Denef, Vincent J: search on Z-Library

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1

Giant virus diversity and host interactions through global metagenomics

Schulz, Frederik, Roux, Simon, Paez-Espino, David, Jungbluth, Sean, Walsh, David A., Denef, Vincent J., McMahon, Katherine D., Konstantinidis, Konstantinos T., Eloe-Fadrosh, Emiley A., Kyrpides, Nikos

Journal:

Year:

2020

File:

PDF, 8.05 MB

2020

2

Population Genomic Analysis of Strain Variation in Leptospirillum Group II Bacteria Involved in Acid Mine Drainage Formation

Simmons, Sheri L., DiBartolo, Genevieve, Denef, Vincent J., Goltsman, Daniela S. Aliaga, Thelen, Michael P., Banfield, Jillian F., Eisen, Jonathan A.

Journal:

Year:

2008

Language:

english

File:

PDF, 957 KB

english, 2008

3

RNA Preservation Agents and Nucleic Acid Extraction Method Bias Perceived Bacterial Community Composition

McCarthy, Ann, Chiang, Edna, Schmidt, Marian L., Denef, Vincent J., Green, Stefan J.

Journal:

Year:

2015

Language:

english

File:

PDF, 728 KB

english, 2015

4

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

VerBerkmoes, Nathan C., Denef, Vincent J., Hettich, Robert L., Banfield, Jillian F.

Journal:

Nature Reviews Microbiology

Year:

2009

Language:

english

File:

PDF, 494 KB

english, 2009

5

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

Props, Ruben, Schmidt, Marian L., Heyse, Jasmine, Vanderploeg, Henry A., Boon, Nico, Denef, Vincent J.

Journal:

Environmental Microbiology

Year:

2017

Language:

english

File:

PDF, 566 KB

english, 2017

6

Genome Evolution and Host Microbiome Shifts Correspond with Intraspecific Niche Divergence within Harmful Algal Bloom‐Forming Microcystis aeruginosa

Jackrel, Sara L., White, Jeffrey D., Evans, Jacob T., Buffin, Kyle, Hayden, Kristen, Sarnelle, Orlando, Denef, Vincent J.

Journal:

Molecular Ecology

Year:

2019

File:

PDF, 1018 KB

2019

7

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

Denef, Vincent J., Fujimoto, Masanori, Berry, Michelle A., Schmidt, Marian L.

Journal:

Frontiers in Microbiology

Year:

2016

Language:

english

File:

PDF, 4.56 MB

english, 2016

8

Environmentally relevant parameters affecting PCB degradation: carbon source- and growth phase-mitigated effects of the expression of the biphenyl pathway and associated genes inBurkholderia xenovoransLB400

J. Jacob Parnell, Vincent J. Denef, Joonhong Park, Tamara Tsoi, James M. Tiedje

Journal:

Year:

2010

Language:

english

File:

PDF, 266 KB

english, 2010

9

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

Schmidt, Marian L., White, Jeffrey D., Denef, Vincent J.

Journal:

Environmental Microbiology

Year:

2016

Language:

english

File:

PDF, 810 KB

english, 2016

10

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

Wu, Chia-Chen, Ghosh, Sudeshna, Martin, Kelly J., Pinto, Ameet J., Denef, Vincent J., Olson, Terese M., Love, Nancy G.

Journal:

Environmental Science Water Research & Technology

Year:

2017

Language:

english

File:

PDF, 2.40 MB

english, 2017

11

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

Denef, Vincent J, Mueller, Ryan S, Banfield, Jillian F

Journal:

The ISME Journal

Year:

2010

Language:

english

File:

PDF, 825 KB

english, 2010

12

Temperature and Nutrient Levels Correspond with Lineage-Specific Microdiversification in the Ubiquitous and Abundant Freshwater Genus Limnohabitans

Props, Ruben, Denef, Vincent J., Nojiri, Hideaki

Journal:

Applied and Environmental Microbiology

Year:

2020

File:

PDF, 4.28 MB

2020

13

Host specificity of microbiome assembly and its fitness effects in phytoplankton

Jackrel, Sara L., Yang, Jinny W., Schmidt, Kathryn C., Denef, Vincent J.

Journal:

The ISME Journal

Year:

2020

File:

PDF, 1.43 MB

2020

14

The dynamic genetic repertoire of microbial communities

Paul Wilmes, Sheri L. Simmons, Vincent J. Denef, Jillian F. Banfield

Journal:

FEMS Microbiology Reviews

Year:

2009

Language:

english

File:

PDF, 1.00 MB

english, 2009

15

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

Schmidt, Kathryn C., Jackrel, Sara L., Smith, Derek J., Dick, Gregory J., Denef, Vincent J.

Journal:

Year:

2020

File:

PDF, 2.40 MB

2020

16

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

Schmidt, Marian L, Biddanda, Bopaiah A, Weinke, Anthony D, Chiang, Edna, Januska, Fallon, Props, Ruben, Denef, Vincent J

Journal:

FEMS Microbiology Ecology

Year:

2020

Language:

english

File:

PDF, 2.32 MB

english, 2020

17

Microbiomes Reduce Their Hostâs Sensitivity to Interspecific Interactions

Jackrel, Sara L., Schmidt, Kathryn C., Cardinale, Bradley J., Denef, Vincent J., Cooper, Vaughn S.

Journal:

Year:

2020

File:

PDF, 766 KB

2020

18

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

Belnap, Christopher P, Pan, Chongle, Denef, Vincent J, Samatova, Nagiza F, Hettich, Robert L, Banfield, Jillian F

Journal:

The ISME Journal

Year:

2011

Language:

english

File:

PDF, 526 KB

english, 2011

19

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

Berry, Michelle A., White, Jeffrey D., Davis, Timothy W., Jain, Sunit, Johengen, Thomas H., Dick, Gregory J., Sarnelle, Orlando, Denef, Vincent J.

Journal:

Frontiers in Microbiology

Year:

2017

Language:

english

File:

PDF, 1.16 MB

english, 2017

20

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

Mueller, Ryan S, Denef, Vincent J, Kalnejais, Linda H, Suttle, K Blake, Thomas, Brian C, Wilmes, Paul, Smith, Richard L, Nordstrom, D Kirk, McCleskey, R Blaine, Shah, Manesh B, VerBerkmoes, Nathan C,

Journal:

Molecular Systems Biology

Year:

2010

Language:

english

File:

PDF, 2.01 MB

english, 2010

21

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

Cory, Rose M., Davis, Timothy W., Dick, Gregory J., Johengen, Thomas, Denef, Vincent J., Berry, Michelle A., Page, Sarah E., Watson, Susan B., Yuhas, Kate, Kling, George W.

Journal:

Frontiers in Marine Science

Year:

2016

Language:

english

File:

PDF, 2.23 MB

english, 2016

22

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

Vincent J. Denef, Nathan C. VerBerkmoes, Manesh B. Shah, Paul Abraham, Mark Lefsrud, Robert L. Hettich, Jillian F. Banfield

Journal:

Environmental Microbiology

Year:

2009

Language:

english

File:

PDF, 19.75 MB

english, 2009

23

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

Yelton, Alexis P, Comolli, Luis R, Justice, Nicholas B, Castelle, Cindy, Denef, Vincent J, Thomas, Brian C, Banfield, Jillian F

Journal:

Year:

2013

Language:

english

File:

PDF, 585 KB

english, 2013

24

Chloroflexi CL500-11 populations that predominate deep lake hypolimnion bacterioplankton rely on nitrogen-rich DOM metabolism and C1 compound oxidation.

Denef, Vincent J., Mueller, Ryan S., Chiang, Edna, Liebig, James R., Vanderploeg, Henry A.

Journal:

Applied and Environmental Microbiology

Year:

2015

Language:

english

File:

PDF, 2.36 MB

english, 2015

25

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

Berry, Michelle A., Davis, Timothy W., Cory, Rose M., Duhaime, Melissa B., Johengen, Thomas H., Kling, George W., Marino, John A., Den Uyl, Paul A., Gossiaux, Duane, Dick, Gregory J., Denef, Vincent J

Journal:

Environmental Microbiology

Year:

2017

Language:

english

File:

PDF, 1.50 MB

english, 2017

26

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

Michael J. Morowitz, Vincent J. Denef, Elizabeth K. Costello, Brian C. Thomas, Valeriy Poroyko, David A. Relman, Jillian F. Banfield and Jeffrey I. Gordon

Journal:

Proceedings of the National Academy of Sciences

Year:

2011

Language:

english

File:

PDF, 1.65 MB

english, 2011

27

Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria

Lo, Ian, Denef, Vincent J., VerBerkmoes, Nathan C., Shah, Manesh B., Goltsman, Daniela, DiBartolo, Genevieve, Tyson, Gene W., Allen, Eric E., Ram, Rachna J., Detter, J. Chris

Journal:

Year:

2007

Language:

english

File:

PDF, 2.29 MB

english, 2007

28

Spatiotemporal distribution of bacterioplankton functional groups along a freshwater estuary to pelagic gradient in Lake Michigan

Fujimoto, Masanori, Cavaletto, Joann, Liebig, James R., McCarthy, Ann, Vanderploeg, Henry A., Denef, Vincent J.

Journal:

Journal of Great Lakes Research

Year:

2016

Language:

english

File:

PDF, 3.99 MB

english, 2016

29

Ecological engineering helps maximize function in algal oil production

Jackrel, Sara L., Narwani, Anita, Bentlage, Bastian, Levine, Robert B., Hietala, David C., Savage, Phillip E., Oakley, Todd H., Denef, Vincent J., Cardinale, Bradley J.

Journal:

Applied and Environmental Microbiology

Year:

2018

Language:

english

File:

PDF, 2.26 MB

english, 2018

30

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

Cory, Rose M., Davis, Timothy W., Dick, Gregory J., Johengen, Tom, Denef, Vincent J., Berry, Michelle, Page, Sarah E., Watson, Susan B., Yuhas, Kate, Kling, George W.

Journal:

Frontiers in Marine Science

Year:

2017

Language:

english

File:

PDF, 162 KB

english, 2017

31

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

Vincent J. Denef, Joonhong Park, Jorge L. M. Rodrigues, Tamara V. Tsoi, Syed A. Hashsham, James M. Tiedje

Journal:

Environmental Microbiology

Year:

2003

Language:

english

File:

PDF, 468 KB

english, 2003

32

[Population Genomics] || Peering into the Genetic Makeup of Natural Microbial Populations Using Metagenomics

Denef, Vincent J.

Year:

2018

Language:

english

File:

PDF, 536 KB

english, 2018

33

Proteogenomic Basis for Ecological Divergence of Closely Related Bacteria in Natural Acidophilic Microbial Communities

Vincent J. Denef, Linda H. Kalnejais, Ryan S. Mueller, Paul Wilmes, Brett J. Baker, Brian C. Thomas, Nathan C. VerBerkmoes, Robert L. Hettich, Julian F. Banfield and Julian F. Banfield

Journal:

Proceedings of the National Academy of Sciences

Year:

2010

Language:

english

File:

PDF, 1.80 MB

english, 2010

34

To Dereplicate or Not To Dereplicate?

Evans, Jacob T., Denef, Vincent J., McMahon, Katherine

Journal:

Year:

2020

File:

PDF, 495 KB

2020

35

Implications of Strain- and Species-Level Sequence Divergence for Community and Isolate Shotgun Proteomic Analysis

Denef, Vincent J., Shah, Manesh B., VerBerkmoes, Nathan C., Hettich, Robert L., Banfield, Jillian F.

Journal:

Journal of Proteome Research

Year:

2007

Language:

english

File:

PDF, 401 KB

english, 2007

36

Persisting Viral Sequences Shape Microbial CRISPR-based Immunity

Weinberger, Ariel D., Sun, Christine L., Pluciński, Mateusz M., Denef, Vincent J., Thomas, Brian C., Horvath, Philippe, Barrangou, Rodolphe, Gilmore, Michael S., Getz, Wayne M., Banfield, Jillian F.,

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 5.31 MB

english, 2012

37

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

Denef, Vincent J., Carrick, Hunter J., Cavaletto, Joann, Chiang, Edna, Johengen, Thomas H., Vanderploeg, Henry A., Kent, Angela D.

Journal:

Year:

2017

Language:

english

File:

PDF, 645 KB

english, 2017

38

Gene Expansion and Positive Selection as Bacterial Adaptations to Oligotrophic Conditions

Props, Ruben, Monsieurs, Pieter, Vandamme, Peter, Leys, Natalie, Denef, Vincent J., Boon, Nico, Tringe, Susannah Green

Journal:

Year:

2019

File:

PDF, 2.46 MB

2019

39

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

Chiang, Edna, Schmidt, Marian L., Berry, Michelle A., Biddanda, Bopaiah A., Burtner, Ashley, Johengen, Thomas H., Palladino, Danna, Denef, Vincent J., Smidt, Hauke

Journal:

Year:

2018

Language:

english

File:

PDF, 4.25 MB

english, 2018

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