Jed A. Fuhrman - Publications

Affiliations: 
1981-1988 Stony Brook University, Stony Brook, NY, United States 
 1988- University of Southern California, Los Angeles, CA, United States 
Area:
Oceanography Biology, Microbiology Biology
Website:
https://dornsife.usc.edu/cf/faculty-and-staff/faculty.cfm?pid=1003269

162 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Wang Z, Wang Y, Fuhrman JA, Sun F, Zhu S. Corrigendum to: Assessment of metagenomic assemblers based on hybrid reads of real and simulated metagenomic sequences. Briefings in Bioinformatics. PMID 32379299 DOI: 10.1093/bib/bbaa085  0.6
2019 Dekas AE, Parada AE, Mayali X, Fuhrman JA, Wollard J, Weber PK, Pett-Ridge J. Characterizing Chemoautotrophy and Heterotrophy in Marine Archaea and Bacteria With Single-Cell Multi-isotope NanoSIP. Frontiers in Microbiology. 10: 2682. PMID 31920997 DOI: 10.3389/fmicb.2019.02682  0.32
2019 Gómez-Consarnau L, Raven JA, Levine NM, Cutter LS, Wang D, Seegers B, Arístegui J, Fuhrman JA, Gasol JM, Sañudo-Wilhelmy SA. Microbial rhodopsins are major contributors to the solar energy captured in the sea. Science Advances. 5: eaaw8855. PMID 31457093 DOI: 10.1126/sciadv.aaw8855  0.32
2019 Gómez-Consarnau L, Needham DM, Weber PK, Fuhrman JA, Mayali X. Influence of Light on Particulate Organic Matter Utilization by Attached and Free-Living Marine Bacteria. Frontiers in Microbiology. 10: 1204. PMID 31214143 DOI: 10.3389/fmicb.2019.01204  0.52
2019 Sieradzki ET, Ignacio-Espinoza JC, Needham DM, Fichot EB, Fuhrman JA. Dynamic marine viral infections and major contribution to photosynthetic processes shown by spatiotemporal picoplankton metatranscriptomes. Nature Communications. 10: 1169. PMID 30862830 DOI: 10.1038/s41467-019-09106-z  0.52
2019 Wang Z, Wang Y, Fuhrman JA, Sun F, Zhu S. Assessment of metagenomic assemblers based on hybrid reads of real and simulated metagenomic sequences. Briefings in Bioinformatics. PMID 30860572 DOI: 10.1093/bib/bbz025  0.6
2018 Roux S, Adriaenssens EM, Dutilh BE, Koonin EV, Kropinski AM, Krupovic M, Kuhn JH, Lavigne R, Brister JR, Varsani A, Amid C, Aziz RK, Bordenstein SR, Bork P, Breitbart M, ... ... Fuhrman JA, et al. Minimum Information about an Uncultivated Virus Genome (MIUViG). Nature Biotechnology. PMID 30556814 DOI: 10.1038/nbt.4306  0.56
2018 Sieradzki ET, Fuhrman JA, Rivero-Calle S, Gómez-Consarnau L. Proteorhodopsins dominate the expression of phototrophic mechanisms in seasonal and dynamic marine picoplankton communities. Peerj. 6: e5798. PMID 30370186 DOI: 10.7717/peerj.5798  0.32
2018 Brown MV, van de Kamp J, Ostrowski M, Seymour JR, Ingleton T, Messer LF, Jeffries T, Siboni N, Laverock B, Bibiloni-Isaksson J, Nelson TM, Coman F, Davies CH, Frampton D, Rayner M, ... ... Fuhrman JA, et al. Systematic, continental scale temporal monitoring of marine pelagic microbiota by the Australian Marine Microbial Biodiversity Initiative. Scientific Data. 5: 180130. PMID 30015804 DOI: 10.1038/sdata.2018.130  0.52
2018 Needham DM, Fichot EB, Wang E, Berdjeb L, Cram JA, Fichot CG, Fuhrman JA. Dynamics and interactions of highly resolved marine plankton via automated high-frequency sampling. The Isme Journal. PMID 29899514 DOI: 10.1038/s41396-018-0169-y  0.52
2018 Hernando-Morales V, Varela MM, Needham DM, Cram J, Fuhrman JA, Teira E. Vertical and Seasonal Patterns Control Bacterioplankton Communities at Two Horizontally Coherent Coastal Upwelling Sites off Galicia (NW Spain). Microbial Ecology. PMID 29675703 DOI: 10.1007/s00248-018-1179-z  0.52
2018 Gómez-Consarnau L, Sachdeva R, Gifford SM, Cutter LS, Fuhrman JA, Sañudo-Wilhelmy SA, Moran MA. Mosaic patterns of B-vitamin synthesis and utilization in a natural marine microbial community. Environmental Microbiology. PMID 29659156 DOI: 10.1111/1462-2920.14133  0.32
2018 Yeh YC, Needham DM, Sieradzki ET, Fuhrman JA. Taxon Disappearance from Microbiome Analysis Reinforces the Value of Mock Communities as a Standard in Every Sequencing Run. Msystems. 3. PMID 29629423 DOI: 10.1128/mSystems.00023-18  0.52
2018 Berdjeb L, Parada A, Needham DM, Fuhrman JA. Short-term dynamics and interactions of marine protist communities during the spring-summer transition. The Isme Journal. PMID 29599520 DOI: 10.1038/s41396-018-0097-x  0.52
2017 Lu YY, Lv J, Fuhrman JA, Sun F. Towards enhanced and interpretable clustering/classification in integrative genomics. Nucleic Acids Research. PMID 28977511 DOI: 10.1093/nar/gkx767  0.6
2017 Wigington CH, Sonderegger D, Brussaard CPD, Buchan A, Finke JF, Fuhrman JA, Lennon JT, Middelboe M, Suttle CA, Stock C, Wilson WH, Wommack KE, Wilhelm SW, Weitz JS. Author Correction: Re-examination of the relationship between marine virus and microbial cell abundances. Nature Microbiology. PMID 28974689 DOI: 10.1038/s41564-017-0042-1  0.56
2017 Parada AE, Fuhrman JA. Marine archaeal dynamics and interactions with the microbial community over 5 years from surface to seafloor. The Isme Journal. PMID 28731479 DOI: 10.1038/ismej.2017.104  0.32
2017 Ren J, Ahlgren NA, Lu YY, Fuhrman JA, Sun F. VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data. Microbiome. 5: 69. PMID 28683828 DOI: 10.1186/s40168-017-0283-5  0.6
2017 Lu YY, Tang K, Ren J, Fuhrman JA, Waterman MS, Sun F. CAFE: aCcelerated Alignment-FrEe sequence analysis. Nucleic Acids Research. PMID 28472388 DOI: 10.1093/nar/gkx351  0.6
2017 Ahlgren NA, Chen Y, Needham DM, Parada AE, Sachdeva R, Trinh V, Chen T, Fuhrman JA. Genome and epigenome of a novel marine Thaumarchaeota strain suggest viral infection, phosphorothioation DNA modification, and multiple restriction systems. Environmental Microbiology. PMID 28418097 DOI: 10.1111/1462-2920.13768  0.52
2017 Needham DM, Sachdeva R, Fuhrman JA. Ecological dynamics and co-occurrence among marine phytoplankton, bacteria and myoviruses shows microdiversity matters. The Isme Journal. PMID 28398348 DOI: 10.1038/ismej.2017.29  0.52
2017 Zhang M, Yang L, Ren J, Ahlgren NA, Fuhrman JA, Sun F. Prediction of virus-host infectious association by supervised learning methods. Bmc Bioinformatics. 18: 60. PMID 28361670 DOI: 10.1186/s12859-017-1473-7  0.6
2016 Ahlgren NA, Ren J, Lu YY, Fuhrman JA, Sun F. Alignment-free $d_2^*$ oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences. Nucleic Acids Research. PMID 27899557 DOI: 10.1093/nar/gkw1002  0.6
2016 Needham DM, Fuhrman JA. Pronounced daily succession of phytoplankton, archaea and bacteria following a spring bloom. Nature Microbiology. 1: 16005. PMID 27572439 DOI: 10.1038/nmicrobiol.2016.5  0.52
2016 Wigington CH, Sonderegger D, Brussaard CP, Buchan A, Finke JF, Fuhrman JA, Lennon JT, Middelboe M, Suttle CA, Stock C, Wilson WH, Wommack KE, Wilhelm SW, Weitz JS. Re-examination of the relationship between marine virus and microbial cell abundances. Nature Microbiology. 1: 15024. PMID 27572161 DOI: 10.1038/nmicrobiol.2015.24  0.56
2016 Lu YY, Chen T, Fuhrman JA, Sun F. COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment, and paired-end read LinkAge. Bioinformatics (Oxford, England). PMID 27256312 DOI: 10.1093/bioinformatics/btw290  0.6
2016 Weiss S, Van Treuren W, Lozupone C, Faust K, Friedman J, Deng Y, Xia LC, Xu ZZ, Ursell L, Alm EJ, Birmingham A, Cram JA, Fuhrman JA, Raes J, Sun F, et al. Correlation detection strategies in microbial data sets vary widely in sensitivity and precision. The Isme Journal. PMID 26905627 DOI: 10.1038/ismej.2015.235  1
2016 Cram JA, Parada AE, Fuhrman JA. Dilution reveals how viral lysis and grazing shape microbial communities Limnology and Oceanography. 61: 889-905. DOI: 10.1002/lno.10259  1
2015 Gómez-Consarnau L, González JM, Riedel T, Jaenicke S, Wagner-Döbler I, Sañudo-Wilhelmy SA, Fuhrman JA. Proteorhodopsin light-enhanced growth linked to vitamin-B1 acquisition in marine Flavobacteria. The Isme Journal. PMID 26574687 DOI: 10.1038/ismej.2015.196  1
2015 Xia LC, Ai D, Cram JA, Liang X, Fuhrman JA, Sun F. Statistical significance approximation in local trend analysis of high-throughput time-series data using the theory of Markov chains. Bmc Bioinformatics. 16: 301. PMID 26390921 DOI: 10.1186/s12859-015-0732-8  1
2015 Parada AE, Needham DM, Fuhrman JA. Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. Environmental Microbiology. PMID 26271760 DOI: 10.1111/1462-2920.13023  1
2015 Kopf A, Bicak M, Kottmann R, Schnetzer J, Kostadinov I, Lehmann K, Fernandez-Guerra A, Jeanthon C, Rahav E, Ullrich M, Wichels A, Gerdts G, Polymenakou P, Kotoulas G, Siam R, ... ... Fuhrman JA, et al. The ocean sampling day consortium. Gigascience. 4: 27. PMID 26097697 DOI: 10.1186/s13742-015-0066-5  1
2015 Cram JA, Xia LC, Needham DM, Sachdeva R, Sun F, Fuhrman JA. Cross-depth analysis of marine bacterial networks suggests downward propagation of temporal changes. The Isme Journal. PMID 25989373 DOI: 10.1038/ismej.2015.76  1
2015 Fuhrman JA, Cram JA, Needham DM. Marine microbial community dynamics and their ecological interpretation. Nature Reviews. Microbiology. 13: 133-46. PMID 25659323 DOI: 10.1038/nrmicro3417  1
2015 Weitz JS, Stock CA, Wilhelm SW, Bourouiba L, Coleman ML, Buchan A, Follows MJ, Fuhrman JA, Jover LF, Lennon JT, Middelboe M, Sonderegger DL, Suttle CA, Taylor BP, Frede Thingstad T, et al. A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes. The Isme Journal. 9: 1352-64. PMID 25635642 DOI: 10.1038/ismej.2014.220  1
2015 Cram JA, Chow CE, Sachdeva R, Needham DM, Parada AE, Steele JA, Fuhrman JA. Seasonal and interannual variability of the marine bacterioplankton community throughout the water column over ten years. The Isme Journal. 9: 563-80. PMID 25203836 DOI: 10.1038/ismej.2014.153  1
2014 Chow CE, Kim DY, Sachdeva R, Caron DA, Fuhrman JA. Top-down controls on bacterial community structure: microbial network analysis of bacteria, T4-like viruses and protists. The Isme Journal. 8: 816-29. PMID 24196323 DOI: 10.1038/ismej.2013.199  1
2013 Hatosy SM, Martiny JB, Sachdeva R, Steele J, Fuhrman JA, Martiny AC. Beta diversity of marine bacteria depends on temporal scale. Ecology. 94: 1898-904. PMID 24279260 DOI: 10.1890/12-2125.1  1
2013 Pagarete A, Chow CET, Johannessen T, Fuhrman JA, Thingstad TF, Sandaa RA. Strong seasonality and interannual recurrence in marine myovirus communities Applied and Environmental Microbiology. 79: 6253-6259. PMID 23913432 DOI: 10.1128/AEM.01075-13  1
2013 Harwood VJ, Boehm AB, Sassoubre LM, Vijayavel K, Stewart JR, Fong TT, Caprais MP, Converse RR, Diston D, Ebdon J, Fuhrman JA, Gourmelon M, Gentry-Shields J, Griffith JF, Kashian DR, et al. Performance of viruses and bacteriophages for fecal source determination in a multi-laboratory, comparative study. Water Research. 47: 6929-43. PMID 23886543 DOI: 10.1016/j.watres.2013.04.064  1
2013 Chow CE, Sachdeva R, Cram JA, Steele JA, Needham DM, Patel A, Parada AE, Fuhrman JA. Temporal variability and coherence of euphotic zone bacterial communities over a decade in the Southern California Bight. The Isme Journal. 7: 2259-73. PMID 23864126 DOI: 10.1038/ismej.2013.122  1
2013 Riedel T, Gómez-Consarnau L, Tomasch J, Martin M, Jarek M, González JM, Spring S, Rohlfs M, Brinkhoff T, Cypionka H, Göker M, Fiebig A, Klein J, Goesmann A, Fuhrman JA, et al. Genomics and physiology of a marine flavobacterium encoding a proteorhodopsin and a xanthorhodopsin-like protein. Plos One. 8: e57487. PMID 23526944 DOI: 10.1371/journal.pone.0057487  1
2013 Needham DM, Chow CE, Cram JA, Sachdeva R, Parada A, Fuhrman JA. Short-term observations of marine bacterial and viral communities: patterns, connections and resilience. The Isme Journal. 7: 1274-85. PMID 23446831 DOI: 10.1038/ismej.2013.19  1
2013 Xia LC, Ai D, Cram J, Fuhrman JA, Sun F. Efficient statistical significance approximation for local similarity analysis of high-throughput time series data. Bioinformatics (Oxford, England). 29: 230-7. PMID 23178636 DOI: 10.1093/bioinformatics/bts668  1
2013 Amend AS, Oliver TA, Amaral-Zettler LA, Boetius A, Fuhrman JA, Horner-Devine MC, Huse SM, Welch DBM, Martiny AC, Ramette A, Zinger L, Sogin ML, Martiny JBH. Macroecological patterns of marine bacteria on a global scale Journal of Biogeography. 40: 800-811. DOI: 10.1111/jbi.12034  1
2013 Fuhrman JA, Needham DM, Hewson I. Plankton Viruses Reference Module in Earth Systems and Environmental Sciences. DOI: 10.1016/B978-0-12-409548-9.04291-3  1
2012 Fuhrman JA. Metagenomics and its connection to microbial community organization. F1000 Biology Reports. 4: 15. PMID 22912649 DOI: 10.3410/B4-15  1
2012 Brown MV, Lauro FM, DeMaere MZ, Muir L, Wilkins D, Thomas T, Riddle MJ, Fuhrman JA, Andrews-Pfannkoch C, Hoffman JM, McQuaid JB, Allen A, Rintoul SR, Cavicchioli R. Global biogeography of SAR11 marine bacteria. Molecular Systems Biology. 8: 595. PMID 22806143 DOI: 10.1038/msb.2012.28  1
2012 Knight R, Jansson J, Field D, Fierer N, Desai N, Fuhrman JA, Hugenholtz P, van der Lelie D, Meyer F, Stevens R, Bailey MJ, Gordon JI, Kowalchuk GA, Gilbert JA. Unlocking the potential of metagenomics through replicated experimental design. Nature Biotechnology. 30: 513-20. PMID 22678395 DOI: 10.1038/nbt.2235  1
2012 Chang Q, Luan Y, Chen T, Fuhrman JA, Sun F. Computational methods for the analysis of tag sequences in metagenomics studies. Frontiers in Bioscience (Scholar Edition). 4: 1333-43. PMID 22652875  1
2012 Hanson CA, Fuhrman JA, Horner-Devine MC, Martiny JB. Beyond biogeographic patterns: processes shaping the microbial landscape. Nature Reviews. Microbiology. 10: 497-506. PMID 22580365 DOI: 10.1038/nrmicro2795  1
2012 Chow CE, Fuhrman JA. Seasonality and monthly dynamics of marine myovirus communities. Environmental Microbiology. 14: 2171-83. PMID 22507260 DOI: 10.1111/j.1462-2920.2012.02744.x  1
2012 Freitas S, Hatosy S, Fuhrman JA, Huse SM, Welch DB, Sogin ML, Martiny AC. Global distribution and diversity of marine Verrucomicrobia. The Isme Journal. 6: 1499-505. PMID 22318305 DOI: 10.1038/ismej.2012.3  1
2012 Gilbert JA, Steele JA, Caporaso JG, Steinbrück L, Reeder J, Temperton B, Huse S, McHardy AC, Knight R, Joint I, Somerfield P, Fuhrman JA, Field D. Defining seasonal marine microbial community dynamics. The Isme Journal. 6: 298-308. PMID 21850055 DOI: 10.1038/ismej.2011.107  1
2012 Romero IC, Jacobson M, Fuhrman JA, Fogel M, Capone DG. Long-term nitrogen and phosphorus fertilization effects on N 2 fixation rates and nifH gene community patterns in mangrove sediments Marine Ecology. 33: 117-127. DOI: 10.1111/j.1439-0485.2011.00465.x  1
2011 Xia LC, Steele JA, Cram JA, Cardon ZG, Simmons SL, Vallino JJ, Fuhrman JA, Sun F. Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates. Bmc Systems Biology. 5: S15. PMID 22784572 DOI: 10.1186/1752-0509-5-S2-S15  1
2011 Xia LC, Cram JA, Chen T, Fuhrman JA, Sun F. Accurate genome relative abundance estimation based on shotgun metagenomic reads. Plos One. 6: e27992. PMID 22162995 DOI: 10.1371/journal.pone.0027992  1
2011 Zinger L, Amaral-Zettler LA, Fuhrman JA, Horner-Devine MC, Huse SM, Welch DB, Martiny JB, Sogin M, Boetius A, Ramette A. Global patterns of bacterial beta-diversity in seafloor and seawater ecosystems. Plos One. 6: e24570. PMID 21931760 DOI: 10.1371/journal.pone.0024570  1
2011 Yilmaz P, Kottmann R, Field D, Knight R, Cole JR, Amaral-Zettler L, Gilbert JA, Karsch-Mizrachi I, Johnston A, Cochrane G, Vaughan R, Hunter C, Park J, Morrison N, Rocca-Serra P, ... ... Fuhrman JA, et al. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nature Biotechnology. 29: 415-20. PMID 21552244 DOI: 10.1038/nbt.1823  1
2011 Steele JA, Countway PD, Xia L, Vigil PD, Beman JM, Kim DY, Chow CE, Sachdeva R, Jones AC, Schwalbach MS, Rose JM, Hewson I, Patel A, Sun F, Caron DA, ... Fuhrman JA, et al. Marine bacterial, archaeal and protistan association networks reveal ecological linkages. The Isme Journal. 5: 1414-25. PMID 21430787 DOI: 10.1038/ismej.2011.24  1
2011 Beman JM, Steele JA, Fuhrman JA. Co-occurrence patterns for abundant marine archaeal and bacterial lineages in the deep chlorophyll maximum of coastal California. The Isme Journal. 5: 1077-85. PMID 21228895 DOI: 10.1038/ismej.2010.204  1
2011 Danovaro R, Corinaldesi C, Dell'anno A, Fuhrman JA, Middelburg JJ, Noble RT, Suttle CA. Marine viruses and global climate change. Fems Microbiology Reviews. 35: 993-1034. PMID 21204862 DOI: 10.1111/j.1574-6976.2010.00258.x  1
2011 Beman JM, Chow CE, King AL, Feng Y, Fuhrman JA, Andersson A, Bates NR, Popp BN, Hutchins DA. Global declines in oceanic nitrification rates as a consequence of ocean acidification. Proceedings of the National Academy of Sciences of the United States of America. 108: 208-13. PMID 21173255 DOI: 10.1073/pnas.1011053108  1
2011 Gilbert JA, Bailey M, Field D, Fierer N, Fuhrman JA, Hu B, Jansson J, Knight R, Kowalchuk GA, Kyrpides NC, Meyer F, Stevens R. The Earth Microbiome Project: The Meeting Report for the 1st International Earth Microbiome Project Conference, Shenzhen, China, June 13th-15th 2011 Standards in Genomic Sciences. 5: 243-247. DOI: 10.4056/sigs.2134923  1
2011 Perrings C, Naeem S, Ahrestani FS, Bunker DE, Burkill P, Canziani G, Elmqvist T, Fuhrman JA, Jaksic FM, Kawabata Z, Kinzig A, Mace GM, Mooney H, Prieur-Richard AH, Tschirhart J, et al. Ecosystem services, targets, and indicators for the conservation and sustainable use of biodiversity Frontiers in Ecology and the Environment. 9: 512-520. DOI: 10.1890/100212  1
2011 Fuhrman JA. Oceans of crenarchaeota: A personal history describing this paradigm shift Microbe. 6: 531-537.  1
2010 Beman JM, Sachdeva R, Fuhrman JA. Population ecology of nitrifying archaea and bacteria in the Southern California Bight. Environmental Microbiology. 12: 1282-92. PMID 20192962 DOI: 10.1111/j.1462-2920.2010.02172.x  1
2010 Griffith JF, Schiff KC, Lyon GS, Fuhrman JA. Microbiological water quality at non-human influenced reference beaches in southern California during wet weather. Marine Pollution Bulletin. 60: 500-8. PMID 20015517 DOI: 10.1016/j.marpolbul.2009.11.015  1
2010 Bertics VJ, Sohm JA, Treude T, Chow CET, Capone DG, Fuhrman JA, Ziebis W. Burrowing deeper into benthic nitrogen cycling: The impact of Bioturbation on nitrogen fixation coupled to sulfate reduction Marine Ecology Progress Series. 409: 1-15. DOI: 10.3354/meps08639  1
2009 Brown MV, Philip GK, Bunge JA, Smith MC, Bissett A, Lauro FM, Fuhrman JA, Donachie SP. Microbial community structure in the North Pacific ocean. The Isme Journal. 3: 1374-86. PMID 19626056 DOI: 10.1038/ismej.2009.86  1
2009 Fuhrman JA. Microbial community structure and its functional implications. Nature. 459: 193-9. PMID 19444205 DOI: 10.1038/nature08058  1
2009 Böer SI, Hedtkamp SI, van Beusekom JE, Fuhrman JA, Boetius A, Ramette A. Time- and sediment depth-related variations in bacterial diversity and community structure in subtidal sands. The Isme Journal. 3: 780-91. PMID 19340087 DOI: 10.1038/ismej.2009.29  1
2008 Fuhrman JA, Steele JA, Hewson I, Schwalbach MS, Brown MV, Green JL, Brown JH. A latitudinal diversity gradient in planktonic marine bacteria. Proceedings of the National Academy of Sciences of the United States of America. 105: 7774-8. PMID 18509059 DOI: 10.1073/pnas.0803070105  1
2008 Fuhrman JA, Schwalbach MS, Stingl U. Proteorhodopsins: an array of physiological roles? Nature Reviews. Microbiology. 6: 488-94. PMID 18475306 DOI: 10.1038/nrmicro1893  1
2008 Fuhrman JA, Steele JA. Community structure of marine bacterioplankton: Patterns, networks, and relationships to function Aquatic Microbial Ecology. 53: 69-81. DOI: 10.3354/ame01222  1
2008 Hewson I, Fuhrman JA. Viruses, Bacteria, and the Microbial Loop Nitrogen in the Marine Environment. 1097-1134. DOI: 10.1016/B978-0-12-372522-6.00025-6  1
2008 Fuhrman JA, Hagström A. Bacterial and Archaeal Community Structure and its Patterns Microbial Ecology of the Oceans: Second Edition. 45-90. DOI: 10.1002/9780470281840.ch3  1
2007 Horner-Devine MC, Silver JM, Leibold MA, Bohannan BJ, Colwell RK, Fuhrman JA, Green JL, Kuske CR, Martiny JB, Muyzer G, OvreÃ¥s L, Reysenbach AL, Smith VH. A comparison of taxon co-occurrence patterns for macro- and microorganisms. Ecology. 88: 1345-53. PMID 17601127 DOI: 10.1890/06-0286  1
2007 Patel A, Noble RT, Steele JA, Schwalbach MS, Hewson I, Fuhrman JA. Virus and prokaryote enumeration from planktonic aquatic environments by epifluorescence microscopy with SYBR Green I. Nature Protocols. 2: 269-76. PMID 17406585 DOI: 10.1038/nprot.2007.6  1
2007 Hewson I, Jacobson Meyers ME, Fuhrman JA. Diversity and biogeography of bacterial assemblages in surface sediments across the San Pedro Basin, Southern California Borderlands. Environmental Microbiology. 9: 923-33. PMID 17359264 DOI: 10.1111/j.1462-2920.2006.01214.x  1
2007 Hewson I, Fuhrman JA. Characterization of lysogens in bacterioplankton assemblages of the southern California borderland. Microbial Ecology. 53: 631-8. PMID 17345141 DOI: 10.1007/s00248-006-9148-3  1
2007 Hewson I, Fuhrman JA. Covariation of viral parameters with bacterial assemblage richness and diversity in the water column and sediments Deep-Sea Research Part I: Oceanographic Research Papers. 54: 811-830. DOI: 10.1016/j.dsr.2007.02.003  1
2006 Fuhrman JA, Hewson I, Schwalbach MS, Steele JA, Brown MV, Naeem S. Annually reoccurring bacterial communities are predictable from ocean conditions. Proceedings of the National Academy of Sciences of the United States of America. 103: 13104-9. PMID 16938845 DOI: 10.1073/pnas.0602399103  1
2006 Ruan Q, Dutta D, Schwalbach MS, Steele JA, Fuhrman JA, Sun F. Local similarity analysis reveals unique associations among marine bacterioplankton species and environmental factors. Bioinformatics (Oxford, England). 22: 2532-8. PMID 16882654 DOI: 10.1093/bioinformatics/btl417  1
2006 Ruan Q, Steele JA, Schwalbach MS, Fuhrman JA, Sun F. A dynamic programming algorithm for binning microbial community profiles. Bioinformatics (Oxford, England). 22: 1508-14. PMID 16567364 DOI: 10.1093/bioinformatics/btl114  1
2006 Noble RT, Griffith JF, Blackwood AD, Fuhrman JA, Gregory JB, Hernandez X, Liang X, Bera AA, Schiff K. Multitiered approach using quantitative PCR to track sources of fecal pollution affecting Santa Monica Bay, California. Applied and Environmental Microbiology. 72: 1604-12. PMID 16461716 DOI: 10.1128/AEM.72.2.1604-1612.2006  1
2006 Hewson I, Fuhrman JA. Improved strategy for comparing microbial assemblage fingerprints. Microbial Ecology. 51: 147-53. PMID 16437287 DOI: 10.1007/s00248-005-0144-9  1
2006 Martiny JB, Bohannan BJ, Brown JH, Colwell RK, Fuhrman JA, Green JL, Horner-Devine MC, Kane M, Krumins JA, Kuske CR, Morin PJ, Naeem S, Ovreås L, Reysenbach AL, Smith VH, et al. Microbial biogeography: putting microorganisms on the map. Nature Reviews. Microbiology. 4: 102-12. PMID 16415926 DOI: 10.1038/nrmicro1341  1
2006 Hewson I, Steele JA, Capone DG, Fuhrman JA. Temporal and spatial scales of variation in bacterioplankton assemblages of oligotrophic surface waters Marine Ecology Progress Series. 311: 67-77. DOI: 10.3354/meps311067  1
2006 Hewson I, Fuhrman JA. Spatial and vertical biogeography of coral reef sediment bacterial and diazotroph communities Marine Ecology Progress Series. 306: 79-86. DOI: 10.3354/meps306079  1
2006 Honjo M, Matsui K, Ueki M, Nakamura R, Fuhrman JA, Kawabata Z. Diversity of virus-like agents killing Microcystis aeruginosa in a hyper-eutrophic pond Journal of Plankton Research. 28: 407-412. DOI: 10.1093/plankt/fbi128  1
2006 Hewson I, Winget DM, Williamson KE, Fuhrman JA, Wommack KE. Viral and bacterial assemblage covariance in oligotrophic waters of the West Florida Shelf (Gulf of Mexico) Journal of the Marine Biological Association of the United Kingdom. 86: 591-603. DOI: 10.1017/S0025315406013506  1
2006 Hewson I, Fuhrman JA. Viral impacts upon marine bacterioplankton assemblage structure Journal of the Marine Biological Association of the United Kingdom. 86: 577-589. DOI: 10.1017/S002531540601349X  1
2006 Hewson I, Capone DG, Steele JA, Fuhrman JA. Influence of Amazon and Orinoco offshore surface water plumes on oligotrophic bacterioplankton diversity in the west tropical Atlantic Aquatic Microbial Ecology. 43: 11-22.  1
2006 Hewson I, Steele JA, Capone DG, Fuhrman JA. Remarkable heterogeneity in meso- and bathypelagic bacterioplankton assemblage composition Limnology and Oceanography. 51: 1274-1283.  1
2005 Brown MV, Schwalbach MS, Hewson I, Fuhrman JA. Coupling 16S-ITS rDNA clone libraries and automated ribosomal intergenic spacer analysis to show marine microbial diversity: development and application to a time series. Environmental Microbiology. 7: 1466-79. PMID 16104869 DOI: 10.1111/j.1462-2920.2005.00835.x  1
2005 Fuhrman JA, Liang X, Noble RT. Rapid detection of enteroviruses in small volumes of natural waters by real-time quantitative reverse transcriptase PCR. Applied and Environmental Microbiology. 71: 4523-30. PMID 16085845 DOI: 10.1128/AEM.71.8.4523-4530.2005  1
2005 Steele JA, Ozis F, Fuhrman JA, Devinny JS. Structure of microbial communities in ethanol biofilters Chemical Engineering Journal. 113: 135-143. DOI: 10.1016/j.cej.2005.04.011  1
2005 Schwalbach MS, Fuhrman JA. Wide-ranging abundances of aerobic anoxygenic phototrophic bacteria in the world ocean revealed by epifluorescence microscopy and quantitative PCR Limnology and Oceanography. 50: 620-628.  1
2005 Brown MV, Fuhrman JA. Marine bacterial microdiversity as revealed by internal transcribed spacer analysis Aquatic Microbial Ecology. 41: 15-23.  1
2005 Schwalbach MS, Brown M, Fuhrman JA. Impact of light on marine bacterioplankton community structure Aquatic Microbial Ecology. 39: 235-245.  1
2004 Hewson I, Fuhrman JA. Richness and diversity of bacterioplankton species along an estuarine gradient in Moreton Bay, Australia. Applied and Environmental Microbiology. 70: 3425-33. PMID 15184140 DOI: 10.1128/AEM.70.6.3425-3433.2004  1
2004 Schwalbach MS, Hewson I, Fuhrman JA. Viral effects on bacterial community composition in marine plankton microcosms Aquatic Microbial Ecology. 34: 117-127.  1
2004 Hewson I, Govil SR, Capone DG, Carpenter EJ, Fuhrman JA. Evidence of Trichodesmium viral lysis and potential significance for biogeochemical cycling in the oligotrophic ocean Aquatic Microbial Ecology. 36: 1-8.  1
2003 Hewson I, Vargo GA, Fuhrman JA. Bacterial diversity in shallow oligotrophic marine benthos and overlying waters: effects of virus infection, containment, and nutrient enrichment. Microbial Ecology. 46: 322-36. PMID 14502411 DOI: 10.1007/s00248-002-1067-3  1
2003 Hewson I, Fuhrman JA. Viriobenthos production and virioplankton sorptive scavenging by suspended sediment particles in coastal and pelagic waters. Microbial Ecology. 46: 337-47. PMID 14502409 DOI: 10.1007/s00248-002-1041-0  1
2003 González JM, Covert JS, Whitman WB, Henriksen JR, Mayer F, Scharf B, Schmitt R, Buchan A, Fuhrman JA, Kiene RP, Moran MA. Silicibacter pomeroyi sp. nov. and Roseovarius nubinhibens sp. nov., dimethylsulfoniopropionate-demethylating bacteria from marine environments. International Journal of Systematic and Evolutionary Microbiology. 53: 1261-9. PMID 13130004 DOI: 10.1099/ijs.0.02491-0  1
2003 Jiang S, Fu W, Chu W, Fuhrman JA. The vertical distribution and diversity of marine bacteriophage at a station off Southern California Microbial Ecology. 45: 399-410. PMID 12704560 DOI: 10.1007/s00248-002-1059-3  1
2003 Fuhrman JA, Schwalbach M. Viral influence on aquatic bacterial communities Biological Bulletin. 204: 192-195. PMID 12700152  1
2003 Boehm AB, Fuhrman JA, Mrse RD, Grant SB. Tiered approach for identification of a human fecal pollution source at a recreational beach: case study at Avalon Bay, Catalina Island, California. Environmental Science & Technology. 37: 673-80. PMID 12636264 DOI: 10.1021/es025934x  1
2002 Fuhrman JA. Community structure and function in prokaryotic marine plankton. Antonie Van Leeuwenhoek. 81: 521-7. PMID 12448747 DOI: 10.1023/A:1020513506777  1
2002 Fuhrman JA, Griffith JF, Schwalbach MS. Prokaryotic and viral diversity patterns in marine plankton Ecological Research. 17: 183-194. DOI: 10.1046/j.1440-1703.2002.00478.x  1
2001 Fuhrman JA, Capone DG. Nifty nanoplankton Nature. 412: 593-594. PMID 11493900 DOI: 10.1038/35088159  1
2001 Noble RT, Fuhrman JA. Enteroviruses detected by reverse transcriptase polymerase chain reaction from the coastal waters of Santa Monica Bay, California: Low correlation to bacterial indicator levels Hydrobiologia. 460: 175-184. DOI: 10.1023/A:1013121416891  1
2001 Hewson I, O'Neil JM, Fuhrman JA, Dennison WC. Virus-like particle distribution and abundance in sediments and overlying waters along eutrophication gradients in two subtropical estuaries Limnology and Oceanography. 46: 1734-1746.  1
2000 Ouverney CC, Fuhrman JA. Marine planktonic archaea take up amino acids. Applied and Environmental Microbiology. 66: 4829-33. PMID 11055931 DOI: 10.1128/AEM.66.11.4829-4833.2000  1
2000 Noble RT, Fuhrman JA. Rapid virus production and removal as measured with fluorescently labeled viruses as tracers Applied and Environmental Microbiology. 66: 3790-3797. PMID 10966392 DOI: 10.1128/AEM.66.9.3790-3797.2000  1
1999 Gasol JM, Li Zweifel U, Peters F, Fuhrman JA, Hagström Å. Significance of size and nucleic acid content heterogeneity as measured by flow cytometry in natural planktonic bacteria Applied and Environmental Microbiology. 65: 4475-4483. PMID 10508078  1
1999 Fuhrman JA. Marine viruses and their biogeochemical and ecological effects Nature. 399: 541-548. PMID 10376593 DOI: 10.1038/21119  1
1999 Ouverney CC, Fuhrman JA. Combined microautoradiography-16S rRNA probe technique for determination of radioisotope uptake by specific microbial cell types in situ. Applied and Environmental Microbiology. 65: 1746-52. PMID 10103276  1
1999 Noble RT, Fuhrman JA. Breakdown and microbial uptake of marine viruses and other lysis products Aquatic Microbial Ecology. 20: 1-11.  1
1999 Noble RT, Middelboe M, Fuhrman JA. Effects of viral enrichment on the mortality and growth of heterotrophic bacterioplankton Aquatic Microbial Ecology. 18: 1-13.  1
1998 Fuhrman JA, Campbell U. Microbial microdiversity Nature. 393: 410-411. DOI: 10.1038/30839  1
1998 Fuhrman JA, Ouverney CC. Marine microbial diversity studied via 16S rRNA sequences: Cloning results from coastal waters and counting of native archaea with fluorescent single cell probes Aquatic Ecology. 32: 3-15. DOI: 10.1023/A:1009974817127  1
1998 Noble RT, Fuhrman JA. Use of SYBR Green I for rapid epifluorescence counts of marine viruses and bacteria Aquatic Microbial Ecology. 14: 113-118.  1
1997 Fuhrman JA, Davis AA. Widespread Archaea and novel Bacteria from the deep sea as shown by 16S rRNA gene sequences Marine Ecology Progress Series. 150: 275-285.  1
1997 Ouverney CC, Fuhrman JA. Increase in fluorescence intensity of 16S rRNA in situ hybridization in natural samples treated with chloramphenicol Applied and Environmental Microbiology. 63: 2735-2740.  1
1997 Karner M, Fuhrman JA. Determination of active marine bacterioplankton: A comparison of universal 16S rRNA probes, autoradiography, and nucleoid staining Applied and Environmental Microbiology. 63: 1208-1213.  1
1997 Noble RT, Fuhrman JA. Virus decay and its causes in coastal waters Applied and Environmental Microbiology. 63: 77-83.  1
1996 Thingstad TF, Dolan JR, Fuhrman JA. Loss rate of an oligotrophic bacterial assemblage as measured by 3H-thymidine and 32PO4: Good agreement and near-balance with production Aquatic Microbial Ecology. 10: 29-36.  1
1995 Fuhrman JA, McCallum K, Davis AA. Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific oceans. Applied and Environmental Microbiology. 61: 4517. PMID 8534122  1
1995 Fuhrman JA, Noble RT. Viruses and protists cause similar bacterial mortality in coastal seawater Limnology and Oceanography. 40: 1236-1242.  1
1995 Lee S, Kang YC, Fuhrman JA. Imperfect retention of natural bacterioplankton cells by glass fiber filters Marine Ecology Progress Series. 119: 285-290.  1
1994 Fuhrman JA, Lee SH, Masuchi Y, Davis AA, Wilcox RM. Characterization of marine prokaryotic communities via DNA and RNA. Microbial Ecology. 28: 133-45. PMID 24186438 DOI: 10.1007/BF00166801  1
1994 Wilcox RM, Fuhrman JA. Bacterial viruses in coastal seawater: Lytic rather than lysogenic production Marine Ecology Progress Series. 114: 35-46.  1
1993 Proctor LM, Okubo A, Fuhrman JA. Calibrating estimates of phage-induced mortality in marine bacteria: Ultrastructural studies of marine bacteriophage development from one-step growth experiments. Microbial Ecology. 25: 161-82. PMID 24189813 DOI: 10.1007/BF00177193  1
1993 Fuhrman JA, McCallum K, Davis AA. Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific Oceans. Applied and Environmental Microbiology. 59: 1294-302. PMID 7685997  1
1992 Fuhrman JA, McCallum K, Davis AA. Novel major archaebacterial group from marine plankton. Nature. 356: 148-9. PMID 1545865 DOI: 10.1038/356148a0  1
1992 Kristiansen K, Nielsen H, Riemann B, Fuhrman JA. Growth efficiencies of freshwater bacterioplankton Microbial Ecology. 24: 145-160. DOI: 10.1007/BF00174451  1
1992 Proctor LM, Fuhrman JA. Mortality of marine bacteria in response to enrichments of the virus size fraction from seawater Marine Ecology Progress Series. 87: 283-293.  1
1991 Proctor LM, Fuhrman JA. Roles of viral infection in organic particle flux Marine Ecology Progress Series. 69: 133-142.  1
1991 Fuhrman JA, Capone DG. Possible biogeochemical consequences of ocean fertilization Limnology &Amp; Oceanography. 36: 1951-1959.  1
1991 Sanghoon Lee, Fuhrman JA. Spatial and temporal variation of natural bacterioplankton assemblages studied by total genomic DNA cross-hybridization Limnology &Amp; Oceanography. 36: 1277-1287.  1
1991 Glibert PM, Garside C, Fuhrman JA, Roman MR. Time-dependent coupling of inorganic and organic nitrogen uptake and regeneration in the plume of the Chesapeake Bay estuary and its regulation by large heterotrophs Limnology &Amp; Oceanography. 36: 895-909.  1
1990 Lee S, Fuhrman JA. DNA hybridization to compare species compositions of natural bacterioplankton assemblages Applied and Environmental Microbiology. 56: 739-746. PMID 2317044  1
1990 Proctor LM, Fuhrman JA. Viral mortality of marine bacteria and cyanobacteria Nature. 343: 60-62.  1
1990 Mitchell JG, Okubo A, Fuhrman JA. Gyrotaxis as a new mechanism for generating spatial heterogeneity and migration in microplankton Limnology &Amp; Oceanography. 35: 123-130.  1
1990 Suttle CA, Fuhrman JA, Capone DG. Rapid ammonium cycling and concentration-dependent partitioning of ammonium and phosphate: implications for carbon transfer in planktonic communities Limnology & Oceanography. 35: 424-433.  1
1989 Mitchell JG, Okubo A, Fuhrman JA, Cochlan W. The contribution of phytoplankton to ocean density gradients Deep Sea Research Part a, Oceanographic Research Papers. 36: 1277-1282. DOI: 10.1016/0198-0149(89)90106-4  1
1988 McManus GB, Fuhrman JA. Control of marine bacterioplankton populations: Measurement and significance of grazing Hydrobiologia. 159: 51-62. DOI: 10.1007/BF00007367  1
1986 Riemann B, Jørgensen NO, Lampert W, Fuhrman JA. Zooplankton induced changes in dissolved free amino acids and in production rates of freshwater bacteria. Microbial Ecology. 12: 247-58. PMID 24212678 DOI: 10.1007/BF02011168  1
1986 Mcmanus GB, Fuhrman JA. Photosynthetic pigments in the ciliate Laboea strobila from Long Island Sound, USA Journal of Plankton Research. 8: 317-327. DOI: 10.1093/plankt/8.2.317  1
1986 Légier-Visser MF, Mitchell JG, Okubo A, Fuhrman JA. Mechanoreception in calanoid copepods - A mechanism for prey detection Marine Biology. 90: 529-535. DOI: 10.1007/BF00409273  1
1986 Fuhrman JA, Ducklow HW, Kirchman DL, Hudak J, McManus GB, Kramer J. Does adenine incorporation into nucleic acids measure total microbial production? Limnology & Oceanography. 31: 627-636.  1
1985 Mitchell JG, Okubo A, Fuhrman JA. Microzones surrounding phytoplankton form the basis for a stratified marine microbial ecosystem Nature. 316: 58-59. DOI: 10.1038/316058a0  1
1984 Fuhrman JA, McManus GB. Do bacteria-sized marine eukaryotes consume significant bacterial production? Science. 224: 1257-1260.  1
1982 Fuhrman JA, Azam F. Thymidine incorporation as a measure of heterotrophic bacterioplankton production in marine surface waters: Evaluation and field results Marine Biology. 66: 109-120. DOI: 10.1007/BF00397184  1
1981 Hodson RE, Azam F, Carlucci AF, Fuhrman JA, Karl DM, Holm-Hansen O. Microbial uptake of dissolved organic matter in Mcmurdo Sound, Antarctica Marine Biology. 61: 89-94. DOI: 10.1007/BF00386648  1
1980 Hollibaugh JT, Carruthers AB, Fuhrman JA, Azam F. Cycling of organic nitrogen in marine plankton communities studied in enclosed water columns Marine Biology. 59: 15-21. DOI: 10.1007/BF00396978  1
1980 Fuhrman JA, Ammerman JW, Azam F. Bacterioplankton in the coastal euphotic zone: Distribution, activity and possible relationships with phytoplankton Marine Biology. 60: 201-207. DOI: 10.1007/BF00389163  1
1980 Fuhrman JA, Azam F. Bacterioplankton secondary production estimates for coastal waters of British Columbia, Antarctica, and California Applied and Environmental Microbiology. 39: 1085-1095.  1
1978 Fuhrman JA, Chisholm SW, Guillard RRL. Marine alga Platymonas sp. accumulates silicon without apparent requirement Nature. 272: 195. DOI: 10.1038/272244a0  1
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