J. Fuhrman

发表

Viral and bacterial assemblage covariance in oligotrophic waters of the West Florida Shelf (Gulf of Mexico)

I. Hewson, Danielle M. Winget, Kurt E. Williamson, 2006, Journal of the Marine Biological Association of the United Kingdom.

Bacterial Diversity in Shallow Oligotrophic Marine Benthos and Overlying Waters: Effects of Virus Infection, Containment, and Nutrient Enrichment

I. Hewson, J. Fuhrman, G. Vargo, 2003, Microbial Ecology.

Bacterial viruses in coastal seawater: lytic rather than lysogenic production

J. Fuhrman, R. Wilcox, 1994 .

A communal catalogue reveals Earth’s multiscale microbial diversity

Rick L. Stevens, William A. Walters, Nicole M. Gaudelli, 2017, Nature.

Correlation detection strategies in microbial data sets vary widely in sensitivity and precision

Sophie J. Weiss, J. Raes, L. Ursell, 2016, The ISME Journal.

Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage

Nicole M. Gaudelli, David R. Liu, Jose A Navas-Molina, 2017, Nature.

The ocean sampling day consortium

Rachelle M. Jensen, G. Cochrane, A. Wichels, 2015, GigaScience.

Microbial biogeography: putting microorganisms on the map

James H. Brown, Robert K. Colwell, R. K. Colwell, 2006, Nature Reviews Microbiology.

General Distributions and the 'rare Biosphere' Microbial Community Structure and Its Functional Implications Review Insight

J. Fuhrman, 2022 .

Identifying viruses from metagenomic data by deep learning.

Fengzhu Sun, Jed A. Fuhrman, Nathan A. Ahlgren, 2018, 1806.07810.

Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples.

J. Fuhrman, Alma E. Parada, D. Needham, 2016, Environmental microbiology.

Ecological dynamics and co-occurrence among marine phytoplankton, bacteria and myoviruses shows microdiversity matters

J. Fuhrman, D. Needham, R. Sachdeva, 2017, The ISME Journal.

Taxon Disappearance from Microbiome Analysis Reinforces the Value of Mock Communities as a Standard in Every Sequencing Run

J. Fuhrman, Yi-Chun Yeh, D. Needham, 2018, mSystems.

Dynamics and interactions of highly resolved marine plankton via automated high-frequency sampling

J. Fuhrman, Jacob A. Cram, D. Needham, 2017, The ISME Journal.

Taxon disappearance from microbiome analysis indicates need for mock communities as a standard in every sequencing run

J. Fuhrman, Yi-Chun Yeh, D. Needham, 2017, bioRxiv.

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

Emily S. Charlson, Chris I. Hunter, B. Birren, 2011, Nature Biotechnology.

Ecosystem services, targets, and indicators for the conservation and sustainable use of biodiversity

H. Mooney, Fabian M Jaksic, A. Kinzig, 2011 .

Proteorhodopsin light-enhanced growth linked to vitamin-B1 acquisition in marine Flavobacteria

S. Jaenicke, J. Fuhrman, T. Riedel, 2015, The ISME Journal.

Marine viruses and their biogeochemical and ecological effects

J. Fuhrman, 1999, Nature.

Improved Strategy for Comparing Microbial Assemblage Fingerprints

I. Hewson, J. Fuhrman, 2006, Microbial Ecology.

Annually reoccurring bacterial communities are predictable from ocean conditions

I. Hewson, J. Fuhrman, Mark V Brown, 2006, Proceedings of the National Academy of Sciences.

Bacterial and Archaeal Community Structure and its Patterns

J. Fuhrman, Å. Hagström, 2008 .

Global biogeography of SAR11 marine bacteria

Matthew Z. DeMaere, C. Andrews-Pfannkoch, J. Fuhrman, 2012, Molecular systems biology.

Short-term observations of marine bacterial and viral communities: patterns, connections and resilience

J. Fuhrman, Jacob A. Cram, Alma E. Parada, 2013, The ISME Journal.

Marine bacterial, archaeal and protistan association networks reveal ecological linkages

D. Caron, Fengzhu Sun, I. Hewson, 2011, The ISME Journal.

Use of SYBR Green I for rapid epifluorescence counts of marine viruses and bacteria

J. Fuhrman, R. Noble, 1998 .

Virus and prokaryote enumeration from planktonic aquatic environments by epifluorescence microscopy with SYBR Green I

I. Hewson, J. Fuhrman, J. Steele, 2007, Nature Protocols.

Unlocking the potential of metagenomics through replicated experimental design

Rick L. Stevens, R. Knight, J. Gilbert, 2012, Nature Biotechnology.

VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data

Yang Young Lu, Fengzhu Sun, J. Fuhrman, 2017, Microbiome.

Global Patterns of Bacterial Beta-Diversity in Seafloor and Seawater Ecosystems

Susan M. Huse, A. Boetius, M. Sogin, 2011, PloS one.

Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys

William A. Walters, R. Knight, J. Gilbert, 2015, mSystems.

EMOSE (2017) Inter-Comparison of Marine Plankton Metagenomic Analysis Methods

J. Poulain, J. Fuhrman, S. Pesant, 2016 .

Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes.

Karoline Faust, Mohammad Bahram, Miklós Bálint, 2016, FEMS microbiology reviews.

A latitudinal diversity gradient in planktonic marine bacteria

James H Brown, James H. Brown, Jed A Fuhrman, 2008, Proceedings of the National Academy of Sciences.

Short-term dynamics and interactions of marine protist communities during the spring–summer transition

J. Fuhrman, Alma E. Parada, D. Needham, 2018, The ISME Journal.

Seasonal and interannual variability of the marine bacterioplankton community throughout the water column over ten years

J. Fuhrman, Jacob A. Cram, Alma E. Parada, 2014, The ISME Journal.

Marine microbial community dynamics and their ecological interpretation

Jed A. Fuhrman, J. Fuhrman, Jacob A. Cram, 2015, Nature Reviews Microbiology.

Bacterial secondary production in freshwater measured by3H-thymidine incorporation method

J. Fuhrman, F. Azam, B. Riemann, 1982, Microbial Ecology.

Accurate Genome Relative Abundance Estimation Based on Shotgun Metagenomic Reads

Li C. Xia, Ting Chen, Fengzhu Sun, 2011, PloS one.

A network-based integrated framework for predicting virus–prokaryote interactions

Fengzhu Sun, J. Fuhrman, J. Braun, 2020, NAR genomics and bioinformatics.

A network-based integrated framework for predicting virus-host interactions

Jie Ren, Fengzhu Sun, Jed A. Fuhrman, 2018, bioRxiv.

Pronounced daily succession of phytoplankton, archaea and bacteria following a spring bloom

J. Fuhrman, D. Needham, 2016, Nature Microbiology.

Richness and Diversity of Bacterioplankton Species along an Estuarine Gradient in Moreton Bay, Australia

Jed A. Fuhrman, I. Hewson, J. Fuhrman, 2004, Applied and Environmental Microbiology.

Minimum Information about an Uncultivated Virus Genome (MIUViG)

Natalia N. Ivanova, Evelien M. Adriaenssens, G. Cochrane, 2018, Nature Biotechnology.

Ecosystem Services for 2020

P. Burkill, H. Mooney, Fabian M Jaksic, 2010, Science.

Re-examination of the relationship between marine virus and microbial cell abundances

J. Weitz, C. Stock, J. Fuhrman, 2016, Nature Microbiology.

Estimating maximal microbial growth rates from cultures, metagenomes, and single cells via codon usage patterns

J. Fuhrman, Shengwei Hou, Jake L. Weissman, 2020, Proceedings of the National Academy of Sciences.

Corrigendum to: Assessment of metagenomic assemblers based on hybrid reads of real and simulated metagenomic sequences

Ying Wang, Shanfeng Zhu, Ziye Wang, 2020, Briefings Bioinform..

Section 8 update: Correlating single-cell count with function in mixed natural microbial communities through STARFISH

J. Fuhrman, C. Ouverney, 2004 .

Bacterioplankton in the coastal euphotic zone: Distribution, activity and possible relationships with phytoplankton

J. Fuhrman, F. Azam, J. Ammerman, 1980 .

Gyrotaxis as a new mechanism for generating spatial heterogeneity and migration in microplankton

A. Ōkubo, J. Fuhrman, James G. Mitchell, 1990 .

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Jie Ren, Fengzhu Sun, Yang Young Lu, 2016, Nucleic acids research.

Ribosome-linked mRNA-rRNA chimeras reveal active novel virus host associations

J. Fuhrman, Yi-Chun Yeh, J. C. Ignacio-Espinoza, 2020, bioRxiv.

Long-term stability and Red Queen-like strain dynamics in marine viruses

J. Fuhrman, N. A. Ahlgren, J. C. Ignacio-Espinoza, 2019, Nature Microbiology.

Discovery of several novel, widespread, and ecologically distinct marine Thaumarchaeota viruses that encode amoC nitrification genes

J. Fuhrman, N. A. Ahlgren, G. Rocap, 2018, The ISME Journal.

A comparative study of culture-independent, library-independent genotypic methods of fecal source tracking.

Linda K. Dick, J. Fuhrman, K. Field, 2003, Journal of water and health.

Metagenomics and quantitative stable isotope probing offer insights into metabolism of polycyclic aromatic hydrocarbons degraders in chronically polluted seawater

J. Fuhrman, E. Sieradzki, Michael Morando, 2020, bioRxiv.

Computational methods for the analysis of tag sequences in metagenomics studies.

Ting Chen, Fengzhu Sun, J. Fuhrman, 2012, Frontiers in bioscience.

A Comprehensive Assessment of Biologicals Contained Within Commercial Airliner Cabin Air

G. Bearman, J. Fuhrman, G. Andersen, 2006 .

Close coupling between release and uptake of dissolved free amino acids in seawater studied by an isotope dilution approach

J. Fuhrman, 1987 .

Increase in Fluorescence Intensity of 16S rRNA In Situ Hybridization in Natural Samples Treated with Chloramphenicol

J. Fuhrman, C. Ouverney, 1997, Applied and environmental microbiology.

Towards enhanced and interpretable clustering/classification in integrative genomics

Yang Young Lu, Fengzhu Sun, Jinchi Lv, 2017, Nucleic acids research.

Microbial tropicalization driven by a strengthening western ocean boundary current

I. Paulsen, J. Fuhrman, Mark V Brown, 2020, Global change biology.

Community structure: bacteria and archaea.

J. Fuhrman, 2007 .

Multitiered Approach Using Quantitative PCR To Track Sources of Fecal Pollution Affecting Santa Monica Bay, California

Angie A. Bera, J. Fuhrman, K. Schiff, 2006, Applied and Environmental Microbiology.

Composition and Biogeography of Planktonic Pro- and Eukaryotic Communities in the Atlantic Ocean: Primer Choice Matters

J. Fuhrman, Jesse Mcnichol, M. Simon, 2022, Frontiers in Microbiology.

Optimizing de novo genome assembly from PCR-amplified metagenomes

R. Malmstrom, J. Fuhrman, M. Sullivan, 2018, PeerJ.

Microbiological water quality at non-human influenced reference beaches in southern California during wet weather.

J. Fuhrman, K. Schiff, J. Griffith, 2010, Marine pollution bulletin.

Communitiesin Marine Myovirus Strong Seasonality and Interannual

J. Fuhrman, R. Sandaa, T. Thingstad, 2013 .

Strong Seasonality and Interannual Recurrence in Marine Myovirus Communities

J. Fuhrman, R. Sandaa, Cheryl-Emiliane Chow, 2013, Applied and Environmental Microbiology.

Marine archaeal dynamics and interactions with the microbial community over 5 years from surface to seafloor

J. Fuhrman, Alma E. Parada, A. Parada, 2017, The ISME Journal.

Top-down controls on bacterial community structure: microbial network analysis of bacteria, T4-like viruses and protists

D. Caron, J. Fuhrman, R. Sachdeva, 2013, The ISME Journal.

Effects of four organic pollutants on the growth of natural marine bacterioplankton populations

J. Fuhrman, J. Hudak, 1988 .

Beta diversity of marine bacteria depends on temporal scale.

J. Fuhrman, J. Martiny, A. Martiny, 2013, Ecology.

Benchmarking community-wide estimates of growth potential from metagenomes using codon usage statistics

J. Fuhrman, Tyler P. Barnum, Jake L. Weissman, 2022, bioRxiv.

The “Minimum Information about an ENvironmental Sequence” (MIENS) specification

Chris I. Hunter, B. Birren, G. Cochrane, 2010 .

Dynamics of finely resolved, abundant symbiotic marine plankton and other interacting microbes via automated high-frequency sampling

J. Fuhrman, Jacob A. Cram, D. Needham, 2017 .

Temporal variability and coherence of euphotic zone bacterial communities over a decade in the Southern California Bight

J. Fuhrman, Jacob A. Cram, Alma E. Parada, 2013, The ISME Journal.

Seasonality and monthly dynamics of marine myovirus communities.

J. Fuhrman, Cheryl-Emiliane Chow, Cheryl-Emiliane T. Chow, 2012, Environmental microbiology.

Community structure of marine bacterioplankton: patterns, networks, and relationships to function

J. Fuhrman, J. Steele, 2008 .

Imperfect retention of natural bacterioplankton cells by glass fiber filters

J. Fuhrman, S. Lee, Y. Kang, 1995 .

Mineralization potentials of aromatic hydrocarbons by estuarine microorganisms: variations with season, location, and bacterioplankton production

J. Fuhrman, S. Lee, J. Hudak, 1988 .

Do Bacteria-Sized Marine Eukaryotes Consume Significant Bacterial Production?

J. Fuhrman, G. McManus, 1984, Science.

Diel variations in bacterioplankton, phytoplankton, and related parameters in the Southern California Bight.

J. Fuhrman, F. Azam, R. Eppley, 1985 .

Defining seasonal marine microbial community dynamics

R. Knight, J. Gilbert, J. Caporaso, 2011, The ISME Journal.

Benchmarking metagenomic marine microbial growth prediction from codon usage bias and peak-to-trough ratios

J. Fuhrman, J. C. Ignacio-Espinoza, Shengwei Hou, 2019, bioRxiv.

Benchmarking Community-Wide Estimates of Growth Potential from Metagenomes Using Codon Usage Statistics

J. Fuhrman, Tyler P. Barnum, Jake L. Weissman, 2022, bioRxiv.

Does adenine incorporation into nucleic acids measure total microbial production

H. Ducklow, D. Kirchman, J. Fuhrman, 1986 .

Origins of Dissolved Organic Matter in Southern California Coastal Waters: Experiments on the Role of Zooplankton

J. Fuhrman, K. Sellner, R. Eppley, 1981 .

Influence of Method on the Apparent Size Distribution of Bacterioplankton Cells: Epifluorescence Microscopy Compared to Scanning Electron Microscopy

J. Fuhrman, 1981 .

Radioactively labeling of natural assemblages of bacterioplankton for use in trophic studies1

J. Fuhrman, F. Azam, J. Hollibaugh, 1980 .

Adaptations of bacteria to marine subsurface waters studied by temperature response

J. Fuhrman, F. Azam, 1983 .

Microbial uptake of dissolved organic matter in Mcmurdo Sound, Antarctica

J. Fuhrman, F. Azam, D. Karl, 1981 .

Cycling of organic nitrogen in marine plankton communities studied in enclosed water columns

J. Fuhrman, F. Azam, J. Hollibaugh, 1980 .

Microbial rhodopsins are major contributors to the solar energy captured in the sea

J. Fuhrman, J. Raven, J. Gasol, 2019, Science Advances.

Zooplankton induced changes in dissolved free amino acids and in production rates of freshwater bacteria

J. Fuhrman, N. Jørgensen, B. Riemann, 1986, Microbial Ecology.

Use of 13N as tracer for bacterial and algal uptake of ammonium from sea-water

J. Fuhrman, D. Capone, S. Horrigan, 1988 .

Influence of Light on Particulate Organic Matter Utilization by Attached and Free-Living Marine Bacteria

J. Fuhrman, P. Weber, D. Needham, 2019, Frontiers in microbiology.

Diel changes in bacterial biomass and growth rates in coastal environments, determined by means of thymidine incorporation into DNA, frequency of dividing cells (FDC), and microautoradiography

J. Fuhrman, B. Riemann, B. Marcussen, 1984 .

Control of marine bacterioplankton populations: Measurement and significance of grazing

J. Fuhrman, G. McManus, 1988, Hydrobiologia.

Dependent coupling of inorganic and organic nitrogen uptake and regeneration in the plume of the Chesapeake Bay estuary and its regulation by large heterotrophs

J. Fuhrman, P. Glibert, M. Roman, 1991 .

Marine alga Platymonas sp. accumulates silicon without apparent requirement

J. Fuhrman, R. Guillard, S. Chisholm, 1978 .

Dissolved free amino acid cycling in an estuarine outflow plume

J. Fuhrman, 1990 .

Biological considerations in the measurement of dissolved free amino acids in seawater and implications for chemical and microbiological studies

J. Fuhrman, T. Bell, 1985 .

A dynamic programming algorithm for binning microbial community proﬁles

Fengzhu Sun, J. Fuhrman, J. Steele, 2006 .

Proteorhodopsins dominate the expression of phototrophic mechanisms in seasonal and dynamic marine picoplankton communities

J. Fuhrman, E. Sieradzki, S. Rivero-Calle, 2018, PeerJ.

of Naturally Derived Marine Bacterioplankton Relationships between Biovolume and Biomass

J. Fuhrman, Sanghoon Lee, 2014 .

Clearance of bacteria-sized particles by natural populations of nanoplankton in the Chesapeake Bay outflow plume

J. Fuhrman, G. McManus, 1988 .

Oceans of Crenarchaeota: a Personal History Describing This Paradigm Shift: Studies of marine archaea during the past two decades unveil the distinctive biology of these diverse and abundant microorganisms

J. Fuhrman, 2011 .

Symbiotic diazotrophic UCYN-A strains co-occurred with El Niño, relaxed upwelling, and varied eukaryotes over 10 years off Southern California Bight

J. Fuhrman, Yi-Chun Yeh, Colette Fletcher-Hoppe, 2022, bioRxiv.

VIRUSES SYSTEMS IN MARINE PLANKTONIC

J. Fuhrman, C. Suttle, 1993 .

Thymidine incorporation as a measure of heterotrophic bacterioplankton production in marine surface waters: Evaluation and field results

J. Fuhrman, F. Azam, 1982 .

Growth efficiencies of freshwater bacterioplankton

J. Fuhrman, B. Riemann, K. Kristiansen, 1992, Microbial Ecology.

Structure of microbial communities in ethanol biofilters

J. Fuhrman, J. Steele, J. Devinny, 2005 .

Phage–bacterial contig association prediction with a convolutional neural network

Fengzhu Sun, J. Fuhrman, Shengwei Hou, 2022, Bioinformatics.

Effects of phytoplankton, viral communities, and warming on free-living and particle-associated marine prokaryotic community structure

J. Fuhrman, Yi-Chun Yeh, 2022, Nature communications.

Photosynthetic pigments in the ciliate Laboea strobila from Long Island Sound, USA

J. Fuhrman, G. McManus, 1986 .

Marine Bacterial, Archaeal, and Protistan Association Networks

Fengzhu Sun, J. Fuhrman, Jacob A. Cram, 2014 .

ViralCC retrieves complete viral genomes and virus-host pairs from metagenomic Hi-C data

J. Fuhrman, Fengzhu Sun, Yuxuan Du, 2023, Nature Communications.

Mosaic Patterns of B-vitamin Synthesis and Utilization in a Natural Marine Microbial Community

J. Fuhrman, M. Moran, S. Gifford, 2018, bioRxiv.

Mosaic Patterns of B-vitamin Synthesis and Utilization in a Natural Marine Microbial Community

J. Fuhrman, M. Moran, S. Gifford, 2018, bioRxiv.

Enteroviruses detected by reverse transcriptase polymerase chain reaction from the coastal waters of Santa Monica Bay, California: low correlation to bacterial indicator levels

Jed A. Fuhrman, Rachel T. Noble, J. Fuhrman, 2001, Hydrobiologia.

Defining seasonal marine microbial community dynamics

Susan M. Huse, R. Knight, J. Gilbert, 2011, The ISME Journal.

Viruses and protists cause similar bacterial mortality in coastal seawater

J. Fuhrman, R. Noble, 1995 .

Characterizing Chemoautotrophy and Heterotrophy in Marine Archaea and Bacteria With Single-Cell Multi-isotope NanoSIP

J. Fuhrman, P. Weber, J. Pett‐Ridge, 2019, Front. Microbiol..

Dissolved free amino acids in the Sargasso Sea: uptake and respiration rates, turnover times, and concentrations

Jed A. Fuhrman, Curtis A. Suttle, J. Fuhrman, 1991 .

A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes

Maureen L. Coleman, J. Weitz, C. Stock, 2015, The ISME Journal.

Wide‐ranging abundances of aerobic anoxygenic phototrophic bacteria in the world ocean revealed by epifluorescence microscopy and quantitative PCR

J. Fuhrman, M. Schwalbach, M. S. Schwalbach, 2005 .

Characterization of marine prokaryotic communities via DNA and RNA

J. Fuhrman, R. Wilcox, Y. Masuchi, 1994, Microbial Ecology.

Identifying viruses from metagenomic data using deep learning

Chao Deng, Kai Song, Yi Li, 2020, Quantitative Biology.

Beyond biogeographic patterns: processes shaping the microbial landscape

J. Fuhrman, J. Martiny, M. C. Horner-Devine, 2012, Nature Reviews Microbiology.

Extraction from Natural Planktonic Microorganisms of DNA Suitable for Molecular Biological Studies

J. Fuhrman, A. M. Chan, Å. Hagström, 1988, Applied and environmental microbiology.

DNA hybridization to compare species compositions of natural bacterioplankton assemblages

J. Fuhrman, S. Lee, Sanghoon Lee, 1990, Applied and environmental microbiology.

Roles of viral infection in organic particle flux

J. Fuhrman, L. Proctor, 1991 .

Significance of Size and Nucleic Acid Content Heterogeneity as Measured by Flow Cytometry in Natural Planktonic Bacteria

J. Fuhrman, Francesc Peters, J. Gasol, 1999, Applied and Environmental Microbiology.

Heterotrophic Planktonic Microbes: Virus, Bacteria, Archaea, and Protozoa

D. Caron, J. Fuhrman, 2016 .

Determination of Active Marine Bacterioplankton: a Comparison of Universal 16S rRNA Probes, Autoradiography, and Nucleoid Staining

J. Fuhrman, M. Karner, M Karner, 1997, Applied and environmental microbiology.

Dominance of bacterial biomass in the Sargasso Sea and its ecological implications

J. Fuhrman, C. Carlson, L. Proctor, 1989 .

Marine bacterial microdiversity as revealed by internal transcribed spacer analysis

J. Fuhrman, Mark V Brown, 2005 .

Rapid Detection of Enteroviruses in Small Volumes of Natural Waters by Real-Time Quantitative Reverse Transcriptase PCR

J. Fuhrman, R. Noble, Xiaolin Liang, 2005, Applied and Environmental Microbiology.

Effects of viral enrichment on the mortality and growth of heterotrophic bacterioplankton

J. Fuhrman, M. Middelboe, R. Noble, 1999 .

Spatial and temporal variation of natural bacterioplankton assemblages studied by total genomic DNA cross‐hybridization

J. Fuhrman, Sanghoon Lee, 1991 .

Proteorhodopsins: an array of physiological roles?

Jed A. Fuhrman, Michael S. Schwalbach, U. Stingl, 2008, Nature Reviews Microbiology.

Bacterioplankton Secondary Production Estimates for Coastal Waters of British Columbia, Antarctica, and California

J. Fuhrman, F. Azam, 1980, Applied and environmental microbiology.

Microbial community structure in the North Pacific ocean

J. Bunge, J. Fuhrman, F. Lauro, 2009, The ISME Journal.

Planktonic food web structure at a coastal time-series site: I. Partitioning of microbial abundances and carbon biomass

D. Caron, J. Fuhrman, Paige E. Connell, 2017 .

Bacterioplankton growth in seawater: I.Growth kinetics and cellular characteristics in seawater cultures

J. Fuhrman, F. Azam, Å. Hagström, 1984 .

Mesoscale and seasonal variability of heterotrophic nanoflagellate abundance in an estuarine outflow plume

J. Fuhrman, G. McManus, 1990 .

Bacterivory in seawater studied with the use of inert fluorescent particles1

J. Fuhrman, G. McManus, 1986 .

Viruses in the Marine Environment

J. Fuhrman, 2003 .

Viral mortality of marine bacteria and cyanobacteria

Jed A. Fuhrman, Lita M. Proctor, J. Fuhrman, 1990, Nature.

Relationships between Biovolume and Biomass of Naturally Derived Marine Bacterioplankton

J. Fuhrman, Sanghoon Lee, 1987 .

Diversity of virus-like agents killing Microcystis aeruginosa in a hyper-eutrophic pond

J. Fuhrman, Z. Kawabata, K. Matsui, 2006 .

Rapid ammonium cycling and concentration‐dependent partitioning of ammonium and phosphate: Implications for carbon transfer in planktonic communities

J. Fuhrman, C. Suttle, D. Capone, 1990 .

Mechanoreception in calanoid copepods

A. Ōkubo, J. Fuhrman, J. G. Mitchell, 1986 .

Genomics and Physiology of a Marine Flavobacterium Encoding a Proteorhodopsin and a Xanthorhodopsin-Like Protein

S. Spring, A. Goesmann, J. Fuhrman, 2013, PloS one.

CAFE: aCcelerated Alignment-FrEe sequence analysis

Jed A. Fuhrman, Jie Ren, Yang Young Lu, 2017, Nucleic Acids Res..

Marine viruses and global climate change.

Roberto Danovaro, Cinzia Corinaldesi, Curtis A Suttle, 2011, FEMS microbiology reviews.

Re-examination of the relationship between marine virus and microbial cell abundances

Joshua S Weitz, Alison Buchan, Curtis A Suttle, 2016, Nature Microbiology.

Re-examining the relationship between virus and microbial cell abundances in the global oceans

J. Weitz, C. Stock, J. Fuhrman, 2015, bioRxiv.

Alteration of Oceanic Nitrification Under Elevated Carbon Dioxide Concentrations

J. Fuhrman, D. Hutchins, J. Beman, 2008 .

Calibrating estimates of phage-induced mortality in marine bacteria: Ultrastructural studies of marine bacteriophage development from one-step growth experiments

Jed A. Fuhrman, Akira Okubo, Lita M. Proctor, 1993, Microbial Ecology.

Viriobenthos Production and Virioplankton Sorptive Scavenging by Suspended Sediment Particles in Coastal and Pelagic Waters

I. Hewson, J. Fuhrman, 2003, Microbial Ecology.

Virus‐like particle distribution and abundance in sediments and overlying waters along eutrophication gradients in two subtropical estuaries

W. Dennison, I. Hewson, J. Fuhrman, 2001 .

Rapid Virus Production and Removal as Measured with Fluorescently Labeled Viruses as Tracers

J. Fuhrman, R. Noble, 2000, Applied and Environmental Microbiology.

Breakdown and microbial uptake of marine viruses and other lysis products

J. Fuhrman, R. Noble, 1999 .

Virus decay and its causes in coastal waters

J. Fuhrman, R. Noble, Rachel T. Noble, 1997, Applied and environmental microbiology.

Bacterioplankton Roles in Cycling of Organic Matter: The Microbial Food Web

J. Fuhrman, 1992 .

Viral Influence on Aquatic Bacterial Communities

J. Fuhrman, M. Schwalbach, 2003, The Biological Bulletin.

Viruses in Marine Planktonic Systems

Jed A. Fuhrman, Curtis A. Suttle, J. Fuhrman, 1993 .

Ecological Role of Viruses in Aquatic Ecosystems

I. Hewson, J. Fuhrman, Cheryl-Emiliane Chow, 2010 .

Viral impacts upon marine bacterioplankton assemblage structure

I. Hewson, J. Fuhrman, 2006, Journal of the Marine Biological Association of the United Kingdom.

Viral effects on bacterial community composition in marine plankton microcosms

I. Hewson, J. Fuhrman, M. Schwalbach, 2004 .

Evaluating and Improving Small Subunit rRNA PCR Primer Coverage for Bacteria, Archaea, and Eukaryotes Using Metagenomes from Global Ocean Surveys

P. Berube, S. Biller, J. Fuhrman, 2021, mSystems.

Evaluating and Improving SSU rRNA PCR Primer Coverage via Metagenomes from Global Ocean Surveys

P. Berube, S. Biller, J. Fuhrman, 2020, bioRxiv.

Faculty Opinions recommendation of IMG/M: the integrated metagenome data management and comparative analysis system.

Jed Fuhrman, J. Fuhrman, 2012 .

Immune lag is a major cost of prokaryotic adaptive immunity during viral outbreaks

J. Fuhrman, E. Westra, S. Meaden, 2020, bioRxiv.

DeepMicrobeFinder Sorts Metagenomes into Prokaryotes, Eukaryotes and Viruses, with Marine Applications

Ting Chen, Fengzhu Sun, J. Fuhrman, 2021 .

Estimating global variation in the maximum growth rates of eukaryotic microbes from cultures and metagenomes via codon usage patterns

Arianna I. Krinos, D. Caron, J. Fuhrman, 2021, bioRxiv.

Assessment of metagenomic assemblers based on hybrid reads of real and simulated metagenomic sequences

Ying Wang, Shanfeng Zhu, Fengzhu Sun, 2019, Briefings Bioinform..

Prediction of virus-host infectious association by supervised learning methods

Jie Ren, Lianping Yang, Fengzhu Sun, 2017, BMC Bioinformatics.

Multi-year dynamics of fine-scale marine cyanobacterial populations are more strongly explained by phage interactions than abiotic, bottom-up factors.

J. Fuhrman, Yi-Chun Yeh, J. Perelman, 2019, Environmental microbiology.

Dynamic marine viral infections and major contribution to photosynthetic processes shown by spatiotemporal picoplankton metatranscriptomes

J. Fuhrman, D. Needham, E. Fichot, 2019, Nature Communications.

Discovery of several novel, widespread, and ecologically distinct marine Thaumarchaeota viruses that encode amoC nitrification genes

J. Fuhrman, G. Rocap, C. Fuchsman, 2018, The ISME Journal.

Genome and epigenome of a novel marine Thaumarchaeota strain suggest viral infection, phosphorothioation DNA modification and multiple restriction systems

J. Fuhrman, Ting Chen, Vickie Trinh, 2017, Environmental microbiology.

Marine Planktonic Archaea Take Up Amino Acids

J. Fuhrman, C. Ouverney, 2000, Applied and Environmental Microbiology.

COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO‐alignment and paired‐end read LinkAge

Ting Chen, Fengzhu Sun, Jed A. Fuhrman, 2016, Bioinform..

Marine microbial diversity studied via 16S rRNA sequences: cloning results from coastal waters and counting of native archaea with fluorescent single cell probes

J. Fuhrman, C. Ouverney, 1998, Aquatic Ecology.

Widespread Archaea and novel Bacteria from the deep sea as shown by 16S rRNA gene sequences

J. Fuhrman, A. Davis, 1997 .

Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific Oceans

J. Fuhrman, J A Fuhrman, K McCallum, 1993, Applied and environmental microbiology.

Cross-depth analysis of marine bacterial networks suggests downward propagation of temporal changes

Fengzhu Sun, Jed A Fuhrman, Fengzhu Sun, 2015, The ISME Journal.

Dynamics and interactions of highly resolved marine plankton via automated high-frequency sampling

J. Fuhrman, Jacob A. Cram, D. Needham, 2018, The ISME Journal.

Contrasting diversity patterns of prokaryotes and protists over time and depth at the San-Pedro Ocean Time series

J. Fuhrman, Yi-Chun Yeh, 2022, ISME Communications.

Dynamic marine viral infections and major contribution to photosynthetic processes shown by regional and seasonal picoplankton metatranscriptomes

J. Fuhrman, D. Needham, E. Fichot, 2017, bioRxiv.

Viruses, Bacteria, and the Microbial Loop

I. Hewson, J. Fuhrman, 2008 .

A comparison of taxon co-occurrence patterns for macro- and microorganisms.

Gerard Muyzer, Anna-Louise Reysenbach, Jed A Fuhrman, 2007, Ecology.

Coupling 16S-ITS rDNA clone libraries and automated ribosomal intergenic spacer analysis to show marine microbial diversity: development and application to a time series.

Jed A Fuhrman, I. Hewson, J. Fuhrman, 2005, Environmental microbiology.

Influence of Light on Particulate Organic Matter Utilization by Attached and Free-Living Marine Bacteria

J. Fuhrman, P. Weber, D. Needham, 2019, bioRxiv.

Covariation of viral parameters with bacterial assemblage richness and diversity in the water column and sediments

I. Hewson, J. Fuhrman, 2007 .

Characterization of Lysogens in Bacterioplankton Assemblages of the Southern California Borderland

I. Hewson, J. Fuhrman, 2007, Microbial Ecology.

Mortality of marine bacteria in response to enrichments of the virus size fraction from seawater

J. Fuhrman, L. Proctor, 1992 .

Comprehensive single-PCR 16S and 18S rRNA community analysis validated with mock communities, and estimation of sequencing bias against 18S.

J. Fuhrman, Yi-Chun Yeh, Jesse Mcnichol, 2021, Environmental microbiology.

Silicibacter pomeroyi sp. nov. and Roseovarius nubinhibens sp. nov., dimethylsulfoniopropionate-demethylating bacteria from marine environments.

J. Fuhrman, M. Moran, W. Whitman, 2003, International journal of systematic and evolutionary microbiology.

Benchmarking microbial growth rate predictions from metagenomes

J. Fuhrman, J. C. Ignacio-Espinoza, Shengwei Hou, 2020, The ISME journal.

Benchmarking microbial growth rate predictions from metagenomes

J. Fuhrman, J. C. Ignacio-Espinoza, Shengwei Hou, 2020, The ISME Journal.

Microbial Desulfurization of a Crude Oil Middle-Distillate Fraction: Analysis of the Extent of Sulfur Removal and the Effect of Removal on Remaining Sulfur

J. Fuhrman, C. Ouverney, 1999, Applied and Environmental Microbiology.

HiCzin: Normalizing metagenomic Hi-C data and detecting spurious contacts using zero-inflated negative binomial regression

Fengzhu Sun, J. Fuhrman, Yuxuan Du, 2021, bioRxiv.

Fluid-dynamics driving saline water in the North East German Basin

J. Fuhrman, A. Pekdeger, V. Clausnitzer, 2005 .

Remarkable heterogeneity in meso‐ and bathypelagic bacterioplankton assemblage composition

I. Hewson, J. Fuhrman, D. Capone, 2006 .

Metagenomics and Quantitative Stable Isotope Probing Offer Insights into Metabolism of Polycyclic Aromatic Hydrocarbon Degraders in Chronically Polluted Seawater

J. Fuhrman, Michael Morando, Ella T. Sieradzki, 2021, mSystems.

Metagenomics and stable isotope probing offer insights into metabolism of polycyclic aromatic hydrocarbons degraders in chronically polluted seawater

J. Fuhrman, Michael Morando, Ella T. Sieradzki, 2019 .

Global distribution and diversity of marine Verrucomicrobia

Susan M. Huse, M. Sogin, J. Fuhrman, 2012, The ISME Journal.

Systematic, continental scale temporal monitoring of marine pelagic microbiota by the Australian Marine Microbial Biodiversity Initiative

Jason Koval, Levente Bodrossy, Martin Ostrowski, 2018, Scientific Data.

Performance of viruses and bacteriophages for fecal source determination in a multi-laboratory, comparative study.

Lauren M. Sassoubre, J. Fuhrman, V. Harwood, 2013, Water research.

Tiered approach for identification of a human fecal pollution source at a recreational beach: case study at Avalon Bay, Catalina Island, California.

S. Grant, J. Fuhrman, A. Boehm, 2003, Environmental science & technology.

Community structure and function in prokaryotic marine plankton

J. Fuhrman, 2002, Antonie van Leeuwenhoek.

Prokaryotic and viral diversity patterns in marine plankton

J. Fuhrman, J. Griffith, M. Schwalbach, 2002, Ecological Research.

for Determination of Radioisotope Uptake by Specific Microbial Cell Types In Situ

J. Fuhrman, C. Ouverney, 1998 .

Macroecological patterns of marine bacteria on a global scale

Jed A. Fuhrman, Susan M. Huse, Mitchell L. Sogin, 2013 .

Metagenomics and its connection to microbial community organization

J. Fuhrman, 2012, F1000 biology reports.

Co-occurrence patterns for abundant marine archaeal and bacterial lineages in the deep chlorophyll maximum of coastal California

Jed A Fuhrman, J. Fuhrman, J. Beman, 2011, The ISME Journal.

A A Davis Pacific Oceans . microbial communities from the Atlantic and Phylogenetic diversity of subsurface marine

J. Fuhrman, K. McCallum, A. Davis, 1993 .

Diversity and biogeography of bacterial assemblages in surface sediments across the San Pedro Basin, Southern California Borderlands.

I. Hewson, J. Fuhrman, Myrna E Jacobson Meyers, 2007, Environmental microbiology.

Spatial and vertical biogeography of coral reef sediment bacterial and diazotroph communities

I. Hewson, J. Fuhrman, 2006 .

Marine ecology: Microbial microdiversity

J. Fuhrman, L. Campbell, 1998, Nature.

Debojyoti Dutta, Fengzhu Sun, Jed A. Fuhrman, 2006, Bioinform..

A dynamic programming algorithm for binning microbial community profiles

Fengzhu Sun, Jed A. Fuhrman, Quansong Ruan, 2006, Bioinform..

Time- and sediment depth-related variations in bacterial diversity and community structure in subtidal sands

A. Boetius, J. Fuhrman, A. Ramette, 2009, The ISME Journal.

Vertical and Seasonal Patterns Control Bacterioplankton Communities at Two Horizontally Coherent Coastal Upwelling Sites off Galicia (NW Spain)

J. Fuhrman, Jacob A. Cram, D. Needham, 2018, Microbial Ecology.

A hydrocarbon contaminated aquifer reveals a Piggyback-the-Persistent viral strategy.

James G. Mitchell, J. Fuhrman, J. Paterson, 2019, FEMS microbiology ecology.

Dynamics and interactions of highly resolved marine plankton via automated high-frequency sampling

J. Fuhrman, Jacob A. Cram, D. Needham, 2018, The ISME Journal.

Dynamic marine viral infections and major contribution to photosynthetic processes shown by spatiotemporal picoplankton metatranscriptomes

J. Fuhrman, D. Needham, E. Fichot, 2019, Nature Communications.

Efficient statistical significance approximation for local similarity analysis of high-throughput time series data

Dongmei Ai, Fengzhu Sun, Li Charlie Xia, 2013, Bioinform..

Global declines in oceanic nitrification rates as a consequence of ocean acidification

J. Fuhrman, D. Hutchins, A. King, 2010, Proceedings of the National Academy of Sciences.

Distribution of Extracellular Flavins in a Coastal Marine Basin and Their Relationship to Redox Gradients and Microbial Community Members.

J. Fuhrman, J. Sylvan, J Jotautas Baronas, 2018, Environmental science & technology.

Measurement of Bacterioplankton Growth in the Sea and Its Regulation by Environmental Conditions

J. Fuhrman, F. Azam, 1984 .

Short-term dynamics and interactions of marine protist communities during the spring–summer transition

J. Fuhrman, D. Needham, Lyria Berdjeb, 2018, The ISME Journal.

Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific oceans

J. Fuhrman, J A Fuhrman, K McCallum, 1993, Applied and environmental microbiology.

Influence of Amazon and Orinoco offshore surface water plumes on oligotrophic bacterioplankton diversity in the west tropical Atlantic

I. Hewson, J. Fuhrman, D. Capone, 2006 .

Impact of light on marine bacterioplankton community structure

J. Fuhrman, Mark V Brown, M. Schwalbach, 2005 .

Population ecology of nitrifying archaea and bacteria in the Southern California Bight.

J. Fuhrman, J. Beman, R. Sachdeva, 2010, Environmental microbiology.

Phylogenetic Diversity of Diazotrophs along an Experimental Nutrient Gradient in Mangrove Sediments

J. Fuhrman, D. Capone, I. Romero, 2015 .

Possible biogeochemical consequences of ocean fertilization

Jed A. Fuhrman, J. Fuhrman, D. Capone, 1991 .

Physics and microbial ecology of a buoyant estuarine plume on the continental shelf

Jed A. Fuhrman, Michael R. Roman, Thomas C. Malone, 1987 .

The contribution of phytoplankton to ocean density gradients

A. Ōkubo, J. Fuhrman, James G. Mitchell, 1989 .

The Vertical Distribution and Diversity of Marine Bacteriophage at a Station off Southern California

J. Fuhrman, S. Jiang, W. Chu, 2003, Microbial Ecology.

Temporal and spatial scales of variation in bacterioplankton assemblages of oligotrophic surface waters

I. Hewson, J. Fuhrman, D. Capone, 2006 .

Whither or wither geomicrobiology in the era of 'community metagenomics'

Jed Fuhrman, John F. Stolz, Ronald S. Oremland, 2005, Nature Reviews Microbiology.

The founding charter of the Genomic Observatories Network

Renzo Kottmann, Frank Oliver Glöckner, Norman Morrison, 2014, GigaScience.

Genome sequences from the sea

Jed Fuhrman, J. Fuhrman, 2003, Nature.

Ecosystem Services for 2020 - Response to Faith

H. Mooney, Fabian M Jaksic, A. Kinzig, 2010 .

Microzones surrounding phytoplankton form the basis for a stratified marine microbial ecosystem

A. Ōkubo, J. Fuhrman, James G. Mitchell, 1985, Nature.

Evidence of Trichodesmium viral lysis and potential significance for biogeochemical cycling in the oligotrophic ocean

Jed A. Fuhrman, Edward J. Carpenter, E. Carpenter, 2004 .

Enumeration of virus particles in aquatic or sediment samples by epifluorescence microscopy

J. Fuhrman, C. Suttle, 2010 .

Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates

Fengzhu Sun, Li Charlie Xia, Jacob Cram, 2011, BMC Systems Biology.

Dilution reveals how viral lysis and grazing shape microbial communities

J. Fuhrman, Jacob A. Cram, A. Parada, 2016 .

Marine proteorhodopsins rival photosynthesis in solar energy capture

J. Fuhrman, J. Gasol, J. Arístegui, 2017, bioRxiv.

Centimeter scale vertical heterogeneity in bacteria and chlorophyll a

J. Fuhrman, James G. Mitchell, 1989 .

Production, consumption and nutrient cycling in a laboratory mesocosm

H. Ducklow, J. Fuhrman, T. Malone, 1988 .

Long-term nitrogen and phosphorus fertilization effects on N 2 fixation rates and nifH gene community patterns in mangrove sediments

J. Fuhrman, D. Capone, M. Jacobson, 2012 .

Burrowing deeper into benthic nitrogen cycling: the impact of bioturbation on nitrogen fixation coupled to sulfate reduction

T. Treude, J. Fuhrman, W. Ziebis, 2010 .

Symbiotic UCYN-A strains co-occurred with El Niño, relaxed upwelling, and varied eukaryotes over 10 years off Southern California

J. Fuhrman, Yi-Chun Yeh, Colette Fletcher-Hoppe, 2023, ISME communications.

Normalizing Metagenomic Hi-C Data and Detecting Spurious Contacts Using Zero-Inflated Negative Binomial Regression

Fengzhu Sun, J. Fuhrman, S. Laperriere, 2022, J. Comput. Biol..

Statistical significance approximation in local trend analysis of high-throughput time-series data using the theory of Markov chains

Fengzhu Sun, J. Fuhrman, L. C. Xia, 2015, BMC Bioinformatics.

Constraining the composition and quantity of organic matter used by abundant marine Thaumarchaeota.

J. Fuhrman, A. Santoro, J. Pett‐Ridge, 2022, Environmental microbiology.

Diverse Marine T4-like Cyanophage Communities Are Primarily Comprised of Low-Abundance Species Including Species with Distinct Seasonal, Persistent, Occasional, or Sporadic Dynamics

J. Fuhrman, Emily Dart, N. Ahlgren, 2023, Viruses.

Comprehensive single-PCR 16S and 18S rRNA community analysis validated with mock communities and denoising algorithms

J. Fuhrman, Yi-Chun Yeh, Jesse Mcnichol, 2019, bioRxiv.

Applying “-omics” Data in Marine Microbial Oceanography

M. Follows, J. Fuhrman, S. Forde, 2013 .

Gene cloning and production of active recombinant Brugia malayi microfilarial chitinase.

J. Fuhrman, P. Robbins, M. Southworth, 1996, Gene.

Microbiological Water Quality at Non-Human Impacted Reference Beaches in Southern California During wet Weather

J. Fuhrman, K. Schiff, J. Griffith, 2009 .

VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data

Yang Young Lu, Fengzhu Sun, J. Fuhrman, 2017, Microbiome.

Inter-comparison of marine microbiome sampling protocols.

J. Poulain, J. Fuhrman, S. Pesant, 2023, ISME communications.

LSU LSU A communal catalogue reveals Earth's multiscale microbial A communal catalogue reveals Earth's multiscale microbial diversity diversity

Se Jin Song, Luke R. Thompson, James T. Morton, 2021 .

Global biogeography of SAR 11 marine bacteria

Matthew Z. DeMaere, C. Andrews-Pfannkoch, J. Fuhrman, 2012 .

Relationships between Biovolume and Biomass of Naturally Derived Marine Bacterioplankton.

J. Fuhrman, J. Fuhrman, S. Lee, 1987, Applied and environmental microbiology.

Statistical significance approximation in local trend analysis of high-throughput time-series data using the theory of Markov chains

Dongmei Ai, Fengzhu Sun, Li Charlie Xia, 2015, BMC Bioinformatics.

Marine ecology: Microbial microdiversity

J. Fuhrman, L. Campbell, 1998, Nature.

Bacterial community structure and its patterns.

J. Fuhrman, Å. Hagström, 2008 .

Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes.

R. O’Hara, M. Sogin, J. Fuhrman, 2016, FEMS microbiology reviews.

DeepMicroClass sorts metagenomes into prokaryotes, eukaryotes and viruses, with marine applications

Ting Chen, J. Fuhrman, Shengwei Hou, 2021, bioRxiv.

Microbial community structure and its functional implications

J. Fuhrman, 2009, Nature.

A latitudinal diversity gradient in planktonic marine bacteria

James H. Brown, I. Hewson, J. Fuhrman, 2008, Proceedings of the National Academy of Sciences.

A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes

Maureen L. Coleman, J. Weitz, C. Stock, 2015, The ISME Journal.

Marine viruses and global climate change.

J. Fuhrman, C. Suttle, J. Middelburg, 2011, FEMS microbiology reviews.

Characterization of marine prokaryotic communities via DNA and RNA

J. Fuhrman, R. Wilcox, Y. Masuchi, 1994, Microbial Ecology.

Author Correction: Re-examination of the relationship between marine virus and microbial cell abundances

J. Weitz, C. Stock, J. Fuhrman, 2017, Nature Microbiology.

Ecosystem Services for 2020

H. Mooney, Fabian M Jaksic, A. Kinzig, 2010, Science.

Predictable functional biogeography of marine microbial heterotrophs

J. Fuhrman, S. Dutkiewicz, E. Zakem, 2024, bioRxiv.

Phylogenetic proximity drives temporal succession of marine giant viruses in a five-year metagenomic time-series

J. Fuhrman, Shengwei Hou, S. Laperriere, 2024, bioRxiv.

Variational inference for microbiome survey data with application to global ocean data

J. Fuhrman, Christian L. Müller, Aditya Mishra, 2024, bioRxiv.