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Items: 1 to 50 of 122

1.

GPU acceleration of a model-based iterative method for Digital Breast Tomosynthesis.

Cavicchioli R, Hu JC, Loli Piccolomini E, Morotti E, Zanni L.

Sci Rep. 2020 Jan 8;10(1):43. doi: 10.1038/s41598-019-56920-y.

2.

Unexpected host dependency of Antarctic Nanohaloarchaeota.

Hamm JN, Erdmann S, Eloe-Fadrosh EA, Angeloni A, Zhong L, Brownlee C, Williams TJ, Barton K, Carswell S, Smith MA, Brazendale S, Hancock AM, Allen MA, Raftery MJ, Cavicchioli R.

Proc Natl Acad Sci U S A. 2019 Jul 16;116(29):14661-14670. doi: 10.1073/pnas.1905179116. Epub 2019 Jun 28.

3.

Scientists' warning to humanity: microorganisms and climate change.

Cavicchioli R, Ripple WJ, Timmis KN, Azam F, Bakken LR, Baylis M, Behrenfeld MJ, Boetius A, Boyd PW, Classen AT, Crowther TW, Danovaro R, Foreman CM, Huisman J, Hutchins DA, Jansson JK, Karl DM, Koskella B, Mark Welch DB, Martiny JBH, Moran MA, Orphan VJ, Reay DS, Remais JV, Rich VI, Singh BK, Stein LY, Stewart FJ, Sullivan MB, van Oppen MJH, Weaver SC, Webb EA, Webster NS.

Nat Rev Microbiol. 2019 Sep;17(9):569-586. doi: 10.1038/s41579-019-0222-5. Epub 2019 Jun 18. Review.

PMID:
31213707
4.

The urgent need for microbiology literacy in society.

Timmis K, Cavicchioli R, Garcia JL, Nogales B, Chavarría M, Stein L, McGenity TJ, Webster N, Singh BK, Handelsman J, de Lorenzo V, Pruzzo C, Timmis J, Martín JLR, Verstraete W, Jetten M, Danchin A, Huang W, Gilbert J, Lal R, Santos H, Lee SY, Sessitsch A, Bonfante P, Gram L, Lin RTP, Ron E, Karahan ZC, van der Meer JR, Artunkal S, Jahn D, Harper L.

Environ Microbiol. 2019 May;21(5):1513-1528. doi: 10.1111/1462-2920.14611. Epub 2019 Apr 11. No abstract available.

PMID:
30912268
5.

Sucrose Metabolism in Haloarchaea: Reassessment Using Genomics, Proteomics, and Metagenomics.

Williams TJ, Allen MA, Liao Y, Raftery MJ, Cavicchioli R.

Appl Environ Microbiol. 2019 Mar 6;85(6). pii: e02935-18. doi: 10.1128/AEM.02935-18. Print 2019 Mar 15.

6.

Genomic variation and biogeography of Antarctic haloarchaea.

Tschitschko B, Erdmann S, DeMaere MZ, Roux S, Panwar P, Allen MA, Williams TJ, Brazendale S, Hancock AM, Eloe-Fadrosh EA, Cavicchioli R.

Microbiome. 2018 Jun 20;6(1):113. doi: 10.1186/s40168-018-0495-3.

7.

A vision for a 'microbcentric' future.

Cavicchioli R.

Microb Biotechnol. 2019 Jan;12(1):26-29. doi: 10.1111/1751-7915.13262. Epub 2018 Apr 2.

8.

A plasmid from an Antarctic haloarchaeon uses specialized membrane vesicles to disseminate and infect plasmid-free cells.

Erdmann S, Tschitschko B, Zhong L, Raftery MJ, Cavicchioli R.

Nat Microbiol. 2017 Oct;2(10):1446-1455. doi: 10.1038/s41564-017-0009-2. Epub 2017 Aug 21.

PMID:
28827601
9.
10.

Cold adaptation of the Antarctic haloarchaea Halohasta litchfieldiae and Halorubrum lacusprofundi.

Williams TJ, Liao Y, Ye J, Kuchel RP, Poljak A, Raftery MJ, Cavicchioli R.

Environ Microbiol. 2017 Jun;19(6):2210-2227. doi: 10.1111/1462-2920.13705. Epub 2017 Mar 28.

PMID:
28217912
11.

Morphological and proteomic analysis of biofilms from the Antarctic archaeon, Halorubrum lacusprofundi.

Liao Y, Williams TJ, Ye J, Charlesworth J, Burns BP, Poljak A, Raftery MJ, Cavicchioli R.

Sci Rep. 2016 Nov 22;6:37454. doi: 10.1038/srep37454.

12.

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses.

Paez-Espino D, Chen IA, Palaniappan K, Ratner A, Chu K, Szeto E, Pillay M, Huang J, Markowitz VM, Nielsen T, Huntemann M, K Reddy TB, Pavlopoulos GA, Sullivan MB, Campbell BJ, Chen F, McMahon K, Hallam SJ, Denef V, Cavicchioli R, Caffrey SM, Streit WR, Webster J, Handley KM, Salekdeh GH, Tsesmetzis N, Setubal JC, Pope PB, Liu WT, Rivers AR, Ivanova NN, Kyrpides NC.

Nucleic Acids Res. 2017 Jan 4;45(D1):D457-D465. doi: 10.1093/nar/gkw1030. Epub 2016 Oct 30.

13.

Glycerol metabolism of haloarchaea.

Williams TJ, Allen M, Tschitschko B, Cavicchioli R.

Environ Microbiol. 2017 Mar;19(3):864-877. doi: 10.1111/1462-2920.13580. Epub 2016 Nov 13. Review.

PMID:
27768817
14.

Virus-mediated archaeal hecatomb in the deep seafloor.

Danovaro R, Dell'Anno A, Corinaldesi C, Rastelli E, Cavicchioli R, Krupovic M, Noble RT, Nunoura T, Prangishvili D.

Sci Adv. 2016 Oct 12;2(10):e1600492. eCollection 2016 Oct.

15.

Developing a genetic manipulation system for the Antarctic archaeon, Halorubrum lacusprofundi: investigating acetamidase gene function.

Liao Y, Williams TJ, Walsh JC, Ji M, Poljak A, Curmi PM, Duggin IG, Cavicchioli R.

Sci Rep. 2016 Oct 6;6:34639. doi: 10.1038/srep34639.

16.

Complete genome sequence of the Antarctic Halorubrum lacusprofundi type strain ACAM 34.

Anderson IJ, DasSarma P, Lucas S, Copeland A, Lapidus A, Del Rio TG, Tice H, Dalin E, Bruce DC, Goodwin L, Pitluck S, Sims D, Brettin TS, Detter JC, Han CS, Larimer F, Hauser L, Land M, Ivanova N, Richardson P, Cavicchioli R, DasSarma S, Woese CR, Kyrpides NC.

Stand Genomic Sci. 2016 Sep 10;11(1):70. doi: 10.1186/s40793-016-0194-2. eCollection 2016.

17.

Corrigendum: Characterization of a temperature-responsive two component regulatory system from the Antarctic archaeon, Methanococcoides burtonii.

Najnin T, Siddiqui KS, Taha, Elkaid N, Kornfeld G, Curmi PM, Cavicchioli R.

Sci Rep. 2016 Jun 10;6:27162. doi: 10.1038/srep27162. No abstract available.

18.

Characterization of a temperature-responsive two component regulatory system from the Antarctic archaeon, Methanococcoides burtonii.

Najnin T, Siddiqui KS, Taha T, Elkaid N, Kornfeld G, Curmi PM, Cavicchioli R.

Sci Rep. 2016 Apr 7;6:24278. doi: 10.1038/srep24278. Erratum in: Sci Rep. 2016 Jun 10;6:27162.

19.

Ecophysiological Distinctions of Haloarchaea from a Hypersaline Antarctic Lake as Determined by Metaproteomics.

Tschitschko B, Williams TJ, Allen MA, Zhong L, Raftery MJ, Cavicchioli R.

Appl Environ Microbiol. 2016 May 16;82(11):3165-73. doi: 10.1128/AEM.00473-16. Print 2016 Jun 1.

20.

Aptamer based peptide enrichment for quantitative analysis of gonadotropin-releasing hormone by LC-MS/MS.

Richards SL, Cawley AT, Cavicchioli R, Suann CJ, Pickford R, Raftery MJ.

Talanta. 2016 Apr 1;150:671-80. doi: 10.1016/j.talanta.2016.01.006. Epub 2016 Jan 7.

PMID:
26838458
21.

Single TRAM domain RNA-binding proteins in Archaea: functional insight from Ctr3 from the Antarctic methanogen Methanococcoides burtonii.

Taha, Siddiqui KS, Campanaro S, Najnin T, Deshpande N, Williams TJ, Aldrich-Wright J, Wilkins M, Curmi PM, Cavicchioli R.

Environ Microbiol. 2016 Sep;18(9):2810-24. doi: 10.1111/1462-2920.13229. Epub 2016 Feb 5.

PMID:
26769275
22.

Microbial ecology of Antarctic aquatic systems.

Cavicchioli R.

Nat Rev Microbiol. 2015 Nov;13(11):691-706. doi: 10.1038/nrmicro3549. Epub 2015 Oct 12. Review. Erratum in: Nat Rev Microbiol. 2015 Dec;13(12):795.

PMID:
26456925
23.

The discovery of Antarctic RNA viruses: a new game changer.

Cavicchioli R, Erdmann S.

Mol Ecol. 2015 Oct;24(19):4809-11. doi: 10.1111/mec.13387.

PMID:
26417900
24.

On the concept of a psychrophile.

Cavicchioli R.

ISME J. 2016 Apr;10(4):793-5. doi: 10.1038/ismej.2015.160. Epub 2015 Sep 15. No abstract available.

25.

Antarctic archaea-virus interactions: metaproteome-led analysis of invasion, evasion and adaptation.

Tschitschko B, Williams TJ, Allen MA, Páez-Espino D, Kyrpides N, Zhong L, Raftery MJ, Cavicchioli R.

ISME J. 2015 Sep;9(9):2094-107. doi: 10.1038/ismej.2015.110. Epub 2015 Jun 30.

26.

Lost cold Antarctic deserts inferred from unusual sulfate formation and isotope signatures.

Sun T, Socki RA, Bish DL, Harvey RP, Bao H, Niles PB, Cavicchioli R, Tonui E.

Nat Commun. 2015 Jun 29;6:7579. doi: 10.1038/ncomms8579.

PMID:
26119082
27.

Viruses of haloarchaea.

Luk AW, Williams TJ, Erdmann S, Papke RT, Cavicchioli R.

Life (Basel). 2014 Nov 13;4(4):681-715. doi: 10.3390/life4040681. Review.

28.

Marine metaproteomics: deciphering the microbial metabolic food web.

Williams TJ, Cavicchioli R.

Trends Microbiol. 2014 May;22(5):248-60. doi: 10.1016/j.tim.2014.03.004. Epub 2014 Apr 11. Review.

PMID:
24731505
29.

Versatile peroxidase degradation of humic substances: use of isothermal titration calorimetry to assess kinetics, and applications to industrial wastes.

Siddiqui KS, Ertan H, Charlton T, Poljak A, Daud Khaled AK, Yang X, Marshall G, Cavicchioli R.

J Biotechnol. 2014 May 20;178:1-11. doi: 10.1016/j.jbiotec.2014.03.002. Epub 2014 Mar 11.

PMID:
24631722
30.

Microbial ecology of an Antarctic hypersaline lake: genomic assessment of ecophysiology among dominant haloarchaea.

Williams TJ, Allen MA, DeMaere MZ, Kyrpides NC, Tringe SG, Woyke T, Cavicchioli R.

ISME J. 2014 Aug;8(8):1645-58. doi: 10.1038/ismej.2014.18. Epub 2014 Feb 20. Erratum in: ISME J. 2014 Aug;8(8):1752.

31.

High level of intergenera gene exchange shapes the evolution of haloarchaea in an isolated Antarctic lake.

DeMaere MZ, Williams TJ, Allen MA, Brown MV, Gibson JA, Rich J, Lauro FM, Dyall-Smith M, Davenport KW, Woyke T, Kyrpides NC, Tringe SG, Cavicchioli R.

Proc Natl Acad Sci U S A. 2013 Oct 15;110(42):16939-44. doi: 10.1073/pnas.1307090110. Epub 2013 Sep 30.

32.

Advection shapes Southern Ocean microbial assemblages independent of distance and environment effects.

Wilkins D, van Sebille E, Rintoul SR, Lauro FM, Cavicchioli R.

Nat Commun. 2013;4:2457. doi: 10.1038/ncomms3457.

PMID:
24036630
33.

Towards real-time image deconvolution: application to confocal and STED microscopy.

Zanella R, Zanghirati G, Cavicchioli R, Zanni L, Boccacci P, Bertero M, Vicidomini G.

Sci Rep. 2013;3:2523. doi: 10.1038/srep02523.

34.

Integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the Chlamydiae.

Lagkouvardos I, Weinmaier T, Lauro FM, Cavicchioli R, Rattei T, Horn M.

ISME J. 2014 Jan;8(1):115-25. doi: 10.1038/ismej.2013.142. Epub 2013 Aug 15.

35.

Shotgun redox proteomics: identification and quantitation of carbonylated proteins in the UVB-resistant marine bacterium, Photobacterium angustum S14.

Matallana-Surget S, Cavicchioli R, Fauconnier C, Wattiez R, Leroy B, Joux F, Raftery MJ, Lebaron P.

PLoS One. 2013 Jul 9;8(7):e68112. doi: 10.1371/journal.pone.0068112. Print 2013.

36.

Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean.

Swan BK, Tupper B, Sczyrba A, Lauro FM, Martinez-Garcia M, González JM, Luo H, Wright JJ, Landry ZC, Hanson NW, Thompson BP, Poulton NJ, Schwientek P, Acinas SG, Giovannoni SJ, Moran MA, Hallam SJ, Cavicchioli R, Woyke T, Stepanauskas R.

Proc Natl Acad Sci U S A. 2013 Jul 9;110(28):11463-8. doi: 10.1073/pnas.1304246110. Epub 2013 Jun 25.

37.

Metagenomic insights into strategies of carbon conservation and unusual sulfur biogeochemistry in a hypersaline Antarctic lake.

Yau S, Lauro FM, Williams TJ, Demaere MZ, Brown MV, Rich J, Gibson JA, Cavicchioli R.

ISME J. 2013 Oct;7(10):1944-61. doi: 10.1038/ismej.2013.69. Epub 2013 Apr 25.

38.

Biogeographic partitioning of Southern Ocean microorganisms revealed by metagenomics.

Wilkins D, Lauro FM, Williams TJ, Demaere MZ, Brown MV, Hoffman JM, Andrews-Pfannkoch C, McQuaid JB, Riddle MJ, Rintoul SR, Cavicchioli R.

Environ Microbiol. 2013 May;15(5):1318-33. doi: 10.1111/1462-2920.12035. Epub 2012 Nov 30.

PMID:
23199136
39.

The role of planktonic Flavobacteria in processing algal organic matter in coastal East Antarctica revealed using metagenomics and metaproteomics.

Williams TJ, Wilkins D, Long E, Evans F, DeMaere MZ, Raftery MJ, Cavicchioli R.

Environ Microbiol. 2013 May;15(5):1302-17. doi: 10.1111/1462-2920.12017. Epub 2012 Nov 6.

PMID:
23126454
40.

Key microbial drivers in Antarctic aquatic environments.

Wilkins D, Yau S, Williams TJ, Allen MA, Brown MV, DeMaere MZ, Lauro FM, Cavicchioli R.

FEMS Microbiol Rev. 2013 May;37(3):303-35. doi: 10.1111/1574-6976.12007. Epub 2012 Nov 20. Review.

41.

Global biogeography of SAR11 marine bacteria.

Brown MV, Lauro FM, DeMaere MZ, Muir L, Wilkins D, Thomas T, Riddle MJ, Fuhrman JA, Andrews-Pfannkoch C, Hoffman JM, McQuaid JB, Allen A, Rintoul SR, Cavicchioli R.

Mol Syst Biol. 2012 Jul 17;8:595. doi: 10.1038/msb.2012.28.

43.

A metagenomic assessment of winter and summer bacterioplankton from Antarctica Peninsula coastal surface waters.

Grzymski JJ, Riesenfeld CS, Williams TJ, Dussaq AM, Ducklow H, Erickson M, Cavicchioli R, Murray AE.

ISME J. 2012 Oct;6(10):1901-15. doi: 10.1038/ismej.2012.31. Epub 2012 Apr 26.

44.

A metaproteomic assessment of winter and summer bacterioplankton from Antarctic Peninsula coastal surface waters.

Williams TJ, Long E, Evans F, Demaere MZ, Lauro FM, Raftery MJ, Ducklow H, Grzymski JJ, Murray AE, Cavicchioli R.

ISME J. 2012 Oct;6(10):1883-900. doi: 10.1038/ismej.2012.28. Epub 2012 Apr 26.

45.

Life and applications of extremophiles.

Cavicchioli R, Amils R, Wagner D, McGenity T.

Environ Microbiol. 2011 Aug;13(8):1903-7. doi: 10.1111/j.1462-2920.2011.02512.x. No abstract available.

PMID:
22236328
46.

Simple high-throughput annotation pipeline (SHAP).

DeMaere MZ, Lauro FM, Thomas T, Yau S, Cavicchioli R.

Bioinformatics. 2011 Sep 1;27(17):2431-2. doi: 10.1093/bioinformatics/btr411. Epub 2011 Jul 19.

PMID:
21775307
47.

Biotechnological uses of enzymes from psychrophiles.

Cavicchioli R, Charlton T, Ertan H, Mohd Omar S, Siddiqui KS, Williams TJ.

Microb Biotechnol. 2011 Jul;4(4):449-60. doi: 10.1111/j.1751-7915.2011.00258.x. Epub 2011 Mar 24. Review.

48.

Proteomics of extremophiles.

Burg D, Ng C, Ting L, Cavicchioli R.

Environ Microbiol. 2011 Aug;13(8):1934-55. doi: 10.1111/j.1462-2920.2011.02484.x. Epub 2011 Apr 25. Review.

PMID:
21518215
49.

Chaperonins from an Antarctic archaeon are predominantly monomeric: crystal structure of an open state monomer.

Pilak O, Harrop SJ, Siddiqui KS, Chong K, De Francisci D, Burg D, Williams TJ, Cavicchioli R, Curmi PM.

Environ Microbiol. 2011 Aug;13(8):2232-49. doi: 10.1111/j.1462-2920.2011.02477.x. Epub 2011 Apr 7.

PMID:
21477108
50.

Virophage control of antarctic algal host-virus dynamics.

Yau S, Lauro FM, DeMaere MZ, Brown MV, Thomas T, Raftery MJ, Andrews-Pfannkoch C, Lewis M, Hoffman JM, Gibson JA, Cavicchioli R.

Proc Natl Acad Sci U S A. 2011 Apr 12;108(15):6163-8. doi: 10.1073/pnas.1018221108. Epub 2011 Mar 28.

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