Bacterial communities of diverse Drosophila species: ecological context of a host-microbe model system von Chandler, James Angus, Lang, Jenna Morgan, Bhatnagar, Srijak, Eisen, Jonathan A, Kopp, Artyom

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Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota von Van Deynze, Allen, Zamora, Pablo, Delaux, Pierre-Marc, Heitmann, Cristobal, Jayaraman, Dhileepkumar, Rajasekar, Shanmugam, Graham, Danielle, Maeda, Junko, Gibson, Donald, Schwartz, Kevin D, Berry, Alison M, Bhatnagar, Srijak, Jospin, Guillaume, Darling, Aaron, Jeannotte, Richard, Lopez, Javier, Weimer, Bart C, Eisen, Jonathan A, Shapiro, Howard-Yana, Ané, Jean-Michel, Bennett, Alan B

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A simple, fast, and accurate method of phylogenomic inference von Wu, Martin, Eisen, Jonathan A

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Research priorities for harnessing plant microbiomes in sustainable agriculture von Busby, Posy E, Soman, Chinmay, Wagner, Maggie R, Friesen, Maren L, Kremer, James, Bennett, Alison, Morsy, Mustafa, Eisen, Jonathan A, Leach, Jan E, Dangl, Jeffery L

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Structure, variation, and assembly of the root-associated microbiomes of rice von Edwards, Joseph, Johnson, Cameron, Santos-Medellín, Christian, Lurie, Eugene, Podishetty, Natraj Kumar, Bhatnagar, Srijak, Eisen, Jonathan A., Sundaresan, Venkatesan

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Systematic identification of gene families for use as "markers" for phylogenetic and phylogeny-driven ecological studies of bacteria and archaea and their major subgroups von Wu, Dongying, Jospin, Guillaume, Eisen, Jonathan A

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Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance von Kembel, Steven W, Wu, Martin, Eisen, Jonathan A, Green, Jessica L

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An integrated pipeline for de novo assembly of microbial genomes von Tritt, Andrew, Eisen, Jonathan A, Facciotti, Marc T, Darling, Aaron E

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Fungi, bacteria and oomycota opportunistically isolated from the seagrass, Zostera marina von Ettinger, Cassandra L, Eisen, Jonathan A

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Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications von Valdés, Jorge, Pedroso, Inti, Quatrini, Raquel, Dodson, Robert J, Tettelin, Herve, Blake, 2nd, Robert, Eisen, Jonathan A, Holmes, David S

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Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices von Lang, Jenna Morgan, Darling, Aaron E, Eisen, Jonathan A

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Marine probiotics: increasing coral resistance to bleaching through microbiome manipulation von Rosado, Phillipe M., Leite, Deborah C. A., Duarte, Gustavo A. S., Chaloub, Ricardo M., Jospin, Guillaume, Nunes da Rocha, Ulisses, P. Saraiva, João, Dini-Andreote, Francisco, Eisen, Jonathan A., Bourne, David G., Peixoto, Raquel S.

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2019 Novel Coronavirus (COVID-19) Pandemic: Built Environment Considerations To Reduce Transmission von Dietz, Leslie, Horve, Patrick F, Coil, David A, Fretz, Mark, Eisen, Jonathan A, Van Den Wymelenberg, Kevin

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Host-associated microbiomes drive structure and function of marine ecosystems von Wilkins, Laetitia G E, Leray, Matthieu, O'Dea, Aaron, Yuen, Benedict, Peixoto, Raquel S, Pereira, Tiago J, Bik, Holly M, Coil, David A, Duffy, J Emmett, Herre, Edward Allen, Lessios, Harilaos A, Lucey, Noelle M, Mejia, Luis C, Rasher, Douglas B, Sharp, Koty H, Sogin, Emilia M, Thacker, Robert W, Vega Thurber, Rebecca, Wcislo, William T, Wilbanks, Elizabeth G, Eisen, Jonathan A

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Accounting for alignment uncertainty in phylogenomics von Wu, Martin, Chatterji, Sourav, Eisen, Jonathan A

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Drivers of bacterial β-diversity depend on spatial scale von Martiny, Jennifer B. H., Eisen, Jonathan A., Penn, Kevin, Allison, Steven D., Horner-Devine, M. Claire, DeLong, Edward F.

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Insights into the phylogeny and coding potential of microbial dark matter von Rinke, Christian, Schwientek, Patrick, Sczyrba, Alexander, Ivanova, Natalia N., Anderson, Iain J., Cheng, Jan-Fang, Darling, Aaron, Malfatti, Stephanie, Swan, Brandon K., Gies, Esther A., Dodsworth, Jeremy A., Hedlund, Brian P., Tsiamis, George, Sievert, Stefan M., Liu, Wen-Tso, Eisen, Jonathan A., Hallam, Steven J., Kyrpides, Nikos C., Stepanauskas, Ramunas, Rubin, Edward M., Hugenholtz, Philip, Woyke, Tanja

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Assembling the marine metagenome, one cell at a time von Woyke, Tanja, Xie, Gary, Copeland, Alex, González, José M, Han, Cliff, Kiss, Hajnalka, Saw, Jimmy H, Senin, Pavel, Yang, Chi, Chatterji, Sourav, Cheng, Jan-Fang, Eisen, Jonathan A, Sieracki, Michael E, Stepanauskas, Ramunas

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Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes von Eisen, Jonathan A

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Global-Scale Structure of the Eelgrass Microbiome von Fahimipour, Ashkaan K, Kardish, Melissa R, Lang, Jenna M, Green, Jessica L, Eisen, Jonathan A, Stachowicz, John J

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