JBPC Publications: 2000 - 2010

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.

Amaral-Zettler, L. A., Peplies, J., Ramette, A., Fuchs, B., Ludwig, W., & Glockner, F. O. (2008). “Proceedings of the international workshop on Ribosomal RNA technology, April 7-9, 2008, Bremen, Germany.” Syst Appl Microbiol, 31(4), 258-268. doi:10.1016/j.syapm.2008.08.00.

Amaral-Zettler, L. A., Rocca, J. D., Lamontagne, M. G., Dennett, M. R., & Gast, R. J. (2008). “Changes in microbial community structure in the wake of Hurricanes Katrina and Rita.” Environ Sci Technol, 42(24), 9072-9078. doi:doi:10.1021/es801904.

Biddle, J. F., Huse, S. M., Sogin, M. L., & Teske, A. (2008). “Archaeal and bacterial diversity of deep marine subsurface sediments analysed by V6-tag sequencing.” Paper presented at the Poster and Abstract at ICOMM Workshop “Assessing marine microbial diversity: problems and solutions”, Amsterdam, The Netherlands.

Claessens, M., Wickham, S. A., Post, A. F., & Reuter, M. (2008). “Ciliate community in the oligotrophic Gulf of Aqaba, Red Sea.” Aquatic Microbial Ecology, 53(2), 181-190. doi:DOI 10.3354/ame0124.

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.

Dethlefsen, L., Huse, S. M., Sogin, M. L., & Relman, D. A. (2008). “The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing.” PLoS Biol, 6(11), e280. doi:10.1371/journal.pbio.006028.

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.

Gil, I. S., Sheldon, W., Schmidt, T., Servilla, M., Aguilar, R., Gries, C., Gray, T., Field, D., Cole, J., Pan, J. Y., 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., & Michener, W. K. (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), 151-156. doi:10.1089/omi.2008.001.

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..

Gradman, R. J., & Reznikoff, W. S. (2008). “Tn5 synaptic complex formation: role of transposase residue W450.” J Bacteriol, 190(4), 1484-1487. doi:10.1128/JB.01488-0.

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.

Jost, M. C., Hillis, D. M., Lu, Y., Kyle, J. W., Fozzard, H. A., & Zakon, H. H. (2008). “Toxin-resistant sodium channels: parallel adaptive evolution across a complete gene family.” Mol Biol Evol, 25(6), 1016-1024. doi:10.1093/molbev/msn02.

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.

Smith, J., & Davidson, E. H. (2008). “Gene regulatory network subcircuit controlling a dynamic spatial pattern of signaling in the sea urchin embryo.” Proc Natl Acad Sci U S A, 105(51), 20089-20094. doi:10.1073/pnas.080644210.

Smith, J., & Davidson, E. H. (2008). “A new method, using cis-regulatory control, for blocking embryonic gene expression.” Dev Biol, 318(2), 360-365. doi:10.1016/j.ydbio.2008.02.05.

Smith, J., Kraemer, E., Liu, H., Theodoris, C., & Davidson, E. (2008). “A spatially dynamic cohort of regulatory genes in the endomesodermal gene network of the sea urchin embryo.” Dev Biol, 313(2), 863-875. doi:10.1016/j.ydbio.2007.10.04.

Stewart, J. R., Gast, R. J., Fujioka, R. S., Solo-Gabriele, H. M., Meschke, J. S., Amaral-Zettler, L. A., Del Castillo, E., Polz, M. F., Collier, T. K., Strom, M. S., Sinigalliano, C. D., Moeller, P. D., & Holland, A. F. (2008). “The coastal environment and human health: microbial indicators, pathogens, sentinels and reservoirs.” Environ Health, 7 Suppl 2, S3. doi:10.1186/1476-069X-7-S2-S.

Suga, K., Mark Welch, D. B., Tanaka, Y., Sakakura, Y., & Hagiwara, A. (2008). “Two circular chromosomes of unequal copy number make up the mitochondrial genome of the rotifer Brachionus plicatilis.” Molecular Biology and Evolution, 25(6), 1129-1137. doi:DOI 10.1093/molbev/msn05.

Tamas, I., Wernegreen, J. J., Nystedt, B., Kauppinen, S. N., Darby, A. C., Gomez-Valero, L., Lundin, D., Poole, A. M., & Andersson, S. G. (2008). “Endosymbiont gene functions impaired and rescued by polymerase infidelity at poly(A) tracts.” Proc Natl Acad Sci U S A, 105(39), 14934-14939. doi:10.1073/pnas.080655410.

Ye, S., MacEachran, D. P., Hamilton, J. W., O’Toole, G. A., & Stanton, B. A. (2008). “Chemotoxicity of doxorubicin and surface expression of P-glycoprotein (MDR1) is regulated by the Pseudomonas aeruginosa toxin Cif.” Am J Physiol Cell Physiol, 295(3), C807-818. doi:10.1152/ajpcell.00234.200.

2007

Adams, C. D., Schnurr, B., Marko, J. F., & Reznikoff, W. S. (2007). “Pulling apart catalytically active Tn5 synaptic complexes using magnetic tweezers.” J Mol Biol, 367(2), 319-327. doi:10.1016/j.jmb.2006.12.06.

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.

Bordenstein, S. R. (2007). “Evolutionary genomics: transdomain gene transfers.” Curr Biol, 17(21), R935-936. doi:10.1016/j.cub.2007.09.02.

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.

Curcio, M. J., & Belfort, M. (2007). “The beginning of the end: links between ancient retroelements and modern telomerases.” Proc Natl Acad Sci U S A, 104(22), 9107-9108. doi:10.1073/pnas.070322410.

Czyz, A., Stillmock, K. A., Hazuda, D. J., & Reznikoff, W. S. (2007). “Dissecting Tn5 transposition using HIV-1 integrase diketoacid inhibitors.” Biochemistry, 46(38), 10776-10789. doi:10.1021/bi700654.

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.

Driscoll, M. E., Romine, M. F., Juhn, F. S., Serres, M. H., McCue, L. A., Beliaev, A. S., Fredrickson, J. K., & Gardner, T. S. (2007). “Identification of diverse carbon utilization pathways in Shewanella oneidensis MR-1 via expression profiling.” Genome Inform, 18, 287-298. doi:9781860949920_0028 [pii.

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.

Ioannidis, P., Dunning Hotopp, J. C., Sapountzis, P., Siozios, S., Tsiamis, G., Bordenstein, S. R., Baldo, L., Werren, J. H., & Bourtzis, K. (2007). “New criteria for selecting the origin of DNA replication in Wolbachia and closely related bacteria.” BMC Genomics, 8, 182. doi:10.1186/1471-2164-8-18.

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.

Leary, P. R., Remsen, D. P., Norton, C. N., Patterson, D. J., & Sarkar, I. N. (2007). “uBioRSS: tracking taxonomic literature using RSS Bioinformatics (Vol.” 23, pp. 1434-1436).

Lo, N., Paraskevopoulos, C., Bourtzis, K., O’Neill, S. L., Werren, J. H., Bordenstein, S. R., & Bandi, C. (2007). “Taxonomic status of the intracellular bacterium Wolbachia pipientis.” Int J Syst Evol Microbiol, 57(Pt 3), 654-657. doi:10.1099/ijs.0.64515-.

Mackey, K. R. M., Calhoun, M., Labiosa, R. G., Street, J. H., Post, A. F., & Paytan, A. (2007). “Phosphorus availability controls phytoplankton community dynamics and taxon specific nutrient status in the Gulf of Aqaba, Red Sea.” Limnology and Oceanography, 52(2), 873-885.

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.

Morrison, H. G., McArthur, A. G., Gillin, F. D., Aley, S. B., Adam, R. D., Olsen, G. J., Best, A. A., Cande, W. Z., Chen, F., Cipriano, M. J., Davids, B. J., Dawson, S. C., Elmendorf, H. G., Hehl, A. B., Holder, M. E., Huse, S. M., Kim, U. U., Lasek-Nesselquist, E., Manning, G., Nigam, A., Nixon, J. E., Palm, D., Passamaneck, N. E., Prabhu, A., Reich, C. I., Reiner, D. S., Samuelson, J., Svard, S. G., & Sogin, M. L. (2007). “Genomic minimalism in the early diverging intestinal parasite Giardia lamblia.” Science, 317(5846), 1921-1926. doi:10.1126/science.114383.

Morrison, H. G., McArthur, A. G., Gillin, F. D., Aley, S. B., Adam, R. D., Olsen, G. J., Best, A. A., Cande, W. Z., Chen, F., Cipriano, M. J., Davids, B. J., Dawson, S. C., Elmendorf, H. G., Hehl, A. B., Holder, M. E., Huse, S. M., Kim, U. U., Lasek-Nesselquist, E., Manning, G., Nigam, A., Nixon, J. E. J., Palm, D., Passamaneck, N. E., Prabhu, A., Reich, C. I., Reiner, D. S., Samuelson, J., Svard, S. G., & Sogin, M. L. (2007). “Genomic Minimalism in the Early Diverging Intestinal Parasite Giardia lamblia.” Science, 317(5846), 1921.

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.

Patterson, D. J., Bhattacharya, D., Cole, J., Dunthorn, M., Logsdon, J., Katz, L., & Wegener-Parfrey, L. (2007). “Classifying protists.” Microbiology today(Feb 07), 44-45.

Patterson, D. J., & Sogin, M. L. (2007). “The micro*scope web tool.” In S. W. T. & J. A. Baross (Ed.), Planets and Life: The emerging Science of Astrobiology (pp. 579-584). Cambridge: Cambridge University Press.

Prabhu, A., Morrison, H. G., Martinez, C. R., 3rd, & Adam, R. D. (2007). “Characterisation of the subtelomeric regions of Giardia lamblia genome isolate WBC6.” Int J Parasitol, 37(5), 503-513. doi:10.1016/j.ijpara.2006.12.01.

Robbins, J. B., Stapleton, M., Stanger, M. J., Smith, D., Dansereau, J. T., Derbyshire, V., & Belfort, M. (2007). “Homing endonuclease I-TevIII: dimerization as a means to a double-strand break.” Nucleic Acids Res, 35(5), 1589-1600. doi:10.1093/nar/gkl117.

Sanogo, Y. O., Dobson, S. L., Bordenstein, S. R., & Novak, R. J. (2007). “Disruption of the Wolbachia surface protein gene wspB by a transposable element in mosquitoes of the Culex pipiens complex (Diptera, Culicidae).” Insect Mol Biol, 16(2), 143-154. doi:10.1111/j.1365-2583.2006.00707..

Simmons, S. L., Bazylinski, D. A., & Edwards, K. J. (2007). “Population dynamics of marine magnetotactic bacteria in a meromictic salt pond described with qPCR.” Environ Microbiol, 9(9), 2162-2174. doi:10.1111/j.1462-2920.2007.01330..

Simmons, S. L., & Edwards, K. J. (2007). “Unexpected diversity in populations of the many-celled magnetotactic prokaryote.” Environ Microbiol, 9(1), 206-215. doi:10.1111/j.1462-2920.2006.01129..

Simmons, S. L., & Edwards, K. J. (2007). “Geobiology of magnetotactic bacteria.” In D. Schüler (Ed.), Magnetoreception and Magnetosomes in Bacteria (pp. 77-102). Berlin: Springer-Verlag.

Sinigalliano, C. D., Gidley, M. L., Shibata, T., Whitman, D., Dixon, T. H., Laws, E., Hou, A., Bachoon, D., Brand, L., Amaral-Zettler, L. A., Gast, R. J., Steward, G. F., Nigro, O. D., Fujioka, R., Betancourt, W. Q., Vithanage, G., Mathews, J., Fleming, L. E., & Solo-Gabriele, H. M. (2007). “Impacts of Hurricanes Katrina and Rita on the microbial landscape of the New Orleans area.” Proc Natl Acad Sci U S A, 104(21), 9029-9034. doi:10.1073/pnas.061055210.

Slagter-Jager, J. G., Puzis, L., Gutgsell, N. S., Belfort, M., & Jain, C. (2007). “Functional defects in transfer RNAs lead to the accumulation of ribosomal RNA precursors.” RNA, 13(4), 597-605. doi:10.1261/rna.31940.

Smith, J., Theodoris, C., & Davidson, E. H. (2007). “A gene regulatory network subcircuit drives a dynamic pattern of gene expression.” Science, 318(5851), 794-797. doi:10.1126/science.114652.

Sogin, M. L., Patterson, D. J., & McArthur, A. (2007). “The origin and diversification of eukaryotes.” In S. W. T. & J. A. Baross (Ed.), Planets and Life: The emerging Science of Astrobiology (pp. 265-274). Cambridge: Cambridge University Press.

Suga, K., Mark Welch, D. B., Tanaka, Y., Sakakura, Y., & Hagiwara, A. (2007). “Analysis of expressed sequence tags of the cyclically parthenogenetic rotifer Brachionus plicatilis.” PLoS One, 2(7), e671. doi:10.1371/journal.pone.000067.

Vaezeslami, S., Sterling, R., & Reznikoff, W. S. (2007). “Site-directed mutagenesis studies of tn5 transposase residues involved in synaptic complex formation.” J Bacteriol, 189(20), 7436-7441. doi:10.1128/JB.00524-0.

Van Roey, P., Pereira, B., Li, Z., Hiraga, K., Belfort, M., & Derbyshire, V. (2007). “Crystallographic and mutational studies of Mycobacterium tuberculosis recA mini-inteins suggest a pivotal role for a highly conserved aspartate residue.” J Mol Biol, 367(1), 162-173. doi:10.1016/j.jmb.2006.12.05.

Wells, L. E., Armstrong, J. C., & Huber, J. A. (2007). “Disciplinary aspirations and educational opportunities.” In W. T. I. Sullivan & J. A. Baross (Ed.), Planets and Life: The Emerging Science of Astrobiology (pp. 547-557). Cambridge: Cambridge University Press.

Wernegreen, J. J. (2007). “Genomic signatures of intracellularity: Evolutionary patterns and paces in bacterial mutalists and parasites.” In M. J. Pallen, K. E. Nelson, & G. M. Preston (Ed.), Bacterial Pathogenomics (pp. 196-212). Washington, DC: ASM Press.

Winterberg, K. M., & Reznikoff, W. S. (2007). “Screening transposon mutant libraries using full-genome oligonucleotide microarrays.” Methods Enzymol, 421, 110-125. doi:10.1016/S0076-6879(06)21011-.

Winterberg, K. M., & Reznikoff, W. S. (2007). “Transposon-based strategies for the identification of essential bacterial genes.” In A. Osterman & S. Gerdes (Ed.), Gene Essentiality at Genome Scale: Protocols and Bioinformatics. Totowa, NJ: Humana Press.

2006

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..

Alliegro, M. C., Alliegro, M. A., & Palazzo, R. E. (2006). “Centrosome-associated RNA in surf clam oocytes.” Proc Natl Acad Sci U S A, 103(24), 9034-9038. doi:10.1073/pnas.060285910.

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..

Arkhipova, I. R. (2006). “Distribution and phylogeny of Penelope-like elements in eukaryotes.” Syst Biol, 55(6), 875-885.

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.

Baldo, L., Dunning Hotopp, J. C., Jolley, K. A., Bordenstein, S. R., Biber, S. A., Choudhury, R. R., Hayashi, C., Maiden, M. C., Tettelin, H., & Werren, J. H. (2006). “Multilocus sequence typing system for the endosymbiont Wolbachia pipientis.” Appl Environ Microbiol, 72(11), 7098-7110. doi:10.1128/AEM.00731-0.

Beauregard, A., Chalamcharla, V. R., Piazza, C. L., Belfort, M., & Coros, C. J. (2006). “Bipolar localization of the group II intron Ll.LtrB is maintained in Escherichia coli deficient in nucleoid condensation, chromosome partitioning and DNA replication.” Mol Microbiol, 62(3), 709-722. doi:10.1111/j.1365-2958.2006.05419..

Biddle, J. F., Lipp, J. S., Lever, M. A., Lloyd, K. G., Sorensen, K. B., Anderson, R., Fredricks, H. F., Elvert, M., Kelly, T. J., Schrag, D. P., Sogin, M. L., Brenchley, J. E., Teske, A., House, C. H., & Hinrichs, K. U. (2006). “Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru.” Proc Natl Acad Sci U S A, 103(10), 3846-3851. doi:10.1073/pnas.060003510.

Bordenstein, S. R., Marshall, M. L., Fry, A. J., Kim, U., & Wernegreen, J. J. (2006). “The tripartite associations between bacteriophage, Wolbachia, and arthropods.” PLoS Pathog, 2(5), e43. doi:10.1371/journal.ppat.002004.

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.

Consortium, S. U. G. S. (2006). “The genome of the sea urchin Strongylocentrotus purpuratus.” Science, 314, 941-952.

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.

Ley, R. E., Harris, J. K., Wilcox, J., Spear, J. R., Miller, S. R., Bebout, B. M., Maresca, J. A., Bryant, D. A., Sogin, M. L., & Pace, N. R. (2006). “Unexpected diversity and complexity of the Guerrero Negro hypersaline microbial mat.” Appl Environ Microbiol, 72(5), 3685-3695. doi:10.1128/AEM.72.5.3685-3695.200.

Liu, Q., Derbyshire, V., Belfort, M., & Edgell, D. R. (2006). “Distance determination by GIY-YIG intron endonucleases: discrimination between repression and cleavage functions.” Nucleic Acids Res, 34(6), 1755-1764. doi:10.1093/nar/gkl07.

Mühling, M., Fuller, N. J., Somerfield, P. J., Post, A. F., Wilson, W. H., Scanlan, D. J., Joint, I., & Mann, N. H. (2006). “High resolution genetic diversity studies of marine Synechococcus using rpoC1-based Restriction Fragment Length Polymorphism.” Aquatic Microbial Ecology, 45, 263-275.

Murray, S., Hoppenrath, M., Preisfeld, A., Larsen, J., Yoshimatsu, S., Toriumi, S., & Patterson, D. J. (2006). “Phylogenetics of Rhinodinium broomeense gen.” et sp nov., a peridinioid, sand-dwelling dinoflagellate (Dinophyceae). Journal of Phycology, 42(4), 934-942. doi:DOI 10.1111/j.1529-8817.2006.00241..

Paraskevopoulos, C., Bordenstein, S. R., Wernegreen, J. J., Werren, J. H., & Bourtzis, K. (2006). “Toward a Wolbachia multilocus sequence typing system: discrimination of Wolbachia strains present in Drosophila species.” Curr Microbiol, 53(5), 388-395. doi:10.1007/s00284-006-0054-.

Patterson, D. J., Remsen, D., Marino, W. A., & Norton, C. (2006). “Taxonomic indexing–extending the role of taxonomy.” Syst Biol, 55(3), 367-373. doi:10.1080/1063515050054168.

Penno, S., Lindell, D., & Post, A. F. (2006). “Diversity of Synechococcus and Prochlorococcus populations determined from DNA sequences of the N-regulatory gene ntcA.” Environ Microbiol, 8(7), 1200-1211. doi:10.1111/j.1462-2920.2006.01010..

Post, A. F. (2006). “The Genus Prochlorococcus.” In M. Dworkin, S. Falkow, E. Rosenberg, K.-H. Schleifer, & E. Stackebrandt (Ed.), The Prokaryotes (pp. 1099-1110): Springer US.

Remsen, D. P., Norton, C., & Patterson, D. J. (2006). “Taxonomic informatics tools for the electronic Nomenclator Zoologicus.” Biol Bull, 210(1), 18-24. doi:210/1/18 [pii.

Reznikoff, W. S. (2006). “Tn5 transposition: a molecular tool for studying protein structure-function.” Biochem Soc Trans, 34(Pt 2), 320-323. doi:10.1042/BST2006032.

Riley, M., Abe, T., Arnaud, M. B., Berlyn, M. K., Blattner, F. R., Chaudhuri, R. R., Glasner, J. D., Horiuchi, T., Keseler, I. M., Kosuge, T., Mori, H., Perna, N. T., Plunkett, G., 3rd, Rudd, K. E., Serres, M. H., Thomas, G. H., Thomson, N. R., Wishart, D., & Wanner, B. L. (2006). “Escherichia coli K-12: a cooperatively developed annotation snapshot–2005.” Nucleic Acids Res, 34(1), 1-9. doi:10.1093/nar/gkj40.

Schon, I., & Arkhipova, I. R. (2006). “Two families of non-LTR retrotransposons, Syrinx and Daphne, from the Darwinulid ostracod, Darwinula stevensoni.” Gene, 371(2), 296-307. doi:10.1016/j.gene.2005.12.00.

Serres, M. H., & Riley, M. (2006). “Genomic analysis of carbon source metabolism of Shewanella oneidensis MR-1: Predictions versus experiments.” J Bacteriol, 188(13), 4601-4609. doi:10.1128/JB.01787-0.

Silva, G. H., Belfort, M., Wende, W., & Pingoud, A. (2006). “From monomeric to homodimeric endonucleases and back: engineering novel specificity of LAGLIDADG enzymes.” J Mol Biol, 361(4), 744-754. doi:10.1016/j.jmb.2006.06.06.

Simmons, S. L., Bazylinski, D. A., & Edwards, K. J. (2006). “South-seeking magnetotactic bacteria in the Northern Hemisphere.” Science, 311(5759), 371-374. doi:10.1126/science.112284.

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.

Sogin, M. L., Morrison, H. G., Huber, J. A., Mark Welch, D. B., Huse, S. M., Neal, P. R., Arrieta, J. M., & Herndl, G. J. (2006). “Microbial diversity in the deep sea and the underexplored “rare biosphere”.” Proc Natl Acad Sci U S A, 103(32), 12115-12120. doi:10.1073/pnas.060512710.

Steiniger, M., Adams, C. D., Marko, J. F., & Reznikoff, W. S. (2006). “Defining characteristics of Tn5 Transposase non-specific DNA binding.” Nucleic Acids Res, 34(9), 2820-2832. doi:10.1093/nar/gkl17.

Steiniger, M., Metzler, J., & Reznikoff, W. S. (2006). “Mutation of Tn5 transposase beta-loop residues affects all steps of Tn5 transposition: the role of conformational changes in Tn5 transposition.” Biochemistry, 45(51), 15552-15562. doi:10.1021/bi061227.

Wegener-Parfrey, L., Barbero, E., Lasser, B., Dunthorn, M., Bhattacharya, D., Patterson, D. J., & Katz, L. (2006). “Evaluating support for the current classification of eukaryotic diversity.” PLOS Genetics, 2, 2062-2073.

2005

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.

Amaral-Zettler, L. A., Laatsch, A. D., Zettler, E., Nerad, T. A., Cole, J., Diaz, F. C., Diaz, J., Janzen, D. H., Sittenfeld, A., Mason, O., & Reysenbach, A. L. (2005). “A microbial observatory of caterpillars: isolation and molecular characterization of protists associated with the saturniid moth caterpillar Rothschildia lebeau.” J Eukaryot Microbiol, 52(2), 107-115. doi:10.1111/j.1550-7408.2005.05202008..

Amils, R., González-Toril, E., Gómez, F., Fernández-Remolar, D., Rodríguez, N., Malki, M., Zuluaga, J., Aguilera, A., & Amaral-Zettler, L. A. (2005). “Importance of Chemolithotrophy for Early Life on Earth: The Tinto River (Iberian Pyritic Belt) Case.” In J. Seckbach (Ed.), Origins (Vol. 6, pp. 463-480): Springer Netherlands.

Arkhipova, I. R. (2005). “Mobile genetic elements and sexual reproduction.” Cytogenet Genome Res, 110(1-4), 372-382. doi:10.1159/00008496.

Arkhipova, I. R., & Meselson, M. (2005). “Diverse DNA transposons in rotifers of the class Bdelloidea.” Proc Natl Acad Sci U S A, 102(33), 11781-11786. doi:10.1073/pnas.050533310.

Arkhipova, I. R., & Meselson, M. (2005). “Deleterious transposable elements and the extinction of asexuals.” Bioessays, 27(1), 76-85. doi:10.1002/bies.2015.

Ason, B., Knauss, D. J., Balke, A. M., Merkel, G., Skalka, A. M., & Reznikoff, W. S. (2005). “Targeting Tn5 transposase identifies human immunodeficiency virus type 1 inhibitors.” Antimicrob Agents Chemother, 49(5), 2035-2043. doi:10.1128/AAC.49.5.2035-2043.200.

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..

Belfort, M. (2005). “Back to Basics: Structure, Function, Evolution and Application of Homing Endonucleases and Inteins.” In M. Belfort, D. Wood, B. Stoddard, & V. Derbyshire (Ed.), Homing Endonucleases and Inteins (pp. 1-10): Springer Berlin Heidelberg.

Blocker, F. J., Mohr, G., Conlan, L. H., Qi, L., Belfort, M., & Lambowitz, A. M. (2005). “Domain structure and three-dimensional model of a group II intron-encoded reverse transcriptase.” RNA, 11(1), 14-28. doi:10.1261/rna.718110.

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-.

Bordenstein, S. R., & Reznikoff, W. S. (2005). “Mobile DNA in obligate intracellular bacteria.” Nat Rev Microbiol, 3(9), 688-699. doi:10.1038/nrmicro123.

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..

Degnan, P. H., Lazarus, A. B., & Wernegreen, J. J. (2005). “Genome sequence of Blochmannia pennsylvanicus indicates parallel evolutionary trends among bacterial mutualists of insects.” Genome Res, 15(8), 1023-1033. doi:10.1101/gr.377130.

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.

Evgen’ev, M. B., & Arkhipova, I. R. (2005). “Penelope-like elements–a new class of retroelements: distribution, function and possible evolutionary significance.” Cytogenet Genome Res, 110(1-4), 510-521. doi:10.1159/00008498.

Fry, A. J., & Wernegreen, J. J. (2005). “The roles of positive and negative selection in the molecular evolution of insect endosymbionts.” Gene, 355, 1-10. doi:10.1016/j.gene.2005.05.02.

Fuller, N. J., Marie, D., Yallop, M., Rivlin, T., West, N. J., Post, A. F., & Scanlan, D. J. (2005). “Dynamics of community structure and P status of picocyanobacterial populations in the Gulf of Aqaba, Red Sea during 1999-2000.” Limnology and Oceanography, 50(1), 363-375.

Gould, R. M., Morrison, H. G., Gilland, E., & Campbell, R. K. (2005). “Myelin tetraspan family proteins but no non-tetraspan family proteins are present in the ascidian (Ciona intestinalis) genome.” Biol Bull, 209(1), 49-66.

Herbeck, J. T., Degnan, P. H., & Wernegreen, J. J. (2005). “Nonhomogeneous model of sequence evolution indicates independent origins of primary endosymbionts within the enterobacteriales (gamma-Proteobacteria).” Mol Biol Evol, 22(3), 520-532. doi:10.1093/molbev/msi03.

Hiraga, K., Derbyshire, V., Dansereau, J. T., Van Roey, P., & Belfort, M. (2005). “Minimization and stabilization of the Mycobacterium tuberculosis recA intein.” J Mol Biol, 354(4), 916-926. doi:10.1016/j.jmb.2005.09.08.

Kolker, E., Picone, A. F., Galperin, M. Y., Romine, M. F., Higdon, R., Makarova, K. S., Kolker, N., Anderson, G. A., Qiu, X., Auberry, K. J., Babnigg, G., Beliaev, A. S., Edlefsen, P., Elias, D. A., Gorby, Y. A., Holzman, T., Klappenbach, J. A., Konstantinidis, K. T., Land, M. L., Lipton, M. S., McCue, L. A., Monroe, M., Pasa-Tolic, L., Pinchuk, G., Purvine, S., Serres, M. H., Tsapin, S., Zakrajsek, B. A., Zhu, W., Zhou, J., Larimer, F. W., Lawrence, C. E., Riley, M., Collart, F. R., Yates, J. R., 3rd, Smith, R. D., Giometti, C. S., Nealson, K. H., Fredrickson, J. K., & Tiedje, J. M. (2005). “Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations.” Proc Natl Acad Sci U S A, 102(6), 2099-2104. doi:10.1073/pnas.040911110.

Kysela, D. T., Palacios, C., & Sogin, M. L. (2005). “Serial analysis of V6 ribosomal sequence tags (SARST-V6): a method for efficient, high-throughput analysis of microbial community composition.” Environ Microbiol, 7(3), 356-364. doi:10.1111/j.1462-2920.2004.00712..

Lee, W. J., Simpson, A. G. B., & Patterson, D. J. (2005). “Free-living heterotrophic flagellates from freshwater sites in Tasmania (Australia), a field survey.” Acta Protozoologica, 44(4), 321-350.

Lindell, D., Penno, S., Al-Qutob, M., David, E., Korpal, T., Lazar, B., & Post, A. F. (2005). “Expression of the N-stress response gene ntcA reveals N-sufficient Synechococcus populations in the oligotrophic northern Red Sea.” Limnology and Oceanography, 50, 1932-1944.

Mark Welch, D. B. (2005). “Bayesian and Maximum Likelihood Analyses of Rotifer–Acanthocephalan Relationships.” Hydrobiologia, 546(1), 47-54. doi:10.1007/s10750-005-4100-.

Mark Welch, D. B., & Mark Welch, J. L. (2005). “The potential of genomic approaches to rotifer ecology.” In A. Herzig, R. Gulati, C. Jersabek, & L. May (Ed.), Rotifera X (Vol. 181, pp. 101-108): Springer Netherlands.

Mehta, M. P., Huber, J. A., & Baross, J. A. (2005). “Incidence of novel and potentially archaeal nitrogenase genes in the deep Northeast Pacific Ocean.” Environ Microbiol, 7(10), 1525-1534. doi:10.1111/j.1462-2920.2005.00836..

Messerli, M. A., Amaral-Zettler, L. A., Zettler, E., Jung, S. K., Smith, P. J., & Sogin, M. L. (2005). “Life at acidic pH imposes an increased energetic cost for a eukaryotic acidophile.” J Exp Biol, 208(Pt 13), 2569-2579. doi:10.1242/jeb.0166.

Miao, J., Wu, W., Spielmann, T., Belfort, M., Derbyshire, V., & Belfort, G. (2005). “Single-step affinity purification of toxic and non-toxic proteins on a fluidics platform.” Lab Chip, 5(3), 248-253. doi:10.1039/b413292.

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.

Murray, S., Flo Jorgensen, M., Ho, S. Y., Patterson, D. J., & Jermiin, L. S. (2005). “Improving the analysis of dinoflagellate phylogeny based on rDNA.” Protist, 156(3), 269-286. doi:10.1016/j.protis.2005.05.00.

Noel, C., Dufernez, F., Gerbod, D., Edgcomb, V. P., Delgado-Viscogliosi, P., Ho, L. C., Singh, M., Wintjens, R., Sogin, M. L., Capron, M., Pierce, R., Zenner, L., & Viscogliosi, E. (2005). “Molecular phylogenies of Blastocystis isolates from different hosts: implications for genetic diversity, identification of species, and zoonosis.” J Clin Microbiol, 43(1), 348-355. doi:10.1128/JCM.43.1.348-355.200.

Post, A. F. (2005). “Nutrient Limitation of Marine Cyanobacteria.” In J. Huisman, H. P. Matthijs, & P. Visser (Ed.), Harmful Cyanobacteria (Vol. 3, pp. 87-107): Springer Netherlands.

Roland, S., Bahr, M., Olendzenski, L., & Patterson, D. J. (2005). “Switch on micro*scope.” The Science Teacher(February ), 47-49.

Schaber, J., Rispe, C., Wernegreen, J. J., Buness, A., Delmotte, F., Silva, F. J., & Moya, A. (2005). “Gene expression levels influence amino acid usage and evolutionary rates in endosymbiotic bacteria.” Gene, 352, 109-117. doi:10.1016/j.gene.2005.04.00.

Serres, M. H., & Riley, M. (2005). “Gene fusions and gene duplications: relevance to genomic annotation and functional analysis.” BMC Genomics, 6, 33. doi:10.1186/1471-2164-6-3.

Sheehan, K. B., Patterson, D. J., Dicks, B. L., & Henson, J. M. (2005). “Seen and unseen: discovering the microbes of Yellowstone.” A Falcon Guide, Montana State University, Helena. Montana, 128.

Smith, D., Zhong, J., Matsuura, M., Lambowitz, A. M., & Belfort, M. (2005). “Recruitment of host functions suggests a repair pathway for late steps in group II intron retrohoming.” Genes Dev, 19(20), 2477-2487. doi:10.1101/gad.134510.

Sogin, M. L., Patterson, D. J., & McArthur, A. G. (2005). “Molecular and traditional approaches in the study of diversity and diversification of eukaryotes.” In J. Barros & W. Sullivan (Ed.), Planets & Life: The Emerging Science of Astrobiology: Cambridge University Press.

Van Roey, P., Belfort, M., & Derbyshire, V. (2005). “Homing endonuclease I-TevI: an atypical zinc finger with a novel function.” In S. Iuchi (Ed.), Zinc finger proteins: from atomic contact to cellular function (Vol. 1, pp. 35-38): Georgetown: Landes Bioscience, New York: Kluwer Academic/Plenum Publishers.

Wagner, R. Jr., & Meselson, M. (2005). “Repair tracts in mismatched DNA heteroduplexes.” 1976. DNA Repair (Amst), 4(1), 126-130; discussion 103-124, 131.

Weiland, M. E., McArthur, A. G., Morrison, H. G., Sogin, M. L., & Svard, S. G. (2005). “Annexin-like alpha giardins: a new cytoskeletal gene family in Giardia lamblia.” Int J Parasitol, 35(6), 617-626. doi:10.1016/j.ijpara.2004.12.00.

Wernegreen, J. J. (2005). “For better or worse: genomic consequences of intracellular mutualism and parasitism.” Curr Opin Genet Dev, 15(6), 572-583. doi:10.1016/j.gde.2005.09.01.

Winterberg, K. M., Luecke, J., Bruegl, A. S., & Reznikoff, W. S. (2005). “Phenotypic screening of Escherichia coli K-12 Tn5 insertion libraries, using whole-genome oligonucleotide microarrays.” Appl Environ Microbiol, 71(1), 451-459. doi:10.1128/AEM.71.1.451-459.200.

2004

Ason, B., & Reznikoff, W. S. (2004). “A high-throughput assay for Tn5 Tnp-induced DNA cleavage.” Nucleic Acids Res, 32(10), e83. doi:10.1093/nar/gnh08.

Ason, B., & Reznikoff, W. S. (2004). “DNA sequence bias during Tn5 transposition.” J Mol Biol, 335(5), 1213-1225. doi:S0022283603014499 [pii.

Best, A. A., Morrison, H. G., McArthur, A. G., Sogin, M. L., & Olsen, G. J. (2004). “Evolution of eukaryotic transcription: insights from the genome of Giardia lamblia.” Genome Res, 14(8), 1537-1547. doi:10.1101/gr.225660.

Bordenstein, S. R., & Wernegreen, J. J. (2004). “Bacteriophage flux in endosymbionts (Wolbachia): infection frequency, lateral transfer, and recombination rates.” Mol Biol Evol, 21(10), 1981-1991. doi:10.1093/molbev/msh21.

Butterfield, D. A., Lilley, M. D., Huber, J. A., Roe, K. K., Embley, R. W., Baross, J. A., & Massoth, G. J. (2004). “Mixing, reaction, and microbial activity in the sub-seafloor revealed by temporal and spatial variation in diffuse flow vents at Axial Volcano.” In W. S. D. Wilcock, E. F. DeLong, D. S. Kelley, J. A. Baross, & S. C. Cary (Ed.), The subseafloor biosphere at mid-ocean ridges (Vol. Geophysical Monograph 144, pp. 269-289). Washington, D.C.: American Geophysical Union.

Crump, B. C., Hopkinson, C. S., Sogin, M. L., & Hobbie, J. E. (2004). “Microbial biogeography along an estuarine salinity gradient: combined influences of bacterial growth and residence time.” Appl Environ Microbiol, 70(3), 1494-1505.

Degnan, P. H., Lazarus, A. B., Brock, C. D., & Wernegreen, J. J. (2004). “Host-symbiont stability and fast evolutionary rates in an ant-bacterium association: cospeciation of camponotus species and their endosymbionts, candidatus blochmannia.” Syst Biol, 53(1), 95-110. doi:JPADCD2N0F198Q0X [pii.

Edgell, D. R., Derbyshire, V., Van Roey, P., LaBonne, S., Stanger, M. J., Li, Z., Boyd, T. M., Shub, D. A., & Belfort, M. (2004). “Intron-encoded homing endonuclease I-TevI also functions as a transcriptional autorepressor.” Nat Struct Mol Biol, 11(10), 936-944. doi:10.1038/nsmb82.

Edgell, D. R., Stanger, M. J., & Belfort, M. (2004). “Coincidence of cleavage sites of intron endonuclease I-TevI and critical sequences of the host thymidylate synthase gene.” J Mol Biol, 343(5), 1231-1241. doi:10.1016/j.jmb.2004.09.00.

Lease, R. A., Smith, D., McDonough, K., & Belfort, M. (2004). “The small noncoding DsrA RNA is an acid resistance regulator in Escherichia coli.” J Bacteriol, 186(18), 6179-6185. doi:10.1128/JB.186.18.6179-6185.200.

Mark Welch, D. B., Cummings, M. P., Hillis, D. M., & Meselson, M. (2004). “Divergent gene copies in the asexual class Bdelloidea (Rotifera) separated before the bdelloid radiation or within bdelloid families.” Proc Natl Acad Sci U S A, 101(6), 1622-1625. doi:10.1073/pnas.213668610.

Mark Welch, J. L., Mark Welch, D. B., & Meselson, M. (2004). “Cytogenetic evidence for asexual evolution of bdelloid rotifers.” Proc Natl Acad Sci U S A, 101(6), 1618-1621. doi:10.1073/pnas.030767710.

Meselson, M. (2004). “Explorations in the land of DNA and beyond.” Nat Med, 10(10), 1034-1037. doi:10.1038/nm1004-103.

Murray, S., & Patterson, D. J. (2004). “Cabra matta, gen.” nov., sp nov., a new benthic, heterotrophic dinoflagellate. European Journal of Phycology, 39(2), 229-234. doi:Doi 10.1080/096702604200020215.

Powell, W. H., Morrison, H. G., Weil, E. J., Karchner, S. I., Sogin, M. L., Stegeman, J. J., & Hahn, M. E. (2004). “Cloning and analysis of the CYP1A promoter from the atlantic killifish (Fundulus heteroclitus).” Mar Environ Res, 58(2-5), 119-124. doi:10.1016/j.marenvres.2004.03.00.

Pyatkov, K. I., Arkhipova, I. R., Malkova, N. V., Finnegan, D. J., & Evgen’ev, M. B. (2004). “Reverse transcriptase and endonuclease activities encoded by Penelope-like retroelements.” Proc Natl Acad Sci U S A, 101(41), 14719-14724. doi:10.1073/pnas.040628110.

Pyatkov, K. I., Arkhipova, I. R., Malkova, N. V., Finnegan, D. J., & Evgen’ev, M. B. (2004). “Reverse transcriptase and endonuclease activities encoded by Penelope-like retroelements.” Proc Natl Acad Sci U S A, 101(41), 14719-14724. doi:10.1073/pnas.040628110.

Reznikoff, W. S., Bordenstein, S. R., & Apodaca, J. (2004). “Comparative sequence analysis of IS50/Tn5 transposase.” J Bacteriol, 186(24), 8240-8247. doi:10.1128/JB.186.24.8240-8247.200.

Reznikoff, W. S., Goryshin, I. Y., & Jendrisak, J. J. (2004). “Tn5 as a molecular genetics tool: In vitro transposition and the coupling of in vitro technologies with in vivo transposition.” Methods Mol Biol, 260, 83-96. doi:10.1385/1-59259-755-6:08.

Serres, M. H., Goswami, S., & Riley, M. (2004). “GenProtEC: an updated and improved analysis of functions of Escherichia coli K-12 proteins.” Nucleic Acids Res, 32(Database issue), D300-302. doi:10.1093/nar/gkh08.

Serres, M. H., & Riley, M. (2004). “Structural domains, protein modules, and sequence similarities enrich our understanding of the Shewanella oneidensis MR-1 proteome.” OMICS, 8(4), 306-321. doi:10.1089/omi.2004.8.30.

Silva, G. H., & Belfort, M. (2004). “Analysis of the LAGLIDADG interface of the monomeric homing endonuclease I-DmoI.” Nucleic Acids Res, 32(10), 3156-3168. doi:10.1093/nar/gkh61.

Silva-Pinhati, A. C., Bacci, M. Jr., Hinkle, G., Sogin, M. L., Pagnocca, F. C., Martins, V. G., Bueno, O. C., & Hebling, M. J. (2004). “Low variation in ribosomal DNA and internal transcribed spacers of the symbiotic fungi of leaf-cutting ants (Attini: Formicidae).” Braz J Med Biol Res, 37(10), 1463-1472. doi:/S0100-879X200400100000.

Simmons, S. L., Sievert, S. M., Frankel, R. B., Bazylinski, D. A., & Edwards, K. J. (2004). “Spatiotemporal distribution of marine magnetotactic bacteria in a seasonally stratified coastal salt pond.” Appl Environ Microbiol, 70(10), 6230-6239. doi:10.1128/AEM.70.10.6230-6239.200.

Steiniger-White, M., Rayment, I., & Reznikoff, W. S. (2004). “Structure/function insights into Tn5 transposition.” Curr Opin Struct Biol, 14(1), 50-57. doi:10.1016/j.sbi.2004.01.00.

Wernegreen, J. J. (2004). “Endosymbiosis: lessons in conflict resolution.” PLoS Biol, 2(3), E68. doi:10.1371/journal.pbio.002006.

Wernegreen, J. J., & Funk, D. J. (2004). “Mutation exposed: a neutral explanation for extreme base composition of an endosymbiont genome.” J Mol Evol, 59(6), 849-858. doi:10.1007/s00239-003-0192-.

2003

Alappat, S. R., Zhang, M., Zhao, X., Alliegro, M. A., Alliegro, M. C., & Burdsal, C. A. (2003). “Mouse pigpen encodes a nuclear protein whose expression is developmentally regulated during craniofacial morphogenesis.” Dev Dyn, 228(1), 59-71. doi:10.1002/dvdy.1035.

Amaral-Zettler, L. A., Messerli, M. A., Laatsch, A. D., Smith, P. J., & Sogin, M. L. (2003). “From genes to genomes: beyond biodiversity in Spain’s Rio Tinto.” Biol Bull, 204(2), 205-209.

Arkhipova, I. R., Pyatkov, K. I., Meselson, M., & Evgen’ev, M. B. (2003). “Retroelements containing introns in diverse invertebrate taxa.” Nat Genet, 33(2), 123-124. doi:10.1038/ng107.

Belfort, M. (2003). “Two for the price of one: a bifunctional intron-encoded DNA endonuclease-RNA maturase.” Genes Dev, 17(23), 2860-2863. doi:10.1101/gad.116250.

Bordenstein, S. R. (2003). “Symbiosis and the origin of species.” In K. Bourtzis & T. Miller (Ed.), Insect Symbiosis (Vol. 1, pp. 283-304). New York: CRC Press.

Bordenstein, S. R., Fitch, D. H., & Werren, J. H. (2003). “Absence of wolbachia in nonfilariid nematodes.” J Nematol, 35(3), 266-270.

Bordenstein, S. R., Uy, J. J., & Werren, J. H. (2003). “Host genotype determines cytoplasmic incompatibility type in the haplodiploid genus Nasonia.” Genetics, 164(1), 223-233.

Busse, I., Patterson, D. J., & Preisfeld, A. (2003). “Phylogeny of phagotrophic euglenids (Euglenozoa): A molecular approach based on culture material and environmental samples.” Journal of Phycology, 39(4), 828-836. doi:DOI 10.1046/j.1529-8817.2003.02178..

Dhillon, A., Teske, A., Dillon, J., Stahl, D. A., & Sogin, M. L. (2003). “Molecular characterization of sulfate-reducing bacteria in the Guaymas Basin.” Appl Environ Microbiol, 69(5), 2765-2772.

Edgell, D. R., Stanger, M. J., & Belfort, M. (2003). “Importance of a single base pair for discrimination between intron-containing and intronless alleles by endonuclease I-BmoI.” Curr Biol, 13(11), 973-978. doi:S0960982203003403 [pii.

Fuller, N. J., Marie, D., Partensky, F., Vaulot, D., Post, A. F., & Scanlan, D. J. (2003). “Clade-specific 16S ribosomal DNA oligonucleotides reveal the predominance of a single marine Synechococcus clade throughout a stratified water column in the Red Sea.” Appl Environ Microbiol, 69(5), 2430-2443.

Gillor, O., Harush, A., Hadas, O., Post, A. F., & Belkin, S. (2003). “A Synechococcus PglnA::luxAB fusion for estimation of nitrogen bioavailability to freshwater cyanobacteria.” Appl Environ Microbiol, 69(3), 1465-1474.

Goryshin, I. Y., Naumann, T. A., Apodaca, J., & Reznikoff, W. S. (2003). “Chromosomal deletion formation system based on Tn5 double transposition: use for making minimal genomes and essential gene analysis.” Genome Res, 13(4), 644-653. doi:10.1101/gr.61140.

Herbeck, J. T., Funk, D. J., Degnan, P. H., & Wernegreen, J. J. (2003). “A conservative test of genetic drift in the endosymbiotic bacterium Buchnera: slightly deleterious mutations in the chaperonin groEL.” Genetics, 165(4), 1651-1660.

Herbeck, J. T., Wall, D. P., & Wernegreen, J. J. (2003). “Gene expression level influences amino acid usage, but not codon usage, in the tsetse fly endosymbiont Wigglesworthia.” Microbiology, 149(Pt 9), 2585-2596.

Huber, J. A., Butterfield, D. A., & Baross, J. A. (2003). “Bacterial diversity in a subseafloor habitat following a deep-sea volcanic eruption.” FEMS Microbiol Ecol, 43(3), 393-409. doi:10.1111/j.1574-6941.2003.tb01080..

Ichiyanagi, K., Beauregard, A., & Belfort, M. (2003). “A bacterial group II intron favors retrotransposition into plasmid targets.” Proc Natl Acad Sci U S A, 100(26), 15742-15747. doi:10.1073/pnas.253665910.

Johnson, H. P., & Party, L. S. (2003). “Probing for life in the ocean crust with the LEXEN program.” Eos, Trans. AGU., 84, 109-112.

Lee, W. J., Brandt, S. M., Vors, N., & Patterson, D. J. (2003). “Darwin’s heterotrophic flagellates.” Ophelia, 57(2), 63-98.

Linz-McGillem, L. A., & Alliegro, M. C. (2003). “Myosin II in retinal pigmented epithelial cells: evidence for an association with membranous vesicles.” Exp Eye Res, 76(5), 543-552. doi:S0014483503000319 [pii.

Liu, Q., Belle, A., Shub, D. A., Belfort, M., & Edgell, D. R. (2003). “SegG endonuclease promotes marker exclusion and mediates co-conversion from a distant cleavage site.” J Mol Biol, 334(1), 13-23. doi:S0022283603011628 [pii.

Man, D., Wang, W., Sabehi, G., Aravind, L., Post, A. F., Massana, R., Spudich, E. N., Spudich, J. L., & Beja, O. (2003). “Diversification and spectral tuning in marine proteorhodopsins.” EMBO J, 22(8), 1725-1731. doi:10.1093/emboj/cdg18.

Mark Welch, D. B., & Meselson, M. (2003). “Oocyte nuclear DNA content and GC proportion in rotifers of the anciently asexual Class Bdelloidea.” Biological Journal of the Linnean Society, 79(1), 85-91. doi:10.1046/j.1095-8312.2003.00180..

Medina, M., Collins, A. G., Taylor, J. W., Valentine, J. W., Lipps, J. H., Amaral-Zettler, L. A., & Sogin, M. L. (2003). “Phylogeny of Opisthokonta and the evolution of multicellularity and complexity in Fungi and Metazoa.” International Journal of Astrobiology, 2, 203-211.

Meselson, M. (2003). “Interview with Matthew Meselson.” Bioessays, 25(12), 1236-1246. doi:10.1002/bies.1037.

Nixon, J. E., Field, J., McArthur, A. G., Sogin, M. L., Yarlett, N., Loftus, B. J., & Samuelson, J. (2003). “Iron-dependent hydrogenases of Entamoeba histolytica and Giardia lamblia: activity of the recombinant entamoebic enzyme and evidence for lateral gene transfer.” Biol Bull, 204(1), 1-9.

Noble, M., Smith, J., Power, J., & Mayer-Proschel, M. (2003). “Redox state as a central modulator of precursor cell function.” Parkinson’s Disease: The Life Cycle of the Dopamine Neuron, 991, 251-271.

Noel, C., Peyronnet, C., Gerbod, D., Edgcomb, V. P., Delgado-Viscogliosi, P., Sogin, M. L., Capron, M., Viscogliosi, E., & Zenner, L. (2003). “Phylogenetic analysis of Blastocystis isolates from different hosts based on the comparison of small-subunit rRNA gene sequences.” Mol Biochem Parasitol, 126(1), 119-123. doi:S0166685102002463 [pii.

O’Kelly, C. J., Silberman, J. D., Amaral-Zettler, L. A., Nerad, T. A., & Sogin, M. L. (2003). “Monopylocystis visvesvarai n.” gen., n. sp. and Sawyeria marylandensis n. gen., n. sp.: two new amitochondrial heterolobosean amoebae from anoxic environments. Protist, 154(2), 281-290. doi:10.1078/14344610332216656.

Patterson, D. J. (2003). “Progressing towards a biological names register.” Nature, 422(6933), 661. doi:10.1038/422661.

Patterson, D. J., Remsen, D., & Norton, C. (2003). “Comment on Zoological record and registration of new names in zoology.” Bulletin of Zoological Nomenclature, 60, 297-299.

Peglar, M. T., Amaral-Zettler, L. A., Anderson, O. R., Nerad, T. A., Gillevet, P. M., Mullen, T. E., Frasca, S. Jr., Silberman, J. D., O’Kelly, C. J., & Sogin, M. L. (2003). “Two new small-subunit ribosomal RNA gene lineages within the subclass gymnamoebia.” J Eukaryot Microbiol, 50(3), 224-232.

Peterson, G., & Reznikoff, W. (2003). “Tn5 transposase active site mutations suggest position of donor backbone DNA in synaptic complex.” J Biol Chem, 278(3), 1904-1909. doi:10.1074/jbc.M20896820.

Reiner, D. S., Hetsko, M. L., Meszaros, J. G., Sun, C. H., Morrison, H. G., Brunton, L. L., & Gillin, F. D. (2003). “Calcium signaling in excystation of the early diverging eukaryote, Giardia lamblia.” J Biol Chem, 278(4), 2533-2540. doi:10.1074/jbc.M20803320.

Reznikoff, W. S. (2003). “Tn5 as a model for understanding DNA transposition.” Mol Microbiol, 47(5), 1199-1206. doi:3382 [pii.

Rocap, G., Larimer, F. W., Lamerdin, J., Malfatti, S., Chain, P., Ahlgren, N. A., Arellano, A., Coleman, M., Hauser, L., Hess, W. R., Johnson, Z. I., Land, M., Lindell, D., Post, A. F., Regala, W., Shah, M., Shaw, S. L., Steglich, C., Sullivan, M. B., Ting, C. S., Tolonen, A., Webb, E. A., Zinser, E. R., & Chisholm, S. W. (2003). “Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation.” Nature, 424(6952), 1042-1047. doi:10.1038/nature0194.

Schroeckh, S., Lee, W. J., & Patterson, D. J. (2003). “Free-living heterotrophic euglenids from freshwater sites in mainland Australia.” Hydrobiologia, 493(1-3), 131-166. doi:Doi 10.1023/A:102545780142.

Seshadri, V., McArthur, A. G., Sogin, M. L., & Adam, R. D. (2003). “Giardia lamblia RNA polymerase II: amanitin-resistant transcription.” J Biol Chem, 278(30), 27804-27810. doi:10.1074/jbc.M30331620.

Sogin, M. L., & Jennings, D. E. (2003). “Introduction.” Biol Bull, 204(2), 159. doi:10.1086/BBLv204n2p15.

Steglich, C., Post, A. F., & Hess, W. R. (2003). “Analysis of natural populations of Prochlorococcus spp.” in the northern Red Sea using phycoerythrin gene sequences. Environ Microbiol, 5(8), 681-690. doi:DOI 10.1046/j.1462-2920.2003.00456..

Teske, A., Dhillon, A., & Sogin, M. L. (2003). “Genomic markers of ancient anaerobic microbial pathways: sulfate reduction, methanogenesis, and methane oxidation.” Biol Bull, 204(2), 186-191.

Walker, G., Silberman, J. D., Karpov, S. A., Preisfeld, A., Foster, P., Ol Frolov, A., Novozhilov, Y., & Sogin, M. L. (2003). “An ultrastructural and molecular study of Hyperamoeba dachnyaya,n.” sp., and its relationship to the mycetozoan slime moulds. European Journal of Protistology, 39, 319-336.

Wernegreen, J. J., Degnan, P. H., Lazarus, A. B., Palacios, C., & Bordenstein, S. R. (2003). “Genome evolution in an insect cell: distinct features of an ant-bacterial partnership.” Biol Bull, 204(2), 221-231.

Zeidner, G., Preston, C. M., Delong, E. F., Massana, R., Post, A. F., Scanlan, D. J., & Beja, O. (2003). “Molecular diversity among marine picophytoplankton as revealed by psbA analyses.” Environ Microbiol, 5(3), 212-216. doi:DOI 10.1046/j.1462-2920.2003.00403..

2002

Al Qassab, S., Lee, W. J., Murray, S., & Patterson, D. J. (2002). “Flagellates from stromatolites and surrounding sediments in Shark Bay, Western Australia.” Acta. Protozoologica, 41, 91-144.

Alliegro, M. C. (2002). “Coiled body heterogeneity induced by G(1) arrest with amiloride + bumetanide.” Exp Cell Res, 279(1), 111-117. doi:S0014482702955989 [pii.

Alliegro, M. C., & Alliegro, M. A. (2002). “Nuclear injection of anti-pigpen antibodies inhibits endothelial cell division.” J Biol Chem, 277(21), 19037-19041. doi:10.1074/jbc.M20073720.

Amaral-Zettler, L. A., Gomez, F., Zettler, E., Keenan, B. G., Amils, R., & Sogin, M. L. (2002). “Microbiology: eukaryotic diversity in Spain’s River of Fire.” Nature, 417(6885), 137. doi:10.1038/417137.

Ason, B., & Reznikoff, W. S. (2002). “Mutational analysis of the base flipping event found in Tn5 transposition.” J Biol Chem, 277(13), 11284-11291. doi:10.1074/jbc.M11111920.

Belfort, M., Derbyshire, V., Cousineau, B., & Lambowitz, A. M. (2002). “Mobile introns: pathway and proteins.” In R. Craig, M. Craigie, Gellert, & A. M. Lambowitz (Ed.), Mobile DNA II (pp. 761-783). Washington, DC: ASM Press.

Boelen, P., Post, A. F., Veldhuis, M. J., & Buma, A. G. (2002). “Diel patterns of UVBR-induced DNA damage in picoplankton size fractions from the Gulf of Aqaba, Red Sea.” Microb Ecol, 44(2), 164-174. doi:10.1007/s00248-002-1002-.

Dean, A. B., Stanger, M. J., Dansereau, J. T., Van Roey, P., Derbyshire, V., & Belfort, M. (2002). “Zinc finger as distance determinant in the flexible linker of intron endonuclease I-TevI.” Proc Natl Acad Sci U S A, 99(13), 8554-8561. doi:10.1073/pnas.08225369.

Delvinquier, B. L. J., & Patterson, D. J. (2002). “Order Slopalinida.” In J. J. Lee, G. F. Leedale, & P. Bradbury (Ed.), An Illustrated Guide to the Protozoa, 2nd edition (pp. 754-759). Lawrence, Kansas: Society of Protozoologists.

Dyer, K. D., Linz-Mcgillem, L. A., Alliegro, M. A., & Alliegro, M. C. (2002). “Receptor-bound uPA is reversibly protected from inhibition by low molecular weight inhibitors.” Cell Biol Int, 26(4), 327-335. doi:10.1006/cbir.2001.085.

Edgcomb, V. P., Kysela, D. T., Teske, A., de Vera Gomez, A., & Sogin, M. L. (2002). “Benthic eukaryotic diversity in the Guaymas Basin hydrothermal vent environment.” Proc Natl Acad Sci U S A, 99(11), 7658-7662. doi:10.1073/pnas.06218639.

Edgcomb, V. P., Simpson, A. G., Zettler, L. A., Nerad, T. A., Patterson, D. J., Holder, M. E., & Sogin, M. L. (2002). “Pelobionts are degenerate protists: insights from molecules and morphology.” Mol Biol Evol, 19(6), 978-982.

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., & 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), 545-556. doi:S1055790302003007 [pii.

Gillor, O., Hadas, O., Post, A. F., & 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., & Hess, W. R. (2002). “Synchronized expression of ftsZ in natural Prochlorococcus populations of the Red Sea.” Environ Microbiol, 4(11), 644-653.

Huber, J. A., Butterfield, D. A., & Baross, J. A. (2002). “Temporal changes in archaeal diversity and chemistry in a mid-ocean ridge subseafloor habitat.” Appl Environ Microbiol, 68(4), 1585-1594.

Ichiyanagi, K., Beauregard, A., Lawrence, S., Smith, D., Cousineau, B., & Belfort, M. (2002). “Retrotransposition of the Ll.LtrB group II intron proceeds predominantly via reverse splicing into DNA targets.” Mol Microbiol, 46(5), 1259-1272.

Katoh, M., & Kuma, M. (2002). “Mafft: a novel method for rapid multiple sequence alignment based on fast Fourier transform.” Nucleic Acids Res, 30. doi:10.1093/nar/gkf43.

Langford, T. D., Silberman, J. D., Weiland, M. E., Svard, S. G., McCaffery, J. M., Sogin, M. L., & 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. doi.

Lee, W. J., & Patterson, D. J. (2002). “Optimising the extraction of bacteria, heterotrophic protists and diatoms, and estimating their abundance and biomass from intertidal sandy sediments.” Journal of the Korean Society of Oceanography, 37, 58-65.

Lee, W. J., & 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), 467-481. doi:10.1007/s00248-002-2000-.

Lindell, D., Erdner, D., Marie, D., Claustre, H., Prasil, O., Le Gall, F., Rippka, R., Partensky, F., Scanlan, D. J., & 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., & Rayment, I. (2002). “Two-metal active site binding of a Tn5 transposase synaptic complex.” Nat Struct Biol, 9(4), 278-281. doi:10.1038/nsb77.

Mark Welch, D. B. (2002). “Rotifera McGraw-Hill Yearbook of Science & Technology (Vol.” 1, pp. 304-306). New York: McGraw Hill.

Mikrjukov, K. A., Patterson, D. J., & Siemensma, F. J. (2002). “Phylum Heliozoa In J.” J. Lee, G. F. Leedale, & P. Bradbury (Ed.), An Illustrated Guide to the Protozoa (2nd ed., pp. 860-871). Lawrence, Kansas: Society of Protozoologists.

Moore, L. R., Post, A. F., Rocap, G., & 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., & 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), 477-491.

Murray, S., & 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. doi:Doi 10.1017/S096702620200359.

Murray, S., & Patterson, D. J. (2002). “Amphidiniopsis korewalensis sp.” nov., a new heterotrophic benthic dinoflagellates. Phycologica, 41, 382-388.

Naumann, T. A., Goryshin, I. Y., & Reznikoff, W. S. (2002). “Production of combinatorial libraries of fused genes by sequential transposition reactions.” Nucleic Acids Res, 30(21), e119.

Naumann, T. A., & Reznikoff, W. S. (2002). “Tn5 transposase active site mutants.” J Biol Chem, 277(20), 17623-17629. doi:10.1074/jbc.M20074220.

Naumann, T. A., & Reznikoff, W. S. (2002). “Tn5 transposase with an altered specificity for transposon ends.” J Bacteriol, 184(1), 233-240.

Nixon, J. E., Wang, A., Field, J., Morrison, H. G., McArthur, A. G., Sogin, M. L., Loftus, B. J., & 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), 181-190.

Nixon, J. E., Wang, A., Morrison, H. G., McArthur, A. G., Sogin, M. L., Loftus, B. J., & Samuelson, J. (2002). “A spliceosomal intron in Giardia lamblia.” Proc Natl Acad Sci U S A, 99(6), 3701-3705. doi:10.1073/pnas.04270029.

Pahl, N., Homsi, S., Morrison, H. G., & Gould, R. M. (2002). “mRNAs located in Squalus acanthias (spiny dogfish) oligodendrocyte processes.” Biol Bull, 203(2), 217-218.

Palacios, C., & Wernegreen, J. J. (2002). “A strong effect of AT mutational bias on amino acid usage in Buchnera is mitigated at high-expression genes.” Mol Biol Evol, 19(9), 1575-1584.

Patterson, D. J. (2002). “Changing views of protistan systematics: the taxonomy of protozoa – an overview.” In J. J. Lee, G. F. Leedale, & P. Bradbury (Ed.), An Illustrated Guide to the Protozoa, 2nd edition (pp. 2-9). Lawrence, Kansas: Society of Protozoologists.

Patterson, D. J. (2002). “Residual heterotrophic stramenopiles.” In J. J. Lee, G. F. Leedale, & P. Bradbury (Ed.), An Illustrated Guide to the Protozoa, 2nd edition (pp. 751-754). Lawrence, Kansas: Society of Protozoologists.

Patterson, D. J., Rogerson, A., & Vors, N. (2002). “Class Heterolobosea.” In J. J. Lee, G. F. Leedale, & P. Bradbury (Ed.), An Illustrated Guide to the Protozoa, 2nd edition (pp. 1104-1111). Lawrence, Kansas: Society of Protozoologists.

Patterson, D. J., Simpson, A. G. B., & Rogerson, A. (2002). “Amoebae of uncertain affinities In J.” J. Lee, G. F. Leedale, & P. Bradbury (Ed.), An Illustrated Guide to the Protozoa, 2nd edition (pp. 804-827). Lawrence, Kansas: Society of Protozoologists.

Patterson, D. J., Vors, N., Simpson, A. G. B., & O’Kelly, C. J. (2002). “Residual free-living and predatory heterotrophic flagellates.” In J. J. Lee, G. F. Leedale, & P. Bradbury (Ed.), An Illustrated Guide to the Protozoa, 2nd edition (2nd edition ed., pp. 1302-1328). Lawrence, Kansas: Society of Protozoologists.

Podar, M., Mullineaux, L., Huang, H. R., Perlman, P. S., & Sogin, M. L. (2002). “Bacterial group II introns in a deep-sea hydrothermal vent environment.” Appl Environ Microbiol, 68(12), 6392-6398.

Post, A. F., Dedej, Z., Gottlieb, R., Li, H., Thomas, D., El-Absawy, M., El-Naggar, A., El-Gharabawi, M., & Sommer, U. (2002). “Spatial and temporal distribution of Trichodesmium spp.” in the stratified waters of the Gulf of Aqaba (northern Red Sea). Marine Ecology Progress Series, 239, 241-250.

Reznikoff, W. S. (2002). “Molecular basis of Tn5 transposition Molecular Genetics Biophysics and Medicine Today, Bresler Memorial Lectures (pp.” 292-297): Russian Academy of Sciences, St. Petersburg Scientific Center RAS, Konstantinov Petersburg Nuclear Physics Institute RAS.

Reznikoff, W. S. (2002). “Tn5 transposition.” In N. Craig, R. Craigie, M. Gellert, & A. Lambowitz (Ed.), Mobile DNA II (pp. 403-421). Washington, DC: ASM Press.

Rogerson, A., & Patterson, D. J. (2002). “The naked ramicristate amoebae (Gymnamoebae) In J.” J. Lee, G. F. Leedale, & P. Bradbury (Ed.), An Illustrated Guide to the Protozoa, 2nd edition (pp. 1023-1053). Lawrence, Kansas: Society of Protozoologists.

Simpson, A. G., Roger, A. J., Silberman, J. D., Leipe, D. D., Edgcomb, V. P., Jermiin, L. S., Patterson, D. J., & 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), 1782-1791.

Simpson, A. G. B., & Patterson, D. J. (2002). “Family Colpodellidae Simpson & Patterson, 19965.” In J. J. Lee, G. F. Leedale, & P. Bradbury (Ed.), An Illustrated Guide to the Protozoa, 2nd edition. Lawrence, Kansas: Society of Protozoologists.

Sommer, U., Berninger, U.-G., Boettger-Schnack, R., Hansen, T., Stibor, H., Schnack-Schiel, S. B., Cornils, A., Hagen, W., Wickham, S., Al-Najjar, T., & Post, A. F. (2002). “Grazing during the spring bloom in the Gulf of Aqaba and the Northern Red Sea.” Marine Ecology Progress Series, 239, 251-261.

Steiniger-White, M., Bhasin, A., Lovell, S., Rayment, I., & Reznikoff, W. S. (2002). “Evidence for “unseen” transposase–DNA contacts.” J Mol Biol, 322(5), 971-982. doi:S002228360200877X [pii.

Tamas, I., Klasson, L., Canback, B., Naslund, A. K., Eriksson, A. S., Wernegreen, J. J., Sandstrom, J. P., Moran, N. A., & Andersson, S. G. (2002). “50 million years of genomic stasis in endosymbiotic bacteria.” Science, 296(5577), 2376-2379. doi:10.1126/science.107127.

Teske, A., Hinrichs, K. U., Edgcomb, V., de Vera Gomez, A., Kysela, D., Sylva, S. P., Sogin, M. L., & 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.

Van Roey, P., Meehan, L., Kowalski, J. C., Belfort, M., & Derbyshire, V. (2002). “Catalytic domain structure and hypothesis for function of GIY-YIG intron endonuclease I-TevI.” Nat Struct Biol, 9(11), 806-811. doi:10.1038/nsb85.

Wernegreen, J. J. (2002). “Genome evolution in bacterial endosymbionts of insects.” Nat Rev Genet, 3(11), 850-861. doi:10.1038/nrg93.

Wernegreen, J. J., Lazarus, A. B., & Degnan, P. H. (2002). “Small genome of Candidatus Blochmannia, the bacterial endosymbiont of Camponotus, implies irreversible specialization to an intracellular lifestyle.” Microbiology, 148(Pt 8), 2551-2556.

Wu, W., Wood, D. W., Belfort, G., Derbyshire, V., & Belfort, M. (2002). “Intein-mediated purification of cytotoxic endonuclease I-TevI by insertional inactivation and pH-controllable splicing.” Nucleic Acids Res, 30(22), 4864-4871.

2001

Alliegro, M. C. (2001). “Pigpen and endothelial cell differentiation.” Cell Biol Int, 25(7), 577-584. doi:10.1006/cbir.2000.073.

Amaral-Zettler, L. A., Nerad, T. A., O’Kelly, C. J., & Sogin, M. L. (2001). “The nucleariid amoebae: more protists at the animal-fungal boundary.” J Eukaryot Microbiol, 48(3), 293-297.

Arkhipova, I. R. (2001). “[Transposable elements in the Animal Kingdom].” Mol Biol (Mosk), 35(2), 196-207.

Arkhipova, I. R. (2001). “Retrotransposons.” In E. C. R. Reeve (Ed.), Encyclopedia of Genetics. London: Fitzroy Dearborn Publishers.

Arkhipova, I. R., & Morrison, H. G. (2001). “Three retrotransposon families in the genome of Giardia lamblia: two telomeric, one dead.” Proc Natl Acad Sci U S A, 98(25), 14497-14502. doi:10.1073/pnas.23149479.

Barbieri, E., Paster, B. J., Hughes, D., Zurek, L., Moser, D. P., Teske, A., & Sogin, M. L. (2001). “Phylogenetic characterization of epibiotic bacteria in the accessory nidamental gland and egg capsules of the squid Loligo pealei (Cephalopoda:Loliginidae).” Environ Microbiol, 3(3), 151-167.

Bordenstein, S. R., & Drapeau, M. D. (2001). “Genotype-by-environment interaction and the Dobzhansky-Muller model of postzygotic isolation.” Journal of Evolutionary Biology, 14(3), 490-501. doi:Doi 10.1046/J.1420-9101.2001.00289..

Bordenstein, S. R., O’Hara, F. P., & Werren, J. H. (2001). “Wolbachia-induced incompatibility precedes other hybrid incompatibilities in Nasonia.” Nature, 409(6821), 707-710. doi:10.1038/3505554.

Brugerolle, G., & Patterson, D. J. (2001). “Ultrastructure of Joenina pulchella Grassi, 1917 (Protista, Parabasalia), a reassessment of evolutionary trends in the parabasalids, and a new order Cristamonadida for devescovinid, calonymphid and lophomonad flagellates.” Organisms Diversity & Evolution, 1(2), 147-160. doi:Doi 10.1078/1439-6092-0001.

Corduneanu, A., & Bishop, C. M. (2001). “Variational Bayesian model selection for mixture distributions.” In T. Jaakkola & T. Richardson (Ed.), Artificial intelligence and statistics 2001. United States: Morgan Kaufmann.

Edgcomb, V. P., Roger, A. J., Simpson, A. G., Kysela, D. T., & Sogin, M. L. (2001). “Evolutionary relationships among “jakobid” flagellates as indicated by alpha- and beta-tubulin phylogenies.” Mol Biol Evol, 18(4), 514-522.

Funk, D. J., Wernegreen, J. J., & Moran, N. A. (2001). “Intraspecific variation in symbiont genomes: bottlenecks and the aphid-buchnera association.” Genetics, 157(2), 477-489.

Gerbod, D., Edgcomb, V. P., Noel, C., Vanacova, S., Wintjens, R., Tachezy, J., Sogin, M. L., & Viscogliosi, E. (2001). “Phylogenetic relationships of class II fumarase genes from trichomonad species.” Mol Biol Evol, 18(8), 1574-1584.

Gerbod, D., Edgcomb, V. P., Noel, C., Zenner, L., Wintjens, R., Delgado-Viscogliosi, P., Holder, M. E., Sogin, M. L., & 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.

Karpov, S. A., Sogin, M. L., & Silberman, J. D. (2001). “Rootlet homology, taxonomy, and phylogeny of bicosoecids based on 18S rRNA gene sequences.” Protistology, 21, 34-47.

Lee, D. D., & Seung, H. S. (2001). “Algorithms for non-negative matrix factorization.” Adv Neural Inf Process Syst, 13.

Lindell, D., & Post, A. F. (2001). “Ecological aspects of ntcA gene expression and its use as an indicator of the nitrogen status of marine Synechococcus spp.” Appl Environ Microbiol, 67(8), 3340-3349. doi:10.1128/AEM.67.8.3340-3349.200.

Mark Welch, D. B. (2001). “Early contributions of molecular phylogenetics to understanding the evolution of Rotifera.” Hydrobiologia, 446-447(1), 315-322. doi:10.1023/A:101750292328.

Mark Welch, D. B., & Meselson, M. (2001). “A survey of introns in three genes of rotifers.” In L. Sanoamuang, H. Segers, R. J. Shiel, & R. D. Gulati (Ed.), Rotifera IX (Vol. 153, pp. 333-336): Springer Netherlands.

Mark Welch, D. B., & Meselson, M. S. (2001). “Rates of nucleotide substitution in sexual and anciently asexual rotifers.” Proc Natl Acad Sci U S A, 98(12), 6720-6724. doi:10.1073/pnas.11114459.

McArthur, A. G., Knodler, L. A., Silberman, J. D., Davids, B. J., Gillin, F. D., & 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), 1455-1463.

Medina, M., Collins, A. G., Silberman, J. D., & Sogin, M. L. (2001). “Evaluating hypotheses of basal animal phylogeny using complete sequences of large and small subunit rRNA.” Proc Natl Acad Sci U S A, 98(17), 9707-9712. doi:10.1073/pnas.17131699.

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

Morrison, H. G., Roger, A. J., Nystul, T. G., Gillin, F. D., & Sogin, M. L. (2001). “Giardia lamblia expresses a proteobacterial-like DnaK homolog.” Mol Biol Evol, 18(4), 530-541.

Patterson, D. J., & Burford, M. A. (2001). “A guide to the protozoa of marine aquaculture ponds.” Collingwood, Australia: CSIRO Publishing.

Pevzner, P., Tang, H., & Waterman, M. (2001). “An Eulerian path approach to DNA fragment assembly.” Proc Natl Acad Sci USA, 98. doi:10.1073/pnas.17128509.

Podar, M., Haddock, S. H., Sogin, M. L., & Harbison, G. R. (2001). “A molecular phylogenetic framework for the phylum Ctenophora using 18S rRNA genes.” Mol Phylogenet Evol, 21(2), 218-230. doi:10.1006/mpev.2001.103.

Schreiter, P., Gillor, O., Post, A. F., Belkin, S., Schmid, R. D., & 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., & Riley, M. (2001). “A functional update of the Escherichia coli K-12 genome.” Genome Biol, 2(9), RESEARCH0035.

Simpson, A. G., & Patterson, D. J. (2001). “On core jakobids and excavate taxa: the ultrastructure of Jakoba incarcerata.” J Eukaryot Microbiol, 48(4), 480-492.

Smith, R., Kavanagh, E., Morrison, H. G., & Gould, R. M. (2001). “Messenger RNAs located in spiny dogfish oligodendrocyte processes.” Biol Bull, 201(2), 255-256.

Stihl, A., Sommer, U., & 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. doi:Doi 10.1046/J.1529-8817.2001.037002310..

Torino, J. L., Burger, M. S., Reznikoff, C. A., & 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), 147-154.

Twining, S. S., Goryshin, I. Y., Bhasin, A., & Reznikoff, W. S. (2001). “Functional characterization of arginine 30, lysine 40, and arginine 62 in Tn5 transposase.” J Biol Chem, 276(25), 23135-23143. doi:10.1074/jbc.M01074820.

Van Roey, P., Waddling, C. A., Fox, K. M., Belfort, M., & Derbyshire, V. (2001). “Intertwined structure of the DNA-binding domain of intron endonuclease I-TevI with its substrate.” EMBO J, 20(14), 3631-3637. doi:10.1093/emboj/20.14.363.

Walker, G., Simpson, A. G. B., Edgcomb, V. P., Sogin, M. L., & 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.

Welling, M., & Weber, M. (2001). “Positive tensor factorization.” Pattern Recognit Lett, 22. doi:10.1016/S0167-8655(01)00070-.

Wernegreen, J. J., & Moran, N. A. (2001). “Vertical transmission of biosynthetic plasmids in aphid endosymbionts (Buchnera).” J Bacteriol, 183(2), 785-790. doi:10.1128/JB.183.2.785-790.200.

Wernegreen, J. J., Richardson, A. O., & Moran, N. A. (2001). “Parallel acceleration of evolutionary rates in symbiont genes underlying host nutrition.” Mol Phylogenet Evol, 19(3), 479-485. doi:10.1006/mpev.2001.092.

West, N. J., Schoenhuber, W. A., Fuller, N. J., Walsby, A. E., Amann, R. I., Rippka, R., Post, A. F., & 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., & 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), 1593-1602. doi:10.1128/MCB.21.5.1593-1602.200.

2000

Alliegro, M. C. (2000). “A C-terminal carbohydrate-binding domain in the endothelial cell regulatory protein, pigpen: new function for an EWS family member.” Exp Cell Res, 255(2), 270-277. doi:10.1006/excr.1999.477.

Alliegro, M. C. (2000). “Effects of dithiothreitol on protein activity unrelated to thiol-disulfide exchange: for consideration in the analysis of protein function with Cleland’s reagent.” Anal Biochem, 282(1), 102-106. doi:10.1006/abio.2000.455.

Amaral-Zettler, L. A., Anderson, O. R., Nerad, T. A., & Sogin, M. L. (2000). “The phylogenetic position of Comandonia operculata and its implications for the taxonomy of the genus Acanthamoeba.” In S. Billot-Bonef, P. A. Cabanes, F. Marciano-Cabral, P. Pernin, & E. Pringuez (Ed.), IXth International Meeting on the Biology and Pathogenicity of Free-Living Amoebae Proceedings (pp. 235-242). Paris, France: John Libbey Eurotext.

Amaral-Zettler, L. A., & Caron, D. A. (2000). “New insights into the phylogeny of the Acantharea based on SSU rRNA gene sequencing.” European Journal of Protistology, 36, 34-39.

Amaral-Zettler, L. A., Nerad, T. A., O’Kelly, C. J., Peglar, M. T., Gillevet, P. M., Silberman, J. D., & Sogin, M. L. (2000). “A molecular reassessment of the Leptomyxid amoebae.” Protist, 151(3), 275-282. doi:10.1078/1434-4610-0002.

Arkhipova, I. R., & Meselson, M. (2000). “Transposable elements in sexual and ancient asexual taxa.” Proc Natl Acad Sci U S A, 97(26), 14473-14477. doi:10.1073/pnas.97.26.1447.

Bernard, C., Simpson, A. G. B., & Patterson, D. J. (2000). “Some free-living flagellates (protista) from anoxic habitats.” Ophelia, 52(2), 113-142.

Bhasin, A., Goryshin, I. Y., Steiniger-White, M., York, D., & Reznikoff, W. S. (2000). “Characterization of a Tn5 pre-cleavage synaptic complex.” J Mol Biol, 302(1), 49-63. doi:10.1006/jmbi.2000.404.

Bordenstein, S. R., Drapeau, M. D., & Werren, J. H. (2000). “Intraspecific variation in sexual isolation in the jewel wasp Nasonia.” Evolution, 54(2), 567-573.

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., & Lewin, H. A. (2000). “Phylogenomic analysis of the alpha proteasome gene family from early-diverging eukaryotes.” J Mol Evol, 51(6), 532-543. doi:10.1007/s002390010117 [pii.

Clark, M. A., Moran, N. A., Baumann, P., & 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), 517-525.

Cousineau, B., Lawrence, S., Smith, D., & Belfort, M. (2000). “Retrotransposition of a bacterial group II intron.” Nature, 404(6781), 1018-1021. doi:10.1038/3501002.

Davies, D. R., Goryshin, I. Y., Reznikoff, W. S., & Rayment, I. (2000). “Three-dimensional structure of the Tn5 synaptic complex transposition intermediate.” Science, 289(5476), 77-85. doi:8656 [pii.

Delgado-Viscogliosi, P., Viscogliosi, E., Gerbod, D., Kulda, J., Sogin, M. L., & 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), 70-75.

Edgell, D. R., Belfort, M., & Shub, D. A. (2000). “Barriers to intron promiscuity in bacteria.” J Bacteriol, 182(19), 5281-5289.

Funk, D. J., Helbling, L., Wernegreen, J. J., & Moran, N. A. (2000). “Intraspecific phylogenetic congruence among multiple symbiont genomes.” Proc Biol Sci, 267(1461), 2517-2521. doi:10.1098/rspb.2000.131.

Goryshin, I. Y., Jendrisak, J., Hoffman, L. M., Meis, R., & Reznikoff, W. S. (2000). “Insertional transposon mutagenesis by electroporation of released Tn5 transposition complexes.” Nat Biotechnol, 18(1), 97-100. doi:10.1038/7201.

Gould, R. M., Freund, C. M., Engler, J., & Morrison, H. G. (2000). “Optimization of homogenization conditions used to isolate mRNAs in processes of myelinating oligodendrocytes.” Biol Bull, 199(2), 215-217.

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

Lease, R. A., & 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), 9919-9924. doi:10.1073/pnas.17028149.

Lease, R. A., & Belfort, M. (2000). “Riboregulation by DsrA RNA: trans-actions for global economy.” Mol Microbiol, 38(4), 667-672.

Lee, W. J., & Patterson, D. J. (2000). “Heterotrophic flagellates (Protista) from marine sediments of Botany Bay, Australia.” Journal of Natural History, 34(4), 483-562. doi:Doi 10.1080/00222930029943.

Liang, P., Serres, M. H., & Riley, M. (2000). “Genes and Proteins of Escherichia coli K-12 (GenProtEC).” Nucleic Acids Research, 26(1), 54.

Mark Welch, D. B. (2000). “Evidence from a protein-coding gene that acanthocephalans are rotifers.” Invertebrate Biology, 119(1), 17-26. doi:10.1111/j.1744-7410.2000.tb00170..

Mark Welch, D. B., & Meselson, M. (2000). “Evidence for the Evolution of Bdelloid Rotifers Without Sexual Reproduction or Genetic Exchange.” Science, 288(5469), 1211-1215. doi:10.1126/science.288.5469.121.

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., & Sogin, M. L. (2000). “The Giardia genome project database.” FEMS Microbiol Lett, 189(2), 271-273.

Mohr, G., Smith, D., Belfort, M., & 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), 559-573.

Moran, N. A., & Wernegreen, J. J. (2000). “Lifestyle evolution in symbiotic bacteria: insights from genomics.” Trends Ecol Evol, 15(8), 321-326. doi:S0169534700019029 [pii.

Naumann, T. A., & Reznikoff, W. S. (2000). “Trans catalysis in Tn5 transposition.” Proc Natl Acad Sci U S A, 97(16), 8944-8949. doi:10.1073/pnas.16010799.

Neal, R. M. (2000). “Markov chain sampling methods for Dirichlet process mixture models.” J Comp Graph, 9.

Noel, R. J. Jr., & Reznikoff, W. S. (2000). “Structural studies of lacUV5-RNA polymerase interactions in vitro.” Ethylation interference and missing nucleoside analysis. J Biol Chem, 275(11), 7708-7712.

Patterson, D. J., & Lee, W. J. (2000). “Geographic distribution and diversity of free-living heterotrophic flagellates.” In J. Green & B. S. C. Leadbeater (Ed.), The Flagellates (pp. 269-287): Taylor and Francis.

Riley, M., & Serres, M. H. (2000). “Interim report on genomics of Escherichia coli.” Annu Rev Microbiol, 54, 341-411. doi:10.1146/annurev.micro.54.1.34.

Serres, M. H., Fladmark, K. E., & Doskeland, S. O. (2000). “An ultrasensitive competitive binding assay for the detection of toxins affecting protein phosphatases.” Toxicon, 38(3), 347-360. doi:DOI: 10.1016/S0041-0101(99)00163-.

Serres, M. H., & Riley, M. (2000). “MultiFun, a multifunctional classification scheme for Escherichia coli K-12 gene products.” Microb Comp Genomics, 5(4), 205-222.

Serres, M. H., Riley, M., M.Dworkin, & et al. (2000). “Genomics and metabolism in Escherichia coli The Prokaryotes: An Evolving Electronic Database for the Microbiological Community (Vol.” 3rd edition (release 3.2), pp. www.prokaryotes.com). New York: Springer-Verlag.

Simpson, A. G. B., Bernard, C., & Patterson, D. J. (2000). “The ultrastructure of Trimastix marina Kent, 1880 (eukaryota), an excavate flagellate.” European Journal of Protistology, 36(3), 229-251.

Sogin, M. L. (2000). “Evolution of Eukaryotic Ribosomal RNA Genes.” In S. Parker (Ed.), McGraw-Hill Yearbook of Science and Technology. New York, NY: McGraw-Hill.

Steiniger-White, M., & Reznikoff, W. S. (2000). “The C-terminal alpha helix of Tn5 transposase is required for synaptic complex formation.” J Biol Chem, 275(30), 23127-23133. doi:10.1074/jbc.M00341120.

Wang, Q., Li, H., & Post, A. F. (2000). “Nitrate assimilation genes of the marine diazotrophic, filamentous cyanobacterium Trichodesmium sp.” strain WH9601. J Bacteriol, 182(6), 1764-1767.

Wernegreen, J. J., & Moran, N. A. (2000). “Decay of mutualistic potential in aphid endosymbionts through silencing of biosynthetic loci: Buchnera of Diuraphis.” Proc Biol Sci, 267(1451), 1423-1431. doi:10.1098/rspb.2000.115.

Wernegreen, J. J., Ochman, H., Jones, I. B., & Moran, N. A. (2000). “Decoupling of genome size and sequence divergence in a symbiotic bacterium.” J Bacteriol, 182(13), 3867-3869.

Wood, D. W., Derbyshire, V., Wu, W., Chartrain, M., Belfort, M., & Belfort, G. (2000). “Optimized single-step affinity purification with a self-cleaving intein applied to human acidic fibroblast growth factor.” Biotechnol Prog, 16(6), 1055-1063. doi:10.1021/bp000085.

Wu, G., McArthur, A. G., Fiser, A., Sali, A., Sogin, M. L., & Mllerm, M. (2000). “Core histones of the amitochondriate protist, Giardia lamblia.” Mol Biol Evol, 17(8), 1156-1163.