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Dr Mike Allen

Dr Mike Allen

Associate Professor of Single Cell Genomics

 Geoffrey Pope 

 

Geoffrey Pope Building, University of Exeter , Stocker Road, Exeter, EX4 4QD, UK

Overview

Professor Mike Allen is an Associate Professor of Single Cell Genomics in the College of Life and Environmental Sciences at University of Exeter, a Merit Scientist at Plymouth Marine Laboratory and an Honorary Fellow of the School of Physics at Bristol University. His interests are varied and encompass both blue skies and applied research topics. Blue skies research focuses mainly on understanding the role of viruses in the ocean using genomic, proteomic, transcriptomic and metabolomic approaches. Applied research focuses on biocatalysis, bioremediation, biotransformation, bioprocessing and technology development.

Mike’s current academic research projects include co-evolution of coccolithophores and coccolithoviruses, sphingolipid biosynthesis, novel protein characterisation, lytic and latent phytoplankton viruses, phytoplankton and virus isolation. Applied projects include biofuel production and processing, bioremediation, water sanitation, high throughput liquid processing and the development of novel photobioreactor technologies for promoting microalgal growth. 

Current and recent funding sources include The Bill and Melinda Gates Foundation, The Roddenberry Foundation, BBSRC and Innovate UK.

For more information on Mike, follow him @Mike_J_Allen on twitter, see his PML web profile.

Research

Publications

Key publications | Publications by category | Publications by year

Publications by category


Books

Wilson WH, Van Etten JL, Allen MJ (2009). The Phycodnaviridae: the story of how tiny giants rule the world. Abstract.

Journal articles

Warwick-Dugdale J, Buchholz H, Allen M, Temperton B (In Press). Host-hijacking and Planktonic Piracy: How Phages Command the Microbial High Seas. Virology Full text.
Piccini M, Raikova S, Allen MJ, Chuck CJ (2019). A synergistic use of microalgae and macroalgae for heavy metal bioremediation and bioenergy production through hydrothermal liquefaction. Sustainable Energy and Fuels, 3(1), 292-301. Abstract.
Raikova S, Knowles TDJ, Allen MJ, Chuck CJ (2019). Co-liquefaction of Macroalgae with Common Marine Plastic Pollutants. ACS Sustainable Chemistry and Engineering, 7(7), 6769-6781. Abstract.
D'Adamo S, Schiano di Visconte G, Lowe G, Szaub-Newton J, Beacham T, Landels A, Allen MJ, Spicer A, Matthijs M (2019). Engineering the unicellular alga Phaeodactylum tricornutum for high-value plant triterpenoid production. Plant Biotechnology Journal, 17(1), 75-87. Abstract.
Phillips ML, Weber SE, Andrews LV, Aronson EL, Allen MF, Allen EB (2019). Fungal community assembly in soils and roots under plant invasion and nitrogen deposition. Fungal Ecology Abstract.
Landels A, Beacham TA, Evans CT, Carnovale G, Raikova S, Cole IS, Goddard P, Chuck C, Allen MJ (2019). Improving electrocoagulation floatation for harvesting microalgae. Algal Research, 39 Abstract.
Abeln F, Fan J, Budarin VL, Briers H, Parsons S, Allen MJ, Henk DA, Clark J, Chuck CJ (2019). Lipid production through the single-step microwave hydrolysis of macroalgae using the oleaginous yeast Metschnikowia pulcherrima. Algal Research, 38 Abstract.
Weber SE, Diez JM, Andrews LV, Goulden ML, Aronson EL, Allen MF (2019). Responses of arbuscular mycorrhizal fungi to multiple coinciding global change drivers. Fungal Ecology Abstract.
Fernandez-Bou AS, Dierick D, Swanson AC, Allen MF, Alvarado AGF, Artavia-León A, Carrasquillo-Quintana O, Lachman DA, Oberbauer S, Pinto-Tomás AA, et al (2019). The Role of the Ecosystem Engineer, the Leaf-Cutter Ant Atta cephalotes, on Soil CO <inf>2</inf> Dynamics in a Wet Tropical Rainforest. Journal of Geophysical Research: Biogeosciences, 124(2), 260-273. Abstract.
Swanson AC, Schwendenmann L, Allen MF, Aronson EL, Artavia-León A, Dierick D, Fernandez-Bou AS, Harmon TC, Murillo-Cruz C, Oberbauer SF, et al (2019). Welcome to the Atta world: a framework for understanding the effects of leaf-cutter ants on ecosystem functions. Functional Ecology Abstract.
Taniguchi T, Kitajima K, Douhan GW, Yamanaka N, Allen MF (2018). A pulse of summer precipitation after the dry season triggers changes in ectomycorrhizal formation, diversity, and community composition in a Mediterranean forest in California, USA. Mycorrhiza, 28(7), 665-677. Abstract.
Evans CT, Payton O, Picco L, Allen MJ (2018). Algal viruses: the (atomic) shape of things to come. Viruses, 10(9). Abstract.  Full text.
Sivri N, Allen MJ, Jones M, Seker DZ, Durmus T, Balci M, Balkis N (2018). Distribution of enteric bacteria by means of gis and detection of Escherichia coli with uida gene in Kapıdağ Peninsula of Marmara sea. Indian Journal of Geo-Marine Sciences, 47(7), 1495-1501. Abstract.  Full text.
Aburto-Oropeza O, Johnson AF, Agha M, Allen EB, Allen MF, González JA, Arenas Moreno DM, Beas-Luna R, Butterfield S, Caetano G, et al (2018). Harnessing cross-border resources to confront climate change. Environmental Science and Policy, 87, 128-132. Abstract.
Teague J, Allen MJ, Scott TB (2018). The potential of low-cost ROV for use in deep-sea mineral, ore prospecting and monitoring. OCEAN ENGINEERING, 147, 333-339. Author URL.
Teague J, Scott TB, Sharma S, Graham G, Allen MJ (2017). An alternative method to niskin sampling for molecular analysis of the marine environment. Journal of Marine Science and Engineering, 5(2). Abstract.  Full text.
Nissimov JI, Pagarete A, Ma F, Cody S, Dunigan DD, Kimmance SA, Allen MJ (2017). Coccolithoviruses: a review of cross‐kingdom genomic thievery and metabolic thuggery. Viruses, 9(3). Abstract.  Full text.
Cagney N, Zhang T, Bransgrove R, Allen MJ, Balabani S (2017). Effects of cell motility and morphology on the rheology of algae suspensions. Journal of Applied Phycology, 29(3), 1145-1157. Abstract.
Hulton VanTassel HL, Bell MD, Rotenberry J, Johnson R, Allen MF (2017). Environmental change, shifting distributions, and habitat conservation plans: a case study of the California gnatcatcher. Ecology and Evolution, 7(23), 10326-10338. Abstract.
Hoffacker MK, Allen MF, Hernandez RR (2017). Land-Sparing Opportunities for Solar Energy Development in Agricultural Landscapes: a Case Study of the Great Central Valley, CA, United States. Environmental Science and Technology, 51(24), 14472-14482. Abstract.
Beacham TA, Sweet JB, Allen MJ (2017). Large scale cultivation of genetically modified microalgae: a new era for environmental risk assessment. Algal Research, 25, 90-100. Abstract.
Weynberg KD, Allen MJ, Wilson WH (2017). Marine prasinoviruses and their tiny plankton hosts: a review. Viruses, 9(3). Abstract.  Full text.
Coma M, Martinez-Hernandez E, Abeln F, Raikova S, Donnelly J, Arnot TC, Allen MJ, Hong DD, Chuck CJ (2017). Organic waste as a sustainable feedstock for platform chemicals. Faraday Discussions, 202, 175-195. Abstract.  Full text.
Raikova S, Le CD, Beacham TA, Jenkins RW, Allen MJ, Chuck CJ (2017). Towards a marine biorefinery through the hydrothermal liquefaction of macroalgae native to the United Kingdom. Biomass and Bioenergy, 107, 244-253. Abstract.
Raikova S, Smith-Baedorf H, Bransgrove R, Barlow O, Santomauro F, Wagner JL, Allen MJ, Bryan CG, Sapsford D, Chuck CJ, et al (2016). Assessing hydrothermal liquefaction for the production of bio-oil and enhanced metal recovery from microalgae cultivated on acid mine drainage. Fuel Processing Technology, 142, 219-227. Abstract.  Full text.
Wang H, Butt L, Rooks P, Khan F, Allen MJ, Ali ST (2016). Characterisation of algicidal bacterial exometabolites against the lipid-accumulating diatom Skeletonema sp. Algal Research, 13, 1-6. Abstract.
Wagner J, Bransgrove R, Beacham TA, Allen MJ, Meixner K, Drosg B, Ting VP, Chuck CJ (2016). Co-production of bio-oil and propylene through the hydrothermal liquefaction of polyhydroxybutyrate producing cyanobacteria. Bioresource Technology, 207, 166-174. Abstract.
Hernandez RR, Hoffacker MK, Murphy-Mariscal ML, Wu GC, Allen MF (2016). Erratum: Solar energy development impacts on land cover change and protected areas (Proceedings of the National Academy of Sciences of the United States of America (2015) 112:44 (13579-13584)). Proceedings of the National Academy of Sciences of the United States of America, 113(12).
Nissimov JI, Napier JA, Allen MJ, Kimmance SA (2016). Intragenus competition between coccolithoviruses: an insight on how a select few can come to dominate many. Environmental Microbiology, 18(1), 133-145. Abstract.
Pivovaroff AL, Santiago LS, Vourlitis GL, Grantz DA, Allen MF (2016). Plant hydraulic responses to long-term dry season nitrogen deposition alter drought tolerance in a Mediterranean-type ecosystem. Oecologia, 181(3), 721-731. Abstract.
Harmon TC, Dierick D, Trahan N, Allen MF, Rundel PW, Oberbauer SF, Schwendenmann L, Zelikova TJ (2015). Low-cost soil CO<inf>2</inf> efflux and point concentration sensing systems for terrestrial ecology applications. Methods in Ecology and Evolution, 6(11), 1358-1362. Abstract.
Murphy-Mariscal ML, Barrows CW, Allen MF (2015). Native Wildlife Use of Highway Underpasses in a Desert Environment. Southwestern Naturalist, 60(4), 340-348. Abstract.
Hernandez RR, Hoffacker MK, Murphy-Mariscal ML, Wu GC, Allen MF (2015). Solar energy development impacts on land cover change and protected areas. Proceedings of the National Academy of Sciences of the United States of America, 112(44), 13579-13584. Abstract.
Thomas SF, Rooks P, Rudin F, Cagney N, Balabani S, Atkinson S, Goddard P, Bransgrove RM, Mason PT, Allen MJ, et al (2015). Swirl flow bioreactor containing dendritic copper-containing alginate beads: a potential rapid method for the eradication of Escherichia coli from waste water streams. Journal of Water Process Engineering, 5, 6-14. Abstract.
Atkinson S, Thomas SF, Goddard P, Bransgrove RM, Mason PT, Oak A, Bansode A, Patankar R, Gleason ZD, Sim MK, et al (2015). Swirl flow bioreactor coupled with Cu-alginate beads: a system for the eradication of Coliform and Escherichia coli from biological effluents. Scientific Reports, 5 Abstract.  Full text.
Hamilton ML, Warwick J, Terry A, Allen MJ, Napier JA, Sayanova O (2015). Towards the industrial production of omega-3 long chain polyunsaturated fatty acids from a genetically modified diatom phaeodactylum tricornutum. PLoS ONE, 10(12). Abstract.
Thomas SF, Rooks P, Rudin F, Atkinson S, Goddard P, Bransgrove RM, Mason PT, Allen MJ (2014). A comparison between ultraviolet disinfection and copper alginate beads within a vortex bioreactor for the deactivation of bacteria in simulated waste streams with high levels of colour, humic acid and suspended solids. PLoS One, 9(12). Abstract.  Author URL.  Full text.
Droser ML, Gehling JG, Dzaugis ME, Kennedy MJ, Rice D, Allen MF (2014). A new ediacaran fossil with a novel sediment displacive life habit. Journal of Paleontology, 88(1), 145-151. Abstract.
Allen MJ (2014). Algal blooms and viruses. Microbiology Today, 41(4), 162-165. Abstract.
Pagarete A, Kusonmano K, Petersen K, Kimmance SA, Martínez Martínez J, Wilson WH, Hehemann JH, Allen MJ, Sandaa RA (2014). Dip in the gene pool: Metagenomic survey of natural coccolithovirus communities. Virology, 466-467, 129-137. Abstract.
Hernandez RR, Easter SB, Murphy-Mariscal ML, Maestre FT, Tavassoli M, Allen EB, Barrows CW, Belnap J, Ochoa-Hueso R, Ravi S, et al (2014). Environmental impacts of utility-scale solar energy. Renewable and Sustainable Energy Reviews, 29, 766-779. Abstract.
Jensen CN, Ali ST, Allen MJ, Grogan G (2014). Exploring nicotinamide cofactor promiscuity in NAD(P)H-dependent flavin containing monooxygenases (FMOs) using natural variation within the phosphate binding loop. Structure and activity of FMOs from Cellvibrio sp. BR and Pseudomonas stutzeri NF13. Journal of Molecular Catalysis B: Enzymatic, 109, 191-198. Abstract.
Allen MF, Kitajima K (2014). Net primary production of ectomycorrhizas in a California forest. Fungal Ecology, 10(1), 81-90. Abstract.
Sivri N, Jones M, Allen MJ (2014). PSEUDOMONAS AERUGINOSA ISOLATED FROM THE MARINE ENVIRONMENTS IN THE ISTANBUL COASTAL AREA (TURKEY). FRESENIUS ENVIRONMENTAL BULLETIN, 23(12B), 3340-3344. Author URL.
Nissimov JI, Napier JA, Kimmance SA, Allen MJ (2014). Permanent draft genomes of four new coccolithoviruses: EhV-18, EhV-145, EhV-156 and EhV-164. Marine Genomics, 15, 7-8. Abstract.
Sivri N, Allen MJ, Jones M, Akbulut V (2014). Potential public health significance of faecal contamination in South-Western Coastal Area in Istanbul, Turkey. Journal of Pure and Applied Microbiology, 8(5), 3789-3796. Abstract.
Kimmance SA, Allen MJ, Pagarete A, Martínez J, Wilson WH (2014). Reduction in photosystem 2 efficiency during a virus-Controlled Emiliania huxleyi bloom. Marine Ecology Progress Series, 495, 65-76. Abstract.
Thomas SF, Rooks P, Rudin F, Atkinson S, Goddard P, Bransgrove R, Mason PT, Allen MJ (2014). The bactericidal effect of dendritic copper microparticles, contained in an alginate matrix, on Escherichia coli. PLoS One, 9(5). Abstract.  Author URL.  Full text.
Kitajima K, Allen MF, Goulden ML (2013). Contribution of hydraulically lifted deep moisture to the water budget in a Southern California mixed forest. Journal of Geophysical Research: Biogeosciences, 118(4), 1561-1572. Abstract.
Hernandez RR, Allen MF (2013). Diurnal patterns of productivity of arbuscular mycorrhizal fungi revealed with the Soil Ecosystem Observatory. New Phytologist, 200(2), 547-557. Abstract.
Reid EL, Weynberg KD, Love J, Isupov MN, Littlechild JA, Wilson WH, Kelly SL, Lamb DC, Allen MJ (2013). Functional and structural characterisation of a viral cytochrome b5. FEBS Lett, 587(22), 3633-3639. Abstract.  Author URL.
Nissimov JI, Jones M, Napier JA, Munn CB, Kimmance SA, Allen MJ (2013). Functional inferences of environmental coccolithovirus biodiversity. Virologica Sinica, 28(5), 291-302. Abstract.
Allen MF, Kitajima K (2013). In situ high-frequency observations of mycorrhizas. New Phytologist, 200(1), 222-228. Abstract.
Nowakowski AJ, Otero Jiménez B, Allen M, Diaz-Escobar M, Donnelly MA (2013). Landscape resistance to movement of the poison frog, Oophaga pumilio, in the lowlands of northeastern Costa Rica. Animal Conservation, 16(2), 188-197. Abstract.
Jensen CN, Ali ST, Allen MJ, Grogan G (2013). Mutations of an NAD(P)H-dependent flavoprotein monooxygenase that influence cofactor promiscuity and enantioselectivity. FEBS Open Bio, 3, 473-478. Abstract.
Estrada-Medina H, Santiago LS, Graham RC, Allen MF, Jiménez-Osornio JJ (2013). Source water, phenology and growth of two tropical dry forest tree species growing on shallow karst soils. Trees - Structure and Function, 27(5), 1297-1307. Abstract.
Estrada-Medina H, Graham RC, Allen MF, Jiménez-Osornio JJ, Robles-Casolco S (2013). The importance of limestone bedrock and dissolution karst features on tree root distribution in northern Yucatán, México. Plant and Soil, 362(1-2), 37-50. Abstract.
Jensen CN, Cartwright J, Ward J, Hart S, Turkenburg JP, Ali ST, Allen MJ, Grogan G (2012). A Flavoprotein Monooxygenase that Catalyses a Baeyer-Villiger Reaction and Thioether Oxidation Using NADH as the Nicotinamide Cofactor. ChemBioChem, 13(6), 872-878. Abstract.
Ladwig LM, Collins SL, Swann AL, Xia Y, Allen MF, Allen EB (2012). Above- and belowground responses to nitrogen addition in a Chihuahuan Desert grassland. Oecologia, 169(1), 177-185. Abstract.
Hernandez RR, Mayernik MS, Murphy-Mariscal ML, Allen MF (2012). Advanced technologies and data management practices in environmental science: Lessons from academia. BioScience, 62(12), 1067-1076. Abstract.
Iversen CM, Murphy MT, Allen MF, Childs J, Eissenstat DM, Lilleskov EA, Sarjala TM, Sloan VL, Sullivan PF (2012). Advancing the use of minirhizotrons in wetlands. Plant and Soil, 352(1-2), 23-39. Abstract.
Querejeta JI, Egerton-Warburton LM, Prieto I, Vargas R, Allen MF (2012). Changes in soil hyphal abundance and viability can alter the patterns of hydraulic redistribution by plant roots. Plant and Soil, 355(1-2), 63-73. Abstract.
Preston KL, Redak RA, Allen MF, Rotenberry JT (2012). Changing distribution patterns of an endangered butterfly: Linking local extinction patterns and variable habitat relationships. Biological Conservation, 152, 280-290. Abstract.
Nissimov JI, Worthy CA, Rooks P, Napier JA, Kimmance SA, Henn MR, Ogata H, Allen MJ (2012). Draft genome sequence of four coccolithoviruses: Emiliania huxleyi virus EhV-88, EhV-201, EhV-207, and EhV-208. Journal of Virology, 86(5), 2896-2897. Abstract.
Nissimov JI, Worthy CA, Rooks P, Napier JA, Kimmance SA, Henn MR, Ogata H, Allen MJ (2012). Draft genome sequence of the coccolithovirus Emiliania huxleyi virus 202. Journal of Virology, 86(4), 2380-2381. Abstract.
Allen MJ, Tait K, Mühling M, Weynberg K, Bradley C, Trivedi U, Gharbi K, Nissimov J, Mavromatis K, Jensen CN, et al (2012). Genome sequence of Stenotrophomonas maltophilia PML168, which displays baeyer-villiger monooxygenase activity. Journal of Bacteriology, 194(17), 4753-4754. Abstract.
Pagarete A, Lanzén A, Puntervoll P, Sandaa RA, Larsen A, Larsen JB, Allen MJ, Bratbak G (2012). Genomic sequence and analysis of EhV-99B1, a new coccolithovirus from the Norwegian fjords. Intervirology, 56(1), 60-66. Abstract.
Allen MJ, Lanzén A, Bratbak G (2011). Characterisation of the coccolithovirus intein. Marine Genomics, 4(1), 1-7. Abstract.
Reid EL, Worthy CA, Probert I, Ali ST, Love J, Napier J, Littlechild JA, Somerfield PJ, Allen MJ (2011). Coccolithophores: functional biodiversity, enzymes and bioprospecting. Mar Drugs, 9(4), 586-602. Abstract.  Author URL.  Full text.
Nissimov JI, Worthy CA, Rooks P, Napier JA, Kimmance SA, Henn MR, Ogata H, Allen MJ (2011). Draft genome sequence of the coccolithovirus EhV-84. Standards in Genomic Sciences, 5(1), 1-11. Abstract.
Nissimov JI, Worthy CA, Rooks P, Napier JA, Kimmance SA, Henn MR, Ogata H, Allen MJ (2011). Draft genome sequence of the coccolithovirus Emiliania huxleyi virus 203. Journal of Virology, 85(24), 13468-13469. Abstract.
Hasselquist NJ, Douhan GW, Allen MF (2011). First report of the ectomycorrhizal status of boletes on the Northern Yucatan Peninsula, Mexico determined using isotopic methods. Mycorrhiza, 21(6), 465-471. Abstract.
Weynberg KD, Allen MJ, Gilg IC, Scanlan DJ, Wilson WH (2011). Genome sequence of Ostreococcus tauri virus OtV-2 throws light on the role of picoeukaryote niche separation in the ocean. Journal of Virology, 85(9), 4520-4529. Abstract.
Sayanova O, Haslam RP, Calerón MV, López NR, Worthy C, Rooks P, Allen MJ, Napier JA (2011). Identification and functional characterisation of genes encoding the omega-3 polyunsaturated fatty acid biosynthetic pathway from the coccolithophore Emiliania huxleyi. Phytochemistry, 72(7), 594-600. Abstract.
Barrows CW, Fleming KD, Allen MF (2011). Identifying habitat linkages to maintain connectivity for corridor dwellers in a fragmented landscape. Journal of Wildlife Management, 75(3), 682-691. Abstract.
Allen MF (2011). Linking water and nutrients through the vadose zone: a fungal interface between the soil and plant systems. Journal of Arid Land, 3(3), 155-163. Abstract.
Temperton B, Thomas S, Tait K, Parry H, Emery M, Allen M, Quinn J, Macgrath J, Gilbert J (2011). Permanent draft genome sequence of Vibrio tubiashii strain NCIMB 1337 (ATCC19106). Standards in Genomic Sciences, 4(2), 183-190. Abstract.  Full text.
Allen M, Pagarete A (2011). Silent killers - the biochemistry of the undead. Biochemist, 33(3), 10-13. Abstract.
Pagarete A, Le Corguillé G, Tiwari B, Ogata H, de Vargas C, Wilson WH, Allen MJ (2011). Unveiling the transcriptional features associated with coccolithovirus infection of natural Emiliania huxleyi blooms. FEMS Microbiology Ecology, 78(3), 555-564. Abstract.
Barrows CW, Rotenberry JT, Allen MF (2010). Assessing sensitivity to climate change and drought variability of a sand dune endemic lizard. Biological Conservation, 143(3), 731-736. Abstract.
Hasselquist NJ, Santiago LS, Allen MF (2010). Belowground nitrogen dynamics in relation to hurricane damage along a tropical dry forest chronosequence. Biogeochemistry, 98(1-3), 89-100. Abstract.
Goode LK, Erhardt EB, Santiago LS, Allen MF (2010). Carbon stable isotopic composition of soluble sugars in Tillandsia epiphytes varies in response to shifts in habitat. Oecologia, 163(3), 583-590. Abstract.
Chen X, Li BL, Allen MF (2010). Characterizing urbanization, and agricultural and conservation land-use change in Riverside County, California, USA. Annals of the New York Academy of Sciences, 1195(SUPPL. 1). Abstract.
McFarland JW, Ruess RW, Kielland K, Pregitzer K, Hendrick R, Allen M (2010). Cross-ecosystem comparisons of in situ plant uptake of amino acid-N and NH<inf>4</inf><sup>+</sup>. Ecosystems, 13(2), 177-193. Abstract.
Vargas R, Baldocchi DD, Querejeta JI, Curtis PS, Hasselquist NJ, Janssens IA, Allen MF, Montagnani L (2010). Ecosystem CO<inf>2</inf> fluxes of arbuscular and ectomycorrhizal dominated vegetation types are differentially influenced by precipitation and temperature. New Phytologist, 185(1), 226-236. Abstract.
Kitajima K, Anderson KE, Allen MF (2010). Effect of soil temperature and soil water content on fine root turnover rate in a California mixed conifer ecosystem. Journal of Geophysical Research: Biogeosciences, 115(4). Abstract.
Vargas R, Hasselquist N, Allen EB, Allen MF (2010). Effects of a hurricane disturbance on aboveground forest structure, arbuscular mycorrhizae and belowground carbon in a restored tropical forest. Ecosystems, 13(1), 118-128. Abstract.
Estrada-Medina H, Tuttle W, Graham RC, Allen MF, Jiménez-Osornio JJ (2010). Identification of underground karst features using ground-penetrating radar in northern Yucatán, México. Vadose Zone Journal, 9(3), 653-661. Abstract.
Vargas R, Baldocchi DD, Allen MF, Bahn M, Black TA, Collins SL, Yuste JC, Hirano T, Jassal RS, Pumpanen J, et al (2010). Looking deeper into the soil: Biophysical controls and seasonal lags of soil CO<inf>2</inf> production and efflux. Ecological Applications, 20(6), 1569-1582. Abstract.
Vargas R, Detto M, Baldocchi DD, Allen MF (2010). Multiscale analysis of temporal variability of soil CO<inf>2</inf> production as influenced by weather and vegetation. Global Change Biology, 16(5), 1589-1605. Abstract.
Allen MF, Allen EB, Lansing JL, Pregitzer KS, Hendrick RL, Ruess RW, Collins SL (2010). Responses to chronic N fertilization of ectomycorrhizal piñon but not arbuscular mycorrhizal juniper in a piñon-juniper woodland. Journal of Arid Environments, 74(10), 1170-1176. Abstract.
Allen M, Wilson W (2010). Survival of the fattest. Planet Earth(SPRING), 14-15. Abstract.
Kegel JU, Blaxter M, Allen MJ, Metfies K, Wilson WH, Valentin K (2010). Transcriptional host-virus interaction of Emiliania huxleyi (Haptophyceae) and EhV-86 deduced from combined analysis of expressed sequence tags and microarrays. European Journal of Phycology, 45(1), 1-12. Abstract.
Hasselquist NJ, Allen MF, Santiago LS (2010). Water relations of evergreen and drought-deciduous trees along a seasonally dry tropical forest chronosequence. Oecologia, 164(4), 881-890. Abstract.
Weynberg KD, Allen MJ, Ashelford K, Scanlan DJ, Wilson WH (2009). From small hosts come big viruses: the complete genome of a second Ostreococcus tauri virus, OtV-1. Environmental Microbiology, 11(11), 2821-2839. Abstract.
Monier A, Pagarete A, De Vargas C, Allen MJ, Read B, Claverie JM, Ogata H (2009). Horizontal gene transfer of an entire metabolic pathway between a eukaryotic alga and its DNA virus. Genome Research, 19(8), 1441-1449. Abstract.
Pagarete A, Allen MJ, Wilson WH, Kimmance SA, De Vargas C (2009). Host-virus shift of the sphingolipid pathway along an Emiliania huxleyi bloom: Survival of the fattest. Environmental Microbiology, 11(11), 2840-2848. Abstract.
Allen MJ, Wilson WH (2008). Aquatic virus diversity accessed through omic techniques: a route map to function. Current Opinion in Microbiology, 11(3), 226-232. Abstract.
Allen MJ, Howard JA, Lilley KS, Wilson WH (2008). Proteomic analysis of the EhV-86 virion. Proteome Science, 6 Abstract.
Frada M, Probert I, Allen MJ, Wilson WH, De Vargas C (2008). The "Cheshire Cat" escape strategy of the coccolithophore Emiliania huxleyi in response to viral infection. Proceedings of the National Academy of Sciences of the United States of America, 105(41), 15944-15949. Abstract.
Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, et al (2008). The minimum information about a genome sequence (MIGS) specification. NATURE BIOTECHNOLOGY, 26(5), 541-547. Author URL.
Kegel J, Allen MJ, Metfies K, Wilson WH, Wolf-Gladrow D, Valentin K (2007). Pilot study of an EST approach of the coccolithophorid Emiliania huxleyi during a virus infection. Gene, 406(1-2), 209-216. Abstract.
Allen MJ, Martinez-Martinez J, Schroeder DC, Somerfield PJ, Wilson WH (2007). Use of microarrays to assess viral diversity: from genotype to phenotype. Environmental Microbiology, 9(4), 971-982. Abstract.
Morrison N, Wood AJ, Hancock D, Shah S, Hakes L, Gray T, Tiwari B, Kille P, Cossins A, Hegarty M, et al (2006). Annotation of environmental OMICS data: Application to the transcriptomics domain. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY, 10(2), 172-178. Author URL.
Allen MJ, Schroeder DC, Holden MTG, Wilson WH (2006). Evolutionary history of the Coccolithoviridae. Molecular Biology and Evolution, 23(1), 86-92. Abstract.
Han G, Gable K, Yan L, Allen MJ, Wilson WH, Moitra P, Harmon JM, Dunn TM (2006). Expression of a novel marine viral single-chain serine palmitoyltransferase and construction of yeast and mammalian single-chain chimera. Journal of Biological Chemistry, 281(52), 39935-39942. Abstract.
Allen MJ, Schroeder DC, Donkin A, Crawfurd KJ, Wilson WH (2006). Genome comparison of two Coccolithoviruses. Virology Journal, 3 Abstract.
Allen MJ, Forster T, Schroeder DC, Hall M, Roy D, Ghazal P, Wilson WH (2006). Locus-specific gene expression pattern suggests a unique propagation strategy for a giant algal virus. Journal of Virology, 80(15), 7699-7705. Abstract.
Allen M (2006). Long live viruses. NEW SCIENTIST, 192(2572), 73-73. Author URL.
Allen MJ, Schroeder DC, Wilson WH (2006). Preliminary characterisation of repeat families in the genome of EhV-86, a giant algal virus that infects the marine microalga Emiliania huxleyi. Archives of Virology, 151(3), 525-535. Abstract.
Allen MJ, Wilson WH (2006). The coccolithovirus microarray: an array of uses. Briefings in Functional Genomics and Proteomics, 5(4), 273-279. Abstract.
Allen MJ, White GF, Morby AP (2006). The response of Escherichia coli to exposure to the biocide polyhexamethylene biguanide. Microbiology, 152(4), 989-1000. Abstract.
Wilson WH, Schroeder DC, Allen MJ, Holden MTG, Parkhill J, Barrell BG, Churcher C, Hamlin N, Mungall K, Norbertczak H, et al (2005). Complete genome sequence and lytic phase transcription profile of a Coccolithovirus. Science, 309(5737), 1090-1092. Abstract.
Allen MJ, Morby AP, White GF (2004). Cooperativity in the binding of the cationic biocide polyhexamethylene biguanide to nucleic acids. Biochemical and Biophysical Research Communications, 318(2), 397-404. Abstract.

Chapters

Allen MF, Allen EB (2016). Mycorrhizal Mediation of Soil Fertility Amidst Nitrogen Eutrophication and Climate Change. In  (Ed) Mycorrhizal Mediation of Soil: Fertility, Structure, and Carbon Storage, 213-231.  Abstract.
Allen MJ (2011). The (CO)Evolutionary Ecology of Viruses. In  (Ed) Studies in Viral Ecology: Animal Host Systems, 127-140.
Allen MJ (2011). The (Co)Evolutionary Ecology of Viruses. In  (Ed) Studies in Viral Ecology: Microbial and Botanical Host Systems, 131-144.
Allen MJ, Cossins AR, Hall N, Blaxter M, Burke T, Field D (2011). Use of microarrays to study environmentally relevant organisms: a UK perspective. In  (Ed) Advances in Environmental Research. Volume 13, 465-480.  Abstract.
Allen MJ, Cossins AR, Hall N, Blaxter M, Burke T, Field D (2011). Use of microarrays to study environmentally relevant organisms: a UK perspective. In  (Ed) Perspectives in Environmental Research, 187-202.  Abstract.
Wilson WH, Allen MJ (2011). Viruses of Eukaryotic Algae. In  (Ed) Studies in Viral Ecology: Microbial and Botanical Host Systems, 189-203.
Wilson WH, Allen MJ (2009). Giant viruses and their genomes. In  (Ed) Viral Genomes: Diversity, Properties and Parameters, 145-157.  Abstract.
Allen MF (2006). Water dynamics of mycorrhizas in arid soils. In  (Ed) Fungi in Biogeochemical Cycles, 74-97.  Abstract.

Conferences

Raikova S, Chuck C, McManus M, Allen M (2018). Hydrothermal liquefaction for marine macroalgal biorefinery.  Author URL.
Zaeuner S, Michaelson LV, Markham JE, Allen MA, Worthy CA, Heinz E, Warnecke D, Napier JA (2012). THE ROLE OF SPHINGOLIPIDS IN VIRUS-INDUCED CELL LYSIS IN EMILIANIA HUXLEYI.  Author URL.
Fischer MG, Allen MJ, Wilson WH, Suttle CA (2010). Giant virus with a remarkable complement of genes infects marine zooplankton.  Abstract.

Publications by year


In Press

Warwick-Dugdale J, Buchholz H, Allen M, Temperton B (In Press). Host-hijacking and Planktonic Piracy: How Phages Command the Microbial High Seas. Virology Full text.

2019

Piccini M, Raikova S, Allen MJ, Chuck CJ (2019). A synergistic use of microalgae and macroalgae for heavy metal bioremediation and bioenergy production through hydrothermal liquefaction. Sustainable Energy and Fuels, 3(1), 292-301. Abstract.
Raikova S, Knowles TDJ, Allen MJ, Chuck CJ (2019). Co-liquefaction of Macroalgae with Common Marine Plastic Pollutants. ACS Sustainable Chemistry and Engineering, 7(7), 6769-6781. Abstract.
D'Adamo S, Schiano di Visconte G, Lowe G, Szaub-Newton J, Beacham T, Landels A, Allen MJ, Spicer A, Matthijs M (2019). Engineering the unicellular alga Phaeodactylum tricornutum for high-value plant triterpenoid production. Plant Biotechnology Journal, 17(1), 75-87. Abstract.
Phillips ML, Weber SE, Andrews LV, Aronson EL, Allen MF, Allen EB (2019). Fungal community assembly in soils and roots under plant invasion and nitrogen deposition. Fungal Ecology Abstract.
Landels A, Beacham TA, Evans CT, Carnovale G, Raikova S, Cole IS, Goddard P, Chuck C, Allen MJ (2019). Improving electrocoagulation floatation for harvesting microalgae. Algal Research, 39 Abstract.
Abeln F, Fan J, Budarin VL, Briers H, Parsons S, Allen MJ, Henk DA, Clark J, Chuck CJ (2019). Lipid production through the single-step microwave hydrolysis of macroalgae using the oleaginous yeast Metschnikowia pulcherrima. Algal Research, 38 Abstract.
Weber SE, Diez JM, Andrews LV, Goulden ML, Aronson EL, Allen MF (2019). Responses of arbuscular mycorrhizal fungi to multiple coinciding global change drivers. Fungal Ecology Abstract.
Fernandez-Bou AS, Dierick D, Swanson AC, Allen MF, Alvarado AGF, Artavia-León A, Carrasquillo-Quintana O, Lachman DA, Oberbauer S, Pinto-Tomás AA, et al (2019). The Role of the Ecosystem Engineer, the Leaf-Cutter Ant Atta cephalotes, on Soil CO <inf>2</inf> Dynamics in a Wet Tropical Rainforest. Journal of Geophysical Research: Biogeosciences, 124(2), 260-273. Abstract.
Swanson AC, Schwendenmann L, Allen MF, Aronson EL, Artavia-León A, Dierick D, Fernandez-Bou AS, Harmon TC, Murillo-Cruz C, Oberbauer SF, et al (2019). Welcome to the Atta world: a framework for understanding the effects of leaf-cutter ants on ecosystem functions. Functional Ecology Abstract.

2018

Taniguchi T, Kitajima K, Douhan GW, Yamanaka N, Allen MF (2018). A pulse of summer precipitation after the dry season triggers changes in ectomycorrhizal formation, diversity, and community composition in a Mediterranean forest in California, USA. Mycorrhiza, 28(7), 665-677. Abstract.
Evans CT, Payton O, Picco L, Allen MJ (2018). Algal viruses: the (atomic) shape of things to come. Viruses, 10(9). Abstract.  Full text.
Sivri N, Allen MJ, Jones M, Seker DZ, Durmus T, Balci M, Balkis N (2018). Distribution of enteric bacteria by means of gis and detection of Escherichia coli with uida gene in Kapıdağ Peninsula of Marmara sea. Indian Journal of Geo-Marine Sciences, 47(7), 1495-1501. Abstract.  Full text.
Aburto-Oropeza O, Johnson AF, Agha M, Allen EB, Allen MF, González JA, Arenas Moreno DM, Beas-Luna R, Butterfield S, Caetano G, et al (2018). Harnessing cross-border resources to confront climate change. Environmental Science and Policy, 87, 128-132. Abstract.
Raikova S, Chuck C, McManus M, Allen M (2018). Hydrothermal liquefaction for marine macroalgal biorefinery.  Author URL.
Teague J, Allen MJ, Scott TB (2018). The potential of low-cost ROV for use in deep-sea mineral, ore prospecting and monitoring. OCEAN ENGINEERING, 147, 333-339. Author URL.

2017

Teague J, Scott TB, Sharma S, Graham G, Allen MJ (2017). An alternative method to niskin sampling for molecular analysis of the marine environment. Journal of Marine Science and Engineering, 5(2). Abstract.  Full text.
Nissimov JI, Pagarete A, Ma F, Cody S, Dunigan DD, Kimmance SA, Allen MJ (2017). Coccolithoviruses: a review of cross‐kingdom genomic thievery and metabolic thuggery. Viruses, 9(3). Abstract.  Full text.
Cagney N, Zhang T, Bransgrove R, Allen MJ, Balabani S (2017). Effects of cell motility and morphology on the rheology of algae suspensions. Journal of Applied Phycology, 29(3), 1145-1157. Abstract.
Hulton VanTassel HL, Bell MD, Rotenberry J, Johnson R, Allen MF (2017). Environmental change, shifting distributions, and habitat conservation plans: a case study of the California gnatcatcher. Ecology and Evolution, 7(23), 10326-10338. Abstract.
Hoffacker MK, Allen MF, Hernandez RR (2017). Land-Sparing Opportunities for Solar Energy Development in Agricultural Landscapes: a Case Study of the Great Central Valley, CA, United States. Environmental Science and Technology, 51(24), 14472-14482. Abstract.
Beacham TA, Sweet JB, Allen MJ (2017). Large scale cultivation of genetically modified microalgae: a new era for environmental risk assessment. Algal Research, 25, 90-100. Abstract.
Weynberg KD, Allen MJ, Wilson WH (2017). Marine prasinoviruses and their tiny plankton hosts: a review. Viruses, 9(3). Abstract.  Full text.
Coma M, Martinez-Hernandez E, Abeln F, Raikova S, Donnelly J, Arnot TC, Allen MJ, Hong DD, Chuck CJ (2017). Organic waste as a sustainable feedstock for platform chemicals. Faraday Discussions, 202, 175-195. Abstract.  Full text.
Raikova S, Le CD, Beacham TA, Jenkins RW, Allen MJ, Chuck CJ (2017). Towards a marine biorefinery through the hydrothermal liquefaction of macroalgae native to the United Kingdom. Biomass and Bioenergy, 107, 244-253. Abstract.

2016

Raikova S, Smith-Baedorf H, Bransgrove R, Barlow O, Santomauro F, Wagner JL, Allen MJ, Bryan CG, Sapsford D, Chuck CJ, et al (2016). Assessing hydrothermal liquefaction for the production of bio-oil and enhanced metal recovery from microalgae cultivated on acid mine drainage. Fuel Processing Technology, 142, 219-227. Abstract.  Full text.
Wang H, Butt L, Rooks P, Khan F, Allen MJ, Ali ST (2016). Characterisation of algicidal bacterial exometabolites against the lipid-accumulating diatom Skeletonema sp. Algal Research, 13, 1-6. Abstract.
Wagner J, Bransgrove R, Beacham TA, Allen MJ, Meixner K, Drosg B, Ting VP, Chuck CJ (2016). Co-production of bio-oil and propylene through the hydrothermal liquefaction of polyhydroxybutyrate producing cyanobacteria. Bioresource Technology, 207, 166-174. Abstract.
Hernandez RR, Hoffacker MK, Murphy-Mariscal ML, Wu GC, Allen MF (2016). Erratum: Solar energy development impacts on land cover change and protected areas (Proceedings of the National Academy of Sciences of the United States of America (2015) 112:44 (13579-13584)). Proceedings of the National Academy of Sciences of the United States of America, 113(12).
Nissimov JI, Napier JA, Allen MJ, Kimmance SA (2016). Intragenus competition between coccolithoviruses: an insight on how a select few can come to dominate many. Environmental Microbiology, 18(1), 133-145. Abstract.
Allen MF, Allen EB (2016). Mycorrhizal Mediation of Soil Fertility Amidst Nitrogen Eutrophication and Climate Change. In  (Ed) Mycorrhizal Mediation of Soil: Fertility, Structure, and Carbon Storage, 213-231.  Abstract.
Pivovaroff AL, Santiago LS, Vourlitis GL, Grantz DA, Allen MF (2016). Plant hydraulic responses to long-term dry season nitrogen deposition alter drought tolerance in a Mediterranean-type ecosystem. Oecologia, 181(3), 721-731. Abstract.

2015

Harmon TC, Dierick D, Trahan N, Allen MF, Rundel PW, Oberbauer SF, Schwendenmann L, Zelikova TJ (2015). Low-cost soil CO<inf>2</inf> efflux and point concentration sensing systems for terrestrial ecology applications. Methods in Ecology and Evolution, 6(11), 1358-1362. Abstract.
Murphy-Mariscal ML, Barrows CW, Allen MF (2015). Native Wildlife Use of Highway Underpasses in a Desert Environment. Southwestern Naturalist, 60(4), 340-348. Abstract.
Hernandez RR, Hoffacker MK, Murphy-Mariscal ML, Wu GC, Allen MF (2015). Solar energy development impacts on land cover change and protected areas. Proceedings of the National Academy of Sciences of the United States of America, 112(44), 13579-13584. Abstract.
Thomas SF, Rooks P, Rudin F, Cagney N, Balabani S, Atkinson S, Goddard P, Bransgrove RM, Mason PT, Allen MJ, et al (2015). Swirl flow bioreactor containing dendritic copper-containing alginate beads: a potential rapid method for the eradication of Escherichia coli from waste water streams. Journal of Water Process Engineering, 5, 6-14. Abstract.
Atkinson S, Thomas SF, Goddard P, Bransgrove RM, Mason PT, Oak A, Bansode A, Patankar R, Gleason ZD, Sim MK, et al (2015). Swirl flow bioreactor coupled with Cu-alginate beads: a system for the eradication of Coliform and Escherichia coli from biological effluents. Scientific Reports, 5 Abstract.  Full text.
Hamilton ML, Warwick J, Terry A, Allen MJ, Napier JA, Sayanova O (2015). Towards the industrial production of omega-3 long chain polyunsaturated fatty acids from a genetically modified diatom phaeodactylum tricornutum. PLoS ONE, 10(12). Abstract.

2014

Thomas SF, Rooks P, Rudin F, Atkinson S, Goddard P, Bransgrove RM, Mason PT, Allen MJ (2014). A comparison between ultraviolet disinfection and copper alginate beads within a vortex bioreactor for the deactivation of bacteria in simulated waste streams with high levels of colour, humic acid and suspended solids. PLoS One, 9(12). Abstract.  Author URL.  Full text.
Droser ML, Gehling JG, Dzaugis ME, Kennedy MJ, Rice D, Allen MF (2014). A new ediacaran fossil with a novel sediment displacive life habit. Journal of Paleontology, 88(1), 145-151. Abstract.
Allen MJ (2014). Algal blooms and viruses. Microbiology Today, 41(4), 162-165. Abstract.
Pagarete A, Kusonmano K, Petersen K, Kimmance SA, Martínez Martínez J, Wilson WH, Hehemann JH, Allen MJ, Sandaa RA (2014). Dip in the gene pool: Metagenomic survey of natural coccolithovirus communities. Virology, 466-467, 129-137. Abstract.
Hernandez RR, Easter SB, Murphy-Mariscal ML, Maestre FT, Tavassoli M, Allen EB, Barrows CW, Belnap J, Ochoa-Hueso R, Ravi S, et al (2014). Environmental impacts of utility-scale solar energy. Renewable and Sustainable Energy Reviews, 29, 766-779. Abstract.
Jensen CN, Ali ST, Allen MJ, Grogan G (2014). Exploring nicotinamide cofactor promiscuity in NAD(P)H-dependent flavin containing monooxygenases (FMOs) using natural variation within the phosphate binding loop. Structure and activity of FMOs from Cellvibrio sp. BR and Pseudomonas stutzeri NF13. Journal of Molecular Catalysis B: Enzymatic, 109, 191-198. Abstract.
Allen MF, Kitajima K (2014). Net primary production of ectomycorrhizas in a California forest. Fungal Ecology, 10(1), 81-90. Abstract.
Sivri N, Jones M, Allen MJ (2014). PSEUDOMONAS AERUGINOSA ISOLATED FROM THE MARINE ENVIRONMENTS IN THE ISTANBUL COASTAL AREA (TURKEY). FRESENIUS ENVIRONMENTAL BULLETIN, 23(12B), 3340-3344. Author URL.
Nissimov JI, Napier JA, Kimmance SA, Allen MJ (2014). Permanent draft genomes of four new coccolithoviruses: EhV-18, EhV-145, EhV-156 and EhV-164. Marine Genomics, 15, 7-8. Abstract.
Sivri N, Allen MJ, Jones M, Akbulut V (2014). Potential public health significance of faecal contamination in South-Western Coastal Area in Istanbul, Turkey. Journal of Pure and Applied Microbiology, 8(5), 3789-3796. Abstract.
Kimmance SA, Allen MJ, Pagarete A, Martínez J, Wilson WH (2014). Reduction in photosystem 2 efficiency during a virus-Controlled Emiliania huxleyi bloom. Marine Ecology Progress Series, 495, 65-76. Abstract.
Thomas SF, Rooks P, Rudin F, Atkinson S, Goddard P, Bransgrove R, Mason PT, Allen MJ (2014). The bactericidal effect of dendritic copper microparticles, contained in an alginate matrix, on Escherichia coli. PLoS One, 9(5). Abstract.  Author URL.  Full text.

2013

Kitajima K, Allen MF, Goulden ML (2013). Contribution of hydraulically lifted deep moisture to the water budget in a Southern California mixed forest. Journal of Geophysical Research: Biogeosciences, 118(4), 1561-1572. Abstract.
Hernandez RR, Allen MF (2013). Diurnal patterns of productivity of arbuscular mycorrhizal fungi revealed with the Soil Ecosystem Observatory. New Phytologist, 200(2), 547-557. Abstract.
Reid EL, Weynberg KD, Love J, Isupov MN, Littlechild JA, Wilson WH, Kelly SL, Lamb DC, Allen MJ (2013). Functional and structural characterisation of a viral cytochrome b5. FEBS Lett, 587(22), 3633-3639. Abstract.  Author URL.
Nissimov JI, Jones M, Napier JA, Munn CB, Kimmance SA, Allen MJ (2013). Functional inferences of environmental coccolithovirus biodiversity. Virologica Sinica, 28(5), 291-302. Abstract.
Allen MF, Kitajima K (2013). In situ high-frequency observations of mycorrhizas. New Phytologist, 200(1), 222-228. Abstract.
Nowakowski AJ, Otero Jiménez B, Allen M, Diaz-Escobar M, Donnelly MA (2013). Landscape resistance to movement of the poison frog, Oophaga pumilio, in the lowlands of northeastern Costa Rica. Animal Conservation, 16(2), 188-197. Abstract.
Jensen CN, Ali ST, Allen MJ, Grogan G (2013). Mutations of an NAD(P)H-dependent flavoprotein monooxygenase that influence cofactor promiscuity and enantioselectivity. FEBS Open Bio, 3, 473-478. Abstract.
Estrada-Medina H, Santiago LS, Graham RC, Allen MF, Jiménez-Osornio JJ (2013). Source water, phenology and growth of two tropical dry forest tree species growing on shallow karst soils. Trees - Structure and Function, 27(5), 1297-1307. Abstract.
Estrada-Medina H, Graham RC, Allen MF, Jiménez-Osornio JJ, Robles-Casolco S (2013). The importance of limestone bedrock and dissolution karst features on tree root distribution in northern Yucatán, México. Plant and Soil, 362(1-2), 37-50. Abstract.

2012

Jensen CN, Cartwright J, Ward J, Hart S, Turkenburg JP, Ali ST, Allen MJ, Grogan G (2012). A Flavoprotein Monooxygenase that Catalyses a Baeyer-Villiger Reaction and Thioether Oxidation Using NADH as the Nicotinamide Cofactor. ChemBioChem, 13(6), 872-878. Abstract.
Ladwig LM, Collins SL, Swann AL, Xia Y, Allen MF, Allen EB (2012). Above- and belowground responses to nitrogen addition in a Chihuahuan Desert grassland. Oecologia, 169(1), 177-185. Abstract.
Hernandez RR, Mayernik MS, Murphy-Mariscal ML, Allen MF (2012). Advanced technologies and data management practices in environmental science: Lessons from academia. BioScience, 62(12), 1067-1076. Abstract.
Iversen CM, Murphy MT, Allen MF, Childs J, Eissenstat DM, Lilleskov EA, Sarjala TM, Sloan VL, Sullivan PF (2012). Advancing the use of minirhizotrons in wetlands. Plant and Soil, 352(1-2), 23-39. Abstract.
Querejeta JI, Egerton-Warburton LM, Prieto I, Vargas R, Allen MF (2012). Changes in soil hyphal abundance and viability can alter the patterns of hydraulic redistribution by plant roots. Plant and Soil, 355(1-2), 63-73. Abstract.
Preston KL, Redak RA, Allen MF, Rotenberry JT (2012). Changing distribution patterns of an endangered butterfly: Linking local extinction patterns and variable habitat relationships. Biological Conservation, 152, 280-290. Abstract.
Nissimov JI, Worthy CA, Rooks P, Napier JA, Kimmance SA, Henn MR, Ogata H, Allen MJ (2012). Draft genome sequence of four coccolithoviruses: Emiliania huxleyi virus EhV-88, EhV-201, EhV-207, and EhV-208. Journal of Virology, 86(5), 2896-2897. Abstract.
Nissimov JI, Worthy CA, Rooks P, Napier JA, Kimmance SA, Henn MR, Ogata H, Allen MJ (2012). Draft genome sequence of the coccolithovirus Emiliania huxleyi virus 202. Journal of Virology, 86(4), 2380-2381. Abstract.
Allen MJ, Tait K, Mühling M, Weynberg K, Bradley C, Trivedi U, Gharbi K, Nissimov J, Mavromatis K, Jensen CN, et al (2012). Genome sequence of Stenotrophomonas maltophilia PML168, which displays baeyer-villiger monooxygenase activity. Journal of Bacteriology, 194(17), 4753-4754. Abstract.
Pagarete A, Lanzén A, Puntervoll P, Sandaa RA, Larsen A, Larsen JB, Allen MJ, Bratbak G (2012). Genomic sequence and analysis of EhV-99B1, a new coccolithovirus from the Norwegian fjords. Intervirology, 56(1), 60-66. Abstract.
Zaeuner S, Michaelson LV, Markham JE, Allen MA, Worthy CA, Heinz E, Warnecke D, Napier JA (2012). THE ROLE OF SPHINGOLIPIDS IN VIRUS-INDUCED CELL LYSIS IN EMILIANIA HUXLEYI.  Author URL.

2011

Allen MJ, Lanzén A, Bratbak G (2011). Characterisation of the coccolithovirus intein. Marine Genomics, 4(1), 1-7. Abstract.
Reid EL, Worthy CA, Probert I, Ali ST, Love J, Napier J, Littlechild JA, Somerfield PJ, Allen MJ (2011). Coccolithophores: functional biodiversity, enzymes and bioprospecting. Mar Drugs, 9(4), 586-602. Abstract.  Author URL.  Full text.
Nissimov JI, Worthy CA, Rooks P, Napier JA, Kimmance SA, Henn MR, Ogata H, Allen MJ (2011). Draft genome sequence of the coccolithovirus EhV-84. Standards in Genomic Sciences, 5(1), 1-11. Abstract.
Nissimov JI, Worthy CA, Rooks P, Napier JA, Kimmance SA, Henn MR, Ogata H, Allen MJ (2011). Draft genome sequence of the coccolithovirus Emiliania huxleyi virus 203. Journal of Virology, 85(24), 13468-13469. Abstract.
Hasselquist NJ, Douhan GW, Allen MF (2011). First report of the ectomycorrhizal status of boletes on the Northern Yucatan Peninsula, Mexico determined using isotopic methods. Mycorrhiza, 21(6), 465-471. Abstract.
Weynberg KD, Allen MJ, Gilg IC, Scanlan DJ, Wilson WH (2011). Genome sequence of Ostreococcus tauri virus OtV-2 throws light on the role of picoeukaryote niche separation in the ocean. Journal of Virology, 85(9), 4520-4529. Abstract.
Sayanova O, Haslam RP, Calerón MV, López NR, Worthy C, Rooks P, Allen MJ, Napier JA (2011). Identification and functional characterisation of genes encoding the omega-3 polyunsaturated fatty acid biosynthetic pathway from the coccolithophore Emiliania huxleyi. Phytochemistry, 72(7), 594-600. Abstract.
Barrows CW, Fleming KD, Allen MF (2011). Identifying habitat linkages to maintain connectivity for corridor dwellers in a fragmented landscape. Journal of Wildlife Management, 75(3), 682-691. Abstract.
Allen MF (2011). Linking water and nutrients through the vadose zone: a fungal interface between the soil and plant systems. Journal of Arid Land, 3(3), 155-163. Abstract.
Temperton B, Thomas S, Tait K, Parry H, Emery M, Allen M, Quinn J, Macgrath J, Gilbert J (2011). Permanent draft genome sequence of Vibrio tubiashii strain NCIMB 1337 (ATCC19106). Standards in Genomic Sciences, 4(2), 183-190. Abstract.  Full text.
Allen M, Pagarete A (2011). Silent killers - the biochemistry of the undead. Biochemist, 33(3), 10-13. Abstract.
Allen MJ (2011). The (CO)Evolutionary Ecology of Viruses. In  (Ed) Studies in Viral Ecology: Animal Host Systems, 127-140.
Allen MJ (2011). The (Co)Evolutionary Ecology of Viruses. In  (Ed) Studies in Viral Ecology: Microbial and Botanical Host Systems, 131-144.
Pagarete A, Le Corguillé G, Tiwari B, Ogata H, de Vargas C, Wilson WH, Allen MJ (2011). Unveiling the transcriptional features associated with coccolithovirus infection of natural Emiliania huxleyi blooms. FEMS Microbiology Ecology, 78(3), 555-564. Abstract.
Allen MJ, Cossins AR, Hall N, Blaxter M, Burke T, Field D (2011). Use of microarrays to study environmentally relevant organisms: a UK perspective. In  (Ed) Advances in Environmental Research. Volume 13, 465-480.  Abstract.
Allen MJ, Cossins AR, Hall N, Blaxter M, Burke T, Field D (2011). Use of microarrays to study environmentally relevant organisms: a UK perspective. In  (Ed) Perspectives in Environmental Research, 187-202.  Abstract.
Wilson WH, Allen MJ (2011). Viruses of Eukaryotic Algae. In  (Ed) Studies in Viral Ecology: Microbial and Botanical Host Systems, 189-203.

2010

Barrows CW, Rotenberry JT, Allen MF (2010). Assessing sensitivity to climate change and drought variability of a sand dune endemic lizard. Biological Conservation, 143(3), 731-736. Abstract.
Hasselquist NJ, Santiago LS, Allen MF (2010). Belowground nitrogen dynamics in relation to hurricane damage along a tropical dry forest chronosequence. Biogeochemistry, 98(1-3), 89-100. Abstract.
Goode LK, Erhardt EB, Santiago LS, Allen MF (2010). Carbon stable isotopic composition of soluble sugars in Tillandsia epiphytes varies in response to shifts in habitat. Oecologia, 163(3), 583-590. Abstract.
Chen X, Li BL, Allen MF (2010). Characterizing urbanization, and agricultural and conservation land-use change in Riverside County, California, USA. Annals of the New York Academy of Sciences, 1195(SUPPL. 1). Abstract.
McFarland JW, Ruess RW, Kielland K, Pregitzer K, Hendrick R, Allen M (2010). Cross-ecosystem comparisons of in situ plant uptake of amino acid-N and NH<inf>4</inf><sup>+</sup>. Ecosystems, 13(2), 177-193. Abstract.
Vargas R, Baldocchi DD, Querejeta JI, Curtis PS, Hasselquist NJ, Janssens IA, Allen MF, Montagnani L (2010). Ecosystem CO<inf>2</inf> fluxes of arbuscular and ectomycorrhizal dominated vegetation types are differentially influenced by precipitation and temperature. New Phytologist, 185(1), 226-236. Abstract.
Kitajima K, Anderson KE, Allen MF (2010). Effect of soil temperature and soil water content on fine root turnover rate in a California mixed conifer ecosystem. Journal of Geophysical Research: Biogeosciences, 115(4). Abstract.
Vargas R, Hasselquist N, Allen EB, Allen MF (2010). Effects of a hurricane disturbance on aboveground forest structure, arbuscular mycorrhizae and belowground carbon in a restored tropical forest. Ecosystems, 13(1), 118-128. Abstract.
Fischer MG, Allen MJ, Wilson WH, Suttle CA (2010). Giant virus with a remarkable complement of genes infects marine zooplankton.  Abstract.
Estrada-Medina H, Tuttle W, Graham RC, Allen MF, Jiménez-Osornio JJ (2010). Identification of underground karst features using ground-penetrating radar in northern Yucatán, México. Vadose Zone Journal, 9(3), 653-661. Abstract.
Vargas R, Baldocchi DD, Allen MF, Bahn M, Black TA, Collins SL, Yuste JC, Hirano T, Jassal RS, Pumpanen J, et al (2010). Looking deeper into the soil: Biophysical controls and seasonal lags of soil CO<inf>2</inf> production and efflux. Ecological Applications, 20(6), 1569-1582. Abstract.
Vargas R, Detto M, Baldocchi DD, Allen MF (2010). Multiscale analysis of temporal variability of soil CO<inf>2</inf> production as influenced by weather and vegetation. Global Change Biology, 16(5), 1589-1605. Abstract.
Allen MF, Allen EB, Lansing JL, Pregitzer KS, Hendrick RL, Ruess RW, Collins SL (2010). Responses to chronic N fertilization of ectomycorrhizal piñon but not arbuscular mycorrhizal juniper in a piñon-juniper woodland. Journal of Arid Environments, 74(10), 1170-1176. Abstract.
Allen M, Wilson W (2010). Survival of the fattest. Planet Earth(SPRING), 14-15. Abstract.
Kegel JU, Blaxter M, Allen MJ, Metfies K, Wilson WH, Valentin K (2010). Transcriptional host-virus interaction of Emiliania huxleyi (Haptophyceae) and EhV-86 deduced from combined analysis of expressed sequence tags and microarrays. European Journal of Phycology, 45(1), 1-12. Abstract.
Hasselquist NJ, Allen MF, Santiago LS (2010). Water relations of evergreen and drought-deciduous trees along a seasonally dry tropical forest chronosequence. Oecologia, 164(4), 881-890. Abstract.

2009

Weynberg KD, Allen MJ, Ashelford K, Scanlan DJ, Wilson WH (2009). From small hosts come big viruses: the complete genome of a second Ostreococcus tauri virus, OtV-1. Environmental Microbiology, 11(11), 2821-2839. Abstract.
Wilson WH, Allen MJ (2009). Giant viruses and their genomes. In  (Ed) Viral Genomes: Diversity, Properties and Parameters, 145-157.  Abstract.
Monier A, Pagarete A, De Vargas C, Allen MJ, Read B, Claverie JM, Ogata H (2009). Horizontal gene transfer of an entire metabolic pathway between a eukaryotic alga and its DNA virus. Genome Research, 19(8), 1441-1449. Abstract.
Pagarete A, Allen MJ, Wilson WH, Kimmance SA, De Vargas C (2009). Host-virus shift of the sphingolipid pathway along an Emiliania huxleyi bloom: Survival of the fattest. Environmental Microbiology, 11(11), 2840-2848. Abstract.
Wilson WH, Van Etten JL, Allen MJ (2009). The Phycodnaviridae: the story of how tiny giants rule the world. Abstract.

2008

Allen MJ, Wilson WH (2008). Aquatic virus diversity accessed through omic techniques: a route map to function. Current Opinion in Microbiology, 11(3), 226-232. Abstract.
Allen MJ, Howard JA, Lilley KS, Wilson WH (2008). Proteomic analysis of the EhV-86 virion. Proteome Science, 6 Abstract.
Frada M, Probert I, Allen MJ, Wilson WH, De Vargas C (2008). The "Cheshire Cat" escape strategy of the coccolithophore Emiliania huxleyi in response to viral infection. Proceedings of the National Academy of Sciences of the United States of America, 105(41), 15944-15949. Abstract.
Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, et al (2008). The minimum information about a genome sequence (MIGS) specification. NATURE BIOTECHNOLOGY, 26(5), 541-547. Author URL.

2007

Kegel J, Allen MJ, Metfies K, Wilson WH, Wolf-Gladrow D, Valentin K (2007). Pilot study of an EST approach of the coccolithophorid Emiliania huxleyi during a virus infection. Gene, 406(1-2), 209-216. Abstract.
Allen MJ, Martinez-Martinez J, Schroeder DC, Somerfield PJ, Wilson WH (2007). Use of microarrays to assess viral diversity: from genotype to phenotype. Environmental Microbiology, 9(4), 971-982. Abstract.

2006

Morrison N, Wood AJ, Hancock D, Shah S, Hakes L, Gray T, Tiwari B, Kille P, Cossins A, Hegarty M, et al (2006). Annotation of environmental OMICS data: Application to the transcriptomics domain. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY, 10(2), 172-178. Author URL.
Allen MJ, Schroeder DC, Holden MTG, Wilson WH (2006). Evolutionary history of the Coccolithoviridae. Molecular Biology and Evolution, 23(1), 86-92. Abstract.
Han G, Gable K, Yan L, Allen MJ, Wilson WH, Moitra P, Harmon JM, Dunn TM (2006). Expression of a novel marine viral single-chain serine palmitoyltransferase and construction of yeast and mammalian single-chain chimera. Journal of Biological Chemistry, 281(52), 39935-39942. Abstract.
Allen MJ, Schroeder DC, Donkin A, Crawfurd KJ, Wilson WH (2006). Genome comparison of two Coccolithoviruses. Virology Journal, 3 Abstract.
Allen MJ, Forster T, Schroeder DC, Hall M, Roy D, Ghazal P, Wilson WH (2006). Locus-specific gene expression pattern suggests a unique propagation strategy for a giant algal virus. Journal of Virology, 80(15), 7699-7705. Abstract.
Allen M (2006). Long live viruses. NEW SCIENTIST, 192(2572), 73-73. Author URL.
Allen MJ, Schroeder DC, Wilson WH (2006). Preliminary characterisation of repeat families in the genome of EhV-86, a giant algal virus that infects the marine microalga Emiliania huxleyi. Archives of Virology, 151(3), 525-535. Abstract.
Allen MJ, Wilson WH (2006). The coccolithovirus microarray: an array of uses. Briefings in Functional Genomics and Proteomics, 5(4), 273-279. Abstract.
Allen MJ, White GF, Morby AP (2006). The response of Escherichia coli to exposure to the biocide polyhexamethylene biguanide. Microbiology, 152(4), 989-1000. Abstract.
Allen MF (2006). Water dynamics of mycorrhizas in arid soils. In  (Ed) Fungi in Biogeochemical Cycles, 74-97.  Abstract.

2005

Wilson WH, Schroeder DC, Allen MJ, Holden MTG, Parkhill J, Barrell BG, Churcher C, Hamlin N, Mungall K, Norbertczak H, et al (2005). Complete genome sequence and lytic phase transcription profile of a Coccolithovirus. Science, 309(5737), 1090-1092. Abstract.

2004

Allen MJ, Morby AP, White GF (2004). Cooperativity in the binding of the cationic biocide polyhexamethylene biguanide to nucleic acids. Biochemical and Biophysical Research Communications, 318(2), 397-404. Abstract.

Mike_Allen Details from cache as at 2019-06-20 20:14:05

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