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Research publications that use VAMPS data

If you use VAMPS in a publication, please cite:
Huse SM, Mark Welch DB, Voorhis A, Shipunova A, Morrison HG, et al. (2014) VAMPS: a website for visualization and analysis of microbial population structures. BMC Bioinformatics 15: 41.
To add your research publication here please send us an email request with the title, authors, journal, pages and date of issue.
1.
Diversity and population structure of sewage derived microorganisms in wastewater treatment plant influent
McLellan, S.L., S.M. Huse, S.R. Mueller-Spitz, E.N. Andreishcheva, and M.L. Sogin
Environmental Microbiology.
Date: in press
2.
Salt marsh sediment diversity: a test of the variability of the rare biosphere among environmental replicates
Bowen, J.L., H.G. Morrison, J.E. Hobbie, and M.L. Sogin
ISME J.
Date: 2012
3.
Prevalence of Streptococci and Increased Polymicrobial Diversity Associated with Cystic Fibrosis Patient Stability
Filkins, L.M., T.H. Hampton, A.H. Gifford, M.J. Gross, D.A. Hogan, M.L. Sogin, H.G. Morrison, B.J. Paster, and G.A. O'Toole
Journal of Bacteriology 194: 4709-4717
Date: 2012
4.
Distance-Decay Relationships Partially Determine Diversity Patterns of Phyllosphere Bacteria on Tamrix Trees across the Sonoran Desert
Finkel, O.M., A.Y. Burch, T. Elad, S.M. Huse, S.E. Lindow, A.F. Post, and S. Belkin
Applied and Environmental Microbiology 78: 6187-6193
Date: 2012
5.
Global distribution and diversity of marine Verrucomicrobia
Freitas, S., S. Hatosy, J.A. Fuhrman, S.M. Huse, D.B. Mark Welch, M.L. Sogin, and A.C. Martiny
ISME J.
Date: 2012
6.
Diversity and dynamics of rare and of resident bacterial populations in coastal sands
Gobet, A., S.I. Boer, S.M. Huse, J.E.E. van Beusekom, C. Quince, M.L. Sogin, A. Boetius, and A. Ramette
ISME J 6: 542-553.
Date: 2012
7.
Serial Analysis of the Gut and Respiratory Microbiome in Cystic Fibrosis in Infancy: Interaction between Intestinal and Respiratory Tracts and Impact of Nutritional Exposures
Madan, J.C., D.C. Koestler, B.A. Stanton, L. Davidson, L.A. Moulton, M.L. Housman, J.H. Moore, M.F. Guill, H.G. Morrison, M.L. Sogin, T.H. Hampton, M.R. Karagas, P.E. Palumbo, J.A. Foster, P.L. Hibberd, and G.A. O'Toole
mBio 3.
Date: 2012
8.
Unique Prokaryotic Consortia in Geochemically Distinct Sediments from Red Sea Atlantis II and Discovery Deep Brine Pools
Siam, R., G.A. Mustafa, H. Sharaf, A. Moustafa, A. Ramadan, A. Antunes, V.B. Bajic, U. Stingl, N.G.R. Marsis, C. M.J.L., M.L. Sogin, A.J. Ferreira, and H. El-Dorry
PLoS ONE in press.
Date: 2012
9.
Millimeter-scale patterns of phylogenetic and trait diversity in a salt marsh microbial mat
Armitage, D.W., K.L. Gallagher, N.D. Youngblut, D.H. Buckley, and S.H. Zinder
Frontiers in Microbiology 3
Date: 2012
10.
Acinetobacter, Aeromonas and Trichococcus populations dominate the microbial community within urban sewer infrastructure
VandeWalle, J.L., G.W. Goetz, S.M. Huse, H.G. Morrison, M.L. Sogin, R.G. Hoffman, K. Yan, and S.L. McLellan
Environmental Microbiology in press.
Date: 2012
11.
Analysis of bacterial and archaeal diversity in coastal microbial mats using massive parallel 16S rRNA gene tag sequencing
Bolhuis, H. and L.J. Stal
ISME J 5: 1701-1712
Date: 2011
12.
Microbial community composition in sediments resists perturbation by nutrient enrichment
Bowen, J.L., B.B. Ward, H.G. Morrison, J.E. Hobbie, I. Valiela, L.A. Deegan, and M.L. Sogin
ISME J 5: 1540-1548
Date: 2011
13.
Exploring the oral microbiota of children at various developmental stages of their dentition in the relation to their oral health
Crielaard, W., E. Zaura, A. Schuller, S. Huse, R. Montijn, and B. Keijser
BMC Medical Genomics 4: 22
Date: 2011
14.
Geographical Location Determines the Population Structure in Phyllosphere Microbial Communities of a Salt-Excreting Desert Tree
Finkel, O.M., A.Y. Burch, S.E. Lindow, A.F. Post, and S. Belkin
Applied and Environmental Microbiology 77: 7647-7655
Date: 2011
15.
Ribosomal tag pyrosequencing of DNA and RNA from benthic coral reef microbiota: community spatial structure, rare members and nitrogen-cycling guilds
Gaidos, E., A. Rusch, and M. Ilardo
Environmental Microbiology 13: 1138-1152.
Date: 2011
16.
Amoebae and Legionella pneumophila in saline environments
Gast, R.J., D.M. Moran, M.R. Dennett, W.A. Wurtsbaugh, and L. Amaral-Zettler
Journal of Water and Health 9: 37-52.
Date: 2011
17.
Defining seasonal marine microbial community dynamics
Gilbert, J.A., J.A. Steele, J.G. Caporaso, L. Steinbruck, J. Reeder, B. Temperton, S. Huse, A.C. McHardy, R. Knight, I. Joint, P. Somerfield, J.A. Fuhrman, and D. Field
ISME J.
Date: 2011
18.
Gut microbial colonisation in premature neonates predicts neonatal sepsis
Madan, J.C., R.C. Salari, D. Saxena, L. Davidson, G.A. O'Toole, J.H. Moore, M.L. Sogin, J.A. Foster, W.H. Edwards, P. Palumbo, and P.L. Hibberd
Archives of Disease in Childhood - Fetal and Neonatal Edition.
Date: 2011
19.
An all-taxon microbial inventory of the Moorea coral reef ecosystem
McCliment, E.A., C.E. Nelson, C.A. Carlson, A.L. Alldredge, J. Witting, and L.A. Amaral-Zettler
ISME J 6: 309-319.
Date: 2011
20.
Lachnospiraceae and Bacteroidales Alternative Fecal Indicators Reveal Chronic Human Sewage Contamination in an Urban Harbor
Newton, R.J., J.L. VandeWalle, M.A. Borchardt, M.H. Gorelick, and S.L. McLellan
Appl. Environ. Microbiol. 77: 6972-6981.
Date: 2011
21.
Eukaryotic Richness in the Abyss: Insights from Pyrotag Sequencing
Pawlowski, J., R. Christen, B.a. Lecroq, D. Bachar, H.R. Shahbazkia, L. Amaral-Zettler, and L. Guillou
PLoS ONE 6: e18169.
Date: 2011
22.
Long term seasonal dynamics of Synechococcus population structure in the Gulf of Aqaba, Northern Red Sea
Post, A.F., S. Penno, K. Zandbank, A. Paytan, S. Huse, and D. Mark Welch
Frontiers in Microbiology 2.
Date: 2011
23.
Community Structures of Fecal Bacteria in Cattle from Different Animal Feeding Operations
Shanks, O.C., C.A. Kelty, S. Archibeque, M. Jenkins, R.J. Newton, S.L. McLellan, S.M. Huse, and M.L. Sogin
Applied and Environmental Microbiology 77: 2992-3001.
Date: 2011
24.
Culture-Independent Analysis of Bacterial Fuel Contamination Provides Insight into the Level of Concordance with the Standard Industry Practice of Aerobic Cultivation
White, J., J. Gilbert, G. Hill, E. Hill, S.M. Huse, A.J. Weightman, and E. Mahenthiralingam
Appl. Environ. Microbiol. 77: 4527-4538.
Date: 2011
25.
The energy-diversity relationship of complex bacterial communities in Arctic deep-sea sediments
Bienhold, C., A. Boetius, and A. Ramette
ISME J 6: 724-732
Date: 2011
26.
Global Patterns of Bacterial Beta-Diversity in Seafloor and Seawater Ecosystems
Zinger, L., L.A. Amaral-Zettler, J.A. Fuhrman, M.C. Horner-Devine, S.M. Huse, D.B.M. Welch, J.B.H. Martiny, M. Sogin, A. Boetius, and A. Ramette
PLoS ONE 6: e24570.
Date: 2011
27.
Variability and Diversity of Nasopharyngeal Microbiota in Children: A Metagenomic Analysis
Bogaert, D., B. Keijser, S. Huse, J. Rossen, R. Veenhoven, E. van Gils, J. Bruin, R. Montijn, M. Bonten, and E. Sanders
PLoS ONE 6: e17035
Date: 2011
28.
Archaea and bacteria with surprising microdiversity show shifts in dominance over 1,000-year time scales in hydrothermal chimneys
Brazelton, W.J., K.A. Ludwig, M.L. Sogin, E.N. Andreishcheva, D.S. Kelley, C.-C. Shen, R.L. Edwards, and J.A. Baross
Proceedings of the National Academy of Sciences
Date: 2010
29.
A global census of marine microbes, in Life in the World's Oceans: Diversity, Distribution and Abundance
Amaral-Zettler, L., L.F. Artigas, J.A. Baross, L. Bharathi, A. Boetius, D. Chandramohan, G.J. Herndl, K. Kogure, P.R. Neal, C. Pedros-Alio, A. Ramette, S. Schouten, L. Stal, A. Thessen, J. de Leeuw, and M.L. Sogin
Blackwell Publishing Ltd: Oxford. p. 223-245
Date: 2010
30.
The taxonomic and functional diversity of microbes at a temperate coastal site: a 'multi-omic' study of seasonal and diel temporal variation
Gilbert, J.A., D. Field, P. Swift, S. Thomas, D. Cummings, B. Temperton, K. Weynberg, S.M. Huse, M. Hughes, I. Joint, P.J. Somerfield, and M. Muhling
PLoS ONE 5.
Date: 2010
31.
Isolated communities of Epsilonproteobacteria in hydrothermal vent fluids of the Mariana Arc seamounts
Huber, J.A., H.V. Cantin, S.M. Huse, D.B. Mark Welch, M.L. Sogin, and D.A. Butterfield
FEMS microbiology ecology 73: 538-549.
Date: 2010
32.
The structure of bacterial communities in the western Arctic Ocean as revealed by pyrosequencing of 16S rRNA genes
Kirchman, D.L., M.T. Cottrell, and C. Lovejoy
Environmental Microbiology 12: 1132-1143.
Date: 2010
33.
Spatial Structure and Activity of Sedimentary Microbial Communities Underlying a Beggiatoa spp. Mat in a Gulf of Mexico Hydrocarbon Seep
Lloyd, K.G., D.B. Albert, J.F. Biddle, J.P. Chanton, O. Pizarro, and A. Teske
PLoS ONE 5: e8738.
Date: 2010
34.
Microbial community structure across the tree of life in the extreme Rio Tinto
Amaral-Zettler, L.A., E.R. Zettler, S.M. Theroux, C. Palacios, A. Aguilera, and R. Amils
ISME J 5: 42-50
Date: 2010
35.
Diversity and population structure of sewage derived microorganisms in wastewater treatment plant influent
McLellan, S.L., S.M. Huse, S.R. Mueller-Spitz, E.N. Andreishcheva, and M.L. Sogin
Environmental Microbiology 12: 378-392.
Date: 2010
36.
Threatened Corals Provide Underexplored Microbial Habitats
Sunagawa, S., C.M. Woodley, and M.n. Medina
PLoS ONE 5: e9554.
Date: 2010
37.
Ecology of the rare microbial biosphere of the Arctic Ocean
Galand, P.E., E.O. Casamayor, D.L. Kirchman, and C. Lovejoy
Proceedings of the National Academy of Sciences 106: 22427-22432.
Date: 2009
38.
The seasonal structure of microbial communities in the Western English Channel
Gilbert, J.A., F. Dawn, S. Paul, N. Lindsay, O. Anna, S. Tim, J.S. Paul, H. Sue, and J. Ian
Environmental Microbiology 11: 3132-3139.
Date: 2009
39.
Metagenomic study of the oral microbiota by Illumina high-throughput sequencing
Lazarevic, V., K. Whiteson, S. Huse, D. Hernandez, L. Farinelli, M. Osteras, J. Schrenzel, and P. Francois
Journal of Microbiological Methods 79: 266-271.
Date: 2009
40.
Diversity and population structure of sewage-derived microorganisms in wastewater treatment plant influent
McLellan, S.L., S.M. Huse, S.R. Mueller-Spitz, E.N. Andreishcheva, and M.L. Sogin
Environmental Microbiology 12: 378-392.
Date: 2009
41.
Reproducible community dynamics of the gastrointestinal microbiota following antibiotic perturbation
Antonopoulos, D.A., S.M. Huse, H.G. Morrison, T.M. Schmidt, M.L. Sogin, and V.B. Young
Infect. Immun. 77: 2367-2375
Date: 2009
42.
Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities
Stoeck, T., A. Behnke, R. Christen, L. Amaral-Zettler, M. Rodriguez-Mora, A. Chistoserdov, W. Orsi, and V. Edgcomb
BMC Biology 7: 72.
Date: 2009
43.
A core gut microbiome in obese and lean twins
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
Nature 457: 480-484.
Date: 2009
44.
The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing
Dethlefsen, L., S. Huse, M.L. Sogin, and D.A. Relman
Date: 2008
45.
An oligarchic microbial assemblage in the anoxic bottom waters of a volcanic subglacial lake
Gaidos, E., V. Marteinsson, T. Thorsteinsson, T. Johannesson, A.R. Runarsson, A. Stefansson, B. Glazer, B. Lanoil, M. Skidmore, S. Han, M. Miller, A. Rusch, and W. Foo
ISME J 3: 486-497.
Date: 2008
46.
Changes in microbial community structure in the wake of Hurricanes Katrina and Rita
Amaral-Zettler, L.A., J.D. Rocca, M.G. Lamontagne, M.R. Dennett, and R.J. Gast
Environmental Science & Technology 42: 9072-9078
Date: 2008
47.
Pyrosequencing analysis of the oral microflora of healthy adults
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, and W. Crielaard
Journal of Dental Research 87: 1016-1020.
Date: 2008
48.
Abundance and diversity of microbial life in ocean crust
Santelli, C.M., B.N. Orcutt, E. Banning, W. Bach, C.L. Moyer, M.L. Sogin, H. Staudigel, and K.J. Edwards
Nature 453: 653-656.
Date: 2008
49.
Microbial Population Structures in the Deep Marine Biosphere
Huber, J.A., D.B. Mark Welch, H.G. Morrison, S.M. Huse, P.R. Neal, D.A. Butterfield, and M.L. Sogin
Science 318: 97-100.
Date: 2007
50.
Pyrosequencing enumerates and contrasts soil microbial diversity
Roesch, L.F.W., R.R. Fulthorpe, A. Riva, G. Casella, A.K.M. Hadwin, A.D. Kent, S.H. Daroub, F.A.O. Camargo, W.G. Farmerie, and E.W. Triplett
ISME Journal 1: 283-290.
Date: 2007
51.
Impacts of Hurricanes Katrina and Rita on the microbial landscape of the New Orleans area
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
Proceedings of the National Academy of Sciences 104: 9029-9034.
Date: 2007
52.
Microbial diversity in the deep sea and the underexplored "rare biosphere"
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
Proceedings of the National Academy of Sciences 103: 12115-12120.
Date: 2006
53.
A molecular view of microbial diversity and the biosphere.
Pace, N.R.
Science 276: 734-40.
Date: 1997