Publications

From projects funded 2012 - present

Aluru N, Deak KL, Jenny MJ, Hahn ME: MicroRNA expression profiling after developmental exposure of zebrafish (Danio rerio) embryos to valproic acid. Neurotoxicology and Teratology 2013, 40:46-58.

From projects funded 2003 - 2011

Acinas, S.G., Sarma-Rupavtarm, R., Klepac-Ceraj, V. and Polz, M.F., 2005. PCR induced sequence artifacts and bias: insights from two 16S rRNA clone libraries constructed from the same sample. Appl. Environ. Microbiol, 71: 8966-8969.

Amaral-Zettler, L.A., Rocca, J.D., LaMontagne, M.G., Dennett, M.R. and Gast, R.J., in press. Changes in microbial community structure in the wake of Hurricanes Katrina and Rita. Environmental Science and Technology.

Anderson, D.M., 2008. Harmful algal blooms and ocean observing systems: needs, present status and future potential. In: Fisheries for Global Welfare and Environment, Terrapub, Tokyo, 317-334 pp.

Anderson, D.M., Burkholder, J.M., Cochlan, W.P., Glibert, P.M., Gobler, C.J., Heil, C.A., Kudela, R., Parsons, M.L., Rensel, J.E., Townsend, D.W., Trainer, V.L., Vargo, G.A., In press. Harmful algal blooms and eutrophication: Examples of linkages from selected coastal regions of the United States. Harmful Algae.

Anderson, D.M., Bruce A. Keafer, Dennis J. McGillicuddy Jr., Michael J. Mickelson, Kenneth E. Keay, P. Scott Libby, James P. Manning, Charles A. Mayo, David K. Whittaker, J. Michael Hickey, Ruoying He, Daniel R. Lynch, Keston W. Smith et al., 2005. Initial observations on the 2005 Alexandrium fundyense bloom in southern New England: general patterns and mechanisms. Deep-Sea Research II(52): 2856-2876.

Aretxabaleta, A.L., McGillicuddy, D.J., Smith, K.W. and Lynch, D.R., 2008. Model Simulations of the Bay of Fundy Gyre: 1. Climatological Results. Journal of Geophysical Research, 113(C10027): doi:10.1029/2007JC004480.

Aretxabaleta, A.L., McGillicuddy, D.J., Smith, K.W., Manning, J.P. and Lynch, D.R., Submitted. Model Simulations of the Bay of Fundy Gyre: 2. Hindcasts for 2005-2007 Reveal Interannual Variability in retentiveness. Journal of Geophysical Research.

Backer, L.C. and McGillicuddy, D.J., 2006. Harmful Algal Blooms: At the Interface Between Coastal Oceanography and Human Health. Oceanography, 19(2): 94-106.

Bogomolni, A.L. Gast, R.J., Ellis, J.C., Dennett, M., Pugliares, K.R., Lentell, B.J., Moore, M.J., 2008. Victims or Vectors: a survey of marine vertebrate zoonoses from coastal waters of the Northwest Atlantic. Diseases of Aquatic Organisms, 81: 13-38.

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

Dyble, J., P., Dusek, E., Hitchcock, G., Holland, F., Laws, E., Lerczak, J., McGillicuddy, D.J., Minnett, P., Moore, S., O’Kelly, C., Solo-Gabriel, H., and J. Wang., 2008. Environmental controls, oceanography and population dynamics of pathogens and harmful algal blooms: Connecting sources to human exposure. Environmental Health, 7(2:55): doi:10.1186/1476-069X-7-S2-S5.

Ehrenreich, I.M., Waterbury, J.B. and Webb, E.A., 2005. Distribution and diversity of natural product genes in marine and freshwater cyanobacterial cultures and genomes. Applied and Environmental Microbiology, 71(11), 7401-7413.

Erdner, D.L. and Anderson, D.M., 2006. Global transcriptional profiling of the toxic dinoflagellate Alexandrium fundyense using Massively Parallel Signature Sequencing. BMC Genomics, 7(88): 1-11.

Erdner, D.L., Dyble, J., Parsons, M.L., Stevens, R.C., Hubbard, K.A., Wrabel, M.L,, Moore, S.K., Lefebvre, K.A., Anderson, D.M., Bienfang, P., Bidigare, R.R., Parker, M.S., Moeller, P., Brand, L.E., Trainer, V.L., 2008. A unified approach to the challenge of harmful algal blooms. Environmental Health, 7(2): S2.

Glibert, P.M., Azanza, R., Burford, M., Furuya, K., Abal, E., Al-Azri, A., Al-Yamani, F., Andersen, P., Anderson, D.M., 2008. Ocean urea fertilization for carbon credits poses high ecological risks. Marine Pollution Bulletin, 56: 1049-1056.

He, R. and McGillicuddy, D.J., 2008. The Historic 2005 Toxic Bloom of Alexandrium fundyense in the western Gulf of Maine - Part 1: In Situ Observations of Coastal Hydrography and Circulation. Journal of Geophysical Research, 113(C07039): doi:10.1029/2007JC004601.

He, R., McGillicuddy, D.J., Keafer, B.A. and Anderson, D.M., 2008. The Historic 2005 Toxic Bloom of Alexandrium fundyense in the Western Gulf of Maine - Part 2: Coupled Bio-physical Numerical Modeling. Journal of Geophysical Research, 113(C07040): doi:10.1029/2007JC004602.

Heisler, J., P. Glibert, J. Burkholder, D. Anderson, W. Cochlan, W. Dennison, C. Gobler, Q. Dortch, C. Heil, E.Humphries, A. Lewitus, R. Magnien, H. Marshall, K. Sellner, D. Stockwell, D. Stoecker, M. Suddleson., In press. Eutrophication and harmful algal blooms: A scientific consensus. Harmful Algae.

Ho, A.Y.T. et al., Submitted. Seasonal variation in size-fractionated phytoplankton biomass and production along a eutrophic gradient in Hong Kong waters. Marine Ecology Progress Series.

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, pp. 97-100.

Hunt, D.E., Klepac-Ceraj, V., Acinas, S.G., Gautier, C., Bertilsson, S., Polz, M.F., 2006. Evaluation of 23S rRNA PCR Primers for Use in Phylogenetic Studies of Bacterial Diversity, Applied and Environmental Microbiology, 72(3), 2221-2225.

Hunt, D.E., 2008. Aquatic microenvironments in bacterial ecology and diversity. Ph.D. Thesis, MIT Cambridge.

Hunt, D.E., Gevers, D., Vahora, N.M. and Polz, M.F., 2008a. Conservation of the chitin utilization pathway in the Vibrionaceae. Applied and Environmental Microbiology, 74(1): 44-51.

Hunt, D.E., L.A. David, D. Gevers, S.P. Preheim, E.J. Alm, M.F. Polz., 2008b. Resource partitioning and sympatric differentiation among closely related bacterioplankton. Science, 320: 1081-1085.

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

Huse, S.M., Huber, J.A., Morrison, H.G., Sogin, M.L. and Welch, D.M., 2007. Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol, 8(7:R143): PMID: 17659080.

Joss, M.J. et al., Submitted. ACID: Annotation of cassette and integron data. Bioinformatics.

Juhl, A.R., Martins, C.A. and Anderson, D.M., 2008. Toxicity of Alexandrium lusitanicum to gastropod larvae is not caused by paralytic-shellfish-poisoning toxins. Harmful Algae, 7: 567-573.

Keijser, B.J.F., E. Zaura, S.M. Huse, J.M.B.M. van der Vossen, F.H.J. Schuren, R.C. Montijn, J.M. ten Cate, W. Crielaard., 2008. Pyrosequencing Analysis of the Oral Microflora of Healthy Adults. Journal of Dental Research, 87(11): 1016-1020.

Kite-Powell, H., L.E. Fleming, L.C. Backer, E.M. Faustman, P. Hoagland, A. Tsuchiya, L.R. Younglove, B.A. Wilcox, R.J. Gast., 2008. Linking the oceans to public health: current efforts and future directions. Environmental Health, 7(Suppl 2): S6, doi:10.1186/1476-069X-7-S2-S6.

Klepac-Ceraj, V., Ceraj, I. and Polz, M.F., 2006. CLUSTERER: extendable java application for sequence grouping and cluster analyses. Online J. of Bioinformatics, 7: 15-21.

Lasek-Nesselquist, E., A. Bogomolni, R. Gast, D.M. Welch, J.C. Ellis, M.L. Sogin, M. Moore., 2008. Molecular characterization of Giardia intestinalis haplotypes in marine animals: variation and zoonotic potential. Diseases of Aquatic Organisms, 81: L39-51.

Laws, E.A., Fleming, L.E. and Stegeman, J.J., 2008. Centers for Oceans and Human Health: Contributions to an emerging discipline. Environmental Health, 7(Suppl 2):S1.

Lerczak, J.A., Geyer, W.R. and Ralston, D.K., In press. The Temporal Response of the Length of a Partially-Stratified Estuary to Changes in River Flow and Tidal Amplitude. Journal of Physical Oceanography.

Lilly, E.L., Halanych, K. and Anderson, D.M., 2007. Species boundaries and global biogeography of the dinoflagellate “A. tamarense” complex of the dinoflagellate genus Alexandrium (Dinophyceae). Journal of Phycology, 43: 1329-1338.

Manning, J.P., McGillicuddy, D.J., Pettigrew, N.R., Churchill, J.H. and Incze, L.S., Submitted. Drifter Observations of the Gulf of Maine Coastal Current. Continental Shelf Research.

Marcelino, L.A., Backman, V., Donaldson, A., Steadman, C., Thompson, J.R., Preheim, S.P., Lien, C., Lim, E., Veneziano, D., Polz, M.F., 2006. Accurately quantifying low-abundant targets amid similar sequences by revealing hidden correlations in oligonucleotide microarray data. Proceedings of the National Academy of Sciences, 103: 13629-13634.

Martins, C.A., 2006. Functional genomics of a non-toxic Alexandrium lusitanicum culture. Ph.D. Thesis, MIT/WHOI Cambridge/Woods Hole.

McCauley, L.A.R., Erdner, D.L., Nagai, S., Richlen, M.L. and Anderson, D.M., In press. Biogeographic analysis of the globally distributed harmful algal bloom species Alexandrium minutum (Dinophyceae) based on rRNA gene sequences and microsatellite markers. J. Phycology.

Messerli, S.M. and Greenberg, R.M., 2006. Cnidarian toxins acting on voltage-gated ion channels. Marine Drugs, 4: 70-81.

Nagai, S., L. McCauley, N. Yasuda, D.L. Erdner, D.M. Kulis, Y. Matsuyama, S. Itakura and D.M. Anderson, 2006. Development of microsatellite markers in the toxic dinoflagellate Alexandrium minutum (Dinophyceae). Molecular Ecology Notes, 6: 756-758.

Polz, M.F., Hunt, D.E., Preheim, S.P. and Weinreich, D.M., 2006. Patterns and mechanisms of genetic and phenotypic differentiation in marine microbes. Royal Society of London, 361: 2009-2021

Pope, W.H., Weigele, P. R., Chang, J., Pedulla, M. L., Ford, M. E., Houtz, J. M., Jiang, W., Chiu, W., Hatfull, G. F., Hendrix, R. W., King, J., 2007. Genome Sequence, Structural Proteins, and Capsid Organization of the Cyanophage Syn5: a "Horned" Bacteriophage of Marine Synechococcus. Journal of Molecular Biol, 368: 966-981.

Ralston D.K., McGillicuddy, D.J. and Townsend, D.W., 2007. Asynchronous vertical migration and bimodal distribution of motile phytoplankton. Journal of Plankton Research, 29(9): 803-821.

Reddy, C.M., Stegeman, J.J. and Hahn, M.E., 2008. Chapter 7: Organic Pollutants: Presence and Effects in Humans and Marine Animals. In: P. Walsh, S. Smith, L. Fleming, H. Solo-Gabriele and W. Gerwick (Editors), Oceans and Human Health: Risks and Remedies from the Seas. Elsevier B.V., pp. 121-144.

Rose, J.M., R.J. Gast, A. Bogomolni, J.C. Ellis, B. Lentell, K. Touhey. M. Moore, In press. Occurrence and patterns of antibiotic resistance in vertebrates off the Northeastern United States coast. FEMS Microbiology Ecology.

Shimeta, J., Gast, R.J. and Rose, J.M., 2007. Community structure of marine sedimentary protist in relation to flow and grain size. Aquatic Microbial Ecology, 48: 91-104.

Sinigalliano, C.D., M. L. Gidley, T. Shibata, D. Whitman, T. H. Dixon, E. Laws, A. Hou, D. Bachoon, L. Brand, L. Amaral-Zettler, R. J. Gast, G. F. Steward, O. D. Nigro, R. Fujioka, W. Q. Betancourt, G. Vithanage, J. Mathews, L. E. Fleming, and H. M. Solo-Gabriele, 2007. Impacts of Hurricane Katrina on the Microbial Landscape of the New Orleans Area. Proceedings of the National Academy of Sciences of the United States of America, 104(21): 9029-9034.

Smith, K.W., McGillicuddy, D.J. and Lynch, D.R., In press. Parameter estimation using an ensemble smoother: the effect of the circulation in biological estimation. Journal of Marine Systems.

Sogin, M.L., H.G. Morrison, J.A. Huber, D.M. Welch, S.M. Huse, P.R. Neal, J.M. Arrieta, and G.J. Herndl, 2006. Microbial diversity in the deep sea and the underexplored "rare biosphere". Proceedings of the National Academy of Sciences of the United States of America, 103(32): 12115-12120.

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., Holland, A.F., 2008. The coastal environment and human health: microbial indicators, pathogens, sentinels and reservoirs. Environmental Health, 7(Suppl 2:S3).

Stock, C.A., McGillicuddy, D.J., Anderson, D.M., Solow, A.M. and Signell, R.P., 2007. Blooms of the toxic dinoflagellate Alexandrium fundyense in the western Gulf of Maine in 1993 and 1994: A comparative modeling study. Continental Shelf Research, 27: 2486-2512.

Stocker, R., Seymour, J.R., Samadani, A., Hunt, D.E. and Polz, M.F., 2008. Rapid chemotactic response enables marine bacteria to exploit ephemeral microscale nutrient patches. Proceedings of the National Academy of Sciences, 105(11): 4209-4214.

Thompson, J.R., 2005. Emergent Patterns of Diversity and Dynamics in Natural Populations of Planktonic Vibrio Bacteria, Ph.D. Thesis, MIT/WHOI Joint Program, Cambridge, MA.

Thompson, J.R., Marcelino, L.A. and Polz, M., 2005. Diversity, sources, and detection of human bacterial pathogens in the marine environment. In: S. Belkin (Editor), Oceans and Health: Pathogens in the Marine Environment. Springer, New York, pp. 29-68.

Thompson, J.R. and Polz, M., 2006. Dynamics of Vibrio populations and their role in environmental nutrient cycling. In: F.L. Thompson, B. Austin and J. Swings (Editors), The Biology of Vibrios. ASM Press, pp. 190-203.

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, in press. A core gut microbiome in obese and lean twins. Nature.

Weigele, P.W., Pope, W. H., Pedulla, M. L., Houtz, J. M., Smith, A. L., King, J., Hatfull, G., Lawrence, J. G., Hendrix, R. W, 2007. Genomic and structural analysis of Syn9, a cyanophage infecting marine Prochlorococcus and Synechococcus. Environ Microbiol, 9: 1675-1695.

Xu, J., A.Y.T. Ho, K. Yin, X. Yuan, D.M. Anderson, P.J. Harrison, 2008. Temporal and spatial variations in nutrient stoichiometry and regulation of phytoplankton biomass in Hong Kong waters: Influence of the Pearl River outflow and sewage inputs. Marine Pollution Bulletin, 57: 335-348.







Last updated: October 31, 2012