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2002 Jun; 148(Pt 6):1903-1913. 2011 Jan; 39(Database issue):D546-51. Baker BJ, Tyson GW, Webb RI, Flanagan J, Hugenholtz P. Genome-directed isolation of the key nitrogen fixer Leptospirillum ferrodiazotrophum sp. 2020 Jun 08. Note that an individual publication can be assigned to more than one field. 2019.
Lo I, Denef VJ, Verberkmoes NC, Shah MB, Goltsman D, DiBartolo G, Tyson GW. De novo sequences of Haloquadratum walsbyi from Lake Tyrrell, Australia, reveal a variable genomic landscape. Diversity and distribution of microbial long-chain fatty acid biosynthetic genes in the marine environment. This graph shows the total number of publications by year.
Genome Announc.
Coates RC, Podell S, Korobeynikov A, Lapidus A, Pevzner P, Sherman DH. Genome Announc.
Archaea.
ISME J. 2015 Dec; 9(12):2697-711. 2013; 8(8):e71952. Podell S, Emerson JB, Jones CM, Ugalde JA, Welch S, Heidelberg KB, Banfield JF.
Location: 4170 Hubbs Hall Tel: 858-534-2570 Fax: 858-534-7313 eallen at ucsd…
ISME J.
2018; 13(4):e0195102.
Minich JJ, Zhu Q, Janssen S, Hendrickson R, Amir A, Vetter R, Hyde J, Doty MM, Stillwell K, Benardini J, Kim JH. Draft Genome Sequence of "Candidatus Halobonum tyrrellensis" Strain G22, Isolated from the Hypersaline Waters of Lake Tyrrell, Australia. Metagenomic and lipid analyses reveal a diel cycle in a hypersaline microbial ecosystem. Minich JJ, Power C, Melanson M, Knight R, Webber C, Rough K, Bott NJ, Nowak B. Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment. 2011 Mar; 13(3):684-95. This site is running Profiles RNS version v2.12.0-792-gbe55c6ce on PROFILES-PWEB01. 2014. Kolody, B, McCrow J, Zeigler Allen L, Aylward F, Fontanez K, Moustafa A, Moniruzzaman M, Chavez F, Scholin C, Allen EE, Worden A, DeLong EF, Allen AE.
FabF is required for piezoregulation of cis-vaccenic acid levels and piezophilic growth of the deep-Sea bacterium Photobacterium profundum strain SS9. Biotechnol Biofuels.
We are investigating the genetics and regulation of bacterial omega-3 PUFA synthesis in several lineages of marine bacteria via bacterial genetic methods to uncover genetic determinants involved in PUFA synthesis and explore the physiological role of these unique marine lipids.
Eloe EA, Fadrosh DW, Novotny M, Zeigler Allen L, Kim M, Lombardo MJ, Yee-Greenbaum J, Yooseph S. Widespread occurrence of secondary lipid biosynthesis potential in microbial lineages. Allemann, MN, Allen EE. Eric Allen is a Professor in the Marine Biology Research Division and Center for Marine Biotechnology & Biomedicine at Scripps Institution of Oceanography, UC San Diego.
mBio. Minich JJ, Humphrey G, Benitez RAS, Sanders J, Swafford A. Pangenomic comparison of globally distributed Poribacteria associated with sponge hosts and marine particles. High-throughput miniaturized 16S rRNA amplicon library preparation reduces costs while preserving microbiome integrity. Minich, JJ, Humphrey G, Benitez RAS, Sanders J, Swafford A, Allen EE, Knight R. 2018. ISME J. Nucleic Acids Res. He became an Assistant Professor in Scripps’ Marine Biology Research Division in 2006. 2014 May; 8(5):979-90. Linkage of Marine Bacterial Polyunsaturated Fatty Acid and Long-Chain Hydrocarbon Biosynthesis. 2013 Dec; 79(23):7491-501. Eric Allen is a professor in the Biology department at University of California San Diego - see what their students are saying about them or leave a rating yourself. Association of rhizobia with a marine polychaete. Mol Ecol. Powered by Altman Clinical and Translational Research Institute, Altman Clinical and Translational Research Institute (ACTRI), Natural Sources and Microbial Transformation of Marine Halogenated Pollutants, Phylogenetic Binning of Metagenomic Sequence Data. Use of plankton-derived vitamin B1 precursors, especially thiazole-related precursor, by key marine picoeukaryotic phytoplankton.
Such investigations include a mix of field-based collections and bioinformatics combined with molecular ecology and genetics. Metabolic versatility of the Riftia pachyptila endosymbiont revealed through metagenomics. PLoS One. Genomic insights into the physiology and ecology of the marine filamentous cyanobacterium Lyngbya majuscula. Palenik B, Brahamsha B, Larimer FW, Land M, Hauser L, Chain P, Lamerdin J, Regala W. Structure and regulation of the omega-3 polyunsaturated fatty acid synthase genes from the deep-sea bacterium Photobacterium profundum strain SS9. He also holds a Professorship at UC San Diego’s Division of Biological Sciences in the Molecular Biology Section. Allemann, MN, Shulse CN, Allen EE.
2010 May 15; 44(10):3752-7.
Lineages of acidophilic archaea revealed by community genomic analysis. Front Microbiol.
ISME J. Research in our laboratory centers upon the use of environmentally-derived genome sequence information (“metagenomics”) to explore the genetic potential, ecology, and evolution of environmental microbial populations.
Archaea.
In addition to the biosynthesis of these compounds, we are also investigating microbial activities that degrade or transform these pollutants within marine animals, e.g. A native of Oregon (born in Eugene and raised in Medford), Allen received a bachelor’s degree in Biology from the University of Oregon in 1995 (Go Ducks!). the fish gut microbiome.
In this work we seek a molecular-level understanding of the microbial genes and enzymatic processes responsible for the biosynthesis of HOCs by marine microorganisms, with the ultimate goal of enabling genetic source tracking through DNA sequence-based biosynthetic signatures, across all trophic levels of the marine food web. UC San Diego 9500 Gilman Dr. La Jolla, CA 92093 (858) 534-2230 Appl Environ Microbiol. Robidart JC, Bench SR, Feldman RA, Novoradovsky A, Podell SB, Gaasterland T. Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. Environ Microbiol. Ugalde JA, Narasingarao P, Kuo S, Podell S. Seasonal fluctuations in ionic concentrations drive microbial succession in a hypersaline lake community. This graph shows the number and percent of publications by field. OC2388528 4 Page. Nat Rev Microbiol. 2015; 2015:875784. Genome Res. Derived automatically from this person's publications.
Environ Microbiol Rep. 2019 06; 11(3):434-447. Environ Microbiol Rep. 2013 Aug; 5(4):492-8. Professor, Scripps Institution of Oceanography Department. As a result, the publication counts in this graph might add up to more than the number of publications the person has written.
We develop and apply bioinformatics tools and pipelines for the annotation and analysis of microbial genomes and metagenomes, collaborating with colleagues in many diverse areas of experimental biology and microbial ecology, as well as marine natural product chemistry and marine geochemistry. Respiration - process of uptake of o2 and release of co2. Spring 2011 ~ Professor Eric Allen ~ 108 Peterson Hall ~ Tues Thurs 3:30 – 4:50 pm. 2014; 5:749.
If you continue to use this site we will assume that you are happy with it. mSystems. 2016; 7:2167. Comparative genomics of cyanobacterial symbionts reveals distinct, specialized metabolism in tropical Dysideidae sponges.
Metagenomic discovery of polybrominated diphenyl ether biosynthesis by marine sponges. ESYS 101 Lecture Notes - Lecture 13: Coconut Crab, Air Sacs, Cuticle. Podell, S, Emerson JB, Jones CM, Ugalde JA, Welch S, Heidelberg KB, Banfield JF, Allen EE. 2018 09; 12(9):2238-2251. Linkage of marine bacterial polyunsaturated fatty acid and long-chain hydrocarbon biosynthesis. This graph shows the total number of publications by year. Front Microbiol. Diversity and composition of intertidal gastropod microbiomes across a major marine biogeographic boundary. Diel transcriptional response of a California Current plankton microbiome to light, low iron, and enduring viral infection. A conjecture of Procesi and the straightening algorithm of Rota. Environ Sci Technol. DATE OPIC. Dynamic viral populations in hypersaline systems as revealed by metagenomic assembly. 2016; 9:258. Proc Natl Acad Sci U S A. Vertically distinct microbial communities in the Mariana and Kermadec trenches. 2019; 10:702. 2011 Oct 10; 6:52.
De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities. Biol Direct. Sierra Nevada mountain lake microbial communities are structured by temperature, resources and geographic location. Community structure and metabolism through reconstruction of microbial genomes from the environment. Allen is also a founding member of the San Diego Center for Algae Biotechnology, which was launched in 2009 to develop new bioenergy solutions. Nat Chem Biol. Nature. Eric Allen is a Professor in the Marine Biology Research Division and Center for Marine Biotechnology & Biomedicine at Scripps Institution of Oceanography, UC San Diego. 2018 Nov-Dec; 3(6). UC San Diego 9500 Gilman Dr. La Jolla, CA 92093 (858) 534-2230, cross-species transmission of microbial genomes, discovery and novelty assignment of secondary metabolite biosynthesis genes. Adaptive laboratory evolution of Escherichia coli K-12 MG1655 for growth at high hydrostatic pressure.
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