78 publications

2021

• Petras, D., Minich, J. J., Cancelada, L. B., Torres, R. R., Kunselman, E., Wang, M. X., ... Dorrestein, P. C. (2021). Non-targeted tandem mass spectrometry enables the visualization of organic matter chemotype shifts in coastal seawater. Chemosphere, 271(129450). doi: 10.1016/j.chemosphere.2020.129450
• Jeremiah, M., Barbara, N., Abigail, E., Rob, K., Stewart, F., & Eric, A. (2021). Impacts of the marine hatchery built environment on mucosal microbiome colonization across ontogeny in yellowtail kingfish, Seriola Lalandi. Research Square. doi: 10.21203/rs.3.rs-75521/v1
• Nayfach, S., Roux, S., Seshadri, R., Udwary, D., Varghese, N., Schulz, F., ... Consortium, I. M. D. (2021). A genomic catalog of Earth’s microbiomes. Nature Biotechnology, 39(4), 499-509. doi: 10.1038/s41587-020-0718-6
• Neu, A. T., Hughes, I. V., Allen, E. E., & Roy, K. (2021). Decade-scale stability and change in a marine bivalve microbiome. Molecular Ecology. doi: 10.1111/mec.15796
• Minich, J. J., Ali, F., Marotz, C., Belda-Ferre, P., Chiang, L., Shaffer, J. P., ... Swafford, A. D. (2021). Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment. Microbiome, 9(1). doi: 10.1186/s40168-020-00960-4

2020

• Minich, J. J., Power, C., Melanson, M., Knight, R., Webber, C., Rough, K., ... Allen, E. E. (2020). The Southern Bluefin Tuna mucosal microbiome is influenced by husbandry method, net pen location, and anti-parasite treatment. Frontiers in Microbiology. doi: 10.1101/2020.05.19.105270
• Podell, S., Blanton, J. M., Oliver, A., Schorn, M. A., Agarwal, V., Biggs, J. S., ... Allen, E. E. (2020). A genomic view of trophic and metabolic diversity in clade-specific Lamellodysidea sponge microbiomes. Microbiome, 8. doi: 10.21203/rs.2.17204/v1
• Allemann, M. N., & Allen, E. E. (2020). Genetic regulation of the bacterial omega-3 polyunsaturated fatty acid biosynthesis pathway. Journal of Bacteriology. doi: 10.1128/JB.00050-20
• Schulhof, M. A., Allen, A. E., Allen, E. E., Mladenov, N., McCrow, J. P., Jones, N. T., ... Shurin, J. B. (2020). Sierra Nevada mountain lake microbial communities are structured by temperature, resources and geographic location. Molecular Ecology. doi: 10.1111/mec.15469
• Fedarko, M. W., Martino, C., Morton, J. T., González, A., Rahman, G., Marotz, C. A., ... Knight, R. (2020). Visualizing ’omic feature rankings and log-ratios using Qurro. NAR Genomics and Bioinformatics, 2(2). doi: 10.1093/nargab/lqaa023
• Minich, J. J., Jantawongsri, K., Johnston, C., Bowie, K., Bowman, J., Knight, R., ... Allen, E. (2020). Microbial ecology of Atlantic salmon (Salmo salar) hatcheries: Impacts of the built environment on fish mucosal microbiota. Applied and Environmental Microbiology, 86(12). doi: 10.1101/828749
• Minich, J., Petrus, S., Michael, J. D., Michael, T. P., Knight, R., & Allen, E. (2020). Temporal, environmental, and biological drivers of the mucosal microbiome in a wild marine fish, Scomber japonicus. mSphere, 5. doi: 10.1128/mSphere.00401-20
• Allemann, M., & Allen, E. (2020). Genetic suppression of lethal mutations in fatty acid synthesis mediated by a secondary lipid synthase. Applied and Environmental Microbiology, 87(12). doi: 10.1128/AEM.00035-21
• Mohanty, I., Podell, S., Biggs, J. S., Garg, N., Allen, E. E., & Agarwal, V. (2020). Multi-omic profiling of melophlus sponges reveals diverse metabolomic and microbiome architectures that are non-overlapping with ecological neighbors. Marine Drugs, 18(2), 124. doi: 10.3390/md18020124

2019

• Podell, S., Blanton, J. M., Neu, A., Agarwal, V., Biggs, J. S., Moore, B. S., & Allen, E. E. (2019). Pangenomic comparison of globally distributed Poribacteria associated with sponge hosts and marine particles. The ISME Journal. doi: 10.1038/s41396-018-0292-9
• Kolody, B. C., McCrow, J. P., Allen, L. Z., Aylward, F. O., Fontanez, K. M., Moustafa, A., ... Allen, A. E. (2019). Diel transcriptional response of a California Current plankton microbiome to light, low iron, and enduring viral infection. The ISME Journal. doi: 10.1038/s41396-019-0472-2
• Schorn, M. A., Jordan, P. A., Podell, S., Blanton, J. M., Agarwal, V., Biggs, J. S., ... Moore, B. S. (2019). Comparative genomics of cyanobacterial symbionts reveals distinct, specialized metabolism in tropical Dysideidae sponges. mBio, 10. doi: 10.1128/mBio.00821-19
• Neu, A. T., Allen, E. E., & Roy, K. (2019). Diversity and composition of intertidal gastropod microbiomes across a major marine biogeographic boundary. Environmental Microbiology Reports, 11(3), 434-447. doi: 10.1111/1758-2229.12743
• Allemann, M. N., Shulse, C. N., & Allen, E. E. (2019). Linkage of marine bacteria polyunsaturated fatty acid and long-chain hydrocarbon biosynthesis. Frontiers in Microbiology, 10(702). doi: 10.3389/fmicb.2019.00702
• Peoples, L. M., Grammatopoulou, E., Pombrol, M., Xu, X. X., Osuntokun, O., Blanton, J., ... Bartlett, D. H. (2019). Microbial community diversity within sediments from two geographically separated hadal trenches. Frontiers in Microbiology, 10(347). doi: 10.3389/fmicb.2019.00347

2018

• Minich, J. J., Humphrey, G., Benitez, R. A. S., Sanders, J., Swofford, A., Allen, E. E., & Knight, R. (2018). High-throughput miniaturized 16S rRNA amplicon library preparation reduces costs while preserving microbiome integrity. Msystems, 3(6). doi: 10.1128/mSystems.00166-18
• Plominsky, A. M., Henriquez-Castillo, C., Delherbe, N., Podell, S., Ramirez-Flandes, S., Ugalde, J. A., ... Trefault, N. (2018). Distinctive archaeal composition of an artisanal crystallizer pond and functional insights into salt-saturated hypersaline environment adaptation. Frontiers in Microbiology, 9(1800). doi: 10.3389/fmicb.2018.01800
• Minich, J. J., Zhu, Q., Xu, Z. Z., Amir, A., Ngochera, M., Simwaka, M., ... Knight, R. (2018). Microbial effects of livestock manure fertilization on freshwater aquaculture ponds rearing tilapia (Oreochromis shiranus) and North African catfish (Clarias gariepinus). MicrobiologyOpen, e00716. doi: 10.1002/mbo3.716
• Guillemette, R., Kaneko, R., Blanton, J., Tan, J., Witt, M., Hamilton, S., ... Azam, F. (2018). Bacterioplankton drawdown of coral mass-spawned organic matter. The ISME Journal. doi: 10.1038/s41396-018-0197-7
• Minich, J. J., Zhu, Q. Y., Janssen, S., Hendrickson, R., Amir, A., Vetter, R., ... Knight, R. (2018). KatharoSeq Enables High-Throughput Microbiome Analysis from Low-Biomass Samples. Msystems, 3(3). doi: 10.1128/mSystems.00218-17
• Peoples, L. M., Donaldson, S., Osuntokun, O., Xia, Q., Nelson, A., Blanton, J., ... Bartlett, D. H. (2018). Vertically distinct microbial communities in the Mariana and Kermadec trenches. Plos One, 13(4). doi: 10.1371/journal.pone.0195102
• Plominsky, A. M., Trefault, N., Podell, S., Blanton, J. M., De la Iglesia, R., Allen, E. E., ... Ulloa, O. (2018). Metabolic potential and in situ transcriptomic profiles of previously uncharacterized key microbial groups involved in coupled carbon, nitrogen and sulfur cycling in anoxic marine zones. Environmental Microbiology. doi: 10.1111/1462-2920.14109
• Allemann, M. N., & Allen, E. E. (2018). Characterization and Application of Marine Microbial Omega-3 Polyunsaturated Fatty Acid Synthesis. Methods in Enzymology (pp. 3-32). : Academic Press. doi: 10.1016/bs.mie.2018.02.018

2017

• Leao, T., Castelao, G., Korobeynikov, A., Monroe, E. A., Podell, S., Glukhov, E., ... Gerwick, L. (2017). Comparative genomics uncovers the prolific and distinctive metabolic potential of the cyanobacterial genus Moorea. Proceedings of the National Academy of Sciences of the United States of America, 114(12), 3198-3203. doi: 10.1073/pnas.1618556114
• Agarwal, V., Blanton, J. M., Podell, S., Taton, A., Schorn, M. A., Busch, J., ... Moore, B. S. (2017). Metagenomic discovery of polybrominated diphenyl ether biosynthesis by marine sponges. Nat Chem Biol, advance online publication. doi: 10.1038/nchembio.2330
• Demidenko, A., Akberdinl, I. R., Allemann, M., Allen, E. E., & Kalyuzhnaya, M. G. (2017). Fatty Acid Biosynthesis Pathways in Methylomicrobium buryatense 5G(B1). Frontiers in Microbiology, 7(2167). doi: 10.3389/fmicb.2016.02167

2016

• Paerl, R. W., Bouget, F., Lozano, J., Verge, V., Schatt, P., Allen, E. E., ... Azam, F. (2016). Use of plankton-derived vitamin B1 precursors, especially thiazole-related precursor, by key marine picoeukaryotic phytoplankton. ISME J. doi: 10.1038/ismej.2016.145
• Traller, J. C., Cokus, S. J., Lopez, D. A., Gaidarenko, O., Smith, S. R., McCrow, J. P., ... Hildebrand, M. (2016). Genome and methylome of the oleaginous diatom Cyclotella cryptica reveal genetic flexibility toward a high lipid phenotype. Biotechnology for Biofuels, 9(1), 258. doi: 10.1186/s13068-016-0670-3
• Hogle, S. L., Bundy, R. M., Blanton, J. M., Allen, E. E., & Barbeau, K. A. (2016). Copiotrophic marine bacteria are associated with strong iron-binding ligand production during phytoplankton blooms. Limnology and Oceanography Letters. doi: 10.1002/lol2.10026
• Fuentes-Valdés, J. J., Plominsky, A. M., Allen, E. E., Tamames, J., & Vásquez, M. (2016). Complete genome sequence of a cylindrospermopsin-producing cyanobacterium, Cylindrospermopsis raciborskii cs505, containing a circular chromosome and a single extrachromosomal element. Genome Announcements, 4(4). doi: 10.1128/genomeA.00823-16

2015

• Andrade, K., Logemann, J., Heidelberg, K. B., Emerson, J. B., Comolli, L. R., Hug, L. A., ... Banfield, J. F. (2015). Metagenomic and lipid analyses reveal a diel cycle in a hypersaline microbial ecosystem. Isme Journal, 9(12), 2697-2711. doi: 10.1038/ismej.2015.66
• Tully, B. J., Emerson, J. B., Andrade, K., Brocks, J. J., Allen, E. E., Banfield, J. F., & Heidelberg, K. B. (2015). De novo sequences of Haloquadratum walsbyi from Lake Tyrrell, Australia, reveal a variable genomic landscape. Archaea.(875784). doi: 10.1155/2015/875784
• Marietou, A., Nguyen, A. T. T., Allen, E. E., & Bartlett, D. H. (2015). Adaptive laboratory evolution of Escherichia coil K-12 MG1655 for growth at high hydrostatic pressure. Frontiers in Microbiology, 5(749). doi: 10.3389/fmicb.2014.00749

2014

• Plominsky, A. M., Delherbe, N., Ugalde, J. A., Allen, E. E., Blanchet, M., Ikeda, P., ... Trefault, N. (2014). Metagenome sequencing of the microbial community of a solar saltern crystallizer pond at Cáhuil Lagoon, Chile. Genome Announcements, 2(6). doi: 10.1128/genomeA.01172-14
• Agarwal, V., El Gamal, A. A., Yamanaka, K., Poth, D., Kersten, R. D., Schorn, M., ... Moore, B. S. (2014). Biosynthesis of polybrominated aromatic organic compounds by marine bacteria. Nat Chem Biol, 10(8), 640-647. doi: 10.1038/nchembio.1564
• Keeling, P. J., Burki, F., Wilcox, H. M., Allam, B., Allen, E. E., Amaral-Zettler, L. A., ... Worden, A. Z. (2014). The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing. PLoS Biol, 12(6), e1001889. doi: 10.1371/journal.pbio.1001889
• Coates, R. C., Podell, S., Korobeynikov, A., Lapidus, A., Pevzner, P., Sherman, D. H., ... Gerwick, W. H. (2014). Characterization of cyanobacterial hydrocarbon composition and distribution of biosynthetic pathways. PLoS ONE, 9(1), e85140. doi: 10.1371/journal.pone.0085140

2013

• Ugalde, J. A., Narasingarao, P., Kuo, S., Podell, S., & Allen, E. E. (2013). Draft genome sequence of “Candidatus halobonum tyrrellensis” strain g22, isolated from the hypersaline waters of Lake Tyrrell, Australia. Genome Announcements, 1(6). doi: 10.1128/genomeA.01001-13
• Podell, S., Emerson, J. B., Jones, C. M., Ugalde, J. A., Welch, S., Heidelberg, K. B., ... Allen, E. E. (2013). Seasonal fluctuations in ionic concentrations drive microbial succession in a hypersaline lake community. ISME J. doi: 10.1038/ismej.2013.221
• Kharbush, J. J., Ugalde, J. A., Hogle, S. L., Allen, E. E., & Aluwihare, L. I. (2013). Composite bacterial hopanoids and their microbial producers across oxygen gradients in the water column of the California Current. Applied and Environmental Microbiology. doi: 10.1128/aem.02367-13
• Ugalde, J. A., Gallardo, M. J., Belmar, C., Munoz, P., Ruiz-Tagle, N., Ferrada-Fuentes, S., ... Gallardo, V. A. (2013). Microbial life in a fjord: Metagenomic analysis of a microbial mat in Chilean Patagonia. Plos One, 8(8). doi: 10.1371/journal.pone.0071952
• Summers, M. M., Katz, S., Allen, E. E., & Rouse, G. W. (2013). Association of rhizobia with a marine polychaete. Environmental Microbiology Reports, 5(4), 492-498. doi: 10.1111/1758-2229.12043
• Emerson, J. B., Andrade, K., Thomas, B. C., Norman, A., Allen, E. E., Heidelberg, K. B., & Banfield, J. F. (2013). Virus-host and CRISPR dynamics in archaea-dominated hypersaline Lake Tyrrell, Victoria, Australia. Archaea-an International Microbiological Journal. doi: 10.1155/2013/370871
• Podell, S., Ugalde, J. A., Narasingarao, P., Banfield, J. F., Heidelberg, K. B., & Allen, E. E. (2013). Assembly-driven community genomics of a hypersaline microbial ecosystem. Plos One, 8(4). doi: 10.1371/journal.pone.0061692

2012

• Emerson, J. B., Thomas, B. C., Andrade, K., Allen, E. E., Heidelberg, K. B., & Banfield, J. F. (2012). Dynamic viral populations in hypersaline systems as revealed by metagenomic assembly. Applied and Environmental Microbiology, 78(17), 6309-6320. doi: 10.1128/aem.01212-12
• Allen, L. Z., Allen, E. E., Badger, J. H., McCrow, J. P., Paulsen, I. T., Elbourne, L. D. H., ... Allen, A. E. (2012). Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic. ISME Journal, 6(7), 1403-1414. doi: 10.1038/ismej.2011.201
• Mosier, A. C., Allen, E. E., Kim, M., Ferriera, S., & Francis, C. A. (2012). Genome Sequence of “Candidatus Nitrosoarchaeum limnia” BG20, a Low-Salinity Ammonia-Oxidizing Archaeon from the San Francisco Bay Estuary. Journal of Bacteriology, 194(8), 2119-2120. doi: 10.1128/jb.00007-12
• Mosier, A. C., Allen, E. E., Kim, M., Ferriera, S., & Francis, C. A. (2012). Genome Sequence of "Candidatus Nitrosopumilus salaria" BD31, an Ammonia-Oxidizing Archaeon from the San Francisco Bay Estuary. Journal of Bacteriology, 194(8), 2121-2122. doi: 10.1128/jb.00013-12
• Ziemert, N., Podell, S., Penn, K., Badger, J. H., Allen, E., & Jensen, P. R. (2012). The Natural Product Domain Seeker NaPDoS: A Phylogeny Based Bioinformatic Tool to Classify Secondary Metabolite Gene Diversity. Plos One, 7(3). doi: 10.1371/journal.pone.0034064
• Narasingarao, P., Podell, S., Ugalde, J. A., Brochier-Armanet, C., Emerson, J. B., Brocks, J. J., ... Allen, E. E. (2012). De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities. ISME Journal, 6(1), 81-93. doi: 10.1038/ismej.2011.78

2011

• Ugalde, J. A., Podell, S., Narasingarao, P., & Allen, E. E. (2011). Xenorhodopsins, an enigmatic new class of microbial rhodopsins horizontally transferred between archaea and bacteria. Biology Direct, 6(52). doi: 10.1186/1745-6150-6-52
• Eloe, E. A., Shulse, C. N., Fadrosh, D. W., Williamson, S. J., Allen, E. E., & Bartlett, D. H. (2011). Compositional differences in particle-associated and free-living microbial assemblages from an extreme deep-ocean environment. Environmental Microbiology Reports, 3(4), 449-458. doi: 10.1111/j.1758-2229.2010.00223.x
• Shulse, C. N., & Allen, E. E. (2011). Widespread Occurrence of Secondary Lipid Biosynthesis Potential in Microbial Lineages. Plos One, 6(5). doi: 10.1371/journal.pone.0020146
• Eloe, E. A., Fadrosh, D. W., Novotny, M., Allen, L. Z., Kim, M., Lombardo, M. J., ... Bartlett, D. H. (2011). Going Deeper: Metagenome of a Hadopelagic Microbial Community. Plos One, 6(5). doi: 10.1371/journal.pone.0020388
• Jones, A. C., Monroe, E. A., Podell, S., Hess, W. R., Klages, S., Esquenazi, E., ... Gerwick, L. (2011). Genomic insights into the physiology and ecology of the marine filamentous cyanobacterium Lyngbya majuscula. Proceedings of the National Academy of Sciences of the United States of America, 108(21), 8815-8820. doi: 10.1073/pnas.1101137108
• Shulse, C. N., & Allen, E. E. (2011). Diversity and distribution of microbial long-chain fatty acid biosynthetic genes in the marine environment. Environmental Microbiology, 13(3), 684-695. doi: 10.1111/j.1462-2920.2010.02373.x
• Sun, S. L., Chen, J., Li, W. Z., Altintas, I., Lin, A., Peltier, S., ... Wooley, J. (2011). Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource. Nucleic Acids Research, 39, D546-D551. doi: 10.1093/nar/gkq1102

2010

• Morin, P. A., Archer, F. I., Foote, A. D., Vilstrup, J., Allen, E. E., Wade, P., ... Harkins, T. (2010). Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species. Genome Research, 20(7), 908-916. doi: 10.1101/gr.102954.109
• Han, S., Narasingarao, P., Obraztsova, A., Gieskes, J., Hartmann, A. C., Tebo, B. M., ... Deheyn, D. D. (2010). Mercury Speciation in Marine Sediments under Sulfate-Limited Conditions. Environmental Science & Technology, 44(10), 3752-3757. doi: 10.1021/es903112m

2009

• Penn, K., Jenkins, C., Nett, M., Udwary, D. W., Gontang, E. A., McGlinchey, R. P., ... Jensen, P. R. (2009). Genomic islands link secondary metabolism to functional adaptation in marine Actinobacteria. Isme Journal, 3(10), 1193-1203. doi: 10.1038/ismej.2009.58

2008

• Podell, S., Gaasterland, T., & Allen, E. E. (2008). A database of phylogenetically atypical genes in archaeal and bacterial genomes, identified using the DarkHorse algorithm. BMC Bioinformatics, 9(419). doi: 10.1186/1471-2105-9-419
• Robidart, J. C., Bench, S. R., Feldman, R. A., Novoradovsky, A., Podell, S. B., Gaasterland, T., ... Felbeck, H. (2008). Metabolic versatility of the Riftia pachyptila endosymbiont revealed through metagenomics. Environmental Microbiology, 10(3), 727-737. doi: 10.1111/j.1462-2920.2007.01496.x

2007

• Lo, I., Denef, V. J., VerBerkmoes, N. C., Shah, M. B., Goltsman, D., DiBartolo, G., ... Banfield, J. F. (2007). Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. Nature, 446(7135), 537-541. doi: 10.1038/nature05624
• Allen, E. E., Tyson, G. W., Whitaker, R. J., Detter, J. C., Richardson, P. M., & Banfield, J. F. (2007). Genome dynamics in a natural archaeal population. Proceedings of the National Academy of Sciences of the United States of America, 104(6), 1883-1888. doi: 10.1073/pnas.0604851104

2006

• Baker, B. J., Tyson, G. W., Webb, R. I., Flanagan, J., Hugenholtz, P., Allen, E. E., & Banfield, J. F. (2006). Lineages of acidophilic archaea revealed by community genomic analysis. Science, 314(5807), 1933-1935. doi: 10.1126/science.1132690

2005

• Tyson, G. W., Lo, I., Baker, B. J., Allen, E. E., Hugenholtz, P., & Banfield, J. F. (2005). Genome-directed isolation of the key nitrogen fixer Leptospirillum ferrodiazotrophum sp nov from an acidophilic microbial community. Applied and Environmental Microbiology, 71(10), 6319-6324. doi: 10.1128/aem.71.10.6319-6324.2005
• Allen, E. E., & Banfield, J. F. (2005). Community genomics in microbial ecology and evolution. Nature Reviews Microbiology, 3(6), 489-498. doi: 10.1038/nrmicro1157
• Banfield, J. R., Tyson, G. W., Allen, E. E., & Whitaker, R. J. (2005). The search for a molecular-level understanding of the processes that underpin the earth's biogeochemical cycles. Molecular Geomicrobiology, 59, 1-7. doi: 10.2138/rmg.2005.59.1

2004

• Tyson, G. W., Chapman, J., Hugenholtz, P., Allen, E. E., Ram, R. J., Richardson, P. M., ... Banfield, J. F. (2004). Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature, 428(6978), 37-43. doi: 10.1038/nature02340

2003

• Palenik, B., Brahamsha, B., Larimer, F. W., Land, M., Hauser, L., Chain, P., ... Waterbury, J. (2003). The genome of a motile marine Synechococcus. Nature, 424, 1037. doi: 10.1038/nature01943

2002

• Allen, E. E., & Bartlett, D. H. (2002). Structure and regulation of the omega-3 polyunsaturated fatty acid synthase genes from the deep-sea bacterium Photobacterium profundum strain SS9. Microbiology-SGM, 148, 1903-1913. doi: 10.1099/00221287-148-6-1903

2000

• Allen, E. E., & Bartlett, D. H. (2000). FabF is required for piezoregulation of cis-vaccenic acid levels and piezophilic growth of the deep-sea bacterium Photobacterium profundum strain SS9. Journal of Bacteriology, 182(5), 1264-1271. doi: 10.1128/jb.182.5.1264-1271.2000

1999

• Allen, E. E., Facciotti, D., & Bartlett, D. H. (1999). Monounsaturated but not polyunsaturated fatty acids are required for growth of the deep-sea bacterium Photobacterium profundum SS9 at high pressure and low temperature. Applied and Environmental Microbiology, 65(4), 1710-1720.