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1. Full Text Microbial community structure and its functional implications
by Fuhrman, Jed A
Nature, ISSN 0028-0836, 05/2009, Volume 459, Issue 7244, pp. 193 - 199
Marine microbial communities are engines of globally important processes, such as the marine carbon, nitrogen and sulphur cycles. Recent data on the structures... 
SPACER ANALYSIS | OCEAN | MULTIDISCIPLINARY SCIENCES | SARGASSO SEA | BACTERIAL COMMUNITIES | MARINE VIRUSES | TIME-SERIES | NORTHWEST ATLANTIC | BACTERIOPLANKTON | LATITUDINAL DIVERSITY GRADIENT | BIOMASS PRODUCTION | Marine Biology | Animals | Ecosystem | Greenhouse Effect | Genomics - methods | Genomics - trends | Water Microbiology | Microorganisms | Biogeochemistry | Microbial populations | Distribution | Microbial mutation | Environmental aspects | Research | Natural history | Studies | Bacteria | Organisms | Microbiology | Genes
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2. Full Text Dynamic marine viral infections and major contribution to photosynthetic processes shown by spatiotemporal picoplankton metatranscriptomes
by Sieradzki, Ella T and Ignacio-Espinoza, J. Cesar and Needham, David M and Fichot, Erin B and Fuhrman, Jed A
Nature Communications, ISSN 2041-1723, 12/2019, Volume 10, Issue 1, pp. 1169 - 9
Viruses provide top-down control on microbial communities, yet their direct study in natural environments was hindered by culture limitations. The advance of... 
BACTERIA | MULTIDISCIPLINARY SCIENCES | LIGHT | GENE-EXPRESSION | SYNECHOCOCCUS | PHOTOSYSTEM-I | CYANOPHAGES | PROTEINS | VIRUSES | GENOME | ABUNDANCE | Microbial activity | Cell culture | Tracking | Cultivation | Viruses | Photosystem II | Genomes | Infections | Oxygen production | Microorganisms | Photosystem | Cyanobacteria | Picoplankton | Photosynthesis | Bioinformatics | Viral infections
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3. Full Text Alignment-free d2∗ oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences
by Ahlgren, Nathan A and Ren, Jie and Lu, Yang Young and Fuhrman, Jed A and Sun, Fengzhu
Nucleic Acids Research, ISSN 0305-1048, 2017, Volume 45, Issue 1, pp. 39 - 53
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4. Full Text CAFE: A C celerated A lignment- F r E e sequence analysis
by Lu, Yang Young and Tang, Kujin and Ren, Jie and Fuhrman, Jed A and Waterman, Michael S and Sun, Fengzhu
Nucleic Acids Research, ISSN 0305-1048, 07/2017, Volume 45, Issue 1, pp. W554 - W559
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5. Full Text Multi‐year dynamics of fine‐scale marine cyanobacterial populations are more strongly explained by phage interactions than abiotic, bottom‐up factors
by Ahlgren, Nathan A and Perelman, Jessica N and Yeh, Yi‐Chun and Fuhrman, Jed A
Environmental Microbiology, ISSN 1462-2912, 08/2019, Volume 21, Issue 8, pp. 2948 - 2963
Summary Currently defined ecotypes in marine cyanobacteria Prochlorococcus and Synechococcus likely contain subpopulations that themselves are ecologically... 
VARIABILITY | TAXONOMIC RESOLUTION | BIOGEOGRAPHY | OCEAN | BACTERIAL COMMUNITIES | PROCHLOROCOCCUS ECOTYPES | MICROBIOLOGY | SYNECHOCOCCUS ECOTYPES | DIVERSITY | VIRUSES | REVEALS | RNA | Analysis | Abiotic factors | rRNA 16S | Populations | Phages | Parameter identification | Seasonal variations | Predators | Partitioning | Water analysis | Dynamics | Network analysis | Ecotypes | Cyanobacteria | Water samples | Nutrients | Predator-prey interactions | Community structure | Subpopulations | Sequences | Niche overlap | rRNA 23S | Environmental factors | Prey | Water sampling | Spacer | Surface water | Niches
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6. Full Text Assessment of metagenomic assemblers based on hybrid reads of real and simulated metagenomic sequences
by Wang, Ziye and Wang, Ying and Fuhrman, Jed A and Sun, Fengzhu and Zhu, Shanfeng
Briefings in bioinformatics, ISSN 1477-4054, 03/2019
In metagenomic studies of microbial communities, the short reads come from mixtures of genomes. Read assembly is usually an essential first step for the... 
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7. Full Text Influence of Light on Particulate Organic Matter Utilization by Attached and Free-Living Marine Bacteria
by Gómez-Consarnau, Laura and Needham, David M and Weber, Peter K and Fuhrman, Jed A and Mayali, Xavier
Frontiers in microbiology, ISSN 1664-302X, 2019, Volume 10, p. 1204
Light plays a central role on primary productivity of aquatic systems. Yet, its potential impact on the degradation of photosynthetically produced biomass is... 
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8. Full Text Proteorhodopsins dominate the expression of phototrophic mechanisms in seasonal and dynamic marine picoplankton communities
by Sieradzki, Ella T and Fuhrman, Jed A and Rivero-Calle, Sara and Gómez-Consarnau, Laura
PeerJ, ISSN 2167-8359, 2018, Volume 2018, Issue 10, p. e5798
The most abundant and ubiquitous microbes in the surface ocean use light as an energy source, capturing it via complex chlorophyll-based photosystems or simple... 
Phototrophy | Spectral tuning | Marine | Expression | Proteorhodopsin | Picoplankton | Metatranscriptome | Metagenome | RHODOPSINS | VISUALIZATION | MULTIDISCIPLINARY SCIENCES | BACTERIOPLANKTON | BACTERIAL | SEA | VARIABILITY | SAR11 | GROWTH | GENE-EXPRESSION | PHYTOPLANKTON | Physiological aspects | Genetic aspects | Research | Gene expression | Population biology | Chlorophyll | Taxonomy | Abundance | Retina | Genomes | Biology | Ribonucleic acid--RNA | Studies | Proteins | Light | RecA protein | Photosynthesis | Bioinformatics | Deoxyribonucleic acid--DNA
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9. Full Text Distribution of Extracellular Flavins in a Coastal Marine Basin and Their Relationship to Redox Gradients and Microbial Community Members
by Monteverde, Danielle R and Sylvan, Jason B and Suffridge, Christopher and Baronas, J. Jotautas and Fichot, Erin and Fuhrman, Jed and Berelson, William and Sañudo-Wilhelmy, Sergio A
Environmental Science & Technology, ISSN 0013-936X, 11/2018, Volume 52, Issue 21, pp. 12265 - 12274
The flavins (including flavin mononucleotide (FMN) and riboflavin (RF)) are a class of organic compounds synthesized by organisms to assist in critical redox... 
RIBOFLAVIN | ENVIRONMENTAL SCIENCES | ELECTRON-TRANSFER | CARBON | COFACTORS | FLUORESCENCE | ENGINEERING, ENVIRONMENTAL | SEDIMENTS | IRON | SAN-PEDRO BASIN | BACTERIAL | SEAWATER
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10. Full Text Mosaic patterns of B-vitamin synthesis and utilization in a natural marine microbial community
: B-vitamin mosaics
by Gómez-Consarnau, Laura and Sachdeva, Rohan and Gifford, Scott M and Cutter, Lynda S and Fuhrman, Jed A and Sañudo-Wilhelmy, Sergio A and Moran, Mary Ann
Environmental Microbiology, ISSN 1462-2912, 08/2018, Volume 20, Issue 8, pp. 2809 - 2823
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11. Full Text Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples
: Primers for marine microbiome studies
by Parada, Alma E and Needham, David M and Fuhrman, Jed A
Environmental Microbiology, ISSN 1462-2912, 05/2016, Volume 18, Issue 5, pp. 1403 - 1414
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12. Full Text Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples
by Parada, Alma E and Needham, David M and Fuhrman, Jed A
Environmental Microbiology, ISSN 1462-2912, 05/2016, Volume 18, Issue 5, pp. 1403 - 1414
Summary Microbial community analysis via high‐throughput sequencing of amplified 16S rRNA genes is an essential microbiology tool. We found the popular primer... 
VARIABILITY | SAR11 | SEQUENCES | SENSITIVITY | PATTERNS | MICROBIOLOGY | DIVERSITY | BACTERIAL | SEASONAL DYNAMICS | PCR | PHYTOPLANKTON | Plankton - isolation & purification | RNA, Ribosomal, 18S - genetics | Archaea - isolation & purification | DNA Primers | Bacteria - genetics | Sequence Analysis, DNA | Bacteria - isolation & purification | Eukaryota - genetics | Microbiota - genetics | Plankton - genetics | RNA, Ribosomal, 16S - genetics | Archaea - genetics | High-Throughput Nucleotide Sequencing | RNA | Analysis
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13. Full Text Proteorhodopsins dominate the expression of phototrophic mechanisms in seasonal and dynamic marine picoplankton communities
by Sieradzki, Ella T and Fuhrman, Jed A and Rivero-Calle, Sara and Gómez-Consarnau, Laura
PeerJ, ISSN 2167-8359, 2018, Volume 6, p. e5798
The most abundant and ubiquitous microbes in the surface ocean use light as an energy source, capturing it via complex chlorophyll-based photosystems or simple... 
Physiological aspects | Genetic aspects | Research | Gene expression | Population biology
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14. Full Text Alignment-free \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$d_2^$\end{document} oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences
by Ahlgren, Nathan A and Ren, Jie and Lu, Yang Young and Fuhrman, Jed A and Sun, Fengzhu
Nucleic Acids Research, ISSN 0305-1048, 1/2017, Volume 45, Issue 1, pp. 39 - 53
Viruses and their host genomes often share similar oligonucleotide frequency (ONF) patterns, which can be used to predict the host of a given virus by finding... 
Computational Biology
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15. Full Text Meeting applying "-omics" data in marine microbial oceanography
by Fuhrman, Jed and Follows, Mick and Forde, Samantha
Eos, ISSN 0096-3941, 07/2013, Volume 94, Issue 27, p. 241
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16. Full Text Marine microbial community dynamics and their ecological interpretation
by Fuhrman, Jed A and Cram, Jacob A and Needham, David M
Nature Reviews Microbiology, ISSN 1740-1526, 03/2015, Volume 13, Issue 3, pp. 133 - 146
Recent advances in studying the dynamics of marine microbial communities have shown that the composition of these communities follows predictable patterns and... 
EUPHOTIC ZONE | ATLANTIC TIME-SERIES | LOCAL SIMILARITY ANALYSIS | STATISTICAL SIGNIFICANCE | SARGASSO SEA | BACTERIAL COMMUNITIES | PROCHLOROCOCCUS ECOTYPES | MICROBIOLOGY | SEASONAL DYNAMICS | OPEN-OCEAN | POPULATION-DYNAMICS | Microbial Interactions | Seawater - microbiology | Biota | Environmental aspects | Environment | Research | Microbial colonies
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