By Professor Torsten Thomas

Journal articles

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 NFW; Thomas T; Curmi PMG; Mattick JS; Kuczek E; Slade R; Davis J; Franzmann PD; Boone D; Rusterholtz K; Feldman R; Gates C; Bench S; Sowers K; 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 Res, 13, pp. 1580 - 1588, http://dx.doi.org/10.1101/gr.1180903

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

Egan S; Torsten T; Holmstrom CG; Kjelleberg S, 2000, 'Phylogenetic relationship and antifouling activity of bacterial epiphytes from the marine alga Ulva lactuca', Environmental Microbiology, 2, pp. 343 - 347

Berchet V; Torsten T; Cavicchioli R; Russell NJ; Gounot A, 2000, 'Structural analysis of the elongation factor G protein from the low-temperature-adapted bacterium Arthrobacter globiformis S155', Extremophiles, 4, pp. 123 - 130

Thomas T; Cavicchioli R, 1998, 'Archaeal cold-adapted proteins: structural and evolutionary analysis of the elongation factor 2 proteins from psychrophilic, mesophilic and thermophilic methanogens.', FEBS letters, 439, pp. 281 - 286, http://dx.doi.org/10.1016/s0014-5793(98)01375-1

Conference Papers

Duarte G; Vilela C; Molodon F; Damasceno T; Hill L; Thomas T; Peixoto R, 2025, 'Culturing deep-sea coral reef bacteria', in BULLETIN OF MARINE SCIENCE, ROSENSTIEL SCH MAR ATMOS SCI

Ribeiro B; Garritano A; Raimundo I; Delgadillo-Ordonez N; Garcias-Bonet N; Villela H; Thomas T; Klautau M; Peixoto R, 2025, 'Not only for corals: Beneficial Microorganisms for Corals (BMC) can also be acquired by sponges', in BULLETIN OF MARINE SCIENCE, ROSENSTIEL SCH MAR ATMOS SCI

Ozkan J; Majzoub M; Coroneo M; Thomas T; Willcox M, 2023, 'Ocular microbiome changes in dry eye disease and meibomian gland dysfunction', Germany, presented at Symposium: The Human Microbiome, European Molecular Biology Laboratory (EMBL), Germany, 20 September 2023

Ozkan J, 2023, 'The conjunctival and lid margin microbiome in meibomian and lacrimal gland dysfunction', USA, presented at Association for Research in Vision and Ophthalmology, USA, 23 April 2023

McKay IR; Coffey MJ; Doumit M; Bramley L; Sharp M; Kasparian N; Chuang S; Stelzer-Braid S; Waters S; Thomas T; Jaffe A; Katz TE; Ooi CY, 2019, 'A GUT FEELING: CORRELATING DIETARY INTAKE WITH THE GASTROINTESTINAL AND RESPIRATORY MICROBIOTA IN CYSTIC FIBROSIS', in PEDIATRIC PULMONOLOGY, WILEY, pp. S261 - S262, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000484544000375&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Coffey MJ; Zhong L; Jaffe A; Ooi CY; Waters S, 2019, 'THE INTESTINAL PROTEOME IN CHILDREN WITH CYSTIC FIBROSIS DIFFERS FROM HEALTHY CONTROLS', in PEDIATRIC PULMONOLOGY, WILEY, pp. S265 - S265, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000484544000385&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Coffey MJ; Nielsen S; Wemheuer B; Garg M; Needham B; Jaffe A; Thomas T; Ooi CY, 2019, 'TAXONOMIC AND FUNCTIONAL INTESTINAL DYSBIOSIS IN CHILDREN WITH CYSTIC FIBROSIS', in GASTROENTEROLOGY, W B SAUNDERS CO-ELSEVIER INC, CA, San Diego, pp. S895 - S895, presented at Digestive Disease Week (DDW), CA, San Diego, 18 May 2019 - 21 May 2019

Ozkan J; Willcox M; Wemheuer B; Wilcsek G; Coroneo M; Thomas T, 2018, 'The biogeography of the human ocular microbiota', Heidelberg, Germany, presented at European Molecular Biology Organisation/European Molecular Biology Laboratory Symposia - The Human Microbiome, Heidelberg, Germany, 16 September 2018 - 19 September 2018, https://www.embo-embl-symposia.org/symposia/2018/EES18-09/programme1/index.html

Cone S; Larkin G; Poulton C; Wemheuer B; Thomas T; Lemberg D; Gupta N; Leach ST; Coffey MJ; Ooi CY, 2018, 'Functional dysbiosis of the gut microbiota in childhood irritable bowel syndrome', in JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY, WILEY, pp. 144 - 145, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000530647800253&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Ozkan J; Willcox M; Wermeuer B; Thomas T; Coroneo MT, 2018, 'What is hiding in your eyes? The microbiome of ocular surface niches', in INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE, ASSOC RESEARCH VISION OPHTHALMOLOGY INC, HI, Honolulu, presented at Annual Meeting of the Association-for-Research-in-Vision-and-Ophthalmology (ARVO), HI, Honolulu, 21 April 2018 - 03 May 2018

Ozkan J; Diez-Vives C; Nielsen S; Coroneo M; Thomas T; Willcox M, 2017, 'A Statistical Model to Filter Contaminant Bacteria in Ocular Microbiome Studies', Portland, Oregon, USA, presented at International Society for Contact Lens Research, Portland, Oregon, USA, 13 August 2017 - 18 August 2017

Ozkan J; Diez-Vives C; Nielsen S; Thomas T; Coroneo MT; Willcox M, 2017, 'THE TEMPORAL STABILITY OF THE OCULAR SURFACE MICROBIOME', in INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE, ASSOC RESEARCH VISION OPHTHALMOLOGY INC, MD, Baltimore, presented at Annual Meeting of the Association-for-Research-in-Vision-and-Ophthalmology (ARVO), MD, Baltimore, 07 May 2017 - 11 May 2017, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000432176306051&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Kaakoush NO; Thomas T; Day AS; Leach ST; Lemberg D; Dowd S; Mitchell HM, 2012, 'MICROBIAL DYSBIOSIS IN PEDIATRIC PATIENTS WITH CROHN'S DISEASE', in HELICOBACTER, WILEY-BLACKWELL, SLOVENIA, Ljubljana, pp. 92 - 92, presented at 25th International Workshop on Helicobacter and Related Bacteria in Chronic Digestive Inflammation and Gastric Cancer, SLOVENIA, Ljubljana, 13 September 2012 - 15 September 2012, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000308581600103&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Jacqueline T; Thomas T; Stuetz RM; Ashbolt NJ, 2011, 'The risk of Free-living amoebe interaction bacterial pathogens in drinking water', in Conference Proceedings, WaterMicro 2011, Rotorua, NZ, presented at Proceeding 16th International Symposium on Health-Related Microbiology, Rotorua, NZ, 18 September 2011 - 23 September 2011

Thomas J; Storey M; Thomas T; Stuetz RM; Ashbolt NJ, 2010, 'Diversity of free-living amoebal pathogen hosts in a dual distribution (drinking and recycled) water system', in Proceedings Water Quality Technology Conference, American Water Works Association (Curran Associates), Washington, presented at Water Quality Technology Conference and Exposition 2010, Savannah, Georgia U.S.A, 14 November 2010 - 18 November 2010

Thomas T; Lim J; March PE; Tillett D; Wiedemann P, 2002, 'A new approach to high through-put DNA sequencing: dLUTE SEQ a method for nanolitre scale reactions', in Takayama K (ed.), School BABS 1st Annual Symposium, Sydney, presented at School of Biotechnology and Biomolecular Sciences 1st Annual Symposium, Sydney, 08 November 2002

Demaere MZ; Lim J; March PE; Thomas T; Tillett D; Wiedemann P; Karunate S, 2002, 'A new approach to high through-put DNA sequencing: UniSEQ a universal approach to primer walking', in Takayama K (ed.), School BABS 1st Annual Symposium, Sydney, presented at School of Biotechnology and Biomolecular Sciences 1st Annual Symposium, Sydney, 08 November 2002

Conference Presentations

Ozkan J; Majzoub M; Coroneo M; Thomas T; Willcox M, 2022, 'The effect of face mask wear on the ocular surface and contact lens microbiome', presented at 21st International Society for Contact Lens Research (ISCLR) Symposium,, 22 August 2022

Ozkan J; Majzoub M; Coroneo M; Thomas T; Willcox M, 2022, 'The comparative ocular surface tissue microbiome in human, mouse, rabbit and guinea pig', presented at Association for Research in Vision and Ophthalmology, 02 May 2022

van Dorst J; McKay I; Coffey M; Doumit M; Paida K; Jaffe A; Thomas T; Katz T; Ooi CY, 2021, 'WS02.4 Evaluating the role of short chain fatty acids in cystic fibrosis', http://dx.doi.org/10.1016/s1569-1993(21)00924-3

Ozkan J; Willcox M; Sandbach J; Coroneo M; Thomas T, 2020, 'Contamination of intravitreal needles by the ocular surface microbiome', presented at Association for Research in Vision and Ophthalmology, 03 May 2020

van Dorst J; McKay I; Coffey M; Doumit M; Bramley L; Paida K; Jaffe A; Thomas T; Katz T; Ooi CY, 2020, 'WS03.6 Does the cystic fibrosis diet contribute to intestinal dysbiosis?', http://dx.doi.org/10.1016/s1569-1993(20)30182-x

Conference Abstracts

van Dorst J; McKay IR; Coffey MJ; Doumit M; Paida K; Jaffe A; Thomas T; Katz TE; Ooi C, 2020, 'CAN THE DIET MODULATE THE GUT-LUNG AXIS AND IMPROVE HEALTH OUTCOMES IN CYSTIC FIBROSIS?', in PEDIATRIC PULMONOLOGY, WILEY, Vol. 55, pp. S135 - S135, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000575294100246&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

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