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Selected Publications

Harrington, C., Del Casale, A., Kennedy, J., Neve, H., Picton, B.E., Mooij, M.J., O'Gara, F., Kulakov, L.A., Larkin, M.J., Dobson, A. D. W. (2012). Evidence of bacteriophage-mediated horizontal transfer of bacterial 16S rRNA genes in the viral metagenome of the marine sponge Hymeniacidon perlevis.  Microbiology-SGM, 158: 2789-2795.

Del Casale, A., Flanagan, P. V., Larkin, M.J., Allen, C.C.R and Kulakov, L.A. (2011). Analysis of transduction in wastewater bacterial populations by targeting the phage-derived 16S rRNA gene sequences.  FEMS Microbiology Ecology, 76: 100-108.

Del Casale, A., Flanagan, P. V., Larkin, M.J., Allen, C.C.R and Kulakov, L.A. (2011). Extent and Variation of Phage-Borne Bacterial 16S rRNA Gene Sequences in Wastewater Environments.  Applied and Environmental Microbiology, 77: 5529-5532.

Curran, T., Coulter, W.A., Wilson, A., Fairley, D.J., Larkin, M.J., et al. (2010). Development of a novel DNA microarray to detect bacterial pathogens in patients with chronic obstructive pulmonary disease (COPD).  Journal of Microbiological Methods, 80: 257-261.

Doherty, R., Kulessa, B. Ferguson , A.S., Larkin, M.J., et al (2010). A microbial fuel cell in contaminated ground delineated by electrical self-potential and normalized induced polarization data.  Journal of Geophysical Research-Biogeosciences, 115: G00G08.

Larkin, M.J., Allen, C.C.R and Kulakov, L.A. (2010). Rhodococcus: Genetics and Functional Genomics. Chapter 38. Handbook of Microbiology of Hydrocarbons, Oils, Lipids, and Derived Compounds. Volume 2, part 11: The Microbes. Kenneth N. Timmis (Ed.). pp 1346-1353. ISBN: 978-3-540-77588. Springer.

Larkin, M.J., Kulakov, L.A and Allen, C.C.R. (2010). Chapter 1. Genomes and plasmids from Rhodococcus in "Biology of Rhodococcus Microbiology Monographs (Springer series) Héctor M. Alvarez (Editor). Volume 16. pp 73-90 ISBN: 3642129366. Springer.

Larkin, M.J., Allen, C.C.R and Kulakov, L.A. (2010). Chapter 13 Rhodococcusbiodegradation. Handbook of Microbiology of Hydrocarbons, Oils, Lipids, and Derived Compounds. Volume 2, part 10: The Microbes. Kenneth N. Timmis (Ed.). pp 1840-1851. ISBN: 978-3-540-77588 Springer.

Huang , W., Ferguson, A.F., Singer, A.C., Lawson, K.A., Thompson, I.P., Kalin, R.M., Larkin, M.J., Bailey, M.J and Whiteley, A.S. (2009). Resolving Genetic Functions within Microbial Populations: In Situ Analyses Using rRNA and mRNA Stable Isotope Probing Coupled with Single-Cell Raman-Fluorescence In Situ Hybridization.  Applied and Environmental Microbiology, 75: 234-241.

Kulakov, L.A., Ksenzenko, V.N., Shlyapnikov, M.G., Larkin, M.J. (2009). Genomes of "phiKMV-like viruses" of Pseudomonas aeruginosa contain localized single-strand interruptions.  Virology, 391: 1-4.

Larkin, M.J., Kulakov, L.A and Allen, C.C.R. (2006). Biodegradation by members of the genus Rhodococcus: Biochemistry, physiology, and genetic adaptation.  Advances in Applied Microbiology, 59: 1-29.

Ferguson, A., Huang, W., Lawson, K.A., Doherty, R., Gilbert, O., Dickson, K., Whiteley, A., Kulakov, L.A., Thompson, I., Kalin, R and Larkin, M.J. (2007). Microbial analysis of soil and groundwater from a gasworks site and comparison to a sequenced biological reactive barrier process (SEREBAR).  J Appl Microbiol, 102: 1227-1238.

Fairley, D.J., Wang , G., Rensing, C., Pepper, I.L and Larkin, M.J. (2006). Expression of genes involved in aromatic degradation in two haloarchaeal genera.  Applied Microbiology and Biotechnology, 73: 691-695.

Kulakov, L.A., Chen , S., Allen, C.C.R and Larkin, M.J. (2005). Web-type evolution of Rhodococcus gene clusters associated with utilization of naphthalene.  Applied and Environmental Microbiology, 71(4): 1754-1764.

Larkin, M.J., Kulakov, L.A and Allen, C.C.R. (2005). Rhodococcus and Biodegradation: Masters of catabolic versatility.  Current Opinions in Biotechnology, 26(3): 2882-290.

Larkin, M.J., Kulakov, L.A and Allen, C.C.R. (2005). Biodegradation by members of the genus Rhodococcus: Biochemistry, physiology and genetic adaptation.  Advances in Applied Microbiology, 59: 1-29.

McDonald, I.R., Kämpfer, P., Warner, K.L, Cox, M.J, Hancock, T.L., Miller, I.G., Ducrocq, V., Larkin, M.J., Harper, D.B., Murrell, J.C and Oremland, R.S (2005). Aminobacter ciceronei sp. nov. and Aminobacter lissarensis sp. nov., halomethane isolated from various terrestrial environments.  International Journal of Systematic and Evolutionary Microbiology, 55: 1827-1832.

Warner, K., Harper, D.B., Larkin, M.J., Murrell, J.C and McDonald, I.R. (2005). Cloning and sequencing the genes involved in methyl halide degradation in Aminobacter strain CC495.  FEMS Microbiology Letters, 251: 45-51.

Gakhar, I., Malik, Z.A., Allen, C.C.R., Lipscomb, D.A., Larkin, M.J. and Ramaswamy, S. (2005). Structure and increased thermostability of Rhodococcus sp. Naphthalene 1,2-dioxygenase.  Journal of Bacteriology, 187: 7222-7231.

Wellington, E.M.H and Larkin, M.J. (2004). Ecology and industrial microbiology - Exploiting the incredible genetic diversity of microorganisms for environmental protection and novel products.  Curr Opin Microbiol, 7(3): 203-205.

Kulakov, L.A and Larkin, M.J. (2003). in Genomics of GC-Rich. Gram-Positive Bacteria Functional Genomics Series Volume 2 Edited by Antoine Danchin. Chapter 2.  Genetic Organization of Rhodococcus pp15 -46 Caister Academic Press (UK) ISBN: 0-9542464-3-8.

Ferguson, A.S., Doherty, R., Larkin, M.J. (2003). Toxicity assessment of a former manufactured gas plant. B Environ Contam Tox., 71(1): 21-30.

Patrick, S., Parkhill, J., McCoy, L.J., Lennard, N., Larkin, M.J., Collins, M., Sczaniecka, M. & Blakely, G. (2003). Multiple inverted DNA repeats of Bacteroides fragilis that control polysaccharide antigenic variation are similar to the hin region inverted repeats of Salmonella typhimurium. Microbiology - UK, 149: 915-924.

Fairley, D.J., Boyd, D.R., Sharma, N.D., Larkin, M.J. et al. (2002). Aerobic metabolism of 4-hydroxybenzoic acid in Archaea via an unusual pathway involving an intramolecular migration (NIH shift). Appl Environ Microb, 68(12): 6246-6255.

Malik, Z.A., Allen, C.C.R., Gakhar, L., Larkin, M.J. et al. (2002). Crystallization and preliminary X-ray diffraction analysis of naphthalene dioxygenase from Rhodococcus sp strain NCIMB 12038. Acta Crystallogr D, 58(12): 2173-2174.

Connery, N., Thompson, A.S., Patrick, S., Larkin, M.J. et al. (2002). Studies of Microthrix parvicella in situ and in laboratory culture: production and use of specific antibodies. Water Sci Technol, 46(1-2): 115-118.

Boyd, D.R., Sharma, N.D., Ljubez, V., Larkin, M.J. et al. (2002). Tandem enzyme-catalysed oxidations of alkyl phenyl sulfides and alkyl benzenes: enantiocomplementary routes to chiral phenols. Chem Commun, 17: 1914-1915.

McAlister, M.B., Kulakov, L.A., O.Hanlon, J.F., Larkin, M.J. et al. (2002). Survival and nutritional requirements of three bacteria isolated from ultrapure water. J Ind Microbiol Biot, 29(2): 75-82.

Kulakov, L.A., McAlister, M.B., Ogden, K.L., Larkin, M.J. et al.(2002). Analysis of bacteria contaminating ultrapure water in industrial systems. Appl Environ Microb, 68(4): 1548-1555.

Barth, J.A.C., Slater, G., Schuth, C., Larkin, M.J. et al. (2002). Carbon isotope fractionation during aerobic biodegradation of trichloroethene by Burkholderia cepacia G4: a tool to map degradation mechanisms. Appl Environ Microb, 68(4): 1728-1734.

McAllister, M.B., Kulakov, L.A., Larkin, M.J. and Ogden, K.L. (2001). Analysis of bacterial contamination in different sections of a high purity water system. Ultrapure Water, 18(1): 18-2.

Kulakov, L.A., McAlister, M.B., Ogden, K.L., Larkin, M.J. et al.(2002) Analysis of bacteria contaminating ultrapure water in industrial systems. Appl Environ Microb, 68(4): 1548-1555.

Irvine, V.A., Kulakov, L.A. and Larkin, M.J. (2001). The diversity of extradiol dioxygenase (edo) genes in cresol degrading rhodococci from a creosote-contaminated site that express a wide range of degradative abilities. Antonie Van Leuvenhoek International Journal of General and Molecular Microbiology, 78: 341-352.

Poelarends, G.J., Kulakov, L.A., Larkin, M.J., Van Hylckama Vleig, J.E.T. & Janssen, D B. (2000). Roles of Horizontal Gene Transfer and Gene Integration in Evolution of 1,3-Dichloropropene- and 1,2-Dibromoethane-Degradative Pathways J. Bacteriol, 182: 2191-2199.

Harper, D.B., Kalin, R.M., Larkin, M.J., Hamilton, J.T.G., Coulter, C. (2000). Microbial transhalogenation: a complicating factor in determination of atmospheric chloro- and bromomethane budgets. Environmental Science and Technology, 34(12): 2525-2527.

Hall, J.A., Kalin, R.M., Larkin, M.J., Allen, C.C.R. and Harper, D.B. (1999). Variation in stable carbon isotope fractionation during aerobic degradation of phenol and benzoate by contaminant degrading bacteria. Organic Geochemistry, 30: 801-811.

Larkin, M J., Allen, C.C.R., Kulakov, L.A. and Lipscomb, D.A. (1999). Purification and characterisation of a novel naphthalene dioxygenase from Rhodococcus sp strain NCIMB12038. J. Bacteriol., 181(19): 6200-6204.

Coulter, C., Hamilton, J.T. G., Mcroberts, W.C., Kulakov, L. A., Larkin, M.J. and Harper, D.B. (1999). Halomethane: Bisulfide/Halide ion methyltransferase, an unusual corrinoid enzyme of environmental significance isolated from an aerobic methylotroph using chloromethane as the sole carbon source. Applied and Environmental Microbiology., 65(10): 4301-4312.