Recent Publications:
Eugene A. Gladyshev and
Irina R. Arkhipova.
A single-copy IS5-like transposon in the genome of a bdelloid rotifer
Molecular Biology and Evolution, MBE Advance Access published on May 14, 2009.
doi:10.1093/molbev/msp104.
Huber, J. A., H. G. Morrison, S. M. Huse,
P. R. Neal, M. L. Sogin, and D. B. Mark Welch. 2009.
Effect of PCR amplicon size on assessments of clone library microbial diversity and community structure. Environmental Microbiology 11:1292-1302.
Dionysios A. Antonopoulos, Susan M. Huse, Hilary G. Morrison, Thomas M. Schmidt,
Mitchell L. Sogin, and Vincent B. Young. 2009.
Reproducible Community Dynamics of the Gastrointestinal Microbiota Following Antibiotic Perturbation.
Infect. Immun doi:10.1128/IAI.01520-08
Gribble, K.E., D.M. Anderson, D.W. Coats. 2009.
Sexual and Asexual Processes in Protoperidinium steidingerae Balech (Dinophyceae), with Observations on Life-History Stages of Protoperidinium depressum (Bailey) Balech (Dinophyceae). Journal of Eukaryotic Microbiology 56(1): 88-103.
Turnbaugh, P.J., M. Hamady, T. Yatsunenko, B.L. Cantarel, A. Duncan, R.E. Ley, M.L. Sogin, W.J.Jones, B.A. Roe, J.P. Affourtit, M.Egholm, B. Henrissat, A.C. Heath, R. Knight and J.I. Gordon. A core gut microbiome in obese and lean twins. Nature 457:480-484 (2009).
Donna E. Akiyoshi, Hilary G. Morrison, Shi Lei, Xiaochuan Feng, Quanshun Zhang, Nicolas
Corradi, Harriet Mayanja, James K. Tumwine, Patrick J. Keeling, Louis M. Weiss, Saul Tzipori.
(2009) Genomic Survey of the Non-Cultivatable Opportunistic Human Pathogen. Enterocytozoon bieneusi.
PLoS Pathog 5(1): e1000261. doi:10.1371/journal.ppat.1000261
Anton A. Turanov, Alexey V. Lobanov, Dmitri E. Fomenko, Hilary G. Morrison,
Mitchell L. Sogin, Lawrence A. Klobutcher,
Dolph L. Hatfield, Vadim N. Gladyshev. (2009).
Genetic Code Supports Targeted Insertion of Two Amino Acids by One Codon.
Science 323 no. 5911. pp. 259-261 DOI:10.1126/science.1164748
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, TK,
Strom, M. S., Sinigalliano, C. D., Moeller P. D. R. and Holland, A. F. 2008.
The coastal environment and human health: Microbial indicators, pathogens,
sentinels and reservoirs. Environmental Health 7(Suppl):S3.
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. Environmental Science and Technology 42: 9072-9078.
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.0003853
Nahum, L.A. and
Pereira, S.L.
(2008)
Phylogenomics, Protein Family Evolution, and the Tree of Life:
An Integrated Approach between Molecular Evolution and Computational Intelligence.
In: Smolinski TG, Milanova MG, Hassanien A-E (eds),
Studies in Computational Intelligence (SCI) 122, 259-279.
Springer-Verlag Berlin Heidelberg.
S.M. Huse, L. Dethlefsen, J.A. Huber, D. Mark Welch, D.A. Relman, M.L. Sogin.
2008 Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable
Tag Sequencing. PLoS Genetics 4(11): e1000255 doi:10.1371/journal.pgen.1000255
L. Dethlefsen, S. Huse, M.L. Sogin, D.A. Relman.
The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA
Sequencing PLoS Biology Vol. 6, No. 11, e280 doi:10.1371/journal.pbio.0060280
B.J.F. Keijser, E. Zaura, S.M. Huse,J.M.B.M. van der Vossen, F.H.J. Schuren,R.C. Montijn, J.M. ten Cate, and W. Crielaard. 2008.
Pyrosequencing analysis of the oral microflora of healthy adults.
Journal of Dental Research 87(11):1016-1020, 2008
Fernan Aguero, Bissan Al-Lazikani, Martin Aslett, Matthew Berriman,
Frederick S. Buckner, Robert K. Campbell, Santiago Carmona, Ian M. Carruthers,
A. W. Edith Chan, Feng Chen, Gregory J. Crowther, Maria A. Doyle,
Christiane Hertz-Fowler, Andrew L. Hopkins, Gregg McAllister, Solomon Nwaka,
John P. Overington, Arnab Pain, Gaia V. Paolini, Ursula Pieper, Stuart A. Ralph,
Aaron Riechers, David S. Roos, Andrej Sali, Dhanasekaran Shanmugam,
Takashi Suzuki, Wesley C. Van Voorhis and Christophe L. M. J. Verlinde.
Genomic-scale prioritization of drug
targets: the TDR Targets database.
Nature Reviews Drug Discovery Volume 7, November 2008, 900-907.
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.,
Hobbie, J., Goldstein, P., Guralnick, R. P., Brunt, J., and Michener W. K.,
Defining linkages between the GSC and NSF's LTER program: How the Ecological
Metadata Language (EML) relates to GCDML and other outcomes. 2008. OMICS A
Journal of Integrative Biology,12(2):151-156.
Huber, J.A. and J.F. Holden.
2008.
Modeling the impact of diffuse vent microorganisms along mid-ocean ridges and flanks.
In Lowell, R.P., J. S. Seewald, A. Metaxas, and M.R. Perfit (eds.), 215-231.
Magma to Microbe: Modeling Hydrothermal Processes at Oceanic Spreading Ridges.
American Geophysical Union Press, Washington, D.C.
Tamas, I., J. J. Wernegreen, B. Nystedt, S. N. Kauppinen, A. C. Darby,
L. Gomez-Valero, D. Lundin, A. M. Poole and S. G. Andersson
(2008).
"Endosymbiont gene functions impaired and rescued by polymerase infidelity at poly(A) tracts."
Proc Natl Acad Sci U S A 105(39): 14934-9.
Cristina Aurrecoechea, John Brestelli, Brian P. Brunk, Jane M. Carlton, Jennifer Dommer, Steve Fischer, Bindu Gajria, Xin Gao,
Alan Gingle, Greg Grant, Omar S. Harb, Mark Heiges, Frank Innamorato, John Iodice, Jessica C. Kissinger, Eileen Kraemer, Wei
Li, John A. Miller, Hilary G. Morrison, Vishal Nayak, Cary Pennington, Deborah F. Pinney, David S. Roos, Chris Ross, Christian
J. Stoeckert, Jr, Steven Sullivan, Charles Treatman and Haiming Wang.
GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis
Nucleic Acids Res. First published online 29 Sep 2008; doi:10.1093/nar/gkn631
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.
Nature Reviews Microbiology,
2008 Aug;6(8):592-603..
Lasek-Nesselquist, E., A. Bogomolni, R. Gast,
D. Mark Welch, J.C. Ellis,
M.L. Sogin, and M. Moore. 2008. Molecular characterization of Giardia intestinalis in marine animals: variation and zoonotic potential. Diseases of Aquatic Organisms 81: 39-51.
E.A. Gladyshev,
M. Meselson, and
I.R. Arkhipova
(2008)
Massive horizontal gene transfer in bdelloid rotifers.
Science 320: 1210-1213.
Cara M. Santelli,
Beth N. Orcutt,
Erin Banning,
Wolfgang Bach,
Craig L. Moyer,
Mitchell L. Sogin,
Hubert Staudigel &
Katrina J. Edwards
Abundance and diversity of microbial life in ocean crust
Nature 453, 653-656 (29 May 2008)
N. Schostak,
K. Pyatkov,
E. Zelentsova,
I. Arkhipova,
D. Shagin,
E. Mudrik,
A. Blintsov,
I. Clark,
D.J. Finnegan,
M. Evgen'ev
(2008)
Molecular dissection of Penelope transposable element regulatory machinery.
Nucleic Acids Res. 36(8): 2522-2529
Suga, K.,
D. B. Mark Welch,
Y. Tanaka, Y. Sakakura,
and A. Hagiwara, 2008.
Two circular chromosomes of unequal copy number make up the mitochondrial genome of the rotifer Brachionus plicatilis.
Molecular Biology and Evolution
2008 25: 1129-1137.
Manda Clair Jost, David M. Hillis, Ying Lu, John W. Kyle, Harry A.
Fozzard, and
Harold H. Zakon, 2008.
Toxin-Resistant Sodium Channels: Parallel Adaptive Evolution across a Complete Gene Family
Molecular Biology and Evolution 2008 25: 1016-1024; doi:10.1093/molbev/msn025.
Riley M.,
Staley J.T., Danchin A., Wang T., Brettin T.S., Hauser L.J., Land M.L., Thompson L.S.
Genomics of an extreme psychrophile, Psychromonas ingrahamii.
BMC Genomics. 2008 May 6;9(1):210
PMID: 18460197.
Alliegro, M.,
Alliegro, M. A., 2008.
Centrosomal RNA correlates with intron-poor nuclear genes in Spisula oocytes.
Proceedings of the National Academy of Sciences
105:6993-6997.
Amaral Zettler, L. A.,
Peplies, J., Ramette,
A. Fuchs, B.,
Ludwig, W., and
Glšckner, F. O.,
Proceedings of the International Workshop on Ribosomal RNA
Technology, April 7-9, 2008, Bremen, Germany, 2008. Syst. Appl. Microbiol.
31(4): 258-268.
Rull, K., Hallast, P., Uuskula, L., Jackson, J., Punab, M., Salumets, A.,
Campbell, R.K., and Laan, M.
Fine scale quantification of hCG beta gene transcription in human trophoblastic and non-malignant non-trophoblastic tissues.
Mol. Human Reprod. 14:23-31. (2008) E-published November 29, 2007.
McKenna, S.D., Feger, G., Kelton, C., Yang, M., Ardissone, V., Cirillo, R., Vitte, P.A., Jiang, X., and Campbell, R.K.
Tumor necrosis factor (TNF)-soluble high-affinity receptor complex as a TNF antagonist.
J. Pharmacol Exp. Ther. 322:822-828. (2007)
Mark Welch D.B, , J.L. Mark Welch, J.L., and M. Melselson. (2008)
Evidence for degenerate tetraploidy in bdelloid rotifers. Proc Nat Acad Sci USA 105: 5145-5149.
Gladyshev, E.,
Meselson, M., 2008.
Extreme resistance of bdelloid rotifers to ionizing radiation
Proceedings of the National Academy of Sciences
10.1073/pnas.0800966105
Huse, S. M.,
J. A. Huber,
Morrison, H. G.,
Sogin, M.L.,
Mark Welch, D.
(2007).
Accuracy and quality of massively-parallel DNA pyrosequencing.
Genome Biology 8: R143.
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 Informatics, 2007;18:287-98..
