Project | Data Management Plan |
---|---|
Investigations of Alexandrium fundyense dynamics in the Gulf of Maine |
Principal Investigator: John J. Stegeman (Woods Hole Oceanographic Institution)
Co-Principal Investigator: Dennis J McGillicuddy
BMC Genomics~2006~7:88~Erdner, D.L. and D.M. Anderson~~1~~~~Global transcriptional profiling of the toxic dinoflagellate Alexandrium fundyense using Massively Parallel Signature Sequencing.~N~~~~~~
Molecular Ecology Notes~2006~6~Nagai, S., L. McCauley, N. Yasuda, D.L. Erdner, D.M. Kulis, Y. Matsuyama, S. Itakura and D.M. Anderson.~~756~~~~Development of microsatellite markers in the toxic dinoflagellate Alexandrium minutum (Dinophyceae)~N~~~~~~
Deep Sea Research II~2005~52~Anderson, D.M., Keafer, B.A., McGillicuddy, D.J., Mickelson, M.J., Keay, K.E., Libby, P.S., Manning, J.P., Mayo, C.A., Whittaker, D.K., Hickey, J.M., He, R., Lynch, D.R., Smith, K.W.~~2856~~~~Initial observations of the 2005 Alexandrium fundyense bloom in southern New England: General patterns and mechanisms~N~~~~~~
Appl. Environ. Microbiol.~2005~71(12)~Acinas, S.G, Sarma-Rupavtarm, R., Klepac-Ceraj, V., Polz, M.F.~~8966~~~~PCR induced sequence artifacts and bias: insights from two 16S rRNA clone libraries constructed from the same sample. Appl. Environ. Microbiol.~N~~~~~~
Online J. Bioinf.~2006~7(1~Klepac-Ceraj, V., Ceraj, I., Polz, M.F.~~15~~~~CLUSTERER: extendable java application for sequence grouping and cluster analyses~N~~~~~~
Appl. Environ. Microbiol.~2006~72(3)~Hunt, D.E., Klepac-Ceraj, V., Acinas, S.G., Gauthier, C., Bertilsson, S., Polz, M.F.~~2221~~~~Evaluation of 23S rRNA PCR Primers for use in Phylogenetic Studies of Bacterial Diversity.~N~~~~~~
Proc. Natl. Acad. Sci. USA~2006~103(37)~Marcelino, L., Backman, V., Donaldson, A., Steadman, C., Thompson, J.R., Paccocha-Preheim, S., Lien, C., Lim, E., Veneziano, D., Polz, M.F.~~13629~~~~Accurate identification of low abundant targets amidst similar sequences by revealing hidden correlations in oligonucleotide microarray data.~N~~~~~~
Phil. Trans. R. Soc. Lond. B.~2006~361~Polz, M.F., Hunt, D.E., Preheim, S.P., Weinreich, D.M.~~2009~~~~Patterns and mechanisms of genetic and phenotypic differentiation in marine microbes. Phil. Trans. R. Soc. Lond. B.~N~~~~~~
Proc. Natl. Acad. Sci. USA~2006~103(32)~Sogin, M.L., H.G. Morrison, J.A. Huber, D.Mark Welch, S.M. Huse, P.R. Neal, J.M. Arrieta, and G.J. Herndl.~~12115~~~~Microbial diversity in the deep sea and the under-explored "rare biosphere.~N~~~~~~
Marine Drugs~2006~4~Messerli, S.M. and Greenberg, R.M.~~70~~~~Cnidarian toxins acting on voltage-gated ion channels.~N~~~~~~
Appl. Environ. Microbiol.~2005~71~Ehrenreich, I.M., J.B. Waterbury, and E.A. Webb~~7401~~~~The Distribution and Diversity of Natural Product Genes in Marine and Freshwater Cyanobacterial Cultures and Genomes.~N~~~~~~
Oceanography~2006~19~Backer, L.C. and McGillicuddy, D.J.,~~94~~~~Harmful Algal Blooms: At the interface between coastal oceanography and human health.~N~~~~~~
Journal of Plankton Research~2007~~Ralston D.K., McGillicuddy, D.J. and D.W. Townsend~~~~~~Asynchronous vertical migration and bimodal distribution of motile phytoplankton.~N~~~~~~
Boston: MWRA Report 2007-10~2007~~Anderson, D.M., Libby, P.S., Mickelson, M.J., Borkman, D.G., He, R., McGillicuddy, D.J.~~~~~~The 2005 New England red tide of Alexandrium fundyense: observations, causes, and potential outfall linkages.~N~~~~~~
Environmental Health~2007~~Dyble, J., Bienfang, P., Dusek, E., Griffiths, W., Hitchcock, G., Holland, F., Laws, E., Lerczak, J., McGillicuddy, D.J., Minnett, P., Moore, S., O?Kelly, C., Solo-Gabriel, H., and J. Wang.~~~~~~Environmental controls, oceanography and population dynamics of pathogens and harmful algal blooms: Connecting sources to human exposure.~N~~~~~~
Aquatic Microbial Ecology~2007~~Shimeta, J., R.J. Gast and J.M. Rose~~~~~~Community structure of marine sedimentary protists in relation to flow and grain size~N~~~~~~
PNAS~2007~~Sinigalliano, CD, Gidley, ML, Shibata, T, Whitman, D, Dixon, TH, Laws, E, Hou, A, Bachoon, D, Brand, L, Amaral-Zettler, L, Gast, R, Steward, GF, Nigro, OD, Fujioka, R, Betancourt, WQ, Vithanage, G, Mathews, J, Fleming, LE and HM Solo-Gabriele.~~~~~~Impact of Hurricanes Katrina and Rita on the microbial landscape of the New Orleans area~N~~~~~~
MTS/IEEE-Boston, Massachusetts September 18-21, 2006~2006~~Bogomolni A, Ellis J, Gast B, Harris R, Pokras M, Touhey K, Moore M~~~~~~Emerging Zoonoses in Marine Mammals and Seabirds of the Northeast U.S. Oceans '06~N~~~~~~
ISME Journal~2007~~Sabehi, G. Kirkup, B. C., Rozenberg, M., Stambler, N., Polz, M.F., Beja, O.~~~~~~Niche adaptation and spectral tuning in marine proteorhodopsins~N~~~~~~
Appl. Environ. Microbiol.~2008~~Hunt, D. E., Gevers, D., Vahora, N. M., Polz, M. F.~~~~~~Conservation of the chitin utilization pathway in the Vibrionaceae.~N~~~~~~
Textbook: 'Oceans Health'~2007~~Thompson, J.T., Marcelino, L., Polz, M.F.~~~~~~Diversity and sources of human bacterial pathogens and overview of methods of their detection and quantification. In: Shimshon Belkin and Rita Colwell (Eds.), Ocean and Health: Pathogens in the Marine Environment.~N~~~~~~
Genome Biology~2007~~Huse, S.M., J.A. Huber , H.G. Morrison, M.L. Sogin and D. Mark Welch~~~~~~Accuracy and quality of massively parallel DNA pyrosequencing.~N~~~~~~
Journal of molecular biology~2007~~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., and King, J.~~~~~~Genome sequence, structural proteins, and capsid organization of the cyanophage Syn5: a "horned" bacteriophage of marine Synechococcus.~N~~~~~~
Environmental microbiology~2007~~Weigele, P. R., Pope, W. H., Pedulla, M. L., Houtz, J. M., Smith, A. L., Conway, J. F., King, J., Hatfull, G. F., Lawrence, J. G., and Hendrix, R. W.~~~~~~Genomic and structural analysis of Syn9, a cyanophage infecting marine Prochlorococcus and Synechococcus.~N~~~~~~
Journal of Plankton Research~2007~29(9)~Ralston D.K., McGillicuddy, D.J. and D.W. Townsend~~80~~~~Asynchronous vertical migration and bimodal distribution of motile phytoplankton~N~~~~~~
Online Journal of Bioinformatics~2006~7(1)~Klepac-Ceraj, V., Ceraj, I., Polz, M.F.~~15~~~~CLUSTERER: extendable java application for sequence grouping and cluster analyses~N~~~~~~
Proc. Natl. Acad. Sci. USA~2006~103(37)~Marcelino, L., Backman, V., Donaldson, A., Steadman, C., Thompson, J.R., Paccocha-Preheim, S., Lien, C., Lim, E., Veneziano, D., Polz, M.F.~~13629~~~~Accurate identification of low abundant targets amidst similar sequences by revealing hidden correlations in oligonucleotide microarray data.~N~~~~~~
Harmful Algae~2008~8~Anderson, D.M., J.M. Burkholder, W.P. Cochlan, P.M. Glibert, C.J. Gobler, C.A. Heil, R. Kudela, M.L. Parsons, J.E. Rensel, D.W. Townsend, V.L. Trainer, and G.A. Vargo (in review).~~39~~~~Harmful algal blooms and eutrophication: Examples of linkages from selected coastal regions of the United States.~N~~~~~~
Environmental Health. Supplement~2007~7~Erdner, D.L., J. Dyble, M.L. Parsons, P. Moeller, R.C. Stevens, K.A. Hubbard, M.L. Wrabel, S.K. Moore, K.A. Lefebvre, D.M. Anderson, P. Bienfang, R.R. Bidigare, M.S. Parker, P. Moeller, L.E. Brand, and V.L. Trainer~~S2~~~~Centers for Oceans and Human Health: A unified approach to the challenge of harmful algal blooms.~N~~~~~~
J. Phycol.~2007~43~Lilly, E.L., K. Halanych, and D.M. Anderson (in press).~~13~~~~Species boundaries and global biogeography of the dinoflagellate "A. tamarense" complex of the dinoflagellate genus Alexandrium (Dinophyceae).~N~~~~~~
Mar. Poll. Bull.~2008~57~Xu, Jie, A.Y.T. Ho, K. Yin, X. Yuan, D.M. Anderson, and P.J. Harrison (in review).~~~~~~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.~N~~~~~~
Oceanography~2006~19(2)~Backer, L.C. and McGillicuddy, D.J.,~~94~~~~Harmful Algal Blooms: At the interface between coastal oceanography and human health.~N~~~~~~
Journal of Marine Systems~2009~76(1-2)~Smith, K.W., McGillicuddy, D.J., and D.R. Lynch.~~162~~~~Parameter estimation using an ensemble smoother: the effect of the circulation in biological estimation.~N~~~~~~
Journal of Geophysical Research~2007~~Aretxabaleta, A.L., McGillicuddy, D.J. , Smith, K.W., and D.R. Lynch~ 10.1029~~~~~Model Simulations of the Bay of Fundy Gyre: 1. Climatological Results~N~~~~~~
Environmental Health~2008~~Dyble, J., Bienfang, P., Dusek, E., Griffiths, W., Hitchcock, G., Holland, F., Laws, E., Lerczak, J., McGillicuddy, D.J., Minnett, P., Moore, S., O'Kelly, C., Solo-Gabriel, H., and J. Wang.~ 10.1186/1476-069x-7-s2-s5~~~~~Environmental controls, oceanography and population dynamics of pathogens and harmful algal blooms: Connecting sources to human exposure.~N~~~~~~
Environmental Health~2008~7(Suppl~Jill R. Stewart, Rebecca J. Gast, Roger S. Fujioka, Helena M. Solo-Gabriele, J. Scott Meschke, Linda A. Amaral-Zettler, Ericka Del Castillo, Martin F. Polz, Tracy K. Collier, Mark S. Strom, Christopher D. Sinigalliano, Peter D. R. Moeller, and A. Fredrick~~~~~~The coastal environment and human health: Microbial indicators, pathogens, sentinels and reservoirs~N~~~~~~
Aquatic Microbial Ecology~2007~48~Shimeta, J., R.J. Gast and J.M. Rose~~91~~~~Community structure of marine sedimentary protists in relation to flow and grain size~N~~~~~~
ISME Journal~2007~1(1)~Sabehi, G. Kirkup, B. C., Rozenberg, M., Stambler, N., Polz, M.F., Beja, O.~~48~~~~Niche adaptation and spectral tuning in marine proteorhodopsins~N~~~~~~
Appl. Environ. Microbiol.~2008~74(1)~Hunt, D. E., Gevers, D., Vahora, N. M., Polz, M. F.~~4~~~~Conservation of the chitin utilization pathway in the Vibrionaceae.~N~~~~~~
Proc. Natl. Acad. Sci.~2008~105(11)~Stocker, R, Seymour, J. R., Samadani, A., Hunt, D. E., Polz, M. F.~~420~~~~Rapid chemotactic response enables marine bacteria to exploit ephemeral microscale nutrient patches.~N~~~~~~
Journal of molecular biology~2007~368~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., and King, J.~~~~~~Genome sequence, structural proteins, and capsid organization of the cyanophage Syn5: a "horned" bacteriophage of marine Synechococcus.~N~~~~~~
Environmental microbiology~2007~9~Weigele, P. R., Pope, W. H., Pedulla, M. L., Houtz, J. M., Smith, A. L., Conway, J. F., King, J., Hatfull, G. F., Lawrence, J. G., and Hendrix, R. W.~~1675~~~~Genomic and structural analysis of Syn9, a cyanophage infecting marine Prochlorococcus and Synechococcus.~N~~~~~~
Environmental Health~2008~7(Suppl~H.L. Kite-Powell, L.E. Fleming, L.C. Backer, E. Faustman, P. Hoagland, A. Tsuchiya, L. Younglove, B.A. Wilcox, and R. Gast.~ 10.1186~~~~~Linking the oceans to public health: current efforts and future directions.~N~~~~~~
Science. 320:1081-1085.~2008~320~Hunt, D. E., Lawrence, A. D., Gevers, D., Preheim, S., Alm, E. J., Polz, M. F.~~1081~~~~Resource partitioning and sympatric differentiation among closely related bacterioplankton.~N~~~~~~
Science. 323:741-746~2009~323~Fraser, C., Alm, E.J., Polz, M.F., Spratt, B., Hanage, W.~~~~~~The bacterial species challenge: Making sense of genetic and ecological diversity.~N~~~~~~
Ethics in Environmental Science and Politics~2009~~Halliday, E.~10.3354/esep00101~~~~~Knowledge is Power? In a world shaped by science, are scientists responsible for keeping the public informed of their research and discoveries?~N~~~~~~
FEMS Microbiology Ecology~2009~67~Rose JM, Gast RJ, Bogomolni A, Ellis J, Lentell B, Touhey K and M Moore.~~421~~~~Occurrence and patterns of antibiotic resistance in vertebrates off the Northeastern United States coast.~N~~~~~~
Environmental Science and Technology.~2008~~Amaral-Zettler LA, Rocca JD, Lamotagne MC, Dennett MR and RJ Gast.~42: 9072-9078.~~~~~Changes in microbial community structure in the wake of Hurricanes Katrina and Rita.~N~~~~~~
Oceanus 47~2008~~Halliday, E.~~~~~~Testing the waters and closing the beaches.~N~~~~~~
Diseases of Aquatic Organisms~2008~~Bogomolni A, Gast RJ, Ellis J, Dennett M, Pugliares K and M Moore.~81(1):13-38~~~~~Vectors or Victims? Marine vertebrate zoonoses from coastal waters of the Northwest Atlantic.~N~~~~~~
Diseases of Aquatic Organisms~2008~81(1)~Lasek-Nesselquist E, Bogomolni A, Gast RJ, Mark Welch D, Ellis J, Sogin ML and M Moore.~~39~~~~Molecular characterization of Giardia intestinalis haplotypes in marine animals: variation and zoonotic potential.~N~~~~~~
Journal of Geophysical Research-Oceans, 113, C07039~2008~~He, R. and D.J. McGillicuddy~10.1029/2007JC004601~~~~~Historic 2005 toxic bloom of Alexandrium fundyense in the west Gulf of Maine: 1. In situ Observations of Coastal Hydrography and Circulation.~N~~~~~~
Journal of Geophysical Research-Oceans, 113, C07040~2008~~He, R., McGillicuddy, D.J.,Keafer, B.A. and D.M. Anderson~10.1029/2007JC004602~~~~~Historic 2005 toxic bloom of Alexandrium fundyense in the western Gulf of Maine: 2. Coupled Biophysical Numerical Modeling.~N~~~~~~
Continental Shelf Research~2009~29 (7)~Manning, J.P., McGillicuddy, D.J., Pettigrew, N.R., Churchill, J.H. and L.S. Incze~~835~~~~Drifter Observations of the Gulf of Maine Coastal Current.~N~~~~~~
Continental Shelf Research~2007~(27)~Stock, C.A., McGillicuddy, D.J., Anderson, D.M., Solow, A.M. and R.P. Signell~~2486~~~~Blooms of the toxic dinoflagellate Alexandrium fundyense in the western Gulf of Maine in 1993 and 1994: A comparative modeling study.~N~~~~~~
Harmful Algae~2008~7~Juhl, A.R., C.A. Martins, and D.M. Anderson.~~567~~~~Toxicity of Alexandrium lusitanicum to gastropod larvae is not caused by paralytic-shellfish-poisoning toxins.~N~~~~~~
Fisheries for Global Welfare and Environment, K. Tsukamoto, T. Kawamura, T. Takeuchi, T.D. Beard, Jr., and M.J. Kaiser (Eds.)~2008~~Anderson, D.M.~~317~~~~Harmful algal blooms and ocean observing systems: needs, present status and future potential.~N~~~~~~
PLoS Biology~2008~6(11)~Dethlefsen, L., S. Huse, M. L. Sogin, and D. A. Relman.~~e280~~~~The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing.~N~~~~~~
Environ Microbiol~2009~~Huber, J. A., H. G. Morrison, S. M. Huse, P. R. Neal, M. L. Sogin, and D. B. Mark Welch.~~~~~~Effect of PCR amplicon size on assessments of clone library microbial diversity and community structure.~N~~~~~~
PLoS Genet~2008~4~Huse, S. M., L. Dethlefsen, J. A. Huber, D. M. Welch, D. A. Relman, and M. L. Sogin.~4:e1000255.~~~~~Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing.~N~~~~~~
Nature~2009~457~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.~~480~~~~A core gut microbiome in obese and lean twins.~N~~~~~~
Marine Pollution Bulletin~2008~56~Glibert, P.M., Azanza, R., Burford, M., Furuya, K., Abal, E., Al-Azri, A., Al-Yamani, F., Andersen, P., Anderson, D.M.~~1049~~~~Ocean urea fertilization for carbon credits poses high ecological risks.~N~~~~~~
Science~2007~~Huber, J.A., Mark Welch D.B., Morrison H.G., Huse S.M., Neal P.R., Butterfield D.A., Sogin M.L.~~97~~~~Microbial population structures in the deep marine biosphere~N~~~~~~
Journal of Dental Research~2008~87(11)~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~~1016~~~~Pyrosequencing Analysis of the Oral Microflora of Healthy Adults.~N~~~~~~
Environmental Health~2008~7 (S2)~Laws, E.A., Fleming, L.E. and Stegeman, J.J.~~~~~~Centers for Oceans and Human Health: Contributions to an emerging discipline.~N~~~~~~
Proc Natl Acad Sci U S A~2006~103(5)~Pukatzki, S. et al.~~1528~~~~Identification of a conserved bacterial protein secretion system in Vibrio cholerae using the Dictyostelium host model system.~N~~~~~~
Proceedings of the National Academy of Sciences of the United States of America~2007~104(21)~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.~~9029~~~~Impacts of Hurricane Katrina on the Microbial Landscape of the New Orleans Area.~N~~~~~~
J. Phycol.~2009~45: 454~McCauley, L.A.R., D.L. Erdner, S. Nagai, M.L. Richlen, and D.M. Anderson~~~~~~Biogeographic analysis of the globally distributed harmful algal bloom species Alexandrium minutum (Dinophyceae) based on rRNA gene sequences and microsatellite markers.~N~~~~~~
Cont. Shelf Res.~2009~29(17)~Li, Y., R. He, D.J. McGillicuddy, Jr., D.M. Anderson, and B.A. Keafer.~~2069-2082~~~~Investigation of the 2006 Alexandrium fundyense bloom in the Gulf of Maine: In situ observations and numerical modeling.~N~~~~~~
Res.~2008~113~He, R., D. J. McGillicuddy, D. Anderson and B. Keafer~10.1029/2007JC004602~C07040,~~~~Gulf of Maine Circulation and Harmful Algal Bloom in Summer 2005- Part 2: Coupled Biophysical Modeling, J. Geophys.~N~~~~~~
Journal of Marine Systems,~2009~76(1-2)~Lynch, D.R., McGillicuddy, D.J., and F.E. Werner,~~1-3~~~~Skill assessment for coupled biological/physical models of marine systems.~N~~~~~~
Journal of Marine Systems~2009~76(1-2)~Stow, C.A., Jolliff, J., McGillicuddy, D.J., Doney, S.C., Allen, J.I., Friedrichs, M.A.M., Rose, K.A., and P. Wallhead~~4-15.~~~~Skill Assessment for Coupled Biological/Physical Models of Marine Systems.~N~~~~~~
Journal of Marine Systems~2009~76(1-2)~Smith, K.W., McGillicuddy, D.J., and D.R. Lynch~~162-170~~~~Parameter estimation using an ensemble smoother: the effect of the circulation in biological estimation.~N~~~~~~
Continental Shelf Research~2009~29(7)~Manning, J.P., McGillicuddy, D.J., Pettigrew, N.R., Churchill, J.H. and L.S. Incze,~~835-845~~~~Drifter Observations of the Gulf of Maine Coastal Current.~N~~~~~~
ournal of Geophysical Researc~2009~Jh 114~Aretxabaleta, A.L., McGillicuddy, D.J., Smith, K.W., Manning J.P. and D.R. Lynch~10.1029/2008JC004948~C09005~~~~Model Simulations of the Bay of Fundy Gyre: 2. Hindcasts for 2005-2007 Reveal Interannual Variability in Retentiveness~N~~~~~~
Continental Shelf Research~2009~29~Li, Y., He, R., McGillicuddy, D.J., Anderson, D.M. and B.A. Keafer~~2069-2082~~~~Investigation of 2006 Alexandrium fundyense bloom in the Gulf of Maine: In-situ observations and numerical modeling~N~~~~~~
BMC Bioinformatics~2008~10~Joss, M. J., Koenig, J., Labbate, M., Polz, M. F., Gillings, M. R., Stokes, H. W., W. Ford Doolittle, W. F., Boucher, Y.~~118~~~~ACID: Annotation of cassette and integron data.~N~~~~~~
Ocean Modelling~2011~36~Aretxabaleta, A. L., K. W. Smith, D. J. McGillicuddy Jr and J. Ballabrera-Poy~~219~~~~Model initialization in a tidally energetic regime: A dynamically adjusted objective analysis~N~~~~~~
Int J Microbiol~2011~~Bienfang, P. K., S. V. Defelice, E. A. Laws, L. E. Brand, R. R. Bidigare, S. Christensen, H. Trapido-Rosenthal, T. K. Hemscheidt, D. J. McGillicuddy, D. M. Anderson, H. M. Solo-Gabriele, A. B. Boehm and L. C. Backer~doi:10.1155/2011/152815~~~~~Prominent human health impacts from several marine microbes: history, ecology, and public health implications~N~~~~~~
MBio~2011~12~Boucher, Y., O. X. Cordero, A. Takemura, D. E. Hunt, K. Schliep, E. Bapteste, P. Lopez, C. L. Tarr and M. F. Polz~doi: 10.1128/mBio.00335-10~~~~~Local Mobile Gene Pools Rapidly Cross Species Boundaries To Create Endemicity within Global Vibrio cholerae Populations~N~~~~~~
Journal of Water and Health~2011~9~Gast, R., D. Moran, M. Dennett, W. Wurtsbaugh and L. Amaral-Zettler~~37~~~~Amoebae and Legionella pneumophila in saline environments~N~~~~~~
Environ Sci Technol.~2011~45~Halliday, E. and R. J. Gast~~370~~~~Bacteria in Beach Sands: An Emerging Challenge in Protecting Coastal Water Quality and Bather Health~N~~~~~~
Environmental Microbiology Reports~2011~3~John, S. G., C. B. Mendez, L. Deng, B. Poulos, A. K. M. Kauffman, S. Kern, J. Brum, M. F. Polz, E. A. Boyle and M. B. Sullivan~~195~~~~A simple and efficient method for concentration of ocean viruses by chemical flocculation~N~~~~~~
BMC Microbiol~2010~10~Kirkup, B. C., Jr., L. Chang, S. Chang, D. Gevers and M. F. Polz~~137~~~~Vibrio chromosomes share common history~N~~~~~~
PLoS One~2011~6~Levinton, J., M. Doall, D. Ralston, A. Starke and B. Allam~doi:10.1371/journal.pone.0018849~~~~~Climate Change, Precipitation and Impacts on an Estuarine Refuge from Disease~N~~~~~~
Journal of Marine Systems~2010~83~McGillicuddy, D. J.~~105~~~~Models of harmful algal blooms: Conceptual, empirical, and numerical approaches~N~~~~~~
Oceanography~2010~3~McGillicuddy, D. J., B. deYoung, S. C. Doney, P. M. Glibert, D. Stammer and F. E. Werner~~126~~~~Models: Tools for Synthesis in International Oceanographic Research Programs~N~~~~~~
Harmful Algae~2011~10~Pan, G., J. Chen, and D.M. Anderson~~381~~~~Modified local sands for the mitigation of harmful algal blooms~N~~~~~~
Environmental Microbiology~2011~13~Preheim, S. P., Y. Boucher, H. Wildschutte, L. A. David, D. Veneziano, E. J. Alm and M. F. Polz~~265~~~~Metapopulation structure of Vibrionaceae among coastal marine invertebrates~N~~~~~~
Harmful Algae~2011~10~Tong, M., D.M. Kulis, E. Fux, J.L Smith, P. Hess, Q. Zhou, and D.M. Anderson~~254~~~~The effects of growth phase and light intensity on toxin production by Dinophysis acuminata from the northeastern United States~N~~~~~~
Proc. Natl. Acad. Sci. USA~2011~108~Wang, L., S. Chen, K. L. Vergin, S. J. Giovannoni, W. Chan, M. S. Demott, K. Taghzadeh, M. Cutler, S. Timberlake, E. J. Alm, M. F. Polz, J. Pinhassi, Z. Deng and P. C. Dedon~~2963~~~~DNA phosphorothioation is ubiquitous feature of bacterial genomes~N~~~~~~
Environmental Microbiology~2010~12~Wildschutte, H., S. P. Preheim, Y. Hernandez and M. F. Polz~~2977~~~~O-antigen diversity and lateral transfer of the wbe region among Vibrio splendidus isolates~N~~~~~~
BMC Genomics~2006~7~Erdner, D.L. and D.M. Anderson~~1~~~~Global transcriptional profiling of the toxic dinoflagellate Alexandrium fundyense using Massively Parallel Signature Sequencing.~N~~~~~~
Molecular Ecology Notes~2006~6~Nagai, S., L. McCauley, N. Yasuda, D.L. Erdner, D.M. Kulis, Y. Matsuyama, S. Itakura and D.M. Anderson.~~756~~~~Development of microsatellite markers in the toxic dinoflagellate Alexandrium minutum (Dinophyceae)~N~~~~~~
Deep Sea Research II~2005~52~Anderson, D.M., Keafer, B.A., McGillicuddy, D.J., Mickelson, M.J., Keay, K.E., Libby, P.S., Manning, J.P., Mayo, C.A., Whittaker, D.K., Hickey, J.M., He, R., Lynch, D.R., Smith, K.W.~~2856~~~~Initial observations of the 2005 Alexandrium fundyense bloom in southern New England: General patterns and mechanisms~N~~~~~~
Journal of Plankton Research~2007~29~Ralston D.K., McGillicuddy, D.J. and D.W. Townsend~~803~~~~Asynchronous vertical migration and bimodal distribution of motile phytoplankton~N~~~~~~
Appl. Environ. Microbiol.~2005~71~Acinas, S.G, Sarma-Rupavtarm, R., Klepac-Ceraj, V., Polz, M.F.~~8966~~~~PCR-induced sequence artifacts and bias: insights from two 16S rRNA clone libraries constructed from the same sample. Appl. Environ. Microbiol.~N~~~~~~
Online Journal of Bioinformatics~2006~7~Klepac-Ceraj, V., Ceraj, I., Polz, M.F.~~15~~~~CLUSTERER: extendable java application for sequence grouping and cluster analyses~N~~~~~~
Applied and Environmental Microbiology~2006~72~Hunt, D.E., Klepac-Ceraj, V., Acinas, S.G., Gauthier, C., Bertilsson, S., Polz, M.F.~~2221~~~~Evaluation of 23S rRNA PCR Primers for use in Phylogenetic Studies of Bacterial Diversity.~N~~~~~~
Proc. Natl. Acad. Sci. USA~2006~103~Marcelino, L., Backman, V., Donaldson, A., Steadman, C., Thompson, J.R., Paccocha-Preheim, S., Lien, C., Lim, E., Veneziano, D., Polz, M.F.~~13629~~~~Accurate identification of low abundant targets amidst similar sequences by revealing hidden correlations in oligonucleotide microarray data~N~~~~~~
Phil. Trans. R. Soc. Lond. B.~2006~361~Polz, M.F., Hunt, D.E., Preheim, S.P., Weinreich, D.M.~~2009~~~~Patterns and mechanisms of genetic and phenotypic differentiation in marine microbes. Phil. Trans. R. Soc. Lond. B.~N~~~~~~
Proceedings of the National Academy of Sciences USA~2006~103~Sogin, M.L., H.G. Morrison, J.A. Huber, D.Mark Welch, S.M. Huse, P.R. Neal, J.M. Arrieta, and G.J. Herndl.~~12115~~~~Microbial diversity in the deep sea and the under-explored "rare biosphere.~N~~~~~~
Marine Drugs~2006~4~Messerli, S.M. and Greenberg, R.M.~~70~~~~Cnidarian toxins acting on voltage-gated ion channels.~N~~~~~~
Applied and Environmental Microbiology~2005~71~Ehrenreich, I.M., J.B. Waterbury, and E.A. Webb~~7401~~~~Distribution and Diversity of Natural Product Genes in Marine and Freshwater Cyanobacterial Cultures and Genomes.~N~~~~~~
Harmful Algae~2008~8~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, and M. Suddleson (in review).~~3~~In press~~Eutrophication and harmful algal blooms: A scientific consensus~N~~~~~~
Journal of Phycology~2007~43~Lilly, E.L., K. Halanych, and D.M. Anderson (in press).~~13~~~~Species boundaries and global biogeography of the dinoflagellate "A. tamarense" complex of the dinoflagellate genus Alexandrium (Dinophyceae).~N~~~~~~
Journal of Phycology~2009~45~McCauley, L.A.R., D.L. Erdner, S. Nagai, and D.M. Anderson~~599~~in press~~Bioegeographic analysis of the globally distributed harmful algal bloom species Alexandrium minutum (Dinophyceae) based on LSU rDNA and ITS sequences, and microsatellite markers.~N~~~~~~
Mar. Poll. Bull.~2008~57~Xu, Jie, A.Y.T. Ho, K. Yin, X. Yuan, D.M. Anderson, and P.J. Harrison (in review).~~335~~~~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.~N~~~~~~
Journal of Geophysical Research~2007~113~Aretxabaleta, A.L., McGillicuddy, D.J. , Smith, K.W., and D.R. Lynch~ 10.1029~~~~~Model Simulations of the Bay of Fundy Gyre: 1. Climatological Results~N~~~~~~
Environmental Health~2008~7~Dyble, J., Bienfang, P., Dusek, E., Griffiths, W., Hitchcock, G., Holland, F., Laws, E., Lerczak, J., McGillicuddy, D.J., Minnett, P., Moore, S., O'Kelly, C., Solo-Gabriel, H., and J. Wang.~ 10.1186/1476-069x-7-s2-s5~~~~~Environmental controls, oceanography and population dynamics of pathogens and harmful algal blooms: Connecting sources to human exposure.~N~~~~~~
Environmental Health~2008~7~Stewart, J. R., R. J. Gast, R. S. Fujioka, H. M. Solo-Gabriele, J. S. Meschke, L. A. Amaral-Zettler, E. Del Castillo, M. F. Polz, T. K. Collier, M. S. Strom, C. D. Sinigalliano, P. D. Moeller and A. F. Holland~~S3~~~~The coastal environment and human health: Microbial indicators, pathogens, sentinels and reservoirs~N~~~~~~
Proceedings of the National Academy of Sciences USA~2007~104~Sinigalliano, CD, Gidley, ML, Shibata, T, Whitman, D, Dixon, TH, Laws, E, Hou, A, Bachoon, D, Brand, L, Amaral-Zettler, L, Gast, R, Steward, GF, Nigro, OD, Fujioka, R, Betancourt, WQ, Vithanage, G, Mathews, J, Fleming, LE and HM Solo-Gabriele.~~9~~~~Impact of Hurricanes Katrina and Rita on the microbial landscape of the New Orleans area~N~~~~~~
Applied and Environmental Microbiology~2008~74~Hunt, D. E., Gevers, D., Vahora, N. M., Polz, M. F.~~4~~~~Conservation of the chitin utilization pathway in the Vibrionaceae.~N~~~~~~
Proceedings of the National Academy of Sciences USA~2008~105~Stocker, R, Seymour, J. R., Samadani, A., Hunt, D. E., Polz, M. F.~~420~~~~Rapid chemotactic response enables marine bacteria to exploit ephemeral microscale nutrient patches.~N~~~~~~
Genome Biology~2007~8~Huse, S.M., J.A. Huber , H.G. Morrison, M.L. Sogin and D. Mark Welch~~R143~~~~Accuracy and quality of massively parallel DNA pyrosequencing.~N~~~~~~
Journal of Molecular Biology~2007~368~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., and King, J.~~966~~~~Genome sequence, structural proteins, and capsid organization of the cyanophage Syn5: a "horned" bacteriophage of marine Synechococcus.~N~~~~~~
Environmental Health~2008~7~Kite-Powell, H. L., L. E. Fleming, L. C. Backer, E. M. Faustman, P. Hoagland, A. Tsuchiya, L. R. Younglove, B. A. Wilcox and R. J. Gast~ 10.1186~S6~~~~Linking the oceans to public health: current efforts and future directions.~N~~~~~~
Science~2008~320~Hunt, D. E., Lawrence, A. D., Gevers, D., Preheim, S., Alm, E. J., Polz, M. F.~~1081~~~~Resource partitioning and sympatric differentiation among closely related bacterioplankton.~N~~~~~~
Science~2009~323~Fraser, C., Alm, E.J., Polz, M.F., Spratt, B., Hanage, W.~~741~~~~The bacterial species challenge: Making sense of genetic and ecological diversity.~N~~~~~~
Environ. Microbiol.~2009~11~LeRoux, F., Zouine, M., Chakroun, N., Binesse, J., Saulnier, D., Bouchier, C., Zidane, N., Ma, L., Rusniok, C., Buchrieser, C., Medigue, C., Polz, M.F., Mazel, D.~~1959~~In Press~~Genome sequence of Vibrio splendidus: a dominant group of bacterioplankton presenting a large genotypic diversity.~N~~~~~~
BMC Bioinformatics~2009~10~Joss, M. J., Koenig, J., Labbate, M., Polz, M. F., Gillings, M. R., Stokes, H. W., W. Ford Doolittle, W. F., Boucher, Y.~~~~In Press.~~ACID: Annotation of cassette and integron data.~N~~~~~~
Environmental Science and Technology.~2008~42~Amaral-Zettler LA, Rocca JD, Lamotagne MC, Dennett MR and RJ Gast.~42: 9072-9078.~9072~~~~Changes in microbial community structure in the wake of Hurricanes Katrina and Rita.~N~~~~~~
Diseases of Aquatic Organisms~2008~81~Bogomolni A, Gast RJ, Ellis J, Dennett M, Pugliares K and M Moore.~81(1):13-38~13~~~~Vectors or Victims? Marine vertebrate zoonoses from coastal waters of the Northwest Atlantic.~N~~~~~~
Journal of Geophysical Research~2009~114~Aretxabaleta, A.L., McGillicuddy, D.J., Smith, K.W., Manning, J.P. and D.R. Lynch.~~c09005~~~~Model Simulations of the Bay of Fundy Gyre: 2. Hindcasts for 2005-2007 Reveal Interannual Variability in retentiveness.~N~~~~~~
Journal of Geophysical Research~2008~113~He, R. and D.J. McGillicuddy~10.1029/2007JC004601~~~~~Historic 2005 toxic bloom of Alexandrium fundyense in the west Gulf of Maine: Part 1. In situ Observations of Coastal Hydrography and Circulation.~N~~~~~~
Journal of Geophysical Research-Oceans, 113, C07040~2008~113~He, R., McGillicuddy, D.J.,Keafer, B.A. and D.M. Anderson~10.1029/2007JC004602~~~~~Historic 2005 toxic bloom of Alexandrium fundyense in the western Gulf of Maine: Part 2. Coupled Biophysical Numerical Modeling.~N~~~~~~
Proceedings of the International Conference on Coastal and Ocean Governance, East Asian Seas Congress, Ocean & Coastal Management~2009~52~Anderson, D.M.~~342~~In Press~~Approaches to monitoring, control, and management of harmful algal blooms (HABs).~N~~~~~~
Karlson, B., Bresnan, E., and Cusack, E., eds., IOC Manuals and Guides, UNESCO, Paris)~2010~55~Tobe, K., D. Kulis, D.M. Anderson, M. Gladstone, and L.K. Medlin.~~59~~In Press~~Detecting intact algal cells with whole cell hybridisation assays. In: Methods for quantitative phytoplankton analysis - estimating cell numbers~N~~~~~~
PLoS Biology~2008~6~Dethlefsen, L., S. Huse, M. L. Sogin, and D. A. Relman.~~e280~~~~The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing.~N~~~~~~
Environ Microbiol~2009~11~Huber, J. A., H. G. Morrison, S. M. Huse, P. R. Neal, M. L. Sogin, and D. B. Mark Welch.~~~~~~Effect of PCR amplicon size on assessments of clone library microbial diversity and community structure.~N~~~~~~
Science~2007~318~Huber, J.A., Mark Welch D.B., Morrison H.G., Huse S.M., Neal P.R., Butterfield D.A., Sogin M.L.~~97~~~~Microbial population structures in the deep marine biosphere~N~~~~~~
Environmental Health~2008~7~Laws, E.A., Fleming, L.E. and Stegeman, J.J.~~~~~~Centers for Oceans and Human Health: Contributions to an emerging discipline.~N~~~~~~
Journal of Physical Oceanography.~2009~39~Lerczak, J.A., Geyer, W.R. and Ralston, D.K.~~915~~~~The Temporal Response of the Length of a Partially-Stratified Estuary to Changes in River Flow and Tidal Amplitude.~N~~~~~~
Journal of Marine Systems~2009~76~Stow, C.A., Jolliff, J., McGillicuddy, D.J., Doney, S.C., Allen, J.I., Friedrichs, M.A.M., Rose, K.A., and P. Wallhead~~4~~~~Skill Assessment for Coupled Biological/Physical Models of Marine Systems.~N~~~~~~
BMC Microbiology~2010~10~Kirkup, B.C. , Chang, L.A., Chang, S., Gevers, D., Polz, M.F.~~~~In press~~Vibrio chromosomes share common history~N~~~~~~
ISME J~2010~4~Man-Aharonovich, D., Philosof, A., Kirkup, B.C., Le Gall, F., Yogev, T., Berman-Frank, I., Polz, M.F., Vaulot, D., Beja� , O.~~1044~~In press~~Diversity of active marine picoeukaryotes in the eastern Mediterranean Sea unveiled using photosystem-II psbA transcripts.~N~~~~~~
Enviornmental Biology~2010~12~Wildschutte, H., Preheim, S.P., Hernandez, Y., Polz, M.F.~~2977~~In press~~0-Antigen Hyper-Variability and Lateral Gene Transfer of the wbe Region Among Vibrio splendidus.~N~~~~~~
MBio~2011~2~Boucher, Y., O. X. Cordero, A. Takemura, D. E. Hunt, K. Schliep, E. Bapteste, P. Lopez, C. L. Tarr and M. F. Polz~doi: 10.1128/mBio.00335-10~~~~~Local Mobile Gene Pools Rapidly Cross Species Boundaries To Create Endemicity within Global Vibrio cholerae Populations~N~~~~~~
ISME J.~2011~52~Bowen, J. L., B. B. Ward, H. G. Morrison, J. E. Hobbie, I. Valiela, L. A. Deegan and M. L. Sogin~~1540~~Epub ahead of print~~Microbial community composition in sediments resists perturbation by nutrient enrichment~N~~~~~~
Cont Shelf Res~2011~31~Gast, R. J., L. Gorrell, B. Raubenheimer and S. Elgar~~1457~~~~Impact of erosion and accretion on the distribution of enterococci in beach sands~N~~~~~~
Deep Sea Research-I~2011~58~Jiang, M., M. Zhou, S.P. Libby, and D.M. Anderson~~1130~~~~Dynamics of a mesoscale eddy off Cape Ann, Massachusetts in May 2005~N~~~~~~
Limnol. & Oceanogr~2011~56~McGillicuddy, Jr., D.J., D.W. Towsend, R. He, B.A. Keafer, J.L. Kleindinst, Y. Li, J.P. Manning, D.G. Mountain, M.A. Thomas, and D.M. Anderson~~2411~~~~Suppression of the 2010 Alexandrium fundyense bloom by changes in physical, biological, and chemical properties of the Gulf of Maine~N~~~~~~
PLoS One~2009~4~Amaral-Zettler, L. A., E. A. McCliment, H. W. Ducklow and S. M. Huse~~e6372~~~~A method for studying protistan diversity using massively parallel sequencing of V9 hypervariable regions of small-subunit ribosomal RNA genes~N~~~~~~
Deep Sea Research Part II: Topical Studies in Oceanography~2010~57~Brosnahan, M. L., D. M. Kulis, A. R. Solow, D. L. Erdner, L. Percy, J. Lewis and D. M. Anderson~~175~~~~Outbreeding lethality between toxic Group I and nontoxic Group III Alexandrium tamarense spp. isolates: Predominance of heterotypic encystment and implications for mating interactions and biogeography~N~~~~~~
Harmful Algae~2011~12~Crespo, B. G., B. A. Keafer, D. K. Ralston, H. Lind, D. Farber and D. M. Anderson~~26~~~~Dynamics of Alexandrium fundyense blooms and shellfish toxicity in the Nauset Marsh System of Cape Cod (Massachusetts, USA)~N~~~~~~
PLoS One~2011~6~Erdner, D. L., M. L. Richlen, L. A. R. McCauley and D. M. Anderson~~e22965~~~~Diversity and Dynamics of a Widespread Bloom of the Toxic Dinoflagellate Alexandrium fundyense~N~~~~~~
Limnology and Oceanography: Methods~2010~8~Halliday, E., J. Griffith and R. Gast~~146~~~~Use of an exogenous plasmid standard and quantitative PCR to monitor spatial and temporal distribution of Enterococcus spp. in beach sands~N~~~~~~
Estuaries and Coasts~2010~33~Ho, A., J. Xu, K. Yin, Y. Jiang, X. Yuan, L. He, D. Anderson, J. Lee and P. Harrison~~170~~~~Phytoplankton Biomass and Production in Subtropical Hong Kong Waters: Influence of the Pearl River Outflow~N~~~~~~
Environmental Health Perspectives~2009~117~Hoagland, P., D. Jin, L. Y. Polansky, B. Kirkpatrick, G. Kirkpatrick, L. E. Fleming, A. Reich, S. M. Watkins, S. G. Ullmann and L. C. Backer~~1239~~~~The costs of respiratory illnesses arising from Florida gulf coast Karenia brevis blooms~N~~~~~~
Environmental Microbiology~2010~12~Huse, S. M., D. M. Welch, H. G. Morrison and M. L. Sogin~~1889~~~~Ironing out the wrinkles in the rare biosphere through improved OTU clustering~N~~~~~~
The Journal of Eukaryotic Microbiology~2009~56~Lasek-Nesselquist, E., D. M. Welch, R. C. Thompson, R. F. Steuart and M. L. Sogin~~504~~~~Genetic exchange within and between assemblages of Giardia duodenalis~N~~~~~~
Environmental Microbiology~2010~12~McLellan, S. L., S. M. Huse, S. R. Mueller-Spitz, E. N. Andreishcheva and M. L. Sogin~~378~~~~Diversity and population structure of sewage-derived microorganisms in wastewater treatment plant influent~N~~~~~~
Molecular and Biochemical Parasitology~2011~180~Perry, D. A., H. G. Morrison and R. D. Adam~~112~~~~Optical map of the genotype A1 WB C6 Giardia lamblia genome isolate~N~~~~~~
BMC Genomics~2009~10~Tzahor, S., D. Man-Aharonovich, B. C. Kirkup, T. Yogev, I. Berman-Frank, M. F. Polz, O. Beja and Y. Mandel-Gutfreund~~229~~~~A supervised learning approach for taxonomic classification of core-photosystem-II genes and transcripts in the marine environment~N~~~~~~
PLoS One~2011~6~Wurch, L. L., E. M. Bertrand, M. A. Saito, B. A. S. Van Mooy and S. T. Dyhrman~~e28949~~~~Proteome Changes Driven by Phosphorus Deficiency and Recovery in the Brown Tide-Forming Alga Aureococcus anophagefferens~N~~~~~~
Harmful Algae~2020~91~Brosnahan, Michael L. and Fischer, Alexis D. and Lopez, Cary B. and Moore, Stephanie K. and Anderson, Donald M.~https://doi.org/10.1016/j.hal.2019.101728~~~~~Cyst-forming dinoflagellates in a warming climate~N~101728~10280280~10280280~OSTI~2021-07-27 13:03:37.363~