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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)

2021

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

Environmental microbiology, 2016-05, Vol.18 (5), p.1403-1414

2016

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Marine microbial community dynamics and their ecological interpretation

Nature reviews. Microbiology, 2015-03, Vol.13 (3), p.133-146

2015

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

Nature microbiology, 2016-02, Vol.1, p.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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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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ViralCC retrieves complete viral genomes and virus-host pairs from metagenomic Hi-C data

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

2023

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

The ISME Journal, 2019-03, Vol.13 (3), p.618-631

2019

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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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Defining seasonal marine microbial community dynamics

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

2012

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

The ISME Journal, 2017-11, Vol.11 (11), p.2510-2525

2017

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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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Accurate genome relative abundance estimation based on shotgun metagenomic reads

PloS one, 2011-12, Vol.6 (12), p.e27992-e27992

2011

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Phage–bacterial contig association prediction with a convolutional neural network

Bioinformatics, 2022-06, Vol.38 (Supplement_1), p.i45-i52

2022

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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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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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Microbial community structure and its functional implications

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

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

Marine microbial community dynamics and their ecological interpretation

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

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

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

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

Beyond biogeographic patterns: processes shaping the microbial landscape

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

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

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

Identifying viruses from metagenomic data using deep learning

Defining seasonal marine microbial community dynamics

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

Benchmarking microbial growth rate predictions from metagenomes

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

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

Accurate genome relative abundance estimation based on shotgun metagenomic reads

Phage–bacterial contig association prediction with a convolutional neural network

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

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

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