(Q41546172)

English

Metabolic Network Analysis and Metatranscriptomics Reveal Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage acI.

scientific article published on July 2017

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scholarly article

1 reference

Europe PubMed Central

3 October 2017

Metabolic Network Analysis and Metatranscriptomics Reveal Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage acI. (English)

1 reference

Europe PubMed Central

3 October 2017

0 references

Joshua J Hamilton

1

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28861526%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

Rex R Malmstrom

7

1 reference

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11 June 2020

Katherine D. McMahon

9

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11 June 2020

Sarahi L. Garcia

2

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11 June 2020

4

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11 June 2020

Stefan Bertilsson

6

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11 June 2020

Katrina T. Forest

8

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Katrina T Forest

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11 June 2020

Brittany Brown Hicks

3

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Brittany S Brown

1 reference

0000-0002-4245-7223

13 November 2023

author name string

Francisco Moya-Flores

5

1 reference

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11 June 2020

publication date

1 July 2017

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3 October 2017

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11 June 2020

2

1 reference

Europe PubMed Central

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11 June 2020

4

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28861526%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

Metabolic network analysis reveals microbial community interactions in anammox granules.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5574706

6 June 2018

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5574706

6 June 2018

Toward a Predictive Understanding of Earth's Microbiomes to Address 21st Century Challenges

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5574706

6 June 2018

Recovering complete and draft population genomes from metagenome datasets

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5574706

6 June 2018

Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5574706

6 June 2018

Auxotrophy and intrapopulation complementary in the 'interactome' of a cultivated freshwater model community.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5574706

6 June 2018

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5574706

6 June 2018

Evaluation of metatranscriptomic protocols and application to the study of freshwater microbial communities

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5574706

6 June 2018

RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5574706

6 June 2018

HTSeq--a Python framework to work with high-throughput sequencing data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5574706

6 June 2018

Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5574706

6 June 2018

PhyloSift: phylogenetic analysis of genomes and metagenomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5574706

6 June 2018

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5574706

6 June 2018

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST).

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5574706

6 June 2018

The transporter classification database

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5574706

6 June 2018

Breaking a paradigm: cosmopolitan and abundant freshwater actinobacteria are low GC.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5574706

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In situ substrate preferences of abundant bacterioplankton populations in a prealpine freshwater lake.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5574706

6 June 2018

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1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5574706

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1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5574706

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1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5574706

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High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5574706

6 June 2018

A guide to the natural history of freshwater lake bacteria

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5574706

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High-throughput generation, optimization and analysis of genome-scale metabolic models

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5574706

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1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5574706

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1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5574706

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1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5574706

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1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5574706

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Large-scale reconstruction and phylogenetic analysis of metabolic environments

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5574706

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1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5574706

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The microbial engines that drive Earth's biogeochemical cycles.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5574706

6 June 2018

Phylogenetic ecology of the freshwater Actinobacteria acI lineage

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5574706

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1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5574706

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Bacterioplankton community composition along a salinity gradient of sixteen high-mountain lakes located on the Tibetan Plateau, China.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5574706

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1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5574706

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1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5574706

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1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5574706

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1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5574706

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1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5574706

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1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5574706

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1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5574706

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1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5574706

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1 reference

https://pubmed.ncbi.nlm.nih.gov/28861526

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1 reference

https://pubmed.ncbi.nlm.nih.gov/28861526

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inferred from PubMed ID database lookup

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1 reference

https://pubmed.ncbi.nlm.nih.gov/28861526

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inferred from PubMed ID database lookup

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1 reference

https://pubmed.ncbi.nlm.nih.gov/28861526

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inferred from PubMed ID database lookup

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1 reference

https://pubmed.ncbi.nlm.nih.gov/28861526

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inferred from PubMed ID database lookup

Identifiers

10.1128/MSYSTEMS.00091-17

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28861526%20AND%20SRC:MED&resulttype=core&format=json

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1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28861526%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

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Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28861526%20AND%20SRC:MED&resulttype=core&format=json

11 June 2020

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