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List of works by Ramunas Stepanauskas

129I in Swedish rivers: distribution and sources

scientific article published on 01 June 2003

A compendium of bacterial and archaeal single-cell amplified genomes from oxygen deficient marine waters

scientific article published on 27 May 2023

A virus or more in (nearly) every cell: ubiquitous networks of virus-host interactions in extreme environments.

scientific article published on 21 February 2018

Ancestral Absence of Electron Transport Chains in Patescibacteria and DPANN

scientific article published on 17 August 2020

Antibiotic resistance in the shellfish pathogen Vibrio parahaemolyticus isolated from the coastal water and sediment of Georgia and South Carolina, USA.

scientific article published in December 2008

Assembling Genomes and Mini-metagenomes from Highly Chimeric Reads

Assembling single-cell genomes and mini-metagenomes from chimeric MDA products

scientific article

Assembling the marine metagenome, one cell at a time

scientific article

Assessing the contribution of wetlands and subsided islands to dissolved organic matter and disinfection byproduct precursors in the Sacramento–San Joaquin River Delta: A geochemical approach

article

Author Correction: Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria

scientific article published on 26 March 2019

Author Correction: Improved genome recovery and integrated cell-size analyses of individual uncultured microbial cells and viral particles

scientific article published on 12 December 2017

Bacterial tolerances to metals and antibiotics in metal-contaminated and reference streams

scientific article published in November 2006

Bioavailability and sources of DOC and DON in macrophyte stands of a tropical coastal lake

Biomass of pelagic fungi in Baltic rivers

article published in 2008

Capturing diversity of marine heterotrophic protists: one cell at a time

scientific article

Capturing single cell genomes of active polysaccharide degraders: an unexpected contribution of Verrucomicrobia.

scientific article

Carboxydotrophy potential of uncultivated Hydrothermarchaeota from the subseafloor crustal biosphere

scientific article published on 07 February 2019

Cell sorting analysis of geographically separated hypersaline environments.

scientific article published on 29 January 2013

Characterization of Two Cryptic Plasmids Isolated in Haiti from Clinical Vibrio cholerae Non-O1/Non-O139.

scientific article published on 23 November 2017

Charting the Complexity of the Marine Microbiome through Single-Cell Genomics

scientific article published on 01 December 2019

Clean room microbiome complexity impacts planetary protection bioburden

scientific article published on 04 December 2021

Co-selection of antibiotic and metal resistance

scientific article

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

scientific article

Comparing effective population sizes of dominant marine alphaproteobacteria lineages

scientific article published on 5 December 2013

Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations

Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations.

scientific article published on 8 December 2017

Correction: Single-cell genomics shedding light on marine Thaumarchaeota diversification

scientific article published on 01 March 2020

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

scientific article published in February 2018

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

article

Coselection for microbial resistance to metals and antibiotics in freshwater microcosms

scientific article published in September 2006

De novo synthesis and functional analysis of the phosphatase-encoding gene acI-B of uncultured Actinobacteria from Lake Stechlin (NE Germany).

scientific article

Decontamination of MDA reagents for single cell whole genome amplification

scientific article

Decoupling of respiration rates and abundance in marine prokaryoplankton

scientific article published in December 2022

Differential Dissolved Organic Nitrogen Availability and Bacterial Aminopeptidase Activity in Limnic and Marine Waters

scientific article published in October 1999

Dissecting the dominant hot spring microbial populations based on community-wide sampling at single-cell genomic resolution

scientific article published in May 2022

Diverse Marinimicrobia bacteria may mediate coupled biogeochemical cycles along eco-thermodynamic gradients.

scientific article published on 15 November 2017

Diversification and niche adaptations of Nitrospina-like bacteria in the polyextreme interfaces of Red Sea brines.

scientific article published on 11 December 2015

Diversification of methanogens into hyperalkaline serpentinizing environments through adaptations to minimize oxidant limitation

scientific article published on 30 November 2020

Ecological Genomics of the Uncultivated Marine Roseobacter Lineage CHAB-I-5.

scientific article

Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics

scientific article published on 29 August 2014

Elevated microbial tolerance to metals and antibiotics in metal-contaminated industrial environments

scientific article published in May 2005

Emergence of trait variability through the lens of nitrogen assimilation in

scientific article published on 01 February 2019

Evolutionary analysis of a streamlined lineage of surface ocean Roseobacters

scientific article

Evolutionary stasis of a deep subsurface microbial lineage

scientific article published in October 2021

Excess of non-conservative amino acid changes in marine bacterioplankton lineages with reduced genomes.

scientific article published on 12 June 2017

Expansion of the global RNA virome reveals diverse clades of bacteriophages

scientific article published in October 2022

Exploring Microdiversity in Novel Kordia sp. (Bacteroidetes) with Proteorhodopsin from the Tropical Indian Ocean via Single Amplified Genomes

scientific article published on 25 July 2017

Flow-cytometric cell sorting and subsequent molecular analyses for culture-independent identification of bacterioplankton involved in dimethylsulfoniopropionate transformations.

scientific article published on March 2005

Four Draft Single-Cell Genome Sequences of Novel, Nearly Identical Strains Isolated from the Continental Deep Subsurface

scientific article published on 14 March 2019

Fundamental differences in diversity and genomic population structure between Atlantic and Pacific Prochlorococcus.

scientific article published on 19 May 2017

Gene exchange networks define species-like units in marine prokaryotes

scientific article published on 10 September 2020

Genome sequencing of a single cell of the widely distributed marine subsurface Dehalococcoidia, phylum Chloroflexi

scientific article published on 22 August 2013

Genomic Analysis of the Yet-Uncultured Binatota Reveals Broad Methylotrophic, Alkane-Degradation, and Pigment Production Capacities

scientific article published on 18 May 2021

Genomic Characterization of Candidate Division LCP-89 Reveals an Atypical Cell Wall Structure, Microcompartment Production, and Dual Respiratory and Fermentative Capacities

scientific article published on 02 May 2019

Genomic Comparison of Two Family-Level Groups of the Uncultivated NAG1 Archaeal Lineage from Chemically and Geographically Disparate Hot Springs.

scientific article published on 31 October 2017

Genomic Variation Influences Fitness in Marine Hydrothermal Systems

scientific article published in 2021

Genomic and metabolic diversity of Marine Group I Thaumarchaeota in the mesopelagic of two subtropical gyres

scientific article published on 17 April 2014

Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems

scientific article published on 06 April 2017

Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems

Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems

Genomic exploration of individual giant ocean viruses

scientific article published on 12 May 2017

Genomic insights into the uncultivated marine Zetaproteobacteria at Loihi Seamount

scientific article

Genomic sequencing of single microbial cells from environmental samples

scientific article

Genomics insights into ecotype formation of ammonia-oxidizing archaea in the deep ocean

scientific article published on 31 January 2019

Hidden diversity in honey bee gut symbionts detected by single-cell genomics

scientific article

Hiding in Plain Sight: The Globally Distributed Bacterial Candidate Phylum PAUC34f

scientific article published on 12 March 2020

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

scientific article

Hydrogen-based metabolism - An ancestral trait in lineages sibling to the Cyanobacteria

Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria

scientific article published in Nature Communications

Hyperactive nanobacteria with host-dependent traits pervade Omnitrophota ⬇️

scientific article published in April 2023

Improved genome recovery and integrated cell-size analyses of individual uncultured microbial cells and viral particles.

scientific article

Influence of industrial contamination on mobile genetic elements: class 1 integron abundance and gene cassette structure in aquatic bacterial communities

scientific article published on 14 February 2008

Insights into the dynamics between viruses and their hosts in a hot spring microbial mat

scientific article published on 13 July 2020

Insights into the environmental resistance gene pool from the genome sequence of the multidrug-resistant environmental isolate Escherichia coli SMS-3-5.

scientific article

Insights into the metabolism, lifestyle and putative evolutionary history of the novel archaeal phylum 'Diapherotrites'

scientific article

Insights into the phylogeny and coding potential of microbial dark matter

scientific article

Landscape scale controls on the vascular plant component of dissolved organic carbon across a freshwater delta

article

Life strategies for Aminicenantia in subseafloor oceanic crust

scientific article published in September 2023

Major role of nitrite-oxidizing bacteria in dark ocean carbon fixation.

scientific article

Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time

scientific article

Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton

scientific article

Methylotrophy, alkane-degradation, and pigment production as defining features of the globally distributed yet-uncultured phylum Binatota

scientific article published on 2 October 2020

Microbial Diversity and Function in Shallow Subsurface Sediment and Oceanic Lithosphere of the Atlantis Massif

scientific article published on 03 August 2021

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

scientific article

Multi-site analysis reveals widespread antibiotic resistance in the marine pathogen Vibrio vulnificus.

scientific article published on 19 July 2008

Nanoarchaeota, Their Sulfolobales Host, and Nanoarchaeota Virus Distribution across Yellowstone National Park Hot Springs

scientific article

New abundant microbial groups in aquatic hypersaline environments

scientific article

Novel Integrative Elements and Genomic Plasticity in Ocean Ecosystems

scientific article published on 08 April 2021

Novel integrative elements and genomic plasticity in ocean ecosystems

scientific article published on 28 December 2020

Novel integrative elements and genomic plasticity in ocean ecosystems

scientific article published in January 2023

Obtaining genomes from uncultivated environmental microorganisms using FACS-based single-cell genomics

scientific article

Occurrence and degradation of peptidoglycan in aquatic environments.

scientific article published in December 2003

Oceanic Crustal Fluid Single Cell Genomics Complements Metagenomic and Metatranscriptomic Surveys With Orders of Magnitude Less Sample Volume

scientific article published in 2021

Omnitrophota encompasses diverse and hyperactive nanobacteria: Potential metabolisms and host-dependent lifestyles

scientific article published on 2 March 2022

Organic matter processing by microbial communities throughout the Atlantic water column as revealed by metaproteomics.

scientific article published on 18 December 2017

Pangenomics Analysis Reveals Diversification of Enzyme Families and Niche Specialization in Globally Abundant SAR202 Bacteria

scientific article published on 07 January 2020

Phosphonate production by marine microbes: Exploring new sources and potential function

scientific article published on 07 March 2022

Phosphonate production by marine microbes: exploring new sources and potential function

scientific article published on 5 November 2020

Phylogenetically and functionally diverse microorganisms reside under the Ross Ice Shelf

scientific article

Phylogenomics suggests oxygen availability as a driving force in Thaumarchaeota evolution

scientific article published on 25 April 2019

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

scientific article

Predominant archaea in marine sediments degrade detrital proteins.

scientific article published on 27 March 2013

Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean

scientific article published on 25 June 2013

Productivity and salinity structuring of the microplankton revealed by comparative freshwater metagenomics

scientific article

Prokaryotic Super Program Advisory Committee DOE Joint Genome Institute, Walnut Creek, CA, March 27, 2013.

scientific article published on 30 July 2013

Re-defining microbial diversity from its single-celled building blocks

scientific article published on February 2015

Replicated life-history patterns and subsurface origins of the bacterial sister phyla Nitrospirota and Nitrospinota

scientific article published in June 2023

Report of the workshop for life detection in samples from Mars

Rokubacteria: Genomic Giants among the Uncultured Bacterial Phyla

scientific article published on 28 November 2017

SAR202 Genomes from the Dark Ocean Predict Pathways for the Oxidation of Recalcitrant Dissolved Organic Matter

scientific article published on 18 April 2017

Single Cell Genomics Reveals Viruses Consumed by Marine Protists

scientific article published on 24 September 2020

Single Cell Genomics-Based Analysis of Gene Content and Expression of Prophages in a Diffuse-Flow Deep-Sea Hydrothermal System

scientific article published on 12 June 2019

Single cell genome sequencing of laboratory mouse microbiota improves taxonomic and functional resolution of this model microbial community

scientific article published on 13 April 2022

Single cell genomes of Prochlorococcus, Synechococcus, and sympatric microbes from diverse marine environments

scientific article published on 04 September 2018

Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population

scientific article published on 22 April 2015

Single cell genomics yields a wide diversity of small planktonic protists across major ocean ecosystems

scientific article published on 15 April 2019

Single cell genomics: an individual look at microbes

scientific article

Single-Cell Genome and Group-Specific dsrAB Sequencing Implicate Marine Members of the Class Dehalococcoidia (Phylum Chloroflexi) in Sulfur Cycling

scientific article published on 03 May 2016

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

scientific article

Single-cell genomics of a rare environmental alphaproteobacterium provides unique insights into Rickettsiaceae evolution

scientific article published on 7 April 2015

Single-cell genomics of co-sorted Nanoarchaeota suggests novel putative host associations and diversification of proteins involved in symbiosis

scientific article published on 17 September 2018

Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans

scientific article published on 22 January 2018

Single-cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade

scientific article

Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus.

scientific article

Single-cell genomics reveals metabolic strategies for microbial growth and survival in an oligotrophic aquifer

scientific article published on February 2014

Single-cell genomics reveals organismal interactions in uncultivated marine protists.

scientific article

Single-cell genomics shedding light on marine Thaumarchaeota diversification.

scientific article published on 7 November 2013

Single-cell genomics-based analysis of virus-host interactions in marine surface bacterioplankton

scientific article

Sources, bioavailability, and photoreactivity of dissolved organic carbon in the Sacramento–San Joaquin River Delta

article

Species-resolved, single-cell respiration rates reveal dominance of sulfate reduction in a deep continental subsurface ecosystem

scientific article published on 9 April 2024

Strategies to improve reference databases for soil microbiomes

scientific article published on 09 December 2016

Synthase-Selective Exploration of a Tunicate Microbiome by Activity-Guided Single-Cell Genomics

scientific article published on 21 May 2021

Targeted sorting of single virus-infected cells of the coccolithophore Emiliania huxleyi

scientific article

The cyanobacterium has divergent light-harvesting antennae and may have evolved in a low-oxygen ocean

scientific article published on 16 March 2021

Thousands of small, novel genes predicted in global phage genomes

scientific article published in 2022

Tuning fresh: radiation through rewiring of central metabolism in streamlined bacteria

scientific article published on 19 January 2016

Ubiquitous Gammaproteobacteria dominate dark carbon fixation in coastal sediments.

scientific article published on 12 February 2016

Unexpected genomic features in widespread intracellular bacteria: evidence for motility of marine chlamydiae

scientific article published on 23 June 2017

Unveiling in situ interactions between marine protists and bacteria through single cell sequencing

scientific article published on 22 September 2011

Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition

scientific article

What's new is old: resolving the identity of Leptothrix ochracea using single cell genomics, pyrosequencing and FISH

scientific article published in 2011

Wiretapping into microbial interactions by single cell genomics

scientific article

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