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Items: 38

1.

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

Rubbens P, Schmidt ML, Props R, Biddanda BA, Boon N, Waegeman W, Denef VJ.

mSystems. 2019 Sep 10;4(5). pii: e00093-19. doi: 10.1128/mSystems.00093-19.

2.

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

Jackrel SL, White JD, Evans JT, Buffin K, Hayden K, Sarnelle O, Denef VJ.

Mol Ecol. 2019 Sep;28(17):3994-4011. doi: 10.1111/mec.15198. Epub 2019 Aug 22.

PMID:
31344288
3.

Gene Expansion and Positive Selection as Bacterial Adaptations to Oligotrophic Conditions.

Props R, Monsieurs P, Vandamme P, Leys N, Denef VJ, Boon N.

mSphere. 2019 Feb 6;4(1). pii: e00011-19. doi: 10.1128/mSphereDirect.00011-19.

4.

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

Chiang E, Schmidt ML, Berry MA, Biddanda BA, Burtner A, Johengen TH, Palladino D, Denef VJ.

PLoS One. 2018 Oct 22;13(10):e0206396. doi: 10.1371/journal.pone.0206396. eCollection 2018.

5.

Ecological Engineering Helps Maximize Function in Algal Oil Production.

Jackrel SL, Narwani A, Bentlage B, Levine RB, Hietala DC, Savage PE, Oakley TH, Denef VJ, Cardinale BJ.

Appl Environ Microbiol. 2018 Jul 17;84(15). pii: e00953-18. doi: 10.1128/AEM.00953-18. Print 2018 Aug 1.

6.

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

Chiang E, Schmidt ML, Berry MA, Biddanda BA, Burtner A, Johengen TH, Palladino D, Denef VJ.

PLoS One. 2018 Mar 28;13(3):e0195112. doi: 10.1371/journal.pone.0195112. eCollection 2018. Erratum in: PLoS One. 2018 Oct 22;13(10):e0206396.

7.

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

Props R, Schmidt ML, Heyse J, Vanderploeg HA, Boon N, Denef VJ.

Environ Microbiol. 2018 Feb;20(2):521-534. doi: 10.1111/1462-2920.13953. Epub 2017 Nov 3.

8.

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

Meyer KA, Davis TW, Watson SB, Denef VJ, Berry MA, Dick GJ.

PLoS One. 2017 Oct 11;12(10):e0183859. doi: 10.1371/journal.pone.0183859. eCollection 2017.

9.

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

Denef VJ, Carrick HJ, Cavaletto J, Chiang E, Johengen TH, Vanderploeg HA.

mSphere. 2017 May 31;2(3). pii: e00189-17. doi: 10.1128/mSphere.00189-17. eCollection 2017 May-Jun.

10.

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

Berry MA, White JD, Davis TW, Jain S, Johengen TH, Dick GJ, Sarnelle O, Denef VJ.

Front Microbiol. 2017 Mar 8;8:365. doi: 10.3389/fmicb.2017.00365. eCollection 2017.

11.

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

Berry MA, Davis TW, Cory RM, Duhaime MB, Johengen TH, Kling GW, Marino JA, Den Uyl PA, Gossiaux D, Dick GJ, Denef VJ.

Environ Microbiol. 2017 Mar;19(3):1149-1162. doi: 10.1111/1462-2920.13640. Epub 2017 Feb 16.

12.

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

Denef VJ, Fujimoto M, Berry MA, Schmidt ML.

Front Microbiol. 2016 Apr 29;7:606. doi: 10.3389/fmicb.2016.00606. eCollection 2016.

13.

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

Denef VJ, Mueller RS, Chiang E, Liebig JR, Vanderploeg HA.

Appl Environ Microbiol. 2015 Dec 18;82(5):1423-32. doi: 10.1128/AEM.03014-15.

14.

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

Schmidt ML, White JD, Denef VJ.

Environ Microbiol. 2016 Apr;18(4):1212-26. doi: 10.1111/1462-2920.13143. Epub 2016 Jan 18.

PMID:
26631909
15.

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

Shetty AR, de Gannes V, Obi CC, Lucas S, Lapidus A, Cheng JF, Goodwin LA, Pitluck S, Peters L, Mikhailova N, Teshima H, Han C, Tapia R, Land M, Hauser LJ, Kyrpides N, Ivanova N, Pagani I, Chain PS, Denef VJ, Woyke T, Hickey WJ.

Stand Genomic Sci. 2015 Aug 15;10:55. doi: 10.1186/s40793-015-0041-x. eCollection 2015.

16.

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

McCarthy A, Chiang E, Schmidt ML, Denef VJ.

PLoS One. 2015 Mar 23;10(3):e0121659. doi: 10.1371/journal.pone.0121659. eCollection 2015.

17.

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

Yelton AP, Comolli LR, Justice NB, Castelle C, Denef VJ, Thomas BC, Banfield JF.

BMC Genomics. 2013 Jul 17;14:485. doi: 10.1186/1471-2164-14-485.

18.

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

Denef VJ, Banfield JF.

Science. 2012 Apr 27;336(6080):462-6. doi: 10.1126/science.1218389.

19.

Persisting viral sequences shape microbial CRISPR-based immunity.

Weinberger AD, Sun CL, Pluciński MM, Denef VJ, Thomas BC, Horvath P, Barrangou R, Gilmore MS, Getz WM, Banfield JF.

PLoS Comput Biol. 2012;8(4):e1002475. doi: 10.1371/journal.pcbi.1002475. Epub 2012 Apr 19.

20.

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

Belnap CP, Pan C, Denef VJ, Samatova NF, Hettich RL, Banfield JF.

ISME J. 2011 Jul;5(7):1152-61. doi: 10.1038/ismej.2010.200. Epub 2011 Jan 13.

21.

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

Morowitz MJ, Denef VJ, Costello EK, Thomas BC, Poroyko V, Relman DA, Banfield JF.

Proc Natl Acad Sci U S A. 2011 Jan 18;108(3):1128-33. doi: 10.1073/pnas.1010992108. Epub 2010 Dec 29. Erratum in: Proc Natl Acad Sci U S A. 2011 Mar 15;108(11):4512.

22.

Metabolome-proteome differentiation coupled to microbial divergence.

Wilmes P, Bowen BP, Thomas BC, Mueller RS, Denef VJ, VerBerkmoes NC, Hettich RL, Northen TR, Banfield JF.

MBio. 2010 Oct 26;1(5). pii: e00246-10. doi: 10.1128/mBio.00246-10.

23.

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

Mueller RS, Denef VJ, Kalnejais LH, Suttle KB, Thomas BC, Wilmes P, Smith RL, Nordstrom DK, McCleskey RB, Shah MB, Verberkmoes NC, Hettich RL, Banfield JF.

Mol Syst Biol. 2010 Jun 8;6:374. doi: 10.1038/msb.2010.30.

24.

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

Denef VJ, Mueller RS, Banfield JF.

ISME J. 2010 May;4(5):599-610. doi: 10.1038/ismej.2009.158. Epub 2010 Feb 18.

PMID:
20164865
25.

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

Denef VJ, Kalnejais LH, Mueller RS, Wilmes P, Baker BJ, Thomas BC, VerBerkmoes NC, Hettich RL, Banfield JF.

Proc Natl Acad Sci U S A. 2010 Feb 9;107(6):2383-90. doi: 10.1073/pnas.0907041107. Epub 2010 Feb 2.

26.

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.

Parnell JJ, Denef VJ, Park J, Tsoi T, Tiedje JM.

Biodegradation. 2010 Feb;21(1):147-56. doi: 10.1007/s10532-009-9289-4. Epub 2009 Aug 12.

PMID:
19672561
27.

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

Goltsman DS, Denef VJ, Singer SW, VerBerkmoes NC, Lefsrud M, Mueller RS, Dick GJ, Sun CL, Wheeler KE, Zemla A, Baker BJ, Hauser L, Land M, Shah MB, Thelen MP, Hettich RL, Banfield JF.

Appl Environ Microbiol. 2009 Jul;75(13):4599-615. doi: 10.1128/AEM.02943-08. Epub 2009 May 8.

28.

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

VerBerkmoes NC, Denef VJ, Hettich RL, Banfield JF.

Nat Rev Microbiol. 2009 Mar;7(3):196-205. doi: 10.1038/nrmicro2080. Review.

PMID:
19219053
29.

The dynamic genetic repertoire of microbial communities.

Wilmes P, Simmons SL, Denef VJ, Banfield JF.

FEMS Microbiol Rev. 2009 Jan;33(1):109-32. doi: 10.1111/j.1574-6976.2008.00144.x. Epub 2008 Nov 24. Review.

30.

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

Denef VJ, VerBerkmoes NC, Shah MB, Abraham P, Lefsrud M, Hettich RL, Banfield JF.

Environ Microbiol. 2009 Feb;11(2):313-25. doi: 10.1111/j.1462-2920.2008.01769.x. Epub 2008 Sep 23.

PMID:
18826438
31.

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

Simmons SL, Dibartolo G, Denef VJ, Goltsman DS, Thelen MP, Banfield JF.

PLoS Biol. 2008 Jul 22;6(7):e177. doi: 10.1371/journal.pbio.0060177.

32.

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

Denef VJ, Shah MB, Verberkmoes NC, Hettich RL, Banfield JF.

J Proteome Res. 2007 Aug;6(8):3152-61. Epub 2007 Jun 28.

PMID:
17602579
33.

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

Lo I, Denef VJ, Verberkmoes NC, Shah MB, Goltsman D, DiBartolo G, Tyson GW, Allen EE, Ram RJ, Detter JC, Richardson P, Thelen MP, Hettich RL, Banfield JF.

Nature. 2007 Mar 29;446(7135):537-41. Epub 2007 Mar 7.

PMID:
17344860
34.

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

Chain PS, Denef VJ, Konstantinidis KT, Vergez LM, Agulló L, Reyes VL, Hauser L, Córdova M, Gómez L, González M, Land M, Lao V, Larimer F, LiPuma JJ, Mahenthiralingam E, Malfatti SA, Marx CJ, Parnell JJ, Ramette A, Richardson P, Seeger M, Smith D, Spilker T, Sul WJ, Tsoi TV, Ulrich LE, Zhulin IB, Tiedje JM.

Proc Natl Acad Sci U S A. 2006 Oct 17;103(42):15280-7. Epub 2006 Oct 9.

35.

Genetic and genomic insights into the role of benzoate-catabolic pathway redundancy in Burkholderia xenovorans LB400.

Denef VJ, Klappenbach JA, Patrauchan MA, Florizone C, Rodrigues JL, Tsoi TV, Verstraete W, Eltis LD, Tiedje JM.

Appl Environ Microbiol. 2006 Jan;72(1):585-95.

36.

Growth substrate- and phase-specific expression of biphenyl, benzoate, and C1 metabolic pathways in Burkholderia xenovorans LB400.

Denef VJ, Patrauchan MA, Florizone C, Park J, Tsoi TV, Verstraete W, Tiedje JM, Eltis LD.

J Bacteriol. 2005 Dec;187(23):7996-8005.

37.

Biphenyl and benzoate metabolism in a genomic context: outlining genome-wide metabolic networks in Burkholderia xenovorans LB400.

Denef VJ, Park J, Tsoi TV, Rouillard JM, Zhang H, Wibbenmeyer JA, Verstraete W, Gulari E, Hashsham SA, Tiedje JM.

Appl Environ Microbiol. 2004 Aug;70(8):4961-70.

38.

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

Denef VJ, Park J, Rodrigues JL, Tsoi TV, Hashsham SA, Tiedje JM.

Environ Microbiol. 2003 Oct;5(10):933-43.

PMID:
14510847

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