Dick, G.J., Duhaime, M.B., Evans, J.T., Errera, R.M., Godwin, C., Kharbush, J.J., Nitschky, H.S., Powers, M.A., Vanderploeg, H.A., Schmidt, K.C., Smith, D.J., Yancey, C.E., Zwiers, C.C., Denef, V.J. 2021. The genetic and ecophysiological diversity of Microcystis.    Environ. Microbiol.

Jackrel, S.L.***, Yang, J.W.**, Schmidt, K.C.*, and V.J. Denef. 2021. Host specificity of microbiome assembly and its fitness effects in phytoplankton.    ISME J

Schmidt, K.C.*, Jackrel, S.L****., Smith, D.J., Dick, G.J., and V.J. Denef. 2020. Genotype and host microbiome alter competitive interactions between Microcystis aeruginosa and Chlorella sorokiniana.   Harmful Algae

Evans, J.T. ****, and V.J. Denef. 2020. To dereplicate or not to dereplicate?    mSphere

Schmidt, M.L.**, Biddanda, B.A., Weinke, A.D., Chiang, E.*, Januska, F., Props, R.**, V.J. Denef. 2020. Microhabitats shape diversity-productivity relationships in freshwater bacterial communities.    FEMS Microbiol. Ecol.

Props, R.**, Boon, N, V.J. Denef. 2020. Strain-resolved analysis of a ubiquitous and abundant freshwater bacterial lineage shows larger genomic divergence across nutrient than temperature gradients.    Appl. Env. Microbiol.

Jackrel, S.L.***, K. Schmidt*, B.J. Cardinale, and V.J. Denef. 2020. Microbiomes Reduce their Host’s Sensitivity to Interspecific Interactions.    mBio

Schulz, F., Roux, S., Paez-Espino, D., Jungbluth, S., Walsh, D., Denef, V.J., McMahon, K.D., Konstantinidis, K.T., Eloe-Fadrosh, E.A., Kyrpides, N., and Woyke, T. 2020. Giant virus diversity and host interactions through global metagenomics.    Nature

Rubbens, P., Schmidt, M.L.**, Props, R.**, Biddanda, B.A., Boon, N., Waegeman, W., V.J. Denef. Randomized lasso associates freshwater lake-system specific bacterial taxa with heterotrophic production through flow cytometry. mSystems, in press. (Rubbens and Schmidt contributed equally)   mSystems

Jackrel, S.L.***, White, J., Buffin, K.*, Hayden, K.*, Sarnelle, O., V.J. Denef. Genome Evolution and Host Microbiome Shifts Correspond with Intraspecific Niche Divergence within Harmful Algal Bloom‐Forming Microcystis aeruginosa. Mol Ecol, in press.   MolEcol

Props, R.**, Monsieurs P., Vandamme, P., Leys, N., Denef, V.J., Boon, N. 2019. Gene Expansion and Positive Selection as Bacterial Adaptations to Oligotrophic Conditions. mSphere 4 (1), e00011-19   mSphere

Jackrel, S.L.***, Narwani, A., Bentlage, B., Levine, R.B., Hietala, D.C., Savage, P.E., Oakley, T.H., Denef, V.J., B.J. Cardinale. 2018. Ecological engineering helps maximize function in algal bio-oil production. Appl Environ Microbiol 00953-18. [AEM spotlight article]   AEM

Chiang, E.*, Schmidt, M.L.**, Berry, M.A.****, Biddanda, B.A., Burtner, A.M., Johengen, T.H., Palladino, D., V.J. Denef. 2018. Verrucomicrobia are prevalent in north-temperate freshwater lakes and display class-level preferences between lake habitats. PLoS ONE 13(3): e0195112.   PLoSOne

Denef, V.J. 2018. Peering into the Genetic Makeup of Natural Microbial Populations Using Metagenomics. Martin F. Polz and Om P. Rajora (eds.), Population Genomics: Microorganisms (Springer).   Book

Props, R.**, M.L. Schmidt**, J. Heyse, H.A. Vanderploeg, N. Boon, and V.J. Denef. 2018. Flow cytometric monitoring of bacterioplankton phenotypic diversity predicts high population‐specific feeding rates by invasive dreissenid mussels. Environ Microbiol 20 (2), 521-534.   EM

Meyer, K.A., Davis, T.W., Watson, S.B., Denef, V.J., Berry, M.A.****, G.J. Dick. 2017. Genome sequences of lower Great Lakes Microcystis sp. reveal strain-specific genes that are present and expressed in western Lake Erie blooms. PloS One 12 (10), e0183859.   PLoSOne

Denef V.J., Carrick H.J., Cavaletto J., Chiang E.*, Johengen T.H., Vanderploeg H.A. 2017. Lake bacterial assemblage composition is sensitive to biological disturbance caused by an invasive filter feeder. mSphere 2 (3), e00189-17.   mSphere

Berry, M.A.****, J.D. White, T.W. Davis, S. Jain, T.H. Johengen, G.J. Dick, O. Sarnelle and V.J Denef. 2017. Are oligotypes meaningful ecological and phylogenetic units? A case study of Microcystis in freshwater lakes. Front Microbiol, 8: 365.   Frontiers

Berry, M.A.****, T.W. Davis, R.M. Cory, M.B. Duhaime, T.H. Johengen, G.W. Kling, J.A. Marino, P.A. Den Uyl, D. Gossiaux, G.J. Dick, V.J. Denef. Cyanobacterial harmful algal blooms are a biological disturbance to western Lake Erie bacterial communities. Environ Microbiol, in press.   EM

CC Wu, S Ghosh, K Martin, AJ Pinto, VJ Denef, TM Olson, N Love. (in press). The microbial colonization of activated carbon block point-of-use (PoU) filters with and without chlorinated phenol disinfection byproducts. Environmental Science: Water Research & Technology   ESWRT

Paez-Espino, D., Chen I.A., Palaniappan, K., Ratner, A., Chu, K., Szeto, E., Pillay, M., Huang, J., Markowitz, V.M. Nielsen, T., Huntemann, M., Reddy, TBK, Pavlopoulos, G.A., Sullivan, M.B., Campbell, B.J., Chen, F. McMahon, K., Hallam, S.J., Denef, V.J., Cavicchioli, R., Caffrey, S.M., Streit, W.R., Webster, J., Handley, K.M., Salekdeh, G.H., Tsesmetzis, N., Setubal, J.C., Pope, P.B., Liu, W., Rivers, A.R., Ivanova, N.N., Kyrpides, N.C. (2017). IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses. Nucl Acids Res 45: D457-D465.   NAR

Fujimoto, M., Cavaletto, J., Liebig, J.R., McCarthy, A., Vanderploeg, H.A., and V.J. Denef. 2016. Spatiotemporal distribution of bacterial functional groups along a freshwater estuary to pelagic gradient in Lake Michigan. J Great Lakes Res, 42 (5), 1036-1048.    JGLR

Denef, V.J., Fujimoto, M., Berry, M.A., and M.L. Schmidt**. (2016). Seasonal succession leads to habitat-dependent differentiation in ribosomal RNA:DNA ratios among freshwater lake bacteria. Front. Microbiol. 7:606.   Frontiers

Cory, R.M., Davis, T.W., Dick, G.J., Johengen, T., Denef, V.J., Berry, M.A., Page, S.E., Watson, S.B., Yuhas, K. and G.W. Kling. (2016). Seasonal dynamics in dissolved organic matter, hydrogen peroxide, and cyanobacterial blooms in Lake Erie. Front. Mar. Sci. 3:54.   Frontiers

Denef, V.J., R.S. Mueller, E. Chiang*, J.R. Liebig, H.A. Vanderploeg. (2016). Chloroflexi CL500-11 populations that predominate deep lake hypolimnion bacterioplankton rely on nitrogen-rich DOM metabolism and C1 compound oxidation. Appl Env Microbiol 82(5):1423-32 [AEM spotlight article]   AEM

Schmidt, M.L.**, J.D. White, and V.J. Denef (2016). Phylogenetic conservation of freshwater lake habitat preference varies between abundant bacterioplankton phyla. Environ Microbiol DOI: 10.1111/1462-2920.13143.   EM

Shetty, A.R., de Gannes, V., Obi, C.C., Lucas, S., Lapidus, A., Cheng, J.F., Goodwin, L.A., Pitluck, S., Peters, L., Mikhailova, N. and Teshima, H., Han, C., Tapia, R., Land, M., Hauser, L.J., Kyrpides, N., Ivanova, N., Pagani, I., Chain, P.S.G., Denef, V.J., Woyke, T., and Hickey, W.J. (2015). Complete genome sequence of the phenanthrene-degrading soil bacterium Delftia acidovorans Cs1-4. Stand Genomic Sci 10(1):1-10.   SIGS

McCarthy A, Chiang E, Schmidt ML, Denef VJ (2015) RNA Preservation Agents and Nucleic Acid Extraction Method Bias Perceived Bacterial Community Composition. PLoS ONE 10(3): e0121659. doi:10.1371/journal.pone.0121659   PLoSOne

Lennon, J.T., and Denef, V.J. (in press). Evolutionary Ecology of Microorganisms: from the Tamed to the Wild. Manual of Environmental Microbiology (ASM Press, Washington, DC).  [Preprint available @ PeerJ Preprints]

A.P. Yelton, L.R. Comolli, N. Justice, C. Castelle, V.J. Denef, B.C. Thomas and J.F. Banfield , J.F. Banfield. 2013. Comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaea. BMC Genomics 14(1):485    Pubmed

Denef V.J., J.F. Banfield. 2012. In situ evolutionary rate measurements show ecological success of recently emerged bacterial hybrids. Science 336(6080):462-466    Pubmed

Weinberger, A.D., C.L. Sun, M.M. Pluciński, V.J. Denef, B.C. Thomas, P. Horvath, R. Barrangou, M.S. Gilmore, W.M. Getz, J.F. Banfield. 2012. Persisting Viral Sequences Shape Microbial CRISPR-based Immunity. PLoS Comput Biol. 8(4):e1002475    Pubmed

Belnap, C.P., C. Pan, V.J. Denef, N.C. VerBerkmoes, N.F. Samatova, R.L. Hettich, J.F. Banfield. 2011. Quantitative proteomic analyses of the response of acidophilic microbial communities to different pH conditions. ISME J. 5(7):1152-1161   Pubmed

Morowitz, M.J., V.J. Denef, E. Costello, B. Thomas, D.A. Relman, J.F. Banfield. 2011. Strain-resolved community genomic analysis of gut microbial colonization in a premature infant. Proc Natl Acad Sci U S A 108(3): 1128–1133   Pubmed

Wilmes P., B.P. Bowen, B.C. Thomas, R.S. Mueller, V.J. Denef, N.C. VerBerkmoes, R.L. Hettich, T.R. Northern,J.F. Banfield. 2010. Metabolome-Proteome Differentiation Coupled to Microbial Divergence. mBio 1(5):e00246-10    Pubmed

Mueller, R.S, V.J. Denef, L.H. Kalnejais, K.B. Suttle, B.C. Thomas, P. Wilmes, R. Smith, D.K. Nordstrom, M.B.Shah, N.C. VerBerkmoes, R.L. Hettich, and J.F. Banfield. 2010. Ecological distribution and population physiology defined by proteomics in a natural microbial community. Molecular Systems Biology 6:374  Pubmed

Denef, V.J., Mueller, R.S., and Banfield J.F. 2010. Winogradsky review: AMD biofilms: using model communities to study microbial evolution and ecological complexity in nature. ISME J. 4(5):599-610.  Pubmed

Denef, V.J., L. Kalnejais, P., Mueller, R.S., Wilmes, B. Baker, Brian C. Thomas, N.C. VerBerkmoes, R.L. Hettich, and J.F. Banfield. 2010. Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities. Proc Natl Acad Sci U S A 107(6):2383-90.  Pubmed

Parnell, J.J., Denef, V.J., Park, J., Tsoi, T.V., and Tiedje, J.M. 2010. Environmentally Relevant Parameters Affecting PCB Degradation: Carbon Source- and Growth Phase-Mitigated Effects of the Expression of the Biphenyl Pathway and Associated Genes in B. xenovorans LB400. Biodegradation 21(1):147-56.  Pubmed

Goltsman, D.S.A., V.J. Denef, S.W. Singer, N.C. VerBerkmoes, M. Lefsrud, R. Muller, G.J. Dick, C. Sun, K. Wheeler, A. Zemla, B.J. Baker, L. Hauser, M. Land, M.B. Shah, M.P. Thelen, R.L. Hettich, and J.F. Banfield. 2009. Community genomic and proteomic analysis of chemoautotrophic, iron-oxidizing "L. rubarum" and L. ferrodiazotrophum in AMD biofilms. Appl. Environ. Microbiol. 75(13): 4599-4615.  Pubmed

VerBerkmoes, N.C., V.J. Denef, R.L. Hettich, and J.F. Banfield. 2009. Community proteomic functional analysis of natural microbial communities. Nat. Rev. Microbiol. 7, 196-205.  Pubmed

Wilmes, P., S.L. Simmons, V.J. Denef, and J.F. Banfield. 2009. The dynamic genetic repertoire of microbialcommunities. FEMS Microbiol Rev 33(1), 109-132.  Pubmed

Denef, V.J., N.C. VerBerkmoes, M.B. Shah, P. Abraham, M. Lefsrud, R.L. Hettich, and J.F. Banfield. 2009. Proteomics-inferred genome typing (PIGT) demonstrates inter-population recombination as a strategy for environmental adaptation. Environ Microbiol. 11(2), 313-325.  Pubmed

Simmons, S., G. DiBartolo, V.J. Denef, D.S.A. Goltsman, M.P. Thelen, and J.F. Banfield. 2008 Population genomic analysis of strain variation in Leptospirillum group II bacteria involved in AMD formation. PLoS Biol. 6(7):e177.  Pubmed

Denef, V.J., M.B Shah, N.C. VerBerkmoes, R.L. Hettich, J.F. Banfield. 2007. Implications of strain- and specieslevel sequence divergence for community and isolate shotgun proteomic analyses. J. Prot. Res. 6(8), 3152-3161.  Pubmed

Lo, I., V.J. Denef, N.C. Verberkmoes, M.B. Shah, D. Goltsman, G. DiBartolo, G.W. Tyson, E.E. Allen, R.J. Ram, J.C. Detter, P.M. Richardson, M.P. Thelen, R.L. Hettich, and J.F. Banfield. 2007. Strain-resolved community proteomics reveals that recombination shapes the genomes of acidophilic bacteria. Nature 446(7135):537-541.  Pubmed

Denef, V.J. Biodegradation of organic anthropogenic pollutants by Burkholderia species. In: Burkholderia: Molecular Biology and Genomics. 2007. Coenye, T. and Vandamme, P., eds. (Horizon Scientific Press, UK)

Chain, P.S.G.*, V.J. Denef*, K.T. Konstantinidis, L.M. Vergez, L. Agullo, V.L. Reyes, L. Hauser, M. Cordova, L. Gomez, M. Gonzalez, M. Land, V. Lao, F. Larimer, J.J. LiPuma, E. Mahenthiralingam, S.A. Malfatti, C.J.Marx, J.J. Parnell, A. Ramette, P. Richardson, M. Seeger, D. Smith, T. Spilker, W.J. Sul, T.V. Tsoi, L.E.Ulrich, I.B. Zhulin, and J.M. Tiedje. 2006. Burkholderia xenovorans LB400 harbors a multi-replicon, 9.7 M bp genome shaped for versatility. Proc. Natl. Acad. Sc. USA 103(42):15280-15287.   Pubmed
*contributed equally

Parnell, J.J., J. Park, V.J. Denef, T.V. Tsoi, S.A Hashsham, J. Quensen III, and J.M. Tiedje. 2006. Coping with PCB toxicity: The physiological and genome-wide response of Burkholderia xenovorans LB400 to PCB (polychlorinated biphenyl)-mediated stress. Appl. Environ. Microbiol. 72(10):6607-6614.  Pubmed

Denef, V.J., J.A. Klappenbach, M.A. Patrauchan, C. Florizone, J.L.M. Rodrigues, T.V. Tsoi, W. Verstraete, L.D.Eltis, and J.M. Tiedje. 2006. Genetic and genomic insights into the role of benzoate-catabolic pathway redundancy in Burkholderia xenovorans LB400. Appl. Environ. Microbiol. 72(1):585-95   Pubmed

Denef, V.J., M.A. Patrauchan, C. Florizone, J. Park, T.V. Tsoi, W. Verstraete, J.M. Tiedje, and L.D. Eltis. 2005. Growth substrate- and phase-specific expression of biphenyl, benzoate and C1 metabolic pathways in Burkholderia xenovorans LB400. J. Bacteriol. 187(23):7996-8005.  Pubmed

Denef, V.J., J. Park, T.V. Tsoi, J.-M. Rouillard, H. Zhang, J.A. Wibbenmeyer, W. Verstraete, E. Gulari, S.A. Hashsham, and J.M. Tiedje. 2004. Biphenyl and benzoate metabolism in a genomic context: Outlining genome-wide metabolic networks in Burkholderia xenovorans LB400. Appl Environ Microbiol 70(8):4961-4970 . Pubmed

Denef, V.J., J. Park, J. L. Rodrigues, T. V. Tsoi, S. A. Hashsham, J. M. Tiedje. 2003. Validation of a more sensitive method for using spotted oligonucleotide DNA microarrays for functional genomics studies on bacterial communities. Environ. Microbiol. 5(10):9339-43.  Pubmed