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(*contributed equally, #corresponding author)

2019

78. Fineran, P.C.# (2019). Resistance is not futile: bacterial ‘innate’ and ‘adaptive’ immune systems. Fleming Prize Award Article. Microbiology. doi: 10.1099/mic.0.000802.

77. Edwards, R.A., Vega, A., … Fineran, P.C. … , Dutilh, B.E. (2019). Global phylogeography and ancient evolution of the widespread human gut virus crAssphage. bioRxiv preprint

76. Jackson, S.A.,# Birkholz, N. Malone, L.M. and Fineran, P.C.# (2019). Imprecise spacer acquisition generates CRISPR-Cas immune diversity through primed adaptation. Cell Host & Microbe doi.org/10.1016/j.chom.2018.12.014

75. Fagerlund, R.D.,# Ferguson, T.J., Maxwell, H.W.R. Opel-Reading, H.K., Krause, K.L. and Fineran, P.C.# (2019). Reconstitution of CRISPR adaptation in vitro and its detection by PCR. Volume 617: CRISPR-Cas Enzymes. Methods in Enzymologydoi.org/10.1016/bs.mie.2018.10.024

74. Fineran, P.C.# (2019) CRISPR-Cas impedes archaeal mating. Nature Microbiology. 4:2-3.

73. Shereen, S., Chyou, D. Fineran, P.C. and Brown, C.M. (2019). Genome-wide correlation analysis suggests different roles of CRISPR-Cas systems in the acquisition of antibiotic resistance genes in diverse species. Philosophical Transactions of the Royal Society B. In press

72. Watson, B.N.J., Easingwood, R.A., Tong, B., Wolf, M., Salmond, G.P.C., Staals, R.H.J., Bostina, M.# and Fineran, P.C.# (2019). Different genetic and morphological outcomes for phages targeted by single or multiple CRISPR-Cas spacers. Philosophical Transactions of the Royal Society B. In press 

2018

71. Dy, R.L.,# Rigano, L. and Fineran, P.C.# (2018). Phage-based biocontrol strategies and their application in agriculture and aquaculture. Biochemical Society Transactions. doi:10.1042/BST20180178

70. Bondy-Denomy, J., Davidson, A.R., Doudna, J.A., Fineran, P.C., Maxwell, K.L., Moineau, S., Peng, X., Sontheimer, E.J. and Wiedenheft, B. (2018). A Unified Resource for Tracking Anti-CRISPR Names. The CRISPR Journal. 1. 304-305.

69. Nicholson, T.J.,* Jackson, S.A.,* Croft, B.I., Staals, R.H.J., Fineran, P.C.# and Brown, C.M.# (2018). Bioinformatic evidence of widespread priming in Type I and II CRISPR-Cas systems. RNA Biology. doi:10.1080/15476286.2018.1509662

68. Hampton, H.G., Jackson, S.A., Fagerlund, R.D., Vogel, A.I.M., Dy, R.L., Blower, T.R. and Fineran, P.C.# (2018). AbiEi binds cooperatively to the Type IV abiE toxin-antitoxin operator via a positively-charged surface and causes DNA bending and negative autoregulation. Journal of Molecular Biology430:1141-1156

67. Watson, B.N.J., Staals, R.H.J. and Fineran, P.C.# (2018). CRISPR-Cas-mediated phage resistance enhances horizontal gene transfer by transduction. mBio 9:e02406-17.
Highlight: Du Toit A. (2018). Viral infection: CRISPR-Cas enhances HGT by transduction. Nature Reviews Microbiology. 16:186

2017

66. Silas, S., Lucas-Elío, P., Jackson, S.A., Aroca-Crevillén, A., Hansen, L.L., Fineran, P.C., Fire, A.Z., Sánchez-Amat, A. (2017).Type III CRISPR-Cas systems can provide redundancy to counteract viral escape from type I systems. eLife. 6:e27601 doi: 10.7554/eLife.27601

65. Fagerlund, R.D.,* Wilkinson, M.E.,* Klykov, O.,* Barendregt, A., Pearce, F.G., Kieper, S.N., Maxwell, H.W.R., Capolupo, A., Heck, A.J.R., Krause, K.L., Bostina, M., Scheltema, R.A., Staals, R.H.J. and Fineran, P.C.# (2017). Spacer capture and integration by a type I-F Cas1:Cas2-3 CRISPR adaptation complex. Proc. Natl. Acad. Sci. (USA). 114. E5122-E5128

64. Jackson, S.A.,* McKenzie, R.E.,* Fagerlund, R.D., Kieper, S.N., Fineran, P.C.# and Brouns, S.J.J.# (2017). CRISPR-Cas: adapting to change. Science. 356.eaal5056

63. Patterson, A.G., Yevstigneyeva, M. and Fineran, P.C.# (2017). Regulation of CRISPR-Cas adaptive immune systems. Current Opinion in Microbiology. 37. 1-7. (invited)

62. Mesarich, C.H., Rees-George, J., Gardner, P.P., Ghomi, F.A., Gerth, M.L., Andersen, M.T., Rikkerink, E.H.A., Fineran,P.C. and Templeton, M.D. (2017). Transposon insertion libraries for the characterization of mutants from the kiwifruit pathogen Pseudomonas syringae pv. actinidiae. PLoS ONE. 12. e0172790

61. Blower, T.R., Chai, R., Przybilski, R., Chindhy, S., Fang, X., Kidman, S., Tan, H., Luisi, B.F., Fineran, P.C. and Salmond, G.P.C. (2017). Bacteriophage phiM1 of Pectobacterium atrosepticum evolves to escape two bifunctional Type III toxin-antitoxin and abortive infection systems through mutations in a single viral gene. Applied and Environmental Microbiology.

2016

60. Patterson, A.G., Jackson, S.A., Taylor, C., Evans, G.B., Salmond, G.P.C., Przybilski, R., Staals, R.H.J. and Fineran, P.C.# (2016). Quorum sensing controls adaptive immunity through the regulation of multiple CRISPR-Cas systems. Molecular Cell. 64. 1102–1108

59. Staals, R.H.J., Jackson, S.A., Biswas, A., Brouns, S.J.J., Brown, C.M. and Fineran, P.C.# (2016). Interference-driven spacer acquisition is dominant over naive and primed adaptation in a native CRISPR-Cas system. Nature Communications. 7. 12853

58. Pawluk, A., Staals, R.H.J., Taylor, C., Watson, B.N.J., Saha, S., Fineran, P.C., Maxwell, K.L. and Davidson, A.R. (2016). Inactivation of CRISPR-Cas systems by anti-CRISPR proteins in diverse bacterial species. Nature Microbiology. 1. 16805

57. Biswas, A., Staals, R.H.J., Morales, S.E., Fineran, P.C. and Brown, C.M. (2016). CRISPRDetect: A flexible algorithm to define CRISPR arrays. BMC Genomics. 17.356

56. Hampton, H.G., McNeil, M.B., Paterson, T.J., Ney, B., Williamson, N.R., Easingwood, R.A., Bostina, M., Salmond, G.P.C. and Fineran, P.C.# (2016). CRISPR-Cas gene editing reveals RsmA and RsmC act through FlhDC to repress the SdhE flavinylation factor and control motility and prodigiosin production in Serratia. Microbiology. 162. 1047-1058

55. Panda, P., Vanga, B.R., Lu, A., Fiers, M., Fineran, P.C., Butler, R., Armstrong, K., Ronson, C.W. and Pitman, A.R. (2016). Pectobacterium atrosepticum and Pectobacterium carotovorum harbor distinct, independently acquired integrative and conjugative elements encoding coronafacic acid that enhance virulence on potato stems. Frontiers in Microbiology. 7. 397

54. Wilkinson, M.E., Nakatani, Y., Staals, R.H.J., Kieper, S.N., Opel-Reading, H.K., McKenzie, R.E., Fineran, P.C.# and Krause, K.L.# (2016). Structural plasticity and in vivo activity of Cas1 from the type I-F CRISPR-Cas system. Biochemical Journal. 473. 1063-1072

2015

53. Fagerlund, R.D., Staals, R.H. and Fineran, P.C.# (2015). The CRISPR-Cas protein Cpf1 expands genome-editing tools. Genome Biology. 16. 251

52. Salmond, G.P.C.# and Fineran, P.C.# (2015). A century of the phage: past, present and future. Nature Reviews Microbiology. 13. 777-786

51. Templeton, M.D., Warren, B.A., Andersen, M.T., Rikkerink, E.H.A. and Fineran,P.C. (2015). The Complete DNA Sequence of Pseudomonas syringae pv. actinidiae the Causal Agent of Kiwifruit Canker Disease. Genome Announcements. 3. e01054-15

50. Holguín, A.V., Rangel, G., Clavijo, V., Prada, C., Mantilla, M., Gomez, M.C., Kutter, E., Taylor, C., Fineran, P.C. González Barrios, A.F. and Vives, M.J. (2015). Phage ΦPan70, a putative temperate phage, controls Pseudomonas aeruginosa in planktonic, biofilm and burn mouse model assays. Viruses. 7. 4602-4623

49. Frampton, R.A.,* Lopez-Acedo, E.,* Young, V.L., Chen, D., Tong, B., Taylor, C., Easingwood, R.A., Pitman, A.R., Kleffmann, T.,  Bostina, M.# and Fineran, P.C.# (2015). Genome, proteome and structure of a T7-like bacteriophage of the kiwifruit canker phytopathogen Pseudomonas syringae pv. actinidiae. Viruses. 7. 3361-3379

48. Patterson, A.G., Chang, J.T., Taylor, C. and Fineran, P.C.# (2015). Regulation of the Type I-F CRISPR-Cas system by CRP-cAMP and GalM controls spacer acquisition and interference. Nucleic Acids Research. 43. 6038-6048

47. Lundgren, M., Charpentier, E. and Fineran, P.C. (Eds) (2015). CRISPR: Methods and Protocols. Methods in Molecular Biology. Volume 1311. Humana Press, 366 pages.

46. Biswas, A., Fineran, P.C. and Brown, C.M. (2015). Computational detection of CRISPR/crRNA targets. Methods in Molecular Biology. 1311:77-89

2014

45. Richter, C.,* Dy, R.L.,* McKenzie, R.E.,* Watson, B.N.J., Taylor, C., Chang, J.T., McNeil, M.B., Staals, R.H.J. and Fineran, P.C.# (2014). Priming in the Type I-F CRISPR-Cas system triggers strand-independent spacer acquisition, bi-directionally from the primed protospacer. Nucleic Acids Research. 42. 8516-8526

44. Dy, R.L., Richter, C., Salmond, G.P.C. and Fineran, P.C.# (2014). Remarkable Mechanisms in Microbes to Resist Viral Infections. Annual Reviews of Virology. 1. 307-331

43. Fineran, P.C.#, Gerritzen, M.J.H., Suárez-Diez, M., Künne, T., Boekhorst, J., van Hijum, S.A.F.T., Staals, R.H.J. and Brouns, S.J.J.# (2014). Degenerate target sites mediate rapid primed CRISPR adaptation. Proc. Natl. Acad. Sci. (USA). 111. E1629–E1638

42. Westra, E.R., Buckling, A. and Fineran, P.C. (2014). CRISPR-Cas: More than Adaptive Immunity. Nature Reviews Microbiology12. 317-326

41. Fineran, P.C.# and Dy, R.L. (2014). Gene regulation by engineered CRISPR-Cas systems. Current Opinion in Microbiology18. 83-89

40. Biswas, A., Fineran, P.C. and Brown, C.M. (2014). Accurate computational prediction of the transcribed strand of CRISPR noncoding RNAs. Bioinformatics. 30. 1805-1813

39. Frampton, R.A., Taylor, C., Holguin Moreno, A.V., Visnovsky, S.B., Petty, N.K., Pitman, A.R. and Fineran, P.C.# (2014). Identification of bacteriophages for the biocontrol of the kiwifrut canker phytopathogen Pseudomonas syringae pv. actinidiae. Applied and Environmental Microbiology80. 2216-2228

38. Dy, R.L., Przybilski, R., Semeijn, K., Salmond, G.P.C. and Fineran, P.C.# (2014). A widespread bacteriophage abortive infection system functions through a Type IV toxin-antitoxin mechanism. Nucleic Acids Research42. 4590-4605

37. McNeil, M.B., Hampton, H.G., Hards, K.J., Watson, B.N.J., Cook, G.M. and Fineran, P.C.# (2014). The succinate dehydrogenase assembly factor, SdhE, is required for the flavinylation and activation of fumarate reductase in bacteria. FEBS Letters588. 514-521

2013

36. Fineran, P.C.,# Iglesias Cans, M.C., Ramsay, J.P., Wilf, N., Cossyleon, D., McNeil, M.B., Williamson, N.R., Monson, R.E., Becher, S.A., Stanton, J.S., Brügger, K, Brown, S.D. and Salmond, G.P.C.# (2013). Draft genome sequence of Serratia sp. strain ATCC 39006, a model bacterium for the analysis of the biosynthesis and regulation of prodigiosin, a carbapenem and gas vesicles. Genome Announcements1. e01039-13

35. Dy, R.L., Pitman, A.R. and Fineran, P.C.# (2013). Chromosomal targeting by CRISPR-Cas can contribute to genome plasticity in bacteria. Mobile Genetic Elements3. e26831

34. Richter, C. and Fineran, P.C.# (2013). The type I-F CRISPR-Cas system influences pathogenicity island retention in Pectobacterium atrosepticum via crRNA generation and Csy complex formation. Biochemical Society Transactions41. 1468-74

33. McNeil, M.B. and Fineran, P.C.# (2013). The conserved RGxxE motif of the bacterial FAD assembly factor SdhE is required for succinate dehydrogenase flavinylation and activity. Biochemistry.52. 7628–40

32. Sangal, V., Fineran, P.C. and Hoskisson, P.A. (2013). Novel configurations of Type I and II CRISPR/Cas systems in Corynebacterium diphtheriae. Microbiology159. 2118-2126

31. McNeil, M.B., Iglesias Cans, M., Clulow, J.S. and Fineran, P.C.# (2013). YgfX (CptA) is a multimeric membrane protein that interacts with the succinate dehydrogenase assembly factor SdhE (YgfY). Microbiology159. 1352-1365

30. Vercoe, R.B., Chang, J.T., Dy, R.L., Taylor, C., Gristwood, T., Clulow, J.S., Richter, C., Przybilski, R., Pitman, A.R. and Fineran, P.C.# (2013). Cytotoxic chromosomal targeting by CRISPR/Cas systems can reshape bacterial genomes and expel or remodel pathogenicity islands. PLOS Genetics9(4): e1003454.

29. Westra, E.R., Staals, R.H.J., Gort, G., Hoegh, S., Neumann, S., de la Cruz, F., Fineran, P.C. and Brouns, S.J.J. (2013). CRISPR-Cas systems preferentially target the leading regions of MOBF conjugative plasmids. RNA Biology10. 22-34.

28. Biswas, A., Gagnon, J.N., Brouns, S.J.J., Fineran, P.C.# and Brown, C.M.# (2013). CRISPRTarget: Bioinformatic prediction and analysis of crRNA targets. RNA Biology10. 82-92.

27. Cook, G.M.,# Robson, J.R., Frampton, R.A., McKenzie, J., Przybilski, R., Fineran, P.C#. and Arcus, V.L.# (2013) Ribonucleases in Bacterial Toxin-Antitoxin Systems. BBA - Gene Regulatory Mechanisms1829. 523-531. (invited review)

26. Short, F.L., Pei, X.Y., Blower, T.R., Ong, S.L., Fineran, P.C., Luisi, B.F. and Salmond, G.P.C. (2013). Self-assembly and selective bacterial toxin inhibition by an antitoxic non-coding RNA pseudoknot. Proc. Natl. Acad. Sci. (USA). 110. E241-9.

25. McNeil, M.B. and Fineran, P.C.# (2013). Prokaryotic assembly factors for the attachment of flavin to complex II. BBA Bioenergetics1827. 637-647. (invited review)

2012

24. Richter, C., Gristwood, T., Clulow, J.S. and Fineran, P.C.# (2012). In vivo protein interactions and complex formation in the Pectobacterium atrosepticum subtype I-F CRISPR/Cas system. PLoS ONE.7. e49549. 

23. Blower, T.R., Short, F.L., Fineran, P.C. and Salmond, G.P.C. (2012). Viral molecular mimicry circumvents abortive infection and suppresses bacterial suicide to make hosts permissive for replication. Bacteriophage2. 234-238.

22. Fineran, P.C.# and Charpentier, E.# (2012). Memory of viral infection by CRISPR-Cas immune systems: acquisition of new information. Virology434. 202-209. 

21. Richter, C., Chang, J.T. and Fineran, P.C.# (2012). The function and regulation of CRISPR/Cas systems. Viruses4. 2291-2311. (invited review)

20. Blower, T.R., Evans, T.J., Przybilski, R., Fineran, P.C. and Salmond, G.P.C. (2012). A bacteriophage-derived non-coding RNA mimics antitoxic activity to inhibit abortive infection by a Type III toxin-antitoxin system. PLoS Genetics8. e1003023. 

19. Frampton, R.A. Pitman, A.R. and Fineran, P.C.# (2012). Advances in Bacteriophage-Mediated Control of Plant Pathogens. International Journal of Microbiology2012. 326452.

18. McNeil, M.B., Clulow, J.S., Wilf, N., Salmond, G.P.C. and Fineran, P.C.# (2012). SdhE is a conserved protein required for the flavinylation of succinate dehydrogenase in bacteria. Journal of Biological Chemistry287. 18418–18428. 

17. Blower, T.R., Short, F.L., Rao, F. Mizoguchi, K., Pei, X.Y., Fineran, P.C., Luisi, B.F. and Salmond, G.P.C. (2012). Identification and classification of bacterial Type III toxin-antitoxin systems and antiviral abortive infection systems encoded in chromosomal and plasmid genomes. Nucleic Acids Research.40. 6158-6173.

2011

16. Przybilski, R., Richter, C., Gristwood, T., Clulow, J.S., Vercoe, R.B. and Fineran, P.C.# (2011). Csy4 is responsible for CRISPR RNA processing in Pectobacterium atrosepticum. RNA Biology8. 517-528. 

15. Gristwood, T., McNeil, M.B., Clulow, J.S., Salmond, G.P.C.# and Fineran, P.C.# (2011). PigS and PigP regulate prodigiosin biosynthesis in Serratia via differential control of divergent operons, which include predicted transporters of sulfur-containing molecules. Journal of Bacteriology193. 1076-1085. 

14. Blower, T.R., Pei, X.Y., Short, F.L., Fineran, P.C., Humpreys, D.P., Luisi, B.F. and Salmond, G.P.C. (2011). A processed non-coding RNA regulates a bacterial antiviral system. Nature Structural and Molecular Biology. 18. 185-190.

2010

13. Blower, T.R., Evans, T.J., Fineran, P.C., Toth, I.K., Foulds, I.J. and Salmond, G.P.C. (2010) Chapter 53. Phage-receptor interactions and phage abortive infection: potential biocontrol factors in a bacterial plant pathogen. In Biology of Molecular Plant-Microbe Interactions. Antoun, H., Avis T., Brisson L., Prévost D. and Trepanier M., eds. International Society for Molecular Plant-Microbe Interactions, St. Paul, MN. Volume 7: 1-7.

2009

12. Fineran, P.C., Petty, N.K. and Salmond, G.P.C. (2009). Transduction: Host DNA Transfer by Bacteriophages. In The Encyclopedia of Microbiology (3rd edition). Edited by Moselio Schaechter. 666-679.

11. Blower, T.R., Fineran, P.C., Johnson, M.J., Toth, I.K., Humpreys, D.P and Salmond, G.P.C. (2009). Mutagenesis and functional characterisation of the RNA and protein components of the toxINabortive infection / toxin-antitoxin locus of Erwinia. Journal of Bacteriology191. 6029-6039. 

10. Gristwood, T., Fineran, P.C., Everson, L., Williamson, N.R. and Salmond, G.P.C. (2009). The PhoBR two-component system regulates antibiotic biosynthesis in Serratia in response to phosphate. BMC Microbiology9. 112. doi:10.1186/1471-2180-9-112.

9. Fineran, P.C., Blower, T.R., Foulds, I.J., Humpreys, D.P., Lilley, K.S. and Salmond, G.P.C. (2009).The phage abortive infection system, ToxIN, functions as a protein-RNA toxin-antitoxin pair. Proc. Natl. Acad. Sci. (USA). 106. 894-899.

2008

8. Gristwood, T., Fineran, P.C., Everson, L. and Salmond, G.P.C. (2008). PigZ, a TetR/AcrR family transcriptional repressor, regulates secondary metabolism via the expression of a putative resistance-nodulation-cell-division efflux pump, ZrpADBC, in Serratia. Molecular Microbiology69. 418-435. 

7. Williamson, N.R.,* Fineran, P.C.,* Ogawa, W., Woodley, LR. and Salmond, G.P.C. (2008). Integrated regulation involving quorum sensing, a two-component system, a GGDEF/EAL domain protein and a post-transcriptional regulator controls swarming and RhlA-dependent surfactant biosynthesis in Serratia. Environmental Microbiology. 10. 1202-1217.

2007

6. Williamson, N.R., Fineran, P.C., Gristwood, T., Chawrai, S.R., Leeper, F.J. and Salmond, G.P.C. (2007). Anticancer and Immunosuppressant Properties of Bacterial Prodiginines. Future Microbiology.2. 605-618. 

5. Fineran, P.C.,* Williamson, N.R.,* Lilley, K.S. and Salmond, G.P.C. (2007). Virulence and prodigiosin antibiotic biosynthesis in Serratia are regulated pleiotropically by the GGDEF/EAL domain protein, PigX. Journal of Bacteriology189. 7653-7662. 

4. Petty, N.K.*, Evans, T.J.,* Fineran, P.C.* and Salmond, G.P.C. (2007). Biotechnological Exploitation of Bacteriophage Research. Trends in Biotechnology25: 7-15. (Cover)

2006

3. Williamson, N.R.,* Fineran, P.C.,* Leeper, F.J. and Salmond, G.P.C. (2006). The Regulation and Biosynthesis of Bacterial Prodiginines. Nature Reviews Microbiology4. 887-899. (Cover)

2005

2. Fineran, P.C., Everson, L., Slater, H., and Salmond, G.P.C. (2005). A GntR family transcriptional regulator (PigT) controls gluconate-mediated repression and defines a new, independent pathway for regulation of the tripyrrole antibiotic, prodigiosin, in Serratia. Microbiology 151. 3833-3845. 

1. Fineran, P.C., Slater, H., Everson, L., Hughes, K., and Salmond, G.P.C. (2005). Biosynthesis of tripyrrole and β-lactam secondary metabolites in Serratia: integration of quorum sensing with multiple new regulatory components in the control of prodigiosin and carbapenem antibiotic production. Molecular Microbiology 56: 1495-1517. (Cover)