List of works by Jed A. Fuhrman

A communal catalogue reveals Earth's multiscale microbial diversity

scientific article published in November 2017

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

scientific article

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

scientific article

A dynamic programming algorithm for binning microbial community profiles

scientific article

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

scientific article published on 01 August 2019

A latitudinal diversity gradient in planktonic marine bacteria

scientific article

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

scientific article published on 30 January 2015

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

scientific article published on 23 June 2020

A non-tailed twist in the viral tale

scientific article published in February 2018

Accurate genome relative abundance estimation based on shotgun metagenomic reads

scientific article

Alignment-free $d_2^*$ oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences.

scientific article

Annually reoccurring bacterial communities are predictable from ocean conditions

scientific article

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

scientific article published on 11 March 2019

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

scientific article published on 3 October 2017

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

scientific article published on September 17, 2003

Benchmarking microbial growth rate predictions from metagenomes

scientific article published on 16 September 2020

Beta diversity of marine bacteria depends on temporal scale

scientific article

Beyond biogeographic patterns: processes shaping the microbial landscape.

scientific article

CAFE: aCcelerated Alignment-FrEe sequence analysis

scientific article published on 3 May 2017

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

scientific article published on 2 June 2016

Characterization of lysogens in bacterioplankton assemblages of the southern California borderland

scientific article published on 8 March 2007

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

scientific article published on 17 December 2019

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

scientific article

Community structure and function in prokaryotic marine plankton

scientific article

Computational methods for the analysis of tag sequences in metagenomics studies

scientific article published on June 2012

Contributors

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

scientific article

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

scientific article published on 07 May 2020

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

scientific article

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

scientific article published on 19 May 2015

Defining seasonal marine microbial community dynamics

scientific article

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

article

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

scientific article published on 15 October 2018

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

scientific article

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

scientific article published on 12 March 2019

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

scientific article published on 13 June 2018

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

scientific article published on 11 April 2017

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

article

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

scientific article

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

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

scientific article

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

scientific article

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

scientific article published on 18 April 2017

Genome sequences from the sea

scientific article published in Nature

Genomics and physiology of a marine flavobacterium encoding a proteorhodopsin and a xanthorhodopsin-like protein

scientific article published on 4 March 2013

Global biogeography of SAR11 marine bacteria

scientific article

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

scientific article (publication date: 4 January 2011)

Global distribution and diversity of marine Verrucomicrobia

scientific article

Global patterns of bacterial beta-diversity in seafloor and seawater ecosystems

scientific article published in 2011

Identifying viruses from metagenomic data using deep learning

scientific article

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

scientific article

Improved strategy for comparing microbial assemblage fingerprints

scientific article

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

scientific article published on 04 June 2019

Local similarity analysis reveals unique associations among marine bacterioplankton species and environmental factors

scientific article

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

scientific article published on 09 December 2019

Macroecological patterns of marine bacteria on a global scale

article by Anthony S. Amend et al published 7 November 2012 in Journal of Biogeography

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

scientific article published on 21 July 2017

Marine bacterial, archaeal and protistan association networks reveal ecological linkages.

scientific article

Marine microbial community dynamics and their ecological interpretation

scientific article published on 9 February 2015

Marine viruses and global climate change

scientific article

Metagenomics and its connection to microbial community organization

scientific article

Microbial biogeography: putting microorganisms on the map

scientific article (publication date: February 2006)

Microbial community structure and its functional implications

scientific article published on May 2009

Microbial community structure in the North Pacific ocean

scientific article published on 23 July 2009

Microbial microdiversity

scientific article published in Nature

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

scientific article published on 07 August 2019

Microbial tropicalization driven by a strengthening western ocean boundary current

scientific article published on 27 July 2020

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

scientific article

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

scientific article published in Nature

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

scientific article

Minimum Information about an Uncultivated Virus Genome (MIUViG)

scientific article published on 17 December 2018

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

scientific article

Mosaic patterns of B-vitamin synthesis and utilization in a natural marine microbial community.

scientific article published on 16 April 2018

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

scientific article published on 18 June 2019

Multitiered approach using quantitative PCR to track sources of fecal pollution affecting Santa Monica Bay, California

scientific article

Optimizing genome assembly from PCR-amplified metagenomes

scientific article published in 2019

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

scientific article published on 04 July 2013

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

scientific article published on May 1, 1993

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

scholarly article by David A. Caron published in March 2017

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

scientific article published on 18 February 2010

Prediction of virus-host infectious association by supervised learning methods.

scientific article

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

scientific article

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

scientific article

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

scientific article published on 23 October 2018

Proteorhodopsins: an array of physiological roles?

scientific article

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

Rapid detection of enteroviruses in small volumes of natural waters by real-time quantitative reverse transcriptase PCR

scientific article

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

scientific article

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

Richness and diversity of bacterioplankton species along an estuarine gradient in Moreton Bay, Australia

scientific article published on June 2004

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

scientific article

Seasonality and monthly dynamics of marine myovirus communities

scientific article published on 17 April 2012

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

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

scientific article published on 29 March 2018

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

scientific article

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

scientific article

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

scientific article

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

article

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

scientific article published on 3 April 2018

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

scientific article

The Earth Microbiome Project: The Meeting Report for the 1st International Earth Microbiome Project Conference, Shenzhen, China, June 13th-15th 2011.

scientific article published on 22 November 2011

The founding charter of the Genomic Observatories Network

scientific article published on 7 March 2014

The ocean sampling day consortium

scientific article published in 2015

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

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

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

scientific article published in February 2003

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

scientific article

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

scientific article

Towards enhanced and interpretable clustering/classification in integrative genomics

scientific article published on 30 August 2017

Unlocking the potential of metagenomics through replicated experimental design

scientific article published on 7 June 2012

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

scientific article published on 19 April 2018

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

scientific article

Viral Influence on Aquatic Bacterial Communities ⬇️

scientific article published on April 1, 2003

Viral mortality of marine bacteria and cyanobacteria

scientific article published in Nature

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

scientific article published on September 17, 2003

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

scientific article published in January 2007

Viruses in Marine Planktonic Systems

scientific article published in 1993

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

scientific article

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