List of works - Eric E. Allen

A database of phylogenetically atypical genes in archaeal and bacterial genomes, identified using the DarkHorse algorithm

scientific article

A genomic view of trophic and metabolic diversity in clade-specific Lamellodysidea sponge microbiomes

scientific article published on 23 June 2020

Adaptive laboratory evolution of Escherichia coli K-12 MG1655 for growth at high hydrostatic pressure.

scientific article

Assembly-driven community genomics of a hypersaline microbial ecosystem

scientific article

Bacterioplankton drawdown of coral mass-spawned organic matter.

scientific article

Biosynthesis of polybrominated aromatic organic compounds by marine bacteria

scientific article

Characterization of cyanobacterial hydrocarbon composition and distribution of biosynthetic pathways

scientific article (publication date: 2014)

Community genomics in microbial ecology and evolution

scientific article

Comparative Genomics of Cyanobacterial Symbionts Reveals Distinct, Specialized Metabolism in Tropical Sponges

scientific article published on 14 May 2019

Comparative genomics uncovers the prolific and distinctive metabolic potential of the cyanobacterial genus Moorea.

scientific article published on 6 March 2017

Complete Genome Sequence of a Cylindrospermopsin-Producing Cyanobacterium, Cylindrospermopsis raciborskii CS505, Containing a Circular Chromosome and a Single Extrachromosomal Element

scientific article published on 25 August 2016

Composite Bacterial Hopanoids and Their Microbial Producers across Oxygen Gradients in the Water Column of the California Current.

scientific article

Composite bacterial hopanoids and their microbial producers across oxygen gradients in the water column of the California Current

scientific article (publication date: December 2013)

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

scientific article published on 24 November 2010

De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities

scientific article

De novo sequences of Haloquadratum walsbyi from Lake Tyrrell, Australia, reveal a variable genomic landscape.

scientific article

Diel transcriptional response of a California Current plankton microbiome to light, low iron, and enduring viral infection

scientific article published on 18 July 2019

Diploid genomic architecture of Nitzschia inconspicua, an elite biomass production diatom

scientific article published on 02 August 2021

Distinctive Archaeal Composition of an Artisanal Crystallizer Pond and Functional Insights Into Salt-Saturated Hypersaline Environment Adaptation

article

Diversity and distribution of microbial long-chain fatty acid biosynthetic genes in the marine environment

scientific article

Draft Genome Sequence of "Candidatus Halobonum tyrrellensis" Strain G22, Isolated from the Hypersaline Waters of Lake Tyrrell, Australia.

scientific article published on 12 December 2013

Dynamic viral populations in hypersaline systems as revealed by metagenomic assembly

scientific article

Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment

scientific article published on 18 August 2020

Fine scale transitions of the microbiota and metabolome along the gastrointestinal tract of herbivorous fishes

scientific article published on 23 May 2022

Genome and methylome of the oleaginous diatom Cyclotella cryptica reveal genetic flexibility toward a high lipid phenotype

scientific article

Genome dynamics in a natural archaeal population

scientific article

Genome sequence of "Candidatus Nitrosoarchaeum limnia" BG20, a low-salinity ammonia-oxidizing archaeon from the San Francisco Bay estuary

scientific article published in April 2012

Genome sequence of "Candidatus Nitrosopumilus salaria" BD31, an ammonia-oxidizing archaeon from the San Francisco Bay estuary

scientific article published in April 2012

Genome-directed isolation of the key nitrogen fixer Leptospirillum ferrodiazotrophum sp. nov. from an acidophilic microbial community

scientific article

Genomic insights into the physiology and ecology of the marine filamentous cyanobacterium Lyngbya majuscula.

scientific article

Genomic islands link secondary metabolism to functional adaptation in marine Actinobacteria

scientific article published on 28 May 2009

Going deeper: metagenome of a hadopelagic microbial community

scientific article

High-Throughput Miniaturized 16S rRNA Amplicon Library Preparation Reduces Costs while Preserving Microbiome Integrity

Impacts of the Marine Hatchery Built Environment, Water and Feed on Mucosal Microbiome Colonization Across Ontogeny in Yellowtail Kingfish, Seriola lalandi

scientific article published on 13 May 2021

Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic

scientific article published on 26 January 2012

KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples.

scientific article published on 13 March 2018

Lineages of acidophilic archaea revealed by community genomic analysis

scientific article

Meeting report: Ocean 'omics science, technology and cyberinfrastructure: current challenges and future requirements (August 20-23, 2013).

scientific article

Metabolic potential and in situ transcriptomic profiles of previously uncharacterized key microbial groups involved in coupled carbon, nitrogen, and sulfur cycling in anoxic marine zones

scientific article published on 24 March 2018

Metabolic versatility of the Riftia pachyptila endosymbiont revealed through metagenomics

scientific article published in March 2008

Metagenome sequencing of the microbial community of a solar saltern crystallizer pond at cáhuil lagoon, chile.

scientific article published on 13 November 2014

Metagenomic and lipid analyses reveal a diel cycle in a hypersaline microbial ecosystem

scientific article published on 28 April 2015

Metagenomic discovery of polybrominated diphenyl ether biosynthesis by marine sponges.

scientific article published on 20 March 2017

Microbial Community Diversity Within Sediments from Two Geographically Separated Hadal Trenches

scientific article published on 15 March 2019

Microbial ecology of Atlantic salmon, Salmo salar, hatcheries: impacts of the built environment on fish mucosal microbiota

scientific article published on 17 April 2020

Microbial effects of livestock manure fertilization on freshwater aquaculture ponds rearing tilapia (Oreochromis shiranus) and North African catfish (Clarias gariepinus)

scientific article published on 31 August 2018

Microbial life in a fjord: metagenomic analysis of a microbial mat in Chilean patagonia

scientific article

Microbiomes of Hadal Fishes across Trench Habitats Contain Similar Taxa and Known Piezophiles

scientific article published in 2022

Multi-Omic Profiling of Melophlus Sponges Reveals Diverse Metabolomic and Microbiome Architectures that Are Non-overlapping with Ecological Neighbors

scientific article published on 19 February 2020

Non-target tandem mass spectrometry enables the prioritization of anthropogenic pollutants in seawater along the northern San Diego coast

Non-targeted tandem mass spectrometry enables the visualization of organic matter chemotype shifts in coastal seawater

scientific article

Pangenomic comparison of globally distributed Poribacteria associated with sponge hosts and marine particles

scientific article published on 05 October 2018

Phenotypic and transcriptional response of Daphnia pulicaria to the combined effects of temperature and predation

scientific article published on 14 July 2022

Seasonal fluctuations in ionic concentrations drive microbial succession in a hypersaline lake community.

scientific article

Sierra Nevada mountain lake microbial communities are structured by temperature, resources and geographic location

scientific article published on 24 June 2020

Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria.

scientific article published on 7 March 2007

Structure and regulation of the omega-3 polyunsaturated fatty acid synthase genes from the deep-sea bacterium Photobacterium profundum strain SS9.

scientific article

Temporal, Environmental, and Biological Drivers of the Mucosal Microbiome in a Wild Marine Fish, Scomber japonicus

scientific article published on 20 May 2020

The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing

scientific article

The Southern Bluefin Tuna Mucosal Microbiome Is Influenced by Husbandry Method, Net Pen Location, and Anti-parasite Treatment

scientific article published on 24 August 2020

The natural product domain seeker NaPDoS: a phylogeny based bioinformatic tool to classify secondary metabolite gene diversity

scientific article

Use of plankton-derived vitamin B1 precursors, especially thiazole-related precursor, by key marine picoeukaryotic phytoplankton

scientific article published on 9 December 2016

Variation in Survival and Gut Microbiome Composition of Hatchery-Grown Native Oysters at Various Locations within the Puget Sound

scientific article published in 2022

Vertically distinct microbial communities in the Mariana and Kermadec trenches.

scientific article

Virus-host and CRISPR dynamics in Archaea-dominated hypersaline Lake Tyrrell, Victoria, Australia

scientific article

Visualizing 'omic feature rankings and log-ratios using Qurro

scientific article published on 28 April 2020

Xenorhodopsins, an enigmatic new class of microbial rhodopsins horizontally transferred between archaea and bacteria

scientific article

List of works by Eric E. Allen

A database of phylogenetically atypical genes in archaeal and bacterial genomes, identified using the DarkHorse algorithm

A genomic view of trophic and metabolic diversity in clade-specific Lamellodysidea sponge microbiomes

Adaptive laboratory evolution of Escherichia coli K-12 MG1655 for growth at high hydrostatic pressure.

Assembly-driven community genomics of a hypersaline microbial ecosystem

Bacterioplankton drawdown of coral mass-spawned organic matter.

Biosynthesis of polybrominated aromatic organic compounds by marine bacteria

Characterization of cyanobacterial hydrocarbon composition and distribution of biosynthetic pathways

Community genomics in microbial ecology and evolution

Comparative Genomics of Cyanobacterial Symbionts Reveals Distinct, Specialized Metabolism in Tropical Sponges

Comparative genomics uncovers the prolific and distinctive metabolic potential of the cyanobacterial genus Moorea.

Complete Genome Sequence of a Cylindrospermopsin-Producing Cyanobacterium, Cylindrospermopsis raciborskii CS505, Containing a Circular Chromosome and a Single Extrachromosomal Element

Composite Bacterial Hopanoids and Their Microbial Producers across Oxygen Gradients in the Water Column of the California Current.

Composite bacterial hopanoids and their microbial producers across oxygen gradients in the water column of the California Current

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

De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities

De novo sequences of Haloquadratum walsbyi from Lake Tyrrell, Australia, reveal a variable genomic landscape.

Diel transcriptional response of a California Current plankton microbiome to light, low iron, and enduring viral infection

Diploid genomic architecture of Nitzschia inconspicua, an elite biomass production diatom

Distinctive Archaeal Composition of an Artisanal Crystallizer Pond and Functional Insights Into Salt-Saturated Hypersaline Environment Adaptation

Diversity and distribution of microbial long-chain fatty acid biosynthetic genes in the marine environment

Draft Genome Sequence of "Candidatus Halobonum tyrrellensis" Strain G22, Isolated from the Hypersaline Waters of Lake Tyrrell, Australia.

Dynamic viral populations in hypersaline systems as revealed by metagenomic assembly

Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment

Fine scale transitions of the microbiota and metabolome along the gastrointestinal tract of herbivorous fishes

Genome and methylome of the oleaginous diatom Cyclotella cryptica reveal genetic flexibility toward a high lipid phenotype

Genome dynamics in a natural archaeal population

Genome sequence of "Candidatus Nitrosoarchaeum limnia" BG20, a low-salinity ammonia-oxidizing archaeon from the San Francisco Bay estuary

Genome sequence of "Candidatus Nitrosopumilus salaria" BD31, an ammonia-oxidizing archaeon from the San Francisco Bay estuary

Genome-directed isolation of the key nitrogen fixer Leptospirillum ferrodiazotrophum sp. nov. from an acidophilic microbial community

Genomic insights into the physiology and ecology of the marine filamentous cyanobacterium Lyngbya majuscula.

Genomic islands link secondary metabolism to functional adaptation in marine Actinobacteria

Going deeper: metagenome of a hadopelagic microbial community

High-Throughput Miniaturized 16S rRNA Amplicon Library Preparation Reduces Costs while Preserving Microbiome Integrity

Impacts of the Marine Hatchery Built Environment, Water and Feed on Mucosal Microbiome Colonization Across Ontogeny in Yellowtail Kingfish, Seriola lalandi

Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic

KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples.

Lineages of acidophilic archaea revealed by community genomic analysis

Meeting report: Ocean 'omics science, technology and cyberinfrastructure: current challenges and future requirements (August 20-23, 2013).

Metabolic potential and in situ transcriptomic profiles of previously uncharacterized key microbial groups involved in coupled carbon, nitrogen, and sulfur cycling in anoxic marine zones

Metabolic versatility of the Riftia pachyptila endosymbiont revealed through metagenomics

Metagenome sequencing of the microbial community of a solar saltern crystallizer pond at cáhuil lagoon, chile.

Metagenomic and lipid analyses reveal a diel cycle in a hypersaline microbial ecosystem

Metagenomic discovery of polybrominated diphenyl ether biosynthesis by marine sponges.

Microbial Community Diversity Within Sediments from Two Geographically Separated Hadal Trenches

Microbial ecology of Atlantic salmon, Salmo salar, hatcheries: impacts of the built environment on fish mucosal microbiota

Microbial effects of livestock manure fertilization on freshwater aquaculture ponds rearing tilapia (Oreochromis shiranus) and North African catfish (Clarias gariepinus)

Microbial life in a fjord: metagenomic analysis of a microbial mat in Chilean patagonia

Microbiomes of Hadal Fishes across Trench Habitats Contain Similar Taxa and Known Piezophiles

Multi-Omic Profiling of Melophlus Sponges Reveals Diverse Metabolomic and Microbiome Architectures that Are Non-overlapping with Ecological Neighbors

Non-target tandem mass spectrometry enables the prioritization of anthropogenic pollutants in seawater along the northern San Diego coast

Non-targeted tandem mass spectrometry enables the visualization of organic matter chemotype shifts in coastal seawater

Pangenomic comparison of globally distributed Poribacteria associated with sponge hosts and marine particles

Phenotypic and transcriptional response of Daphnia pulicaria to the combined effects of temperature and predation

Seasonal fluctuations in ionic concentrations drive microbial succession in a hypersaline lake community.

Sierra Nevada mountain lake microbial communities are structured by temperature, resources and geographic location

Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria.

Structure and regulation of the omega-3 polyunsaturated fatty acid synthase genes from the deep-sea bacterium Photobacterium profundum strain SS9.

Temporal, Environmental, and Biological Drivers of the Mucosal Microbiome in a Wild Marine Fish, Scomber japonicus

The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing

The Southern Bluefin Tuna Mucosal Microbiome Is Influenced by Husbandry Method, Net Pen Location, and Anti-parasite Treatment

The natural product domain seeker NaPDoS: a phylogeny based bioinformatic tool to classify secondary metabolite gene diversity

Use of plankton-derived vitamin B1 precursors, especially thiazole-related precursor, by key marine picoeukaryotic phytoplankton

Variation in Survival and Gut Microbiome Composition of Hatchery-Grown Native Oysters at Various Locations within the Puget Sound

Vertically distinct microbial communities in the Mariana and Kermadec trenches.

Virus-host and CRISPR dynamics in Archaea-dominated hypersaline Lake Tyrrell, Victoria, Australia

Visualizing 'omic feature rankings and log-ratios using Qurro

Xenorhodopsins, an enigmatic new class of microbial rhodopsins horizontally transferred between archaea and bacteria