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List of works by Vincent J Denef

AMD biofilms: using model communities to study microbial evolution and ecological complexity in nature.

scientific article published on 18 February 2010

Are Oligotypes Meaningful Ecological and Phylogenetic Units? A Case Study of Microcystis in Freshwater Lakes

scientific article published on 8 March 2017

Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility

scholarly article

Chloroflexi CL500-11 Populations That Predominate Deep-Lake Hypolimnion Bacterioplankton Rely on Nitrogen-Rich Dissolved Organic Matter Metabolism and C1 Compound Oxidation

scientific article published on 18 December 2015

Community genomic and proteomic analyses of chemoautotrophic iron-oxidizing "Leptospirillum rubarum" (Group II) and "Leptospirillum ferrodiazotrophum" (Group III) bacteria in acid mine drainage biofilms

scientific article

Comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaea

scientific article

Complete genome sequence of the phenanthrene-degrading soil bacterium Delftia acidovorans Cs1-4

scientific article published on 15 August 2015

Coping with polychlorinated biphenyl (PCB) toxicity: Physiological and genome-wide responses of Burkholderia xenovorans LB400 to PCB-mediated stress

scientific article

Correction for Props et al., "Gene Expansion and Positive Selection as Bacterial Adaptations to Oligotrophic Conditions"

scientific article published on 25 November 2020

Correction: Verrucomicrobia are prevalent in north-temperate freshwater lakes and display class-level preferences between lake habitats

scientific article published in PLoS ONE

Cyanobacterial harmful algal blooms are a biological disturbance to Western Lake Erie bacterial communities

scientific article published on 27 December 2016

Ecological distribution and population physiology defined by proteomics in a natural microbial community.

scientific article

Ecological engineering helps maximize function in algal oil production

scientific article published on 17 July 2018

Environmentally relevant parameters affecting PCB degradation: carbon source- and growth phase-mitigated effects of the expression of the biphenyl pathway and associated genes in Burkholderia xenovorans LB400.

scientific article published on 12 August 2009

Flow cytometric monitoring of bacterioplankton phenotypic diversity predicts high population-specific feeding rates by invasive dreissenid mussels

scientific article published on 13 October 2017

Gene Expansion and Positive Selection as Bacterial Adaptations to Oligotrophic Conditions

article

Genome evolution and host-microbiome shifts correspond with intraspecific niche divergence within harmful algal bloom-forming Microcystis aeruginosa

scientific article published on 22 August 2019

Genome sequences of lower Great Lakes Microcystis sp. reveal strain-specific genes that are present and expressed in western Lake Erie blooms

scientific article published on 11 October 2017

Genotype and host microbiome alter competitive interactions between Microcystis aeruginosa and Chlorella sorokiniana

scientific article published on 04 November 2020

Giant virus diversity and host interactions through global metagenomics

scientific article published on 22 January 2020

Host specificity of microbiome assembly and its fitness effects in phytoplankton

scientific article published on 23 October 2020

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses

scientific article published on 30 October 2016

Implications of strain- and species-level sequence divergence for community and isolate shotgun proteomic analysis.

scientific article published on 28 June 2007

In situ evolutionary rate measurements show ecological success of recently emerged bacterial hybrids.

scientific article published in April 2012

Lake Bacterial Assemblage Composition Is Sensitive to Biological Disturbance Caused by an Invasive Filter Feeder ⬇️

scientific article published on 31 May 2017

Metabolome-proteome differentiation coupled to microbial divergence

scientific article

Microbiomes Reduce Their Host's Sensitivity to Interspecific Interactions

scientific article published on 21 January 2020

Microhabitats are associated with diversity-productivity relationships in freshwater bacterial communities

scientific article published on 01 April 2020

Microhabitats shape diversity-productivity relationships in freshwater bacterial communities

Persisting viral sequences shape microbial CRISPR-based immunity

scientific article

Phylogenetic conservation of freshwater lake habitat preference varies between abundant bacterioplankton phyla

scientific article published on 3 December 2015

Population genomic analysis of strain variation in Leptospirillum group II bacteria involved in acid mine drainage formation

scientific article (publication date: 22 July 2008)

Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities.

scientific article

Proteomics-inferred genome typing (PIGT) demonstrates inter-population recombination as a strategy for environmental adaptation.

scientific article published on 23 September 2008

Quantitative proteomic analyses of the response of acidophilic microbial communities to different pH conditions

scientific article

RNA preservation agents and nucleic acid extraction method bias perceived bacterial community composition

scientific article

Randomized Lasso Links Microbial Taxa with Aquatic Functional Groups Inferred from Flow Cytometry

scientific article published on 10 September 2019

Seasonal Dynamics in Dissolved Organic Matter, Hydrogen Peroxide, and Cyanobacterial Blooms in Lake Erie

article

Seasonal Succession Leads to Habitat-Dependent Differentiation in Ribosomal RNA:DNA Ratios among Freshwater Lake Bacteria

scientific article published on 29 April 2016

Strain-resolved community genomic analysis of gut microbial colonization in a premature infant

scientific article

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

scientific article published on 7 March 2007

Systems biology: Functional analysis of natural microbial consortia using community proteomics

scientific article published on March 2009

Temperature and nutrient levels correspond with lineage-specific microdiversification in the ubiquitous and abundant Limnohabitans freshwater genus

scientific article published on 13 March 2020

The dynamic genetic repertoire of microbial communities

scientific article (publication date: 2009)

The microbial colonization of activated carbon block point-of-use (PoU) filters with and without chlorinated phenol disinfection by-products

scientific article

To Dereplicate or Not To Dereplicate?

scientific article published on 20 May 2020

Using machine learning to associate bacterial taxa with functional groups through flow cytometry, 16S rRNA gene sequencing, and productivity data

article

Validation of a more sensitive method for using spotted oligonucleotide DNA microarrays for functional genomics studies on bacterial communities

scientific article published in October 2003

Verrucomicrobia are prevalent in north-temperate freshwater lakes and display class-level preferences between lake habitats.

scientific article published on 28 March 2018

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