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2020

Application of transposon insertion sequencing to agricultural science

Fabian, B. K., Tetu, S. G. & Paulsen, I. T., 18 Mar 2020, In : Frontiers in Plant Science. 11, p. 1-15 15 p., 291.

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A synthesis of bacterial and archaeal phenotypic trait data

Madin, J. S., Nielsen, D. A., Brbic, M., Corkrey, R., Danko, D., Edwards, K., Engqvist, M. K. M., Fierer, N., Geoghegan, J. L., Gillings, M., Kyrpides, N. C., Litchman, E., Mason, C. E., Moore, L., Nielsen, S. L., Paulsen, I. T., Price, N. D., Reddy, T. B. K., Richards, M. A., Rocha, E. P. C. & 9 others, Schmidt, T. M., Shaaban, H., Shukla, M., Supek, F., Tetu, S. G., Vieira-Silva, S., Wattam, A. R., Westfall, D. A. & Westoby, M., 5 Jun 2020, In : Scientific Data. 7, p. 170 8 p., 170.

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Characterizing the mechanism of action of an ancient antimicrobial, manuka honey, against Pseudomonas aeruginosa using modern transcriptomics

Bouzo, D., Cokcetin, N. N., Li, L., Ballerin, G., Bottomley, A. L., Lazenby, J., Whitchurch, C. B., Paulsen, I. T., Hassan, K. A. & Harry, E. J., May 2020, In : mSystems. 5, 3, 16 p., e00106-20.

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Subsurface Stappia: success through defence, specialisation and putative pressure-dependent carbon fixation

Vick, S. H. W., Greenfield, P., Willows, R. D., Tetu, S. G., Midgley, D. J. & Paulsen, I. T., Jul 2020, In : Microbial Ecology. 80, 1, p. 34-46 13 p.

Research output: Contribution to journalArticle

The role of zinc efflux during Acinetobacter baumannii infection

Alquethamy, S. F., Adams, F. G., Naidu, V., Khorvash, M., Pederick, V. G., Zang, M., Paton, J. C., Paulsen, I. T., Hassan, K. A., Cain, A. K., McDevitt, C. A. & Eijkelkamp, B. A., 10 Jan 2020, In : ACS Infectious Diseases. 6, 1, p. 150-158 9 p.

Research output: Contribution to journalArticle

1 Citation (Scopus)
2019
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19 Downloads (Pure)
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2 Citations (Scopus)
11 Downloads (Pure)

Genomic and phenotypic insights point to diverse ecological strategies by facultative anaerobes obtained from subsurface coal seams

Vick, S. H. W., Greenfield, P., Tetu, S. G., Midgley, D. J. & Paulsen, I. T., 7 Nov 2019, In : Scientific Reports. 9, p. 1-13 13 p., 16186.

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Identification of novel Acinetobacter baumannii host fatty acid stress adaptation strategies

Jiang, J-H., Hassan, K. A., Begg, S. L., Rupasinghe, T. W. T., Naidu, V., Pederick, V. G., Khorvash, M., Whittall, J. J., Paton, J. C., Paulsen, I. T., McDevitt, C. A., Peleg, A. Y. & Eijkelkamp, B. A., 2019, In : mBio. 10, 1, p. 1-6 6 p., e02056-18.

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2 Citations (Scopus)
13 Downloads (Pure)

Interactions of an emerging fungal pathogen Scedosporium aurantiacum with human lung epithelial cells

Kaur, J., Kautto, L., Penesyan, A., Meyer, W., Elbourne, L. D. H., Paulsen, I. T. & Nevalainen, H., 22 Mar 2019, In : Scientific Reports. 9, p. 1-10 10 p., 5035.

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1 Citation (Scopus)
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Microbial communities are sensitive indicators for freshwater sediment copper contamination

Sutcliffe, B., Hose, G. C., Harford, A. J., Midgley, D. J., Greenfield, P., Paulsen, I. T. & Chariton, A. A., Apr 2019, In : Environmental Pollution. 247, p. 1028-1038 11 p.

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5 Citations (Scopus)
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10 Citations (Scopus)
22 Downloads (Pure)

QTL analysis of natural Saccharomyces cerevisiae isolates reveals unique alleles involved in lignocellulosic inhibitor tolerance

de Witt, R. N., Kroukamp, H., Van Zyl, W. H., Paulsen, I. T. & Volschenk, H., Aug 2019, In : FEMS Yeast Research. 19, 5, p. 1-14 14 p., foz047.

Research output: Contribution to journalArticle

1 Citation (Scopus)

Rapid microevolution of biofilm cells in response to antibiotics

Penesyan, A., Nagy, S. S., Kjelleberg, S., Gillings, M. R. & Paulsen, I. T., 6 Nov 2019, In : npj Biofilms and Microbiomes. 5, p. 1-14 14 p., 34.

Research output: Contribution to journalArticle

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3 Citations (Scopus)
5 Downloads (Pure)

Short-chain diamines are the physiological substrates of PACE family efflux pumps

Hassan, K. A., Naidu, V., Edgerton, J. R., Mettrick, K. A., Liu, Q., Fahmy, L., Li, L., Jackson, S. M., Ahmad, I., Sharples, D., Henderson, P. J. F. & Paulsen, I. T., 3 Sep 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 36, p. 18015-18020 6 p.

Research output: Contribution to journalArticle

Open Access

Succession patterns and physical niche partitioning in microbial communities from subsurface coal seams

Vick, S. H. W., Greenfield, P., Pinetown, K. L., Sherwood, N., Gong, S., Tetu, S. G., Midgley, D. J. & Paulsen, I. T., 22 Feb 2019, In : iScience. 12, p. 152-167 16 p.

Research output: Contribution to journalArticle

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6 Citations (Scopus)
3 Downloads (Pure)

The role of the copA copper efflux system in Acinetobacter baumannii virulence

Alquethamy, S. F., Khorvash, M., Pederick, V. G., Whittall, J. J., Paton, J. C., Paulsen, I. T., Hassan, K. A., McDevitt, C. A. & Eijkelkamp, B. A., 1 Feb 2019, In : International Journal of Molecular Sciences. 20, 3, p. 1-13 13 p., 575.

Research output: Contribution to journalArticle

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7 Citations (Scopus)
23 Downloads (Pure)

Unicellular cyanobacteria are important components of phytoplankton communities in Australia's Northern oceanic ecoregions

Moore, L. R., Huang, T., Ostrowski, M., Mazard, S., Kumar, S. S., Gamage, H. K. A. H., Brown, M. V., Messer, L. F., Seymour, J. R. & Paulsen, I., 23 Jan 2019, In : Frontiers in Microbiology. 9, p. 1-16 16 p., 3356.

Research output: Contribution to journalArticle

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Who eats what? Unravelling microbial conversion of coal to methane

Vick, S. H. W., Gong, S., Sestak, S., Vergara, T. J., Pinetown, K. L., Li, Z., Greenfield, P., Tetu, S. G., Midgley, D. J. & Paulsen, I. T., Jul 2019, In : FEMS Microbiology Ecology. 95, 7, p. 1-14 14 p., fiz093.

Research output: Contribution to journalArticle

1 Citation (Scopus)
2018

Blueprints for biosensors: design, limitations, and applications

Carpenter, A. C., Paulsen, I. T. & Williams, T. C., Aug 2018, In : Genes. 9, 8, p. 1-28 28 p., 375.

Research output: Contribution to journalArticle

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18 Citations (Scopus)
10 Downloads (Pure)

Crystal structure of a UDP-GlcNAc epimerase for surface polysaccharide biosynthesis in Acinetobacter baumannii

Shah, B. S., Ashwood, H. E., Harrop, S. J., Farrugia, D. N., Paulsen, I. T. & Mabbutt, B. C., 19 Jan 2018, In : PLoS ONE. 13, 1, p. 1-19 19 p., e0191610.

Research output: Contribution to journalArticle

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Diverse fungal lineages in subtropical ponds are altered by sediment-bound copper

Sutcliffe, B., Chariton, A. A., Harford, A. J., Hose, G. C., Greenfield, P., Midgley, D. J. & Paulsen, I. T., Aug 2018, In : Fungal Ecology. 34, p. 28-42 15 p.

Research output: Contribution to journalArticle

5 Citations (Scopus)

Dual transcriptomics of host-pathogen interaction of cystic fibrosis isolate Pseudomonas aeruginosa PASS1 with zebrafish

Kumar, S. S., Tandberg, J. I., Penesyan, A., Elbourne, L. D. H., Suarez-Bosche, N., Don, E., Skadberg, E., Fenaroli, F., Cole, N., Winther-Larsen, H. C. & Paulsen, I. T., 22 Nov 2018, In : Frontiers in Cellular and Infection Microbiology. 8, p. 1-15 15 p., 406.

Research output: Contribution to journalArticle

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Ecological effects of cefepime use during antibiotic cycling on the Gram-negative enteric flora of ICU patients

Venturini, C., Ginn, A. N., Wilson, B. E., Tsafnat, G., Paulsen, I., Partridge, S. R. & Iredell, J. R., 27 Jul 2018, In : Intensive Care Medicine Experimental. 6, p. 1-7 7 p., 19.

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Fiber supplements derived from sugarcane stem, wheat dextrin and psyllium husk have different in vitro effects on the human gut microbiota

Gamage, H. K. A. H., Tetu, S. G., Chong, R. W. W., Bucio-Noble, D., Rosewarne, C. P., Kautto, L., Ball, M. S., Molloy, M. P., Packer, N. H. & Paulsen, I. T., 20 Jul 2018, In : Frontiers in Microbiology. 9, p. 1-16 16 p., 1618.

Research output: Contribution to journalArticle

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3 Citations (Scopus)
22 Downloads (Pure)

Genome-based evolutionary history of Pseudomonas spp

Hesse, C., Schulz, F., Bull, C. T., Shaffer, B. T., Yan, Q., Shapiro, N., Hassan, K. A., Varghese, N., Elbourne, L. D. H., Paulsen, I. T., Kyrpides, N., Woyke, T. & Loper, J. E., Jun 2018, In : Environmental microbiology. 20, 6, p. 2142-2159 18 p.

Research output: Contribution to journalArticle

20 Citations (Scopus)

Insights from the genomes of microbes thriving in uranium-enriched sediments

Sutcliffe, B., Chariton, A. A., Harford, A. J., Hose, G. C., Stephenson, S., Greenfield, P., Midgley, D. J. & Paulsen, I. T., May 2018, In : Microbial Ecology. 75, 4, p. 970–984 15 p.

Research output: Contribution to journalArticle

6 Citations (Scopus)

Long-term irrigation affects the dynamics and activity of the wheat rhizosphere microbiome

Mavrodi, D. V., Mavrodi, O. V., Elbourne, L. D. H., Tetu, S., Bonsall, R. F., Parejko, J., Yang, M., Paulsen, I. T., Weller, D. M. & Thomashow, L. S., 21 Mar 2018, In : Frontiers in Plant Science. 9, p. 1-15 15 p., 345.

Research output: Contribution to journalArticle

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14 Citations (Scopus)
4 Downloads (Pure)

Pacing across the membrane: the novel PACE family of efflux pumps is widespread in Gram-negative pathogens

Hassan, K. A., Liu, Q., Elbourne, L. D. H., Ahmad, I., Sharples, D., Naidu, V., Chan, C. L., Li, L., Harborne, S. P. D., Pokhrel, A., Postis, V. L. G., Goldman, A., Henderson, P. J. F. & Paulsen, I. T., Sep 2018, In : Research in Microbiology. 169, 7-8, p. 450-454 5 p.

Research output: Contribution to journalArticle

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16 Citations (Scopus)
13 Downloads (Pure)

Regulation of the aceI multidrug efflux pump gene in Acinetobacter baumannii

Liu, Q., Hassan, K. A., Ashwood, H. E., Gamage, H. K. A. H., Li, L., Mabbutt, B. C. & Paulsen, I. T., Jun 2018, In : Journal of Antimicrobial Chemotherapy. 73, 6, p. 1492-1500 9 p.

Research output: Contribution to journalArticle

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7 Citations (Scopus)
17 Downloads (Pure)

Screening of candidate substrates and coupling ions of transporters by thermostability shift assays

Majd, H., King, M. S., Palmer, S. M., Smith, A. C., Elbourne, L. D. H., Paulsen, I. T., Sharples, D., Henderson, P. J. F. & Kunji, E. R. S., 15 Oct 2018, In : eLife. 7, p. 1-17 17 p., 38821.

Research output: Contribution to journalArticle

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8 Citations (Scopus)
79 Downloads (Pure)

Stormwater influences phytoplankton assemblages within the diverse, but impacted Sydney Harbour estuary

Varkey, D., Mazard, S., Jeffries, T. C., Hughes, D. J., Seymour, J., Paulsen, I. T. & Ostrowski, M., 26 Dec 2018, In : PLoS ONE. 13, 12, 16 p., e0209857.

Research output: Contribution to journalArticle

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2 Citations (Scopus)
8 Downloads (Pure)

Systematic, continental scale temporal monitoring of marine pelagic microbiota by the Australian Marine Microbial Biodiversity Initiative

Brown, M. V., van de Kamp, J., Ostrowski, M., Seymour, J. R., Ingleton, T., Messer, L. F., Jeffries, T., Siboni, N., Laverock, B., Bibiloni-Isaksson, J., Nelson, T. M., Coman, F., Davies, C. H., Frampton, D., Rayner, M., Goossen, K., Robert, S., Holmes, B., Abell, G. C. J., Craw, P. & 17 others, Kahlke, T., Sow, S. L. S., McAllister, K., Windsor, J., Skuza, M., Crossing, R., Patten, N., Malthouse, P., van Ruth, P. D., Paulsen, I., Fuhrman, J. A., Richardson, A., Koval, J., Bissett, A., Fitzgerald, A., Moltmann, T. & Bodrossy, L., 17 Jul 2018, In : Scientific Data. 5, p. 1-10 10 p., 180130.

Research output: Contribution to journalArticle

Open Access
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11 Citations (Scopus)
2 Downloads (Pure)

The Coal Seam Microbiome (CSMB) reference set, a lingua franca for the microbial coal-to-methane community

Vick, S. H. W., Greenfield, P., Tran-Dinh, N., Tetu, S. G., Midgley, D. J. & Paulsen, I. T., 1 Feb 2018, In : International Journal of Coal Geology. 186, p. 41-50 10 p.

Research output: Contribution to journalArticle

13 Citations (Scopus)

The EcoCyc Database

Karp, P. D., Ong, W. K., Paley, S., Billington, R., Caspi, R., Fulcher, C., Kothari, A., Krummenacker, M., Latendresse, M., Midford, P. E., Subhraveti, P., Gama-Castro, S., Muñiz-Rascado, L., Bonavides-Martinez, C., Santos-Zavaleta, A., Mackie, A., Collado-Vides, J., Keseler, I. M. & Paulsen, I., 12 Nov 2018, In : EcoSal Plus. 8, 1, 19 p.

Research output: Contribution to journalArticle

4 Citations (Scopus)
2017

Cereal products derived from wheat, sorghum, rice and oats alter the infant gut microbiota in vitro

Gamage, H. K. A. H., Tetu, S. G., Chong, R. W. W., Ashton, J., Packer, N. H. & Paulsen, I. T., 30 Oct 2017, In : Scientific Reports. 7, 1, p. 1-12 12 p., 14312.

Research output: Contribution to journalArticle

Open Access
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9 Citations (Scopus)
4 Downloads (Pure)

Characterization and vaccine potential of membrane vesicles produced by Francisella noatunensis subsp. orientalis in an adult zebrafish model

Lagos, L., Tandberg, J. I., Repnik, U., Boysen, P., Ropstad, E., Varkey, D., Paulsen, I. T. & Winther-Larsen, H. C., 1 May 2017, In : Clinical and Vaccine Immunology. 24, 5, p. 1-19 19 p., e00557-16.

Research output: Contribution to journalArticle

Open Access
15 Citations (Scopus)

Effects of uranium concentration on microbial community structure and functional potential

Sutcliffe, B., Chariton, A. A., Harford, A. J., Hose, G. C., Greenfield, P., Elbourne, L. D. H., Oytam, Y., Stephenson, S., Midgley, D. J. & Paulsen, I. T., 1 Aug 2017, In : Environmental microbiology. 19, 8, p. 3323-3341 19 p.

Research output: Contribution to journalArticle

14 Citations (Scopus)

Genomics and the evolution of antibiotic resistance

Gillings, M. R., Paulsen, I. T. & Tetu, S. G., 1 Jan 2017, In : Annals of the New York Academy of Sciences. 1388, 1, p. 92-107 16 p.

Research output: Contribution to journalArticle

20 Citations (Scopus)

Global gene expression profile of Acinetobacter baumannii during bacteremia

Murray, G. L., Tsyganov, K., Kostoulias, X. P., Bulach, D. M., Powell, D., Creek, D. J., Boyce, J. D., Paulsen, I. T. & Peleg, A. Y., 15 Feb 2017, In : The Journal of infectious diseases. 215, Suppl. 1, p. S52-S57 6 p.

Research output: Contribution to journalArticle

19 Citations (Scopus)
Open Access
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The EcoCyc database: reflecting new knowledge about Escherichia coli K-12

Keseler, I. M., Mackie, A., Santos-Zavaleta, A., Billington, R., Bonavides-Martínez, C., Caspi, R., Fulcher, C., Gama-Castro, S., Kothari, A., Krummenacker, M., Latendresse, M., Muñiz-Rascado, L., Ong, Q., Paley, S., Peralta-Gil, M., Subhraveti, P., Velázquez-Ramírez, D. A., Weaver, D., Collado-Vides, J., Paulsen, I. & 1 others, Karp, P. D., Jan 2017, In : Nucleic Acids Research. 45, D1, p. D543-D550 8 p.

Research output: Contribution to journalArticle

Open Access
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143 Citations (Scopus)
79 Downloads (Pure)

The putative drug efflux systems of the Bacillus cereus group

Hassan, K. A., Fagerlund, A., Elbourne, L. D. H., Vörös, A., Kroeger, J. K., Simm, R., Tourasse, N. J., Finke, S., Henderson, P. J. F., Økstad, O. A., Paulsen, I. T. & Kolstø, A-B., 4 May 2017, In : PLoS ONE. 12, 5, p. 1-25 25 p., e0176188.

Research output: Contribution to journalArticle

Open Access
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1 Citation (Scopus)
5 Downloads (Pure)
70 Citations (Scopus)
26 Downloads (Pure)

Zinc stress induces copper depletion in Acinetobacter baumannii

Hassan, K. A., Pederick, V. G., Elbourne, L. D. H., Paulsen, I. T., Paton, J. C., McDevitt, C. A. & Eijkelkamp, B. A., 11 Mar 2017, In : BMC Microbiology. 17, 1, p. 1-15 15 p., 59.

Research output: Contribution to journalArticle

Open Access
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17 Citations (Scopus)
6 Downloads (Pure)
2016

A sample-to-sequence protocol for genus targeted transcriptomic profiling: application to marine Synechococcus

Pitt, F. D., Millard, A., Ostrowski, M., Dervish, S., Mazard, S., Paulsen, I. T., Zubkov, M. V. & Scanlan, D. J., 14 Oct 2016, In : Frontiers in Microbiology. 7, p. 1-15 15 p., 1592.

Research output: Contribution to journalArticle

Comparative analysis of membrane vesicles from three Piscirickettsia salmonis isolates reveals differences in vesicle characteristics

Tandberg, J. I., Lagos, L. X., Langlete, P., Berger, E., Rishovd, A. L., Roos, N., Varkey, D., Paulsen, I. T. & Winther-Larsen, H. C., 20 Oct 2016, In : PLoS ONE. 11, 10, p. 1-27 27 p., e0165099.

Research output: Contribution to journalArticle

Open Access
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7 Citations (Scopus)
25 Downloads (Pure)

Disruption of transporters affiliated with enantio-pyochelin biosynthesis gene cluster of Pseudomonas protegens Pf-5 has pleiotropic effects

Lim, C. K., Penesyan, A., Hassan, K. A., Loper, J. E. & Paulsen, I. T., 21 Jul 2016, In : PLoS ONE. 11, 7, p. 1-16 16 p., e0159884.

Research output: Contribution to journalArticle

Open Access
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2 Citations (Scopus)
3 Downloads (Pure)