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Microbial community structure and its functional implications

Nature, 2009-05, Vol.459 (7244), p.193-199

Fuhrman, Jed A

2009

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

Proceedings of the National Academy of Sciences - PNAS, 2021-03, Vol.118 (12), p.1-10

2021

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

Nature communications, 2022-12, Vol.13 (1), p.7905-7905, Article 7905

2022

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

The ISME Journal, 2017-07, Vol.11 (7), p.1614-1629

2017

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

Bioinformatics (Oxford, England), 2017-03, Vol.33 (6), p.791-798

2017

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

Microbiome, 2017-07, Vol.5 (1), p.69-69, Article 69

2017

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

Nature communications, 2023-01, Vol.14 (1), p.502-11, Article 502

2023

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

Nature microbiology, 2016-02, Vol.1 (4), p.16005, Article 16005

2016

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Beyond biogeographic patterns: processes shaping the microbial landscape

Nature reviews. Microbiology, 2012-07, Vol.10 (7), p.497-506

2012

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

PloS one, 2011-09, Vol.6 (9), p.e24570-e24570

2011

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

The ISME Journal, 2018-08, Vol.12 (8), p.1907-1917

2018

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

The ISME Journal, 2016-07, Vol.10 (7), p.1669-1681

2016

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Identifying viruses from metagenomic data using deep learning

Quantitative biology, 2020-03, Vol.8 (1), p.64-77

2020

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

ISME Communications, 2022-04, Vol.2 (1)

2022

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Defining seasonal marine microbial community dynamics

Nature reviews. Microbiology, 2012-02, Vol.6 (2), p.298-308

2012

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

FEMS microbiology reviews, 2016-09, Vol.40 (5), p.686-700

2016

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

The ISME Journal, 2014-04, Vol.8 (4), p.816-829

2014

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Benchmarking microbial growth rate predictions from metagenomes

The ISME Journal, 2021-01, Vol.15 (1), p.183-195

2021

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

mSystems, 2016-01, Vol.1 (1)

2016

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

The ISME Journal, 2015-03, Vol.9 (3), p.563-580

2015

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

Environmental microbiology, 2019-08, Vol.21 (8), p.2948-2963

2019

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

Nature communications, 2019-03, Vol.10 (1), p.1169-1169, Article 1169

2019

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latitudinal diversity gradient in planktonic marine bacteria

Proceedings of the National Academy of Sciences - PNAS, 2008-06, Vol.105 (22), p.7774-7778

2008

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

Viruses, 2023-02, Vol.15 (2), p.581

2023

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

Bioinformatics, 2013-01, Vol.29 (2), p.230-237

2013

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Microbial community structure and its functional implications

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

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

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

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

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

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

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

Beyond biogeographic patterns: processes shaping the microbial landscape

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

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

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

Identifying viruses from metagenomic data using deep learning

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

Defining seasonal marine microbial community dynamics

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

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

Benchmarking microbial growth rate predictions from metagenomes

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

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

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

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

latitudinal diversity gradient in planktonic marine bacteria

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

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

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