By Professor Torsten Thomas

Journal articles

Fernandes N; Steinberg PD; Rusch D; Kjelleberg S; Thomas T, 2012, 'Community structure and functional gene profile of bacteria on healthy and diseased thalli of the red seaweed Delisea pulchra.', PLoS One, 7, pp. e50854, http://dx.doi.org/10.1371/journal.pone.0050854

Woodhouse JN; Fan L; Brown MV; Thomas T; Neilan BA, 2012, 'Deep sequencing of secondary meta-metabolomes: A preliminary screening tool for determining natural product diversity.', Planta Medica, 78, pp. CL51, http://dx.doi.org/10.1055/s-0032-1320286

Fan L; Reynolds D; Liu M; Stark M; Kjelleberg S; Webster N; Thomas T, 2012, 'Functional equivalence and evolutionary convergence in complex communities of microbial sponge symbionts', Proceedings of the National Academy of Science. USA, 109, pp. 1878 - 1887

McElroy KE; Luciani F; Thomas T, 2012, 'GemSIM: General, Error-Model based SIMulator of next-generation sequencing data', BMC Genomics, 13, pp. 1 - 9, http://dx.doi.org/10.1186/1471-2164-13-74

Brown MV; Lauro FM; Demaere MZ; Muir L; Wilkins D; Thomas T; Riddle M; Fuhrman J; Andrews-Pfannkoch C; Hoffman JM; McQuaid J; Allen A; Rintoul S; Cavicchioli R, 2012, 'Global biogeography of SAR11 marine bacteria', Molecular Systems Biology, 8, pp. 595, http://dx.doi.org/10.1038/msb.2012.28

Thomas T; Gilbert J; Meyer F, 2012, 'Metagenomics - a guide from sampling to data analysis.', BMC Microbial Informatics and Experimentation, 2, pp. 3

Fan L; Liu M; Zhong L; Kjelleberg S; Thomas T, 2012, 'Metaproteogenomic analysis of a community of sponge symbionts', ISME Journal, 6, pp. 1515 - 1525, http://dx.doi.org/10.1038/ismej.2012.1

Thole S; Kalhoefer D; Voget S; Berger M; Engelhardt T; Leisegang H; Wollherr A; Kjelleberg S; Danial R; Meinhardt S; Thomas T; Brinkhoff T, 2012, 'Phaeobacter gallaeciensis genomes from globally opposite locations reveal high similarity of adaptation to surface life', ISME Journal, 6, pp. 2229 - 2244, http://dx.doi.org/10.1038/ismej.2012.62

Fan L; Mcelroy KE; Thomas T, 2012, 'Reconstruction of ribosomal RNA genes from metagenomic data', PLoS ONE, 7, pp. e39948

Thomas T; Kjelleberg S; Yung PY, 2011, 'Phylogenetic Screening of Metagenomic Libraries Using Homing Endonuclease Restriction and Marker Insertion', , pp. 245 - 249, http://dx.doi.org/10.1002/9781118010518.ch29

Yung PY; Kjelleberg S; Thomas T, 2011, 'A polyphasic approach to the exploration of collagenolytic activity in the bacterial community associated with the marine sponge Cymbastela concentrica.', FEMS Microbiology Letters, 321, pp. 24 - 29, http://dx.doi.org/10.1111/j.1574-6968.2011.02306.x

Fan L; Kjelleberg S; Thomas T, 2011, 'Accurate Reconstruction of Microbial Community From Environmental Shotgun Sequences Avoiding Primer Bias', SHORT, pp. 58 - 58

Thomas T; Kindinger I; Yu D; Blackall L; Forehead H; Johnson CR; Manefield MJ; Esvaran M, 2011, 'An experimental model for the spatial structuring and selection of bacterial communities', Journal of Microbiological Methods, 87, pp. 165 - 168, http://dx.doi.org/10.1016/j.mimet.2011.08.010

Lauro FM; Demaere MZ; Yau S; Brown MV; Wilkins D; Ng SC; Raftery MJ; Gibson JA; Andrews-Pfannkoch C; Lewis M; Hoffman JM; Thomas T; Cavicchioli R, 2011, 'An integrative study of a meromictic lake ecosystem in Antarctica', ISME Journal, 5, pp. 879 - 895

Kumar V; Rao D; Thomas T; Kjelleberg S; Egan SG, 2011, 'Antidiatom and antibacterial activity of epiphytic bacteria isolated from Ulva lactuca in tropical waters', World Journal of Microbiology and Biotechnology, 27, pp. 1543 - 1549, http://dx.doi.org/10.1007/s11274-010-0606-1

Burke CM; Steinberg PD; Rusch D; Kjelleberg S; Thomas T, 2011, 'Bacterial community assembly based on functional genes rather than species', Proceedings of the National Academy of Sciences of the United States of America, 108, pp. 14288 - 14293, http://dx.doi.org/10.1073/pnas.1101591108

McElroy K; Luciani F; Hui J; Rice S; Thomas T, 2011, 'Bacteriophage evolution drives Pseudomonas aeruginosa PAO1 biofilm diversification', BMC Bioinformatics, 12, pp. A2 - A2

Schleheck DF; Weiss M; Pitluck S; Bruce D; Land ML; Han S; Saunders E; Tapia R; Detter C; Brettin T; Han J; Woyke T; Goodwin L; Pennacchio L; Nolan M; Cook AM; Kjelleberg S; Thomas T, 2011, 'Complete genome sequence of Parvibaculum lavamentivorans type strain (DS-1T).', Standards in Genomic Sciences, 5, pp. 298 - 310, http://dx.doi.org/10.4056/sigs.2215005

Burke CM; Thomas T; Lewis M; Steinberg PD; Kjelleberg S, 2011, 'Composition, uniqueness and variability of the epiphytic bacterial community of the green alga Ulva australis', ISME Journal, 5, pp. 590 - 600, http://dx.doi.org/10.1038/ismej.2010.164

Liu MY; Kjelleberg S; Thomas T, 2011, 'Functional genomic analysis of an uncultured delta-proteobacterium in the sponge Cymbastela concentrica.', ISME Journal, 5, pp. 427 - 435, http://dx.doi.org/10.1038/ismej.2010.139

Fernandes N; Case RJ; Longford SR; Seyedsayamdost M; Steinberg PD; Kjelleberg S; Thomas T, 2011, 'Genomes and virulence factors of novel bacterial pathogens causing bleaching disease in the marine red alga Delisea pulchra', PLoS ONE, 6, pp. e27387, http://dx.doi.org/10.1371/journal.pone.0027387

Penesyan A; Tebben J; Lee M; Thomas T; Kjelleberg S; Harder T; Egan S, 2011, 'Identification of the antibacterial compound produced by the marine epiphytic bacterium Pseudovibrio sp. D323 and related sponge-associated bacteria.', Marine Drugs, 9, pp. 1391 - 1402, http://dx.doi.org/10.3390/md9081391

Yung PY; Burke CM; Lewis M; Kjelleberg S; Thomas T, 2011, 'Novel antibacterial proteins from the microbial communities associated with the sponge Cymbastela concentrica and the green alga Ulva australis.', Applied and Environmental Microbiology, 77, pp. 1512 - 1515, http://dx.doi.org/10.1128/AEM.02038-10

Naughton S; Parker D; Seemann T; Thomas T; Turnbull L; Rose B; Bye P; Cordwell S; Whitchurch C; Manos J, 2011, 'Pseudomonas aeruginosa AES-1 exhibits increased virulence gene expression during chronic infection of cystic fibrosis lung', PLoS ONE, 6, pp. 1 - 8

Demaere MZ; Lauro FM; Thomas T; Yau S; Cavicchioli R, 2011, 'Simple high-throughput annotation pipeline (SHAP)', Bioinformatics, 27, pp. 2431 - 2432

Yau S; Lauro FM; Demaere MZ; Brown MV; Thomas T; Raftery MJ; Lewis M; Hoffman JM; Gibson J; Cavicchioli R; Andrews-Pfannkoch C, 2011, 'Virophage control of Antarctic algal host–virus dynamics', Proceedings of the National Academy of Sciences of the United States of America, 108, pp. 6163 - 6168, http://www.ncbi.nlm.nih.gov/pubmed/21444812

Thomas TD; Kukk E; Ouchi T; Yamada A; Fukuzawa H; Ueda K; Püttner R; Higuchi I; Tamenori Y; Asahina T; Kuze N; Kato H; Hoshino M; Tanaka H; Lindblad A; Sæthre LJ, 2010, 'Publisher's Note: “Valence photoelectron spectroscopy of N2 and CO: Recoil-induced rotational excitation, relative intensities, and atomic orbital composition of molecular orbitals” [J. Chem. Phys. 133, 174312 (2010)]', The Journal of Chemical Physics, 133, http://dx.doi.org/10.1063/1.3524287

Thomas T; Rusch D; Demaere MZ; Yung PY; Lewis M; Halpern A; Heidelberg KB; Egan SG; Steinberg PD; Kjelleberg S, 2010, 'Functional genomic signatures of sponge bacteria reveal unique and shared features of symbiosis', ISME Journal, 4, pp. 1557 - 1567, http://dx.doi.org/10.1038/ismej.2010.74

Ballestriero F; Thomas T; Burke CM; Egan SG; Kjelleberg S, 2010, 'Identification of Compounds with Bioactivity against the Nematode Caenorhabditis elegans by a Screen Based on the Functional Genomics of the Marine Bacterium Pseudoalteromonas tunicata D2', Applied and Environmental Microbiology, 17, pp. 5710 - 5717, http://dx.doi.org/10.1128/AEM.00695-10

Ng SC; De Maere M; Williams TJ; Lauro FM; Raftery MJ; Gibson J; Andrews-Pfannkoch C; Lewis M; Hoffman J; Thomas T; Cavicchioli R, 2010, 'Metaproteogenomic analysis of a dominant green sulfur bacterium from Ace Lake, Antarctica.', ISME Journal, 4, pp. 1002 - 1019

Tujula NA; Crocetti GR; Burke CM; Thomas T; Holmstrom CG; Kjelleberg S, 2010, 'Variability and abundance of the epiphytic bacterial community associated with a green marine Ulvacean alga', ISME Journal, 4, pp. 301-311, http://dx.doi.org/10.1038/ismej.2009.107

Yung PY; Burke CM; Lewis M; Egan SG; Kjelleberg S; Thomas T, 2009, 'Phylogenetic screening of a bacterial, metagenomic library using homing endonuclease restriction and marker insertion', Nucleic Acids Research, 37, pp. e144, http://dx.doi.org/10.1093/nar/gkp746

Cairns MJ; Thomas T; Beltran C; Tillett D, 2009, 'Primer fabrication using polymerase mediated oligonucleotide synthesis', BMC Genomics, 10

Burke CM; Kjelleberg S; Thomas T, 2009, 'Selective extraction of bacterial DNA from the surfaces of macroalgae', Applied and Environmental Microbiology, 75, pp. 252 - 256

Allen MA; Lauro FM; Williams TJ; Burg DW; Siddiqui KS; De Francisci D; Chong K; Pilak O; Chew H; De Maere M; Ting LL; Katrib M; Ng SC; Sowers KR; Galperin M; Anderson I; Ivanova N; Dalin E; Martinez MP; Lapidus A; Hauser L; Land MH; Thomas T; Cavicchioli R, 2009, 'The genome sequence of the psychrophilic archaeon, Methanococcoides burtonii: The role of genome evolution in cold adaptation', ISME Journal, 3, pp. 1012 - 1035

Lauro FM; McDougald D; Thomas T; Williams TJ; Egan SG; Rice SA; Demaere MZ; Ting LL; Ertan H; Johnson J; Ferriera S; Lapidus A; Anderson IM; Kyrpides N; Munkf A; Detter C; Hang C; Brown M; Robb F; Kjelleberg S; Cavicchioli R, 2009, 'The genomic basis of trophic strategy in marine bacteria', Proceedings of the National Academy of Sciences of the United States of America, 106, pp. 15527 - 15533

Thomas T; Evans FF; Schleheck D; Mai-Prochnow A; Burke C; Penesyan A; Dalisay DS; Stelzer-Braid S; Saunders N; Johnson J; others , 2008, 'Analysis of the Pseudoalteromonas tunicata Genome Reveals Properties of a Surface-Associated Life Style in the Marine Environment', Detail:

Mai-Prochnow AG; Lucas-Elio P; Egan SG; Thomas T; Webb JS; Sanchez-Amat A; Kjelleberg S, 2008, 'Hydrogen peroxide linked to lysine oxidase activity facilitates biofilm differentiation and dispersal in several gram-negative bacteria', Journal of Bacteriology, 190, pp. 5493 - 5501

Egan SG; Thomas T; Kjelleberg S, 2008, 'Unlocking the diversity and biotechnological potential of marine surface associated microbial communities', Current Opinion in Microbiology, 11, pp. 219 - 225

nil Siddiqui KS; De Francisci D; Thomas T, 2007, 'In: Methods in Protein Structure and Stability Analysis ISBN 1-60021-704-4 Editors: V. Uversky and E. Permyakov, pp. 147-158\copyright 2007 Nova Science Publishers, Inc.', Methods in Protein Structure and Stability Analysis: Conformational Stability, Size, Shape and Surface of Protein Molecules, pp. 147 - 147

Thomas T; Egan SG; Burg DW; Ng SC; Ting LL; Cavicchioli R, 2007, 'Integration of genomics and proteomics into marine microbial ecology', Marine Ecology Progress Series, 332, pp. 291 - 299

Cavicchioli R; Demaere MZ; Thomas T, 2007, 'Metagenomic studies reveal the critical and wide-ranging ecological importance of uncultivated archaea: the role of ammonia oxidizers', BioEssays, 29, pp. 11 - 14

Burke CM; Thomas T; Egan SG; Kjelleberg S, 2007, 'The use of functional genomics for the identification of a gene cluster encoding for the biosynthesis of an antifungal tambjamine in the marine bacterium Pseudoalteromonas tunicata', Environmental Microbiology, 9, pp. 814 - 818

Goldberg SMD; Johnson J; Busam D; Feldblyum T; Ferriera S; Friedman R; Halpern A; Khouri H; Kravitz SA; Lauro FM; Li K; Rogers YH; Strausberg R; Sutton G; Tallon L; Thomas T; Venter E; Frazier M; Venter JC, 2006, 'Erratum: A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes (Proceedings of the National Academy of Sciences of the United States of America (July 25, 2006) 30, 103 (11240-11245) DOI: 10.1073/pnas.0604351103)', Proceedings of the National Academy of Sciences of the United States of America, 103, pp. 16057, http://dx.doi.org/10.1073/pnas.0607197103

Goldberg S; Johnson J; Busam D; Feldblyum T; Ferriera S; Friedman R; Halpern A; Khouri H; Kravitz S; Lauro FM; Li KS; Rogers Y; Strausberg R; Sutton G; Tallon L; Thomas T; Venter E; Frazier M; Venter J, 2006, 'A Sanger/pyrosequencing hybrid approach tor the generation of high-quality draft assemblies of marine microbial genomes', Proceedings of the National Academy of Sciences of the United States of America, 103, pp. 11240 - 11245

Saunders NF; Thomas T; Curmi PM; Mattick JS; Kuczek E; Slade R; Davis J; Franzmann PD; Boone D; Rusterholtz K; Feldman R; Gates C; Bench S; Sowers KR; Kadner K; Aerts A; Dehal P; Detter C; Glavina T; Lucas S; Richardson P; Larimer F; Hauser L; Land M; Cavicchioli R, 2003, 'Mechanisms of Thermal Adaptation Revealed from the Genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii', Genome Research, 13, pp. 1580 - 1588

Cavicchioli R; Curmi PM; Saunders NF; Thomas T, 2003, 'Pathogenic archaea: do they exist?', BioEssays, 25, pp. 1119 - 1128

Cavicchioli R; Torsten T; Curmi PM, 2000, 'Cold stress response in Archaea', Extremophiles, 4, pp. 321 - 331

Torsten T; Cavicchioli R, 2000, 'Effect of temperature on the stability and activity of the elongation factor 2 proteins from low-temperature adapted and thermophilic methanogens', Journal of Bacteriology, 182, pp. 1328 - 1332

Lim J; Torsten T; Cavicchioli R, 2000, 'Low temperature regulated DEAD-box RNA Helicase from the Antarctic Archaeon, Methanococcoides burtonii', Journal of Molecular Biology, 297, pp. 553 - 567

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