Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype (Q33801668)

29 July 2017

Single-cell enabled comparative genomics of a deep ocean SAR11 bathytype (English)

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29 July 2017

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7

Ramunas Stepanauskas

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Tanja Woyke

5

object named as

Tanja Woyke

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Brandon K. Swan

object named as

Brandon K Swan

3

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Edward F. DeLong

6

object named as

Edward F DeLong

1 reference

29 July 2017

J Cameron Thrash

1

1 reference

29 July 2017

Ben Temperton

2

1 reference

29 July 2017

Zachary C Landry

4

1 reference

29 July 2017

Stephan J Giovannoni

8

1 reference

29 July 2017

23 January 2014

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29 July 2017

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29 July 2017

8

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29 July 2017

1440-1451

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29 July 2017

7

1 reference

https://scigraph.springernature.com/pub.10.1038/ismej.2013.243

29 July 2017

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Insights into the phylogeny and coding potential of microbial dark matter

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High-resolution SAR11 ecotype dynamics at the Bermuda Atlantic Time-series Study site by phylogenetic placement of pyrosequences

4 July 2018

1 reference

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Complete genome sequence of the facultatively chemolithoautotrophic and methylotrophic alpha Proteobacterium Starkeya novella type strain (ATCC 8093(T)).

4 July 2018

1 reference

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Abundant SAR11 viruses in the ocean.

4 July 2018

1 reference

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Analysis of composition and structure of coastal to mesopelagic bacterioplankton communities in the northern gulf of Mexico

4 July 2018

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The future is now: single-cell genomics of bacteria and archaea

4 July 2018

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CD-HIT: accelerated for clustering the next-generation sequencing data

4 July 2018

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Single cell genomics: an individual look at microbes

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

Streamlining and core genome conservation among highly divergent members of the SAR11 clade

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

Metagenomic analysis of hadopelagic microbial assemblages thriving at the deepest part of Mediterranean Sea, Matapan-Vavilov Deep

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

Global biogeography of SAR11 marine bacteria

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

A metaproteomic assessment of winter and summer bacterioplankton from Antarctic Peninsula coastal surface waters.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

Phylogenomic evidence for a common ancestor of mitochondria and the SAR11 clade

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

Seasonality in ocean microbial communities.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

HandAlign: Bayesian multiple sequence alignment, phylogeny and ancestral reconstruction

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

Metagenomic analysis of a complex marine planktonic thaumarchaeal community from the Gulf of Maine

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

Accelerated Profile HMM Searches

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

A semi-quantitative, synteny-based method to improve functional predictions for hypothetical and poorly annotated bacterial and archaeal genes

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

Independent genome reduction and phylogenetic reclassification of the oceanic SAR11 clade

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

Going deeper: metagenome of a hadopelagic microbial community

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

Evolution and classification of the CRISPR-Cas systems

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

The Thaumarchaeota: an emerging view of their phylogeny and ecophysiology

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

The genomic standards consortium: bringing standards to life for microbial ecology

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

Hal: an automated pipeline for phylogenetic analyses of genomic data

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

Microbial metatranscriptomics in a permanent marine oxygen minimum zone.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

Differential expression analysis for sequence count data

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

Comparative metagenomics of bathypelagic plankton and bottom sediment from the Sea of Marmara

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

The presence of the glycolysis operon in SAR11 genomes is positively correlated with ocean productivity

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

Explaining microbial population genomics through phage predation.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

Comparative metagenomic analysis of a microbial community residing at a depth of 4,000 meters at station ALOHA in the North Pacific subtropical gyre

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

Seasonality and vertical structure of microbial communities in an ocean gyre

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

Latitudinal distribution of prokaryotic picoplankton populations in the Atlantic Ocean.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

Seasonal dynamics of SAR11 populations in the euphotic and mesopelagic zones of the northwestern Sargasso Sea.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

Protein evolution in deep sea bacteria: an analysis of amino acids substitution rates

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

A rapid bootstrap algorithm for the RAxML Web servers

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

Abundance and activity of Chloroflexi-type SAR202 bacterioplankton in the meso- and bathypelagic waters of the (sub)tropical Atlantic

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

Environmental adaptation: genomic analysis of the piezotolerant and psychrotolerant deep-sea iron reducing bacterium Shewanella piezotolerans WP3

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

SAR11 marine bacteria require exogenous reduced sulphur for growth

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

Natural variation in SAR11 marine bacterioplankton genomes inferred from metagenomic data

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

Metagenomics of the deep Mediterranean, a warm bathypelagic habitat

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

High intraspecific recombination rate in a native population of Candidatus pelagibacter ubique (SAR11).

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

Prokaryotic lifestyles in deep sea habitats

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

Pirellula and OM43 are among the dominant lineages identified in an Oregon coast diatom bloom

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

Piezophilic adaptation: a genomic point of view

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

Genomic islands and the ecology and evolution of Prochlorococcus.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

Community genomics among stratified microbial assemblages in the ocean's interior

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

ProtTest: selection of best-fit models of protein evolution

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

MUSCLE: multiple sequence alignment with high accuracy and high throughput

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

Environmental genome shotgun sequencing of the Sargasso Sea

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

SAR11 clade dominates ocean surface bacterioplankton communities.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

Archaeal dominance in the mesopelagic zone of the Pacific Ocean

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

Sulfite:Cytochrome c oxidoreductase from Thiobacillus novellus. Purification, characterization, and molecular biology of a heterodimeric member of the sulfite oxidase family

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

A novel membrane protein influencing cell shape and multicellular swarming of Proteus mirabilis

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

A novel delta-subdivision proteobacterial lineage from the lower ocean surface layer

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

Diversity and depth-specific distribution of SAR11 cluster rRNA genes from marine planktonic bacteria

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

Detection of stratified microbial populations related to Chlorobium and Fibrobacter species in the Atlantic and Pacific oceans.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

16S rRNA genes reveal stratified open ocean bacterioplankton populations related to the Green Non-Sulfur bacteria

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

A cryptic sulfur cycle in oxygen-minimum-zone waters off the Chilean coast.

4 July 2018

1 reference

https://api.crossref.org/works/10.1038%2FISMEJ.2013.243

Nutrient requirements for growth of the extreme oligotroph 'Candidatus Pelagibacter ubique' HTCC1062 on a defined medium

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FISMEJ.2013.243

DNA sequence quality trimming and vector removal.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FISMEJ.2013.243

Compositional differences in particle-associated and free-living microbial assemblages from an extreme deep-ocean environment.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FISMEJ.2013.243

Comparative genomics of two ecotypes of the marine planktonic copiotroph Alteromonas macleodii suggests alternative lifestyles associated with different kinds of particulate organic matter

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FISMEJ.2013.243

Single-cell sequencing in its prime

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FISMEJ.2013.243

Basin-scale patterns in the abundance of SAR11 subclades, marine Actinobacteria (OM1), members of the Roseobacter clade and OCS116 in the South Atlantic

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FISMEJ.2013.243

A comparison of homologous recombination rates in bacteria and archaea.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FISMEJ.2013.243

Adaptation of the membrane lipids of a deep-sea bacterium to changes in hydrostatic pressure

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4069386

Emerging concepts on microbial processes in the bathypelagic ocean – ecology, biogeochemistry, and genomics

30 October 2018

1 reference

https://api.crossref.org/works/10.1038%2FISMEJ.2013.243

Major contribution of autotrophy to microbial carbon cycling in the deep North Atlantic’s interior

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FISMEJ.2013.243

Mesopelagic zone ecology and biogeochemistry – a synthesis

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FISMEJ.2013.243

Direct electrochemistry of a bacterial sulfite dehydrogenase

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24451205

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Complete genome sequence of the facultatively chemolithoautotrophic and methylotrophic alpha Proteobacterium Starkeya novella type strain (ATCC 8093T)

1 reference

https://api.crossref.org/works/10.1038%2FISMEJ.2013.243

inferred from DOI database lookup

7 January 2021

based on heuristic

Identifiers

DOI

10.1038/ISMEJ.2013.243

1 reference

Dimensions Publication ID

29 July 2017

0 references

1 reference

29 July 2017

1 reference