitment by arsenic represses transcription at glucocorticoid receptor-regulated promoters.” PLoS One, 4(8), e6766. doi:10.1371/journal.pone.000676.
Brazelton, W. J., Sogin, M. L., & Baross, J. A. (2009). “Multiple scales of diversification within natural populations of archaea in hydrothermal chimney biofilms.” Environmental Microbiology Reports, 2(2), 236-242.
Claessens, M., Wickham, S. A., Post, A. F., & Reuter, M. (2009). “A paradox of the ciliates?” High ciliate diversity in a resource-poor environment. Marine Biology, 157(3), 483-494. doi:10.1007/s00227-009-1334-.
Dick, G. J., Andersson, A. F., Baker, B. J., Simmons, S. L., Thomas, B. C., Yelton, A. P., & Banfield, J. F. (2009). “Community-wide analysis of microbial genome sequence signatures.” Genome Biol, 10(8), R85. doi:10.1186/gb-2009-10-8-r8.
Gilbert, J. A., Field, D., Swift, P., Newbold, L., Oliver, A., Smyth, T., Somerfield, P. J., Huse, S. M., & Joint, I. (2009). “The seasonal structure of microbial communities in the Western English Channel.” Environ Microbiol, 11(12), 3132-3139. doi:10.1111/j.1462-2920.2009.02017..
Gladyshev, E. A., & Arkhipova, I. R. (2009). “A single-copy IS5-like transposon in the genome of a bdelloid rotifer.” Mol Biol Evol, 26(8), 1921-1929. doi:10.1093/molbev/msp10.
Gladyshev, E. A., & Arkhipova, I. R. (2009). “Rotifer rDNA-specific R9 retrotransposable elements generate an exceptionally long target site duplication upon insertion.” Gene, 448(2), 145-150. doi:10.1016/j.gene.2009.08.01.
Gribble, K. E., Anderson, D. M., & Coats, D. W. (2009). “Sexual and asexual processes in Protoperidinium steidingerae Balech (Dinophyceae), with observations on life-history stages of Protoperidinium depressum (Bailey) Balech (Dinophyceae).” J Eukaryot Microbiol, 56(1), 88-103. doi:10.1111/j.1550-7408.2008.00378..
Hamilton, J. (2009). “The use of microarrays to understand the biology and toxicology of low dose arsenic.” In C. Tomlinson (Ed.), Microarrays: Their design and use, The Biomedical & Life Sciences Collection. Henry Stewart Talks Ltd, London (online at http://hstalks.com/bio).
Huber, J. A., Morrison, H. G., Huse, S. M., Neal, P. R., Sogin, M. L., & Mark Welch, D. B. (2009). “Effect of PCR amplicon size on assessments of clone library microbial diversity and community structure.” Environ Microbiol, 11(5), 1292-1302. doi:10.1111/j.1462-2920.2008.01857..
Hur, J. H., Van Doninck, K., Mandigo, M. L., & Meselson, M. (2009). “Degenerate tetraploidy was established before bdelloid rotifer families diverged.” Mol Biol Evol, 26(2), 375-383. doi:10.1093/molbev/msn26.
Ionescu, D., Penno, S., Hazanov, L., Chernihovsky, M., Rihtman, B., Post, A. F., & Oren, A. (2009). “Distribution of Archaea among the prokaryoplankton in the Gulf of Aqaba.” FEMS Microbiol. Ecol., 69, 425-438.
Kenney, D. E., & Borisy, G. G. (2009). “Thomas Hunt Morgan at the marine biological laboratory: naturalist and experimentalist.” Genetics, 181(3), 841-846. doi:10.1534/genetics.109.10165.
Komarova, Y., De Groot, C. O., Grigoriev, I., Gouveia, S. M., Munteanu, E. L., Schober, J. M., Honnappa, S., Buey, R. M., Hoogenraad, C. C., Dogterom, M., Borisy, G. G., Steinmetz, M. O., & Akhmanova, A. (2009). “Mammalian end binding proteins control persistent microtubule growth.” J Cell Biol, 184(5), 691-706. doi:10.1083/jcb.20080717.
Konstantinidis, K. T., Serres, M. H., Romine, M. F., Rodrigues, J. L., Auchtung, J., McCue, L. A., Lipton, M. S., Obraztsova, A., Giometti, C. S., Nealson, K. H., Fredrickson, J. K., & Tiedje, J. M. (2009). “Comparative systems biology across an evolutionary gradient within the Shewanella genus.” Proc Natl Acad Sci U S A, 106(37), 15909-15914. doi:10.1073/pnas.090200010.
Kozul, C. D., Ely, K. H., Enelow, R. I., & Hamilton, J. W. (2009). “Low-dose arsenic compromises the immune response to influenza A infection in vivo.” Environ Health Perspect, 117(9), 1441-1447. doi:10.1289/ehp.090091.
Kozul, C. D., Hampton, T. H., Davey, J. C., Gosse, J. A., Nomikos, A. P., Eisenhauer, P. L., Weiss, D. J., Thorpe, J. E., Ihnat, M. A., & Hamilton, J. W. (2009). “Chronic exposure to arsenic in the drinking water alters the expression of immune response genes in mouse lung.” Environ Health Perspect, 117(7), 1108-1115. doi:10.1289/ehp.080019.
Lasek-Nesselquist, E., Mark Welch, D. B., Thompson, R. C., Steuart, R. F., & Sogin, M. L. (2009). “Genetic exchange within and between assemblages of Giardia duodenalis.” J Eukaryot Microbiol, 56(6), 504-518. doi:10.1111/j.1550-7408.2009.00443..
Lazarevic, V., Whiteson, K., Huse, S. M., Hernandez, D., Farinelli, L., Osteras, M., Schrenzel, J., & Francois, P. (2009). “Metagenomic study of the oral microbiota by Illumina high-throughput sequencing.” J Microbiol Methods, 79(3), 266-271. doi:10.1016/j.mimet.2009.09.01.
Mackey, K. R. M., Paytan, A., Rivlin, T., & Post, A. F. (2009). “Phytoplankton responses to natural and simulated transitions in nutrient and light regimes in the oligotrophic Red Sea.” Mar. Biol., 156, 1531-1546.
Mark Welch, D. B., Ricci, C., & Meselson, M. (2009). “Bdelloid rotifers: progress in understanding the success of an evolutionary scandal.” In K. Martens, I. Shoen, & P. van Dijk (Ed.), Lost Sex: The Evolutionary Biology of Parthenogenesis (pp. 259-279). Heidelberg: Springer-Verlag.
Nahum, L. A., Goswami, S., & Serres, M. H. (2009). “Protein families reflect the metabolic diversity of organisms and provide support for functional prediction.” Physiol Genomics, 38(3), 250-260. doi:10.1152/physiolgenomics.90244.200.
Paytan, A., Mackey, K. R. M., Chen, Y., Lima, I. D., S.C., D., Mahowald, N., Labiosa, R., & Post, A. F. (2009). “Toxicity of atmospheric aerosols on marine phytoplankton.” Proc Natl Acad Sci U S A, 106(12), 4601-4605. doi:10.1073/pnas.081148610.
Post, A. F., Golan, D., Zandbank, K., & Penno, S. (2009). “Phytoplankton communities of the Gulf of Aqaba, Northern Red Sea.” In F. D. Por (Ed.), A Pocket-Sized Ocean, the Gulf of Aqaba (Eilat), Environment and Biodiversity (pp. 119-134). Jerusalem: Magna Press.
Scanlan, D. J., Ostrowski, M., Mazard, S., Dufresne, A., Garczarek, L., Hess, W. R., Post, A. F., Hagemann, M., Paulsen, I., & Partensky, F. (2009). “Ecological genomics of marine picocyanobacteria.” Microbiol Mol Biol Rev, 73(2), 249-299. doi:10.1128/MMBR.00035-0.
Schober, J. M., Cain, J. M., Komarova, Y. A., & Borisy, G. G. (2009). “Migration and actin protrusion in melanoma cells are regulated by EB1 protein.” Cancer Lett, 284(1), 30-36. doi:10.1016/j.canlet.2009.04.00.
Serres, M. H., Kerr, A. R., McCormack, T. J., & Riley, M. (2009). “Evolution by leaps: gene duplication in bacteria.” Biol Direct, 4, 46. doi:10.1186/1745-6150-4-4.
Smith, J., & Davidson, E. H. (2009). “Regulative recovery in the sea urchin embryo and the stabilizing role of fail-safe gene network wiring.” Proc Natl Acad Sci U S A, 106(43), 18291-18296. doi:10.1073/pnas.091000710.
Snell, T. W., Shearer, T. L., Smith, H. A., Kubanek, J., Gribble, K. E., & Mark Welch, D. B. (2009). “Genetic determinants of mate recognition in Brachionus manjavacas (Rotifera).” BMC Biol, 7, 60. doi:10.1186/1741-7007-7-6.
Sogin, M. L. (2009). “Characterizing Microbial Population Structures through Massively Parallel Sequencing.” In S. S. Epstein (Ed.), Uncultivated Microorganisms (Vol. 10, pp. 278-292): Springe.
Stoeck, T., Behnke, A., Christen, R., Amaral-Zettler, L. A., Rodriguez-Mora, M. J., Chistoserdov, A., Orsi, W., & Edgcomb, V. P. (2009). “Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities.” BMC Biol, 7, 72. doi:10.1186/1741-7007-7-7.
Turanov, A. A., Lobanov, A. V., Fomenko, D. E., Morrison, H. G., Sogin, M. L., Klobutcher, L. A., Hatfield, D. L., & Gladyshev, V. N. (2009). “Genetic code supports targeted insertion of two amino acids by one codon.” Science, 323(5911), 259-261. doi:10.1126/science.116474.
Turnbaugh, P. J., Hamady, M., Yatsunenko, T., Cantarel, B. L., Duncan, A., Ley, R. E., Sogin, M. L., Jones, W. J., Roe, B. A., Affourtit, J. P., Egholm, M., Henrissat, B., Heath, A. C., Knight, R., & Gordon, J. I. (2009). “A core gut microbiome in obese and lean twins.” Nature, 457(7228), 480-484. doi:10.1038/nature0754.
Van Doninck, K., Mandigo, M. L., Hur, J. H., Wang, P., Guglielmini, J., Milinkovitch, M. C., Lane, W. S., & Meselson, M. (2009). “Phylogenomics of unusual histone H2A Variants in Bdelloid rotifers.” PLoS Genet, 5(3), e1000401. doi:10.1371/journal.pgen.100040.
Wernegreen, J. J., Kauppinen, S. N., Brady, S. G., & Ward, P. S. (2009). “One nutritional symbiosis begat another: phylogenetic evidence that the ant tribe Camponotini acquired Blochmannia by tending sap-feeding insects.” BMC Evol Biol, 9(1), 292. doi:10.1186/1471-2148-9-29.
Wernegreen, J. J., & Wheeler, D. E. (2009). “Remaining flexible in old alliances: functional plasticity in constrained mutualisms.” DNA Cell Biol, 28(8), 371-382. doi:10.1089/dna.2009.087.
Whitman, C. T., Wirth, T. E., Meselson, M., Nissen, S. E., Juma, C., & Daley, G. (2009). “Your inbox, Mr President.” Nature, 457(7227), 258-261. doi:10.1038/457258.
Wilmes, P., Simmons, S. L., Denef, V. J., & Banfield, J. F. (2009). “The dynamic genetic repertoire of microbial communities.” FEMS Microbiol Rev, 33(1), 109-132. doi:10.1111/j.1574-6976.2008.00144..
Witek, A., Herlyn, H., Ebersberger, I., Mark Welch, D. B., & Hankeln, T. (2009). “Support for the monophyletic origin of Gnathifera from phylogenomics.” Mol Phylogenet Evol, 53(3), 1037-1041. doi:10.1016/j.ympev.2009.07.03.
Zaura, E., Keijser, B. J., Huse, S. M., & Crielaard, W. (2009). “Defining the healthy “core microbiome” of oral microbial communities.” BMC Microbiol, 9, 259. doi:10.1186/1471-2180-9-25.
2008
Aguero, F., Al-Lazikani, B., Aslett, M., Berriman, M., Buckner, F. S., Campbell, R. K., Carmona, S., Carruthers, I. M., Chan, A. W., Chen, F., Crowther, G. J., Doyle, M. A., Hertz-Fowler, C., Hopkins, A. L., McAllister, G., Nwaka, S., Overington, J. P., Pain, A., Paolini, G. V., Pieper, U., Ralph, S. A., Riechers, A., Roos, D. S., Sali, A., Shanmugam, D., Suzuki, T., Van Voorhis, W. C., & Verlinde, C. L. (2008). “Genomic-scale prioritization of drug targets: the TDR Targets database.” Nat Rev Drug Discov, 7(11), 900-907. doi:10.1038/nrd268.
Alliegro, M. C. (2008). “The implications of centrosomal RNA.” RNA Biol, 5(4), 198-200. doi:6972 [pii.
Alliegro, M. C., & Alliegro, M. A. (2008). “Centrosomal RNA correlates with intron-poor nuclear genes in Spisula oocytes.” Proc Natl Acad Sci U S A, 105(19), 6993-6997. doi:10.1073/pnas.080229310.
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Davey, J. C., Nomikos, A. P., Wungjiranirun, M., Sherman, J. R., Ingram, L., Batki, C., Lariviere, J. P., & Hamilton, J. W. (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), 165-172. doi:10.1289/ehp.1013.
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Dufresne, A., Ostrowski, M., Scanlan, D. J., Garczarek, L., Mazard, S., Palenik, B. P., Paulsen, I. T., de Marsac, N. T., Wincker, P., Dossat, C., Ferriera, S., Johnson, J., Post, A. F., Hess, W. R., & Partensky, F. (2008). “Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria.” Genome Biol, 9(5), R90. doi:10.1186/gb-2008-9-5-r9.
Fredrickson, J. K., Romine, M. F., Beliaev, A. S., Auchtung, J. M., Driscoll, M. E., Gardner, T. S., Nealson, K. H., Osterman, A. L., Pinchuk, G., Reed, J. L., Rodionov, D. A., Rodrigues, J. L., Saffarini, D. A., Serres, M. H., Spormann, A. M., Zhulin, I. B., & Tiedje, J. M. (2008). “Towards environmental systems biology of Shewanella.” Nat Rev Microbiol, 6(8), 592-603. doi:10.1038/nrmicro194.
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Gladyshev, E. A., Meselson, M., & Arkhipova, I. R. (2008). “Massive horizontal gene transfer in bdelloid rotifers.” Science, 320(5880), 1210-1213. doi:10.1126/science.115640.
Gradman, R. J., Ptacin, J. L., Bhasin, A., Reznikoff, W. S., & Goryshin, I. Y. (2008). “A bifunctional DNA binding region in Tn5 transposase.” Mol Microbiol, 67(3), 528-540. doi:10.1111/j.1365-2958.2007.06056..
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Hays, A. M., Lantz, R. C., Rodgers, L. S., Sollome, J. J., Vaillancourt, R. R., Andrew, A. S., Hamilton, J. W., & Camenisch, T. (2008). “Arsenic down-regulates vascular matrix.” Toxicol Pathol 36, 805-817.
Huber, J. A., & Holden, J. F. (2008). “Modeling the impact of diffuse vent microorganisms along mid-ocean ridges and flanks.” In R. P. Lowell, J. S. Seewald, A. Metaxas, & M. R. Perfit (Ed.), Magma to Microbe: Modeling Hydrothermal Processes at Oceanic Spreading Ridges (pp. 215-231). Washington, DC: American Geophysical Union Press.
Huse, S. M., Dethlefsen, L., Huber, J. A., Mark Welch, D. B., Relman, D. A., & Sogin, M. L. (2008). “Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing.” PLoS Genet, 4(11), e1000255. doi:10.1371/journal.pgen.100025.
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Kamennaya, N. A., Chernihovsky, M., & Post, A. F. (2008). “The cyanate utilization capacity of marine unicellular Cyanobacteria.” Limnology and Oceanography, 53(6), 2485-2494. doi:DOI 10.4319/lo.2008.53.6.248.
Keijser, B. J., Zaura, E., Huse, S. M., van der Vossen, J. M., Schuren, F. H., Montijn, R. C., ten Cate, J. M., & Crielaard, W. (2008). “Pyrosequencing analysis of the oral microflora of healthy adults.” J Dent Res, 87(11), 1016-1020. doi:87/11/1016 [pii.
Kozul, C. D., Nomikos, A. P., Hampton, T. H., Warnke, L. A., Gosse, J. A., Davey, J. C., Thorpe, J. E., Jackson, B. P., Ihnat, M. A., & Hamilton, J. W. (2008). “Laboratory diet profoundly alters gene expression and confounds genomic analysis in mouse liver and lung.” Chem Biol Interact, 173(2), 129-140. doi:10.1016/j.cbi.2008.02.00.
Lasek-Nesselquist, E., Bogomolni, A. L., Gast, R. J., Mark Welch, D. B., Ellis, J. C., Sogin, M. L., & Moore, M. J. (2008). “Molecular characterization of Giardia intestinalis haplotypes in marine animals: variation and zoonotic potential.” Dis Aquat Organ, 81(1), 39-51. doi:10.3354/dao0193.
Mark Welch, D. B., Mark Welch, J. L., & Meselson, M. (2008). “Evidence for degenerate tetraploidy in bdelloid rotifers.” Proc Natl Acad Sci U S A, 105(13), 5145-5149. doi:10.1073/pnas.080097210.
Nahum, L. A., & Pereira, S. L. (2008). “Phylogenomics, Protein Family Evolution, and the Tree of Life: An Integrated Approach between Molecular Evolution and Computational Intelligence.” In T. Smolinski, M. Milanova, & A.-E. Hassanien (Ed.), Studies in Computational Intelligence (SCI) (Vol. 122, pp. 259-279). Berlin Heidelberg: Springer-Verlag.
Palacios, C., Zettler, E., Amils, R., & Amaral-Zettler, L. (2008). “Contrasting microbial community assembly hypotheses: a reconciling tale from the Rio Tinto.” PLoS One, 3(12), e3853. doi:10.1371/journal.pone.000385.
Riley, M., Staley, J. T., Danchin, A., Wang, T. Z., Brettin, T. S., Hauser, L. J., Land, M. L., & Thompson, L. S. (2008). “Genomics of an extreme psychrophile, Psychromonas ingrahamii.” BMC Genomics, 9(1), 210. doi:10.1186/1471-2164-9-21.
Rull, K., Hallast, P., Uuskula, L., Jackson, J., Punab, M., Salumets, A., Campbell, R. K., & Laan, M. (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. doi:10.1093/molehr/gam08.
San Gil, I., Sheldon, W., Schmidt, T., Servilla, M., Aguilar, R., Gries, C., Gray, T., Field, D., Cole, J., Yun Pan, J., Palanisamy, G., Henshaw, D., O’Brien, M., Kinkel, L., McMahon, K., Kottmann, R., Amaral-Zettler, L. A., Hobbie, J., Goldstein, P., Guralnick, R. P., Brunt, J., & K., M. W. (2008). “Defining linkages between the GSC and NSF’s LTER program: How the Ecological Metadata Language (EML) relates to GCDML and other outcomes.” OMICS A Journal of Integrative Biology, 12(2), 151-156.
Santelli, C. M., Orcutt, B. N., Banning, E., Bach, W., Moyer, C. L., Sogin, M. L., Staudigel, H., & Edwards, K. J. (2008). “Abundance and diversity of microbial life in ocean crust.” Nature, 453(7195), 653-656. doi:10.1038/nature0689.
Scanlan, D. J., & Post, A. F. (2008). “Chapter 24 – Aspects of Marine Cyanobacterial Nitrogen Physiology and Connection to the Nitrogen Cycle.” In D. G. Capone, D. A. Bronk, M. R. Mulholland, & E. J. Carpenter (Ed.), Nitrogen in the Marine Environment (2nd Edition) (pp. 1073-1095). San Diego: Academic Press.
Schostak, N., Pyatkov, K. I., Zelentsova, E., Arkhipova, I. R., Shagin, D., Shagina, I., Mudrik, E., Blintsov, A., Clark, I., Finnegan, D. J., & Evgen’ev, M. B. (2008). “Molecular dissection of Penelope transposable element regulatory machinery.” Nucleic Acids Res, 36(8), 2522-2529. doi:10.1093/nar/gkm116.
Simmons, S. L., Dibartolo, G., Denef, V. J., Goltsman, D. S., Thelen, M. P., & Banfield, J. F. (2008). “Population genomic analysis of strain variation in Leptospirillum group II bacteria involved in acid mine drainage formation.” PLoS Biol, 6(7), e177. doi:10.1371/journal.pbio.006017.
Smith, J. (2008). “A protocol describing the principles of cis-regulatory analysis in the sea urchin.” Nat Protoc, 3(4), 710-718. doi:10.1038/nprot.2008.3.
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Aguilera, A., Amaral-Zettler, L. A., Souza-Egipsy, V., Zettler, E., & Amils, R. (2007). “Eukaryotic Community Structure from Río Tinto (SW, Spain), a Highly Acidic River.” In J. Seckbach (Ed.), Algae and Cyanobacteria in Extreme Environments (Vol. 11, pp. 465-485): Springer Netherlands.
Aguilera, A., Zettler, E., Gomez, F., Amaral-Zettler, L. A., Rodriguez, N., & Amils, R. (2007). “Distribution and seasonal variability in the benthic eukaryotic community of Rio Tinto (SW, Spain), an acidic, high metal extreme environment.” Syst Appl Microbiol, 30(7), 531-546. doi:10.1016/j.syapm.2007.05.00.
Alliegro, M. C., & Alliegro, M. A. (2007). “Echinonectin is a Del-1-like molecule with regulated expression in sea urchin embryos.” Gene Expr Patterns, 7(6), 651-656. doi:10.1016/j.modgep.2007.03.00.
Baross, J. A., Schrenk, M. O., & Huber, J. A. (2007). “Limits of carbon life on Earth and elsewhere.” In W. T. I. Sullivan & J. A. Baross (Ed.), Planets and Life: The Emerging Science of Astrobiology (pp. 275-291). Cambridge, UK: Cambridge University Press.
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Bordenstein, S. R. (2007). “Discover the microbes within: The Wolbachia Project.” Focus on Microbiology Education 14(1), 4-5.
Bordenstein, S. R., & Werren, J. H. (2007). “Bidirectional incompatibility among divergent Wolbachia and incompatibility level differences among closely related Wolbachia in Nasonia.” Heredity (Edinb), 99(3), 278-287. doi:10.1038/sj.hdy.680099.
Chapman, M., & Alliegro, M. C. (2007). “A symbiogenetic origin for the centrosome?” Symbiosis, 44, 23-31.
Chen, Y., Street, J., Golan, D., Post, A. F., & Paytan, A. (2007). “Estimate of atmospheric dry deposition fluxes and associate input of nutrients in the Gulf of Aqaba.” Journal of Geophysical Research, 112, D04309.
Corradi, N., Akiyoshi, D. E., Morrison, H. G., Feng, X., Weiss, L. M., Tzipori, S., & Keeling, P. J. (2007). “Patterns of genome evolution among the microsporidian parasites Encephalitozoon cuniculi, Antonospora locustae and Enterocytozoon bieneusi.” PLoS One, 2(12), e1277. doi:10.1371/journal.pone.000127.
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D’Hondt, S., Inagaki, F., Ferdelman, T., Barker Jørgensen, B., Kato, K., Kemp, P., Sobecky, P., Sogin, M., & Takai, K. (2007). “Exploring Subseafloor Life with the Integrated Ocean Drilling Program.” Sci. Dril., 5, 26-37. doi:10.2204/iodp.sd.5.03.200.
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Edgcomb, V. P., Molyneaux, S. J., Boer, S., Wirsen, C. O., Saito, M., Atkins, M. S., Lloyd, K., & Teske, A. (2007). “Survival and growth of two heterotrophic hydrothermal vent archaea, Pyrococcus strain GB-D and Thermococcus fumicolans, under low pH and high sulfide concentrations in combination with high temperature and pressure regimes.” Extremophiles, 11(2), 329-342. doi:10.1007/s00792-006-0043-.
Ekanayake, D. K., Mark Welch, D. B., Kieft, R., Hajduk, S., & Dittus, W. P. J. (2007). “Transmission dynamics of Cryptosporidium infection in a natural population of non-human primates at Polonnaruwa, Sri Lanka.” Am J Trop Med Hyg, 77(5), 818-822.
Garczarek, L., Dufresne, A., Rousvoal, S., West, N., Mazard, S., Marie, D., Claustre, H., Raimbault, P., Post, A. F., Scanlan, D., & Partensky, F. (2007). “High vertical and low horizontal microdiversity of Prochlorococcus genotypes in the Mediterranean Sea in summer.” FEMS Microbiology Ecology, 60, 189-206.
Gladyshev, E. A., & Arkhipova, I. R. (2007). “Telomere-associated endonuclease-deficient Penelope-like retroelements in diverse eukaryotes.” Proc Natl Acad Sci U S A, 104(22), 9352-9357. doi:10.1073/pnas.070274110.
Gladyshev, E. A., Meselson, M., & Arkhipova, I. R. (2007). “A deep-branching clade of retrovirus-like retrotransposons in bdelloid rotifers.” Gene, 390(1-2), 136-145. doi:10.1016/j.gene.2006.09.02.
Gribble, K. E., Nolan, G., & Anderson, D. M. (2007). “Biodiversity, biogeography and potential trophic impact of Protoperidinium spp.” (Dinophyceae) off the southwestern coast of Ireland. Journal of Plankton Research, 29(11), 931-947. doi:DOI 10.1093/plankt/fbm07.
Hegreness, M., & Meselson, M. (2007). “What did Sutton see? Thirty years of confusion over the chromosomal basis of Mendelism.” Genetics, 176(4), 1939-1944. doi:10.1534/genetics.104.7972.
Huber, J. A., Mark Welch, D. B., Morrison, H. G., Huse, S. M., Neal, P. R., Butterfield, D. A., & Sogin, M. L. (2007). “Microbial population structures in the deep marine biosphere.” Science, 318(5847), 97-100. doi:10.1126/science.114668.
Huse, S. M., Huber, J. A., Morrison, H. G., Sogin, M. L., & Mark Welch, D. B. (2007). “Accuracy and quality of massively parallel DNA pyrosequencing.” Genome Biol, 8(7), R143. doi:10.1186/gb-2007-8-7-r14.
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Kieft, R., Brand, V., Ekanayake, D. K., Sweeney, K., DiPaolo, C., Reznikoff, W. S., & Sabatini, R. (2007). “JBP2, a SWI2/SNF2-like protein, regulates de novo telomeric DNA glycosylation in bloodstream form Trypanosoma brucei.” Mol Biochem Parasitol, 156(1), 24-31. doi:10.1016/j.molbiopara.2007.06.01.
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Mark Welch, D. B. (2007). “Bdelloidea McGraw-Hill Encyclopedia of Science and Technology (10th Edition ed., Vol.” 1, pp. 1-1): McGraw-Hill.
Meselson, M., & Mark Welch, D. B. (2007). “Evolution.” Stable heterozygosity? Science, 318(5848), 202-203. doi:10.1126/science.115019.
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Panagiotis, I., Hotopp, J. C. D., Sapounizis, P., Siozios, S., Tsiamis, G., Bordenstein, S. R., Baldo, L., Werren, J. H., & Bourtzis, K. (2007). “On the origin of DNA replication of Wolbachia and closely related bacteria.” BMC Genomics, 8, 182.
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Adams, C. D., Schnurr, B., Skoko, D., Marko, J. F., & Reznikoff, W. S. (2006). “Tn5 transposase loops DNA in the absence of Tn5 transposon end sequences.” Mol Microbiol, 62(6), 1558-1568. doi:10.1111/j.1365-2958.2006.05471..
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Amaral-Zettler, L. A., Cole, J., Laatsch, A. D., Nerad, T. A., Anderson, O. R., & Reysenbach, A. L. (2006). “Vannella epipetala n.” sp. isolated from the leaf surface of Spondias mombin (Anacardiaceae) growing in the dry forest of Costa Rica. J Eukaryot Microbiol, 53(6), 522-530. doi:10.1111/j.1550-7408.2006.00143..
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Bach, W., Edwards, K. J., Hayes, J. M., Huber, J. A., Sievert, S. M., & Sogin, M. L. (2006). “Energy in the dark: Fuel for life in the deep ocean and beyond.” Eos Transactions, American Geophysical Union, 87(7), 73-78.
Baldo, L., Bordenstein, S., Wernegreen, J. J., & Werren, J. H. (2006). “Widespread recombination throughout Wolbachia genomes.” Mol Biol Evol, 23(2), 437-449. doi:10.1093/molbev/msj04.
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Cantarel, B. L., Morrison, H. G., & Pearson, W. (2006). “Exploring the relationship between sequence similarity and accurate phylogenetic trees.” Mol Biol Evol, 23(11), 2090-2100. doi:10.1093/molbev/msl08.
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D’Andrea, W. J., Lage, M., Martiny, J. B. H., Laatsch, A. D., Amaral-Zettler, L. A., Sogin, M. L., & Huang, Y. S. (2006). “Alkenone producers inferred from well-preserved 18S rDNA in Greenland lake sediments.” Journal of Geophysical Research-Biogeosciences, 111(G3). doi:Artn G0301310.1029/2005jg00012.
Huber, J. A., Butterfield, D. A., & Baross, J. A. (2006). “Diversity and distribution of subseafloor Thermococcales populations in diffuse hydrothermal vents at an active deep-sea volcano in the northeast Pacific Ocean.” Journal of Geophysical Research-Biogeosciences, 111(G4). doi:ARTN G04016 10.1029/2005jg00009.
Huber, J. A., Johnson, H. P., Butterfield, D. A., & Baross, J. A. (2006). “Microbial life in ridge flank crustal fluids.” Environ Microbiol, 8(1), 88-99. doi:10.1111/j.1462-2920.2005.00872..
Hutchinson, L., Mustard, J., Gendrin, A., Fernandez Remolar, D., Amils, R., & Amaral-Zettler, L. A. (2006). “Finding Mineralogically Interesting Targets for Exploration from Spatially Coarse Visible and Near IR Spectra.” Earth and Planetary Science Letters, 252, 201-214.
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Slagter-Jager, J. G., Allen, G. S., Smith, D., Hahn, I. A., Frank, J., & Belfort, M. (2006). “Visualization of a group II intron in the 23S rRNA of a stable ribosome.” Proc Natl Acad Sci U S A, 103(26), 9838-9843. doi:10.1073/pnas.060395610.
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Alliegro, M. C., & Alliegro, M. A. (2005). “Differential expression of tyrosinated tubulin in Spisula solidissima polar bodies.” Dev Dyn, 232(1), 216-220. doi:10.1002/dvdy.2020.
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Bahr, M., Crump, B. C., Klepac-Ceraj, V., Teske, A., Sogin, M. L., & Hobbie, J. E. (2005). “Molecular characterization of sulfate-reducing bacteria in a New England salt marsh.” Environ Microbiol, 7(8), 1175-1185. doi:10.1111/j.1462-2920.2005.00796..
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Bordenstein, S., & Rosengaus, R. B. (2005). “Discovery of a novel Wolbachia super group in Isoptera.” Curr Microbiol, 51(6), 393-398. doi:10.1007/s00284-005-0084-.
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Casiraghi, M., Bordenstein, S. R., Baldo, L., Lo, N., Beninati, T., Wernegreen, J. J., Werren, J. H., & Bandi, C. (2005). “Phylogeny of Wolbachia pipientis based on gltA, groEL and ftsZ gene sequences: clustering of arthropod and nematode symbionts in the F supergroup, and evidence for further diversity in the Wolbachia tree.” Microbiology, 151(Pt 12), 4015-4022. doi:10.1099/mic.0.28313-.
Conlan, L. H., Stanger, M. J., Ichiyanagi, K., & Belfort, M. (2005). “Localization, mobility and fidelity of retrotransposed Group II introns in rRNA genes.” Nucleic Acids Res, 33(16), 5262-5270. doi:10.1093/nar/gki81.
Coros, C. J., Landthaler, M., Piazza, C. L., Beauregard, A., Esposito, D., Perutka, J., Lambowitz, A. M., & Belfort, M. (2005). “Retrotransposition strategies of the Lactococcus lactis Ll.LtrB group II intron are dictated by host identity and cellular environment.” Mol Microbiol, 56(2), 509-524. doi:10.1111/j.1365-2958.2005.04554..
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Dhillon, A., Goswami, S., Riley, M., Teske, A., & Sogin, M. L. (2005). “Domain evolution and functional diversification of sulfite reductases.” Astrobiology, 5(1), 18-29. doi:10.1089/ast.2005.5.1.
Dhillon, A., Lever, M., Lloyd, K. G., Albert, D. B., Sogin, M. L., & Teske, A. (2005). “Methanogen diversity evidenced by molecular characterization of methyl coenzyme M reductase A (mcrA) genes in hydrothermal sediments of the Guaymas Basin.” Appl Environ Microbiol, 71(8), 4592-4601. doi:10.1128/AEM.71.8.4592-4601.200.
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Mühling, M., Fuller, N. J., Millard, A., Scanlan, D. J., Post, A. F., Wilson, W. H., & Mann, N. H. (2005). “Genetic diversity of marine picoplankton (Synechococcus) blooms and covariance of the associated virioplankton population.” Environ Microbiol, 7(4), 499-508.
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