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  • Ian Paulsen
Article

Addition of Escherichia coli K-12 growth observation and gene essentiality data to the ecocyc database

Mackie, A., Paley, S., Keseler, I. M., Shearer, A., Paulsen, I. T. & Karp, P. D., Mar 2014, In : Journal of Bacteriology. 196, 5, p. 982-988 7 p.

Research output: Contribution to journalArticle

Open Access
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6 Citations (Scopus)
1 Downloads (Pure)

Adherence and motility characteristics of clinical Acinetobacter baumannii isolates

Eijkelkamp, B. A., Stroeher, U. H., Hassan, K. A., Papadimitrious, M. S., Paulsen, I. T. & Brown, M. H., Oct 2011, In : FEMS Microbiology Letters. 323, 1, p. 44-51 8 p.

Research output: Contribution to journalArticle

90 Citations (Scopus)

A genome-scale metabolic flux model of Escherichia coli K-12 derived from the EcoCyc database

Weaver, D. S., Keseler, I. M., Mackie, A., Paulsen, I. T. & Karp, P. D., 30 Jun 2014, In : BMC Systems Biology. 8, p. 1-24 24 p., 79.

Research output: Contribution to journalArticle

Open Access
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25 Citations (Scopus)
24 Downloads (Pure)
Open Access
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11 Citations (Scopus)
18 Downloads (Pure)

Analysis of two marine metagenomes reveals the diversity of plasmids in oceanic environments

Ma, Y., Paulsen, I. T. & Palenik, B., Feb 2012, In : Environmental microbiology. 14, 2, p. 453-466 14 p.

Research output: Contribution to journalArticle

28 Citations (Scopus)
37 Citations (Scopus)
Open Access
File
13 Citations (Scopus)
14 Downloads (Pure)
23 Citations (Scopus)

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.

Research output: Contribution to journalArticle

Open Access
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1 Citation (Scopus)
7 Downloads (Pure)

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

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.

Research output: Contribution to journalArticle

Open Access
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1 Downloads (Pure)

Bacillus cereus efflux protein BC3310 - : a multidrug transporter of the unknown major facilitator family, UMF-2

Kroeger, J. K., Hassan, K., Vörös, A., Simm, R., Saidijam, M., Bettaney, K. E., Bechthold, A., Paulsen, I. T., Henderson, P. J. F. & Kolstø, A. B., 2015, In : Frontiers in Microbiology. 6, 12 p., 1063.

Research output: Contribution to journalArticle

Open Access
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5 Citations (Scopus)
13 Downloads (Pure)

Bacterial subfamily of LuxR regulators that respond to plant compounds

Subramoni, S., Gonzalez, J. F., Johnson, A., Péchy-Tarr, M., Rochat, L., Paulsen, I., Loper, J. E., Keel, C. & Venturi, V., Jul 2011, In : Applied and Environmental Microbiology. 77, 13, p. 4579-4588 10 p.

Research output: Contribution to journalArticle

51 Citations (Scopus)
Open Access
File
1 Citation (Scopus)
23 Downloads (Pure)

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

Open Access
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21 Citations (Scopus)
11 Downloads (Pure)
Open Access
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1 Citation (Scopus)
24 Downloads (Pure)

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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10 Citations (Scopus)
5 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
16 Citations (Scopus)

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.

Research output: Contribution to journalArticle

Open Access
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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
File
7 Citations (Scopus)
27 Downloads (Pure)

Comparative analysis of surface-exposed virulence factors of Acinetobacter baumannii

Eijkelkamp, B. A., Stroeher, U. H., Hassan, K. A., Paulsen, I. T. & Brown, M. H., 25 Nov 2014, In : BMC Genomics. 15, p. 1-12 12 p., 1020.

Research output: Contribution to journalArticle

Open Access
File
56 Citations (Scopus)
12 Downloads (Pure)

Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris

Berka, R. M., Grigoriev, I. V., Otillar, R., Salamov, A., Grimwood, J., Reid, I., Ishmael, N., John, T., Darmond, C., Moisan, M. C., Henrissat, B., Coutinho, P. M., Lombard, V., Natvig, D. O., Lindquist, E., Schmutz, J., Lucas, S., Harris, P., Powlowski, J., Bellemare, A. & 19 others, Taylor, D., Butler, G., De Vries, R. P., Allijn, I. E., Van Den Brink, J., Ushinsky, S., Storms, R., Powell, A. J., Paulsen, I. T., Elbourne, L. D. H., Baker, S. E., Magnuson, J., Laboissiere, S., Clutterbuck, A. J., Martinez, D., Wogulis, M., De Leon, A. L., Rey, M. W. & Tsang, A., Oct 2011, In : Nature Biotechnology. 29, 10, p. 922-929 8 p.

Research output: Contribution to journalArticle

249 Citations (Scopus)

Comparative genomics of plant-associated Pseudomonas spp. insights into diversity and inheritance of traits involved in multitrophic interactions

Loper, J. E., Hassan, K. A., Mavrodi, D. V., Davis, E. W., Lim, C. K., Shaffer, B. T., Elbourne, L. D. H., Stockwell, V. O., Hartney, S. L., Breakwell, K., Henkels, M. D., Tetu, S. G., Rangel, L. I., Kidarsa, T. A., Wilson, N. L., van de Mortel, J. E., Song, C., Blumhagen, R., Radune, D., Hostetler, J. B. & 15 others, Brinkac, L. M., Durkin, A. S., Kluepfel, D. A., Wechter, W. P., Anderson, A. J., Kim, Y. C., Pierson, L. S., Pierson, E. A., Lindow, S. E., Kobayashi, D. Y., Raaijmakers, J. M., Weller, D. M., Thomashow, L. S., Allen, A. E. & Paulsen, I. T., Jul 2012, In : PLoS Genetics. 8, 7, p. 1-27 27 p., e1002784.

Research output: Contribution to journalArticle

337 Citations (Scopus)

Complete sequence of pJIE143, a pir-type plasmid carrying ISEcp1-bla CTX-M-15 from an Escherichia coli ST131 isolate

Partridge, S. R., Ellem, J. A., Tetu, S. G., Zong, Z., Paulsen, I. T. & Iredell, J. R., Dec 2011, In : Antimicrobial Agents and Chemotherapy. 55, 12, p. 5933-5935 3 p.

Research output: Contribution to journalArticle

34 Citations (Scopus)

Crystal structure of an integron gene cassette-associated protein from Vibrio cholerae identifies a cationic drug-binding module

Deshpande, C. N., Harrop, S. J., Boucher, Y., Hassan, K. A., Leo, R. D., Xu, X., Cui, H., Savchenko, A., Chang, C., Labbate, M., Paulsen, I. T., Stokes, H. W., Curmi, P. M. G. & Mabbutt, B. C., 2011, In : PLoS ONE. 6, 3, p. 1-11 11 p., e16934.

Research output: Contribution to journalArticle

8 Citations (Scopus)

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

Open Access
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11 Downloads (Pure)

Dead end metabolites - defining the known unknowns of the E. coli metabolic network

Mackie, A., Keseler, I. M., Nolan, L., Karp, P. D. & Paulsen, I. T., 23 Sep 2013, In : PLoS ONE. 8, 9, p. 1-11 11 p., e75210.

Research output: Contribution to journalArticle

Open Access
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14 Citations (Scopus)
10 Downloads (Pure)
6 Citations (Scopus)

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)
4 Downloads (Pure)

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

6 Citations (Scopus)

Draft genome of Australian environmental strain WM 09.24 of the opportunistic human pathogen Scedosporium aurantiacum

Pérez-Bercoff, Å., Papanicolaou, A., Ramsperger, M., Kaur, J., Patel, H. R., Harun, A., Duan, S. Y., Elbourne, L., Bouchara, J. P., Paulsen, I. T., Nevalainen, H., Meyer, W. & Huttley, G. A., 2015, In : Genome Announcements. 3, 1, p. e01526-1-e01526-2 2 p., e01526-14.

Research output: Contribution to journalArticle

Open Access
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14 Citations (Scopus)
15 Downloads (Pure)

Draft genome sequence of Bacillus alcalophilus AV1934, a classic alkaliphile isolated from human feces in 1934

Attie, O., Jayaprakash, A., Shah, H., Paulsen, I. T., Morino, M., Takahashi, Y., Narumi, I., Sachidanandam, R., Satoh, K., Ito, M. & Krulwich, T. A., 2014, In : Genome Announcements. 2, 6, p. 1-2 2 p., e01175-14.

Research output: Contribution to journalArticle

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

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

Open Access
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6 Downloads (Pure)

EcoCyc: a comprehensive database of Escherichia coli biology

Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P. & 1 others, Karp, P. D., Jan 2011, In : Nucleic Acids Research. 39, SUPPL. 1, p. D583–D590 8 p.

Research output: Contribution to journalArticle

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

EcoCyc: fusing model organism databases with systems biology

Keseler, I. M., Mackie, A., Peralta-Gil, M., Santos-Zavaleta, A., Gama-Castro, S., Bonavides-Martínez, C., Fulcher, C., Huerta, A. M., Kothari, A., Krummenacker, M., Latendresse, M., Muñiz-Rascado, L., Ong, Q., Paley, S., Schröder, I., Shearer, A. G., Subhraveti, P., Travers, M., Weerasinghe, D., Weiss, V. & 4 others, Collado-Vides, J., Gunsalus, R. P., Paulsen, I. & Karp, P. D., 1 Jan 2013, In : Nucleic Acids Research. 41, D1, p. D605-D612 8 p.

Research output: Contribution to journalArticle

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

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.

Research output: Contribution to journalArticle

Open Access
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7 Downloads (Pure)

Effect of tannic acid on the transcriptome of the soil bacterium Pseudomonas protegens Pf-5

Lim, C. K., Penesyan, A., Hassan, K. A., Loper, J. E. & Paulsen, I. T., 2013, In : Applied and Environmental Microbiology. 79, 9, p. 3141-3145 5 p.

Research output: Contribution to journalArticle

8 Citations (Scopus)

Effects of low temperature on tropical and temperate isolates of marine Synechococcus

Varkey, D., Mazard, S., Ostrowski, M., Tetu, S. G., Haynes, P. & Paulsen, I. T., 1 May 2016, In : ISME Journal. 10, 5, p. 1252-1263 12 p.

Research output: Contribution to journalArticle

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

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

Open Access
File
4 Citations (Scopus)
24 Downloads (Pure)

Fluorescence-based flow sorting in parallel with transposon insertion site sequencing identifies multidrug efflux systems in Acinetobacter baumannii

Hassan, K. A., Cain, A. K., Huang, T., Liu, Q., Elbourne, L. D. H., Boinett, C. J., Brzoska, A. J., Li, L., Ostrowski, M., Nhu, N. T. K., Nhu, T. D. H., Baker, S., Parkhill, J. & Paulsen, I. T., Sep 2016, In : mBio. 7, 5, p. 1-6 6 p., e01200-16.

Research output: Contribution to journalArticle

Open Access
File
10 Citations (Scopus)
24 Downloads (Pure)

Genes expressed by the biological control bacterium Pseudomonas protegens Pf-5 on seed surfaces under the control of the global regulators GacA and RpoS

Kidarsa, T. A., Shaffer, B. T., Goebel, N. C., Roberts, D. P., Buyer, J. S., Johnson, A., Kobayashi, D. Y., Zabriskie, T. M., Paulsen, I. & Loper, J. E., Mar 2013, In : Environmental microbiology. 15, 3, p. 716-735 20 p.

Research output: Contribution to journalArticle

26 Citations (Scopus)

Genetically and phenotypically distinct Pseudomonas aeruginosa cystic fibrosis isolates share a core proteomic signature

Penesyan, A., Kumar, S. S., Kamath, K., Shathili, A. M., Venkatakrishnan, V., Krisp, C., Packer, N. H., Molloy, M. P. & Paulsen, I. T., 2 Oct 2015, In : PLoS ONE. 10, 10, p. 1-26 26 p., e0138527.

Research output: Contribution to journalArticle

Open Access
File
9 Citations (Scopus)
19 Downloads (Pure)

Genetic identification of a high-affinity Ni transporter and the transcriptional response to Ni deprivation in synechococcus sp. Strain WH8102

Dupont, C. L., Johnson, D. A., Phillippy, K., Paulsen, I. T., Brahamsha, B. & Palenik, B., Nov 2012, In : Applied and Environmental Microbiology. 78, 22, p. 7822-7832 11 p.

Research output: Contribution to journalArticle

16 Citations (Scopus)

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

27 Citations (Scopus)

Genome of alkaliphilic Bacillus pseudofirmus OF4 reveals adaptations that support the ability to grow in an external pH range from 7.5 to 11.4

Janto, B., Ahmed, A., Ito, M., Liu, J., Hicks, D. B., Pagni, S., Fackelmayer, O. J., Smith, T. A., Earl, J., Elbourne, L. D. H., Hassan, K., Paulsen, I. T., Kolstø, A. B., Tourasse, N. J., Ehrlich, G. D., Boissy, R., Ivey, D. M., Li, G., Xue, Y., Ma, Y. & 2 others, Hu, F. Z. & Krulwich, T. A., Dec 2011, In : Environmental microbiology. 13, 12, p. 3289-3309 21 p.

Research output: Contribution to journalArticle

50 Citations (Scopus)

Genome sequence of the group III Clostridium botulinum strain Eklund-C

Hassan, K. A., Tetu, S. G., Elbourne, L. D. H., Johnson, E. A. & Paulsen, I. T., 2013, In : Genome Announcements. 1, 2, p. 1-2 2 p., e00044-13.

Research output: Contribution to journalArticle

6 Citations (Scopus)