Guy Plunkett III, PhD

[Guy Plunkett III]

“Life is too short, and DNA too long.”
- Michael Crichton, Jurassic Park

Senior Scientist
DNASTAR, Inc.

DNASTAR, Inc.
3801 Regent Street
Madison, WI 53705


608.237.3081 phone
608.258.7439 fax
plunkettg@dnastar.com


[Mon AM, Tues- Thurs]

Senior Scientist
UW-Madison

Genome Center of Wisconsin
Univ of Wisconsin - Madison
425G Henry Mall, Rm 4430
Madison, WI 53706-1580

608.890.0169 phone
608.262.2976 fax
guy@genome.wisc.edu


[Mon PM, all day Fri]
Coordinator • AToL:Enterobacteriaceae
Administrator/Curator/Annotator • ASAP

My Profiles • LinkedIn | ResearcherID

Research Interests

Prokaryotic molecular genetics, bacteriophage-host interactions, genome organization and evolution, genome annotation.
I'm a bacteriologist who stumbled into genomics and bioinformatics when he wasn't looking, and found that he liked it. My expertise lies in the area of prokaryotic genomics, especially within the Enterobacteriaceae. I've been known to refer to myself as a “bioinformaticist without portfolio (or training).”

Member • The American Society For Microbiology
Charter Member • Bergey's International Society For Microbial Systematics (BISMiS)

Degrees and Training

former Senior Scientist • E. coli Genome Project at UW-Madison
former Senior Curator • ERIC (Enteropathogen Resource Integration Center)
 (note: ERIC has since been replaced by PATRIC)

Publications

Search Pubmed for publications by Guy Plunkett III
  1. E. Rotman, E. Kouzminova, G. Plunkett III, & A. Kuzminov (2012) Genome of enterobacteriophage Lula/phi80 and insights into its ability to spread in the laboratory environment. J Bacteriol 194(24):6802-6817. Epub 2012 Oct 5. doi:10.1128/JB.01353-12. [PMID: 23042999]

  2. J. D. Glasner, C. H. Yang, S. Reverchon, N. Hugouvieux-Cotte-Pattat, G. Condemine, J. P. Bohin, F. Van Gijsegem, S. Yang, T. Franza, D. Expert, G. Plunkett III, M. J. San Francisco, A. O. Charkowski, B. Py, K. Bell, L. Rauscher, P. Rodriguez-Palenzuela, A. Toussaint, M. C. Holeva, S. Y. He, V. Douet, M. Boccara, C. Blanco, I. Toth, B. D. Anderson, B. S. Biehl, B. Mau, S. M. Flynn, F. Barras, M. Lindeberg, P. Birch, S. Tsuyumu, X. Shi, M. Hibbing, M. N. Yap, M. Carpentier, E. Dassa, M. Umehara, J. F. Kim, M. Rusch, P. Soni, G. F. Mayhew, D. E. Fouts, S. R. Gill, F. R. Blattner, N. T. Keen, & N. T. Perna (2011) Genome sequence of the plant pathogenic bacterium Dickeya dadantii 3937. J Bacteriol 193(8):2076-2077. Epub 2011 Jan 7. doi:10.1128/JB.01513-10. [PMID: 21217001] [PMC: PMC3133054]

  3. S. Zaremba, M. Ramos-Santacruz, T. Hampton, P. Shetty, J. Fedorko, J. Whitmore, J. M. Greene, N. T. Perna, J. D. Glasner, G. Plunkett III, M. Shaker, & D. Pot (2009) Text-mining of PubMed abstracts by natural language processing to create a public knowledge base on molecular mechanisms of bacterial enteropathogens. BMC Bioinformatics 10(1):177. Epub 2009 June 10. doi:10.1186/1471-2105-10-177. [PMID: 19515247] [PMC: PMC2704210]

  4. T. Durfee, R. Nelson, S. Baldwin, G. Plunkett III, V. Burland, B. Mau, J. F. Petrosino, X. Qin, D. M. Muzny, M. Ayele, R. A. Gibbs, B. Csörgo, G. Pósfai, G. M. Weinstock, & F. R. Blattner (2008) The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse. J Bacteriol 190(7):2597-2606. Epub 2008 Feb 1. doi:10.1128/JB.01695-07. [PMID: 18245285] [PMC: PMC2293198]

  5. J. D. Glasner, G. Plunkett III, B. D. Anderson, D. J. Baumler, B. S. Biehl, V. Burland, E. L. Cabot, A. E. Darling, B. Mau, E. C. Neeno-Eckwall, D. Pot, Y. Qiu, A. I. Rissman, S. Worzella, S. Zaremba, J. Fedorko, T. Hampton, P. Liss, M. Rusch, M. Shaker, L. Shaull, P. Shetty, S. Thotakura, J. Whitmore, F. R. Blattner, J. M. Greene, & N. T. Perna (2008) Enteropathogen Resource Integration Center (ERIC): bioinformatics support for research on biodefense-relevant enterobacteria. Nucleic Acids Res 36(Database issue):D519-523. Epub 2007 Nov 13. doi:10.1093/nar/gkm973. [PMID: 17999997] [PMC: PMC2238966]

  6. J. M. Greene, G. Plunkett III, V. Burland, J. Glasner, E. Cabot, B. Anderson, E. Neeno-Eckwall, Y. Qiu, B. Mau, M. Rusch, P. Liss, T. Hampton, D. Pot, M. Shaker, L. Shaull, P. Shetty, C. Shi, J. Whitmore, M. Wong, S. Zaremba, F. R. Blattner, & N. T. Perna (2007) A new asset for pathogen informatics — the Enteropathogen Resource Integration Center (ERIC), an NIAID Bioinformatics Resource Center for Biodefense and Emerging/Re-emerging Infectious Disease. Adv Exp Med Biol 603:28-42. doi:10.1007/978-0-387-72124-8_4. [PMID: 17966403]
    (Chapter 4 in The Genus Yersinia: From Genomics to Function, R. D. Perry & J. D. Fetherston, eds.; Springer, New York; selected conference papers from the “9th International Symposium on Yersinia” held in Lexington, Kentucky, USA on October 10-14, 2006) [ISBN: 0387721231]

  7. M. R. King, R. P. Vimr, S. M. Steenbergen, L. Spanjaard, G. Plunkett III, F. R. Blattner, & E. R. Vimr (2007) Escherichia coli K1-specific bacteriophage CUS-3 distribution and function in phase-variable capsular polysialic acid O acetylation. J Bacteriol 189(17):6447-6456. Epub 2007 Jun 29. doi:10.1128/JB.00657-07. [PMID: 17601779] [PMC: PMC1951898]

  8. Y. Xie, V. Kolisnychenko, M. Paul-Satyaseela, S. Elliott, G. Parthasarathy, Y. Yao, G. Plunkett III, F. R. Blattner, & K. S. Kim (2006) Identification and characterization of Escherichia coli RS218-derived islands in the pathogenesis of E. coli meningitis. J Infect Dis 194(3):358-364. Epub 2006 Jun 30. doi:10.1086/505429. [PMID: 16826484]

  9. G. Pósfai, G. Plunkett III, T. Fehér, D. Frisch, G. M. Keil, K. Umenhoffer, V. Kolisnychenko, B. Stahl, S. S. Sharma, M. de Arruda, V. Burland, S. W. Harcum, & F. R. Blattner (2006) Emergent properties of reduced-genome Escherichia coli. Science 312(5776):1044-1046. Epub 2006 Apr 27. doi:10.1126/science.1126439. [PMID: 16645050]

  10. M. Riley, T. Abe, M. B. Arnaud, M. K. Berlyn, F. R. Blattner, R. R. Chaudhuri, J. D. Glasner, T. Horiuchi, I. M. Keseler, T. Kosuge, H. Mori, N. T. Perna, G. Plunkett III, K. E. Rudd, M. H. Serres, G. H. Thomas, N. R. Thomson, D. Wishart, & B. L. Wanner (2006) Escherichia coli K-12: a cooperatively developed annotation snapshot--2005. Nucleic Acids Res 34(1):1-9. doi:10.1093/nar/gkj405. [PMID: 16397293] [PMC: PMC1325200]

  11. J. D. Glasner, M. Rusch, P. Liss, G. Plunkett III, E. L. Cabot, A. Darling, B. D. Anderson, P. Infield-Harm, M. C. Gilson, & N. T. Perna (2006) ASAP: a resource for annotating, curating, comparing, and disseminating genomic data. Nucleic Acids Res 34(Database issue):D41-D45. doi:10.1093/nar/gkj164. [PMID: 16381899] [PMC: PMC1347526]

  12. M. B. Lobocka, D. J. Rose, G. Plunkett III, M. Rusin, A. Samojedny, H. Lehnherr, M. B. Yarmolinsky, & F. R. Blattner (2004) Genome of bacteriophage P1. J Bacteriol 186(21):7032-7068. doi:10.1128/JB.186.21.7032-7068.2004. [PMID: 15489417] [PMC: PMC523184]

  13. J. Wei, M. B. Goldberg, V. Burland, M. M. Venkatesan, W. Deng, G. Fournier, G. F. Mayhew, G. Plunkett III, D. J. Rose, A. Darling, B. Mau, N. T. Perna, S. M. Payne, L. J. Runyen-Janecky, S. Zhou, D. C. Schwartz, & F. R. Blattner (2003) Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T. Infect Immun 71(5):2775-2786. doi:10.1128/IAI.71.5.2775-2786.2003. [PMID: 12704152] [PMC: PMC153260]

  14. W. Deng, S.-R. Liou, G. Plunkett III, G. F. Mayhew, D. J. Rose, V. Burland, V. Kodoyianni, D. C. Schwartz, & F. R. Blattner (2003) Comparative genomics of Salmonella enterica serovar Typhi strains Ty2 and CT18. J Bacteriol 185(7):2330-2337. doi:10.1128/JB.185.7.2330-2337.2003. [PMID: 12644504] [PMC: PMC151493]

  15. J. D. Glasner, P. Liss, G. Plunkett III, A. Darling, T. Prasad, M. Rusch, A. Byrnes, M. Gilson, B. Biehl, F. R. Blattner, & N. T. Perna (2003) ASAP, a systematic annotation package for community analysis of genomes. Nucleic Acids Res 31(1):147-151. doi:10.1093/nar/gkg125. [PMID: 12519969] [PMC: PMC165572]

  16. R. A. Welch, V. Burland, G. Plunkett III, P. Redford, P. Roesch, D. Rasko, E. L. Buckles, S.-R. Liou, A. Boutin, J. Hackett, D. Stroud, G. F. Mayhew, D. J. Rose, S. Zhou, D. C. Schwartz, N. T. Perna, H. L. T. Mobley, M. S. Donnenberg & F. R. Blattner (2002) Extensive mosiac structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc Natl Acad Sci USA 99(26):17020-17024. Epub 2002 Dec 5. doi:10.1073/pnas.252529799. [PMID: 12471157] [PMC: PMC139262]

  17. N. T. Perna, J. D. Glasner, V. Burland, & G. Plunkett III (2002) Chapter 1. The Genomes of Escherichia coli K-12 and Pathogenic E. coli. pp. 3-53, in: Escherichia coli: Virulence Mechanisms of a Versatile Pathogen, M. S. Donnenberg, ed. Academic Press, San Diego. [ISBN: 0122207513]

  18. W. Deng, V. Burland, G. Plunkett III, A. Boutin, G. F. Mayhew, P. Liss, N. T. Perna, D. J. Rose, B. Mau, S. Zhou, D. C. Schwartz, J. D. Fetherston, L. E. Lindler, R. R. Brubaker, G. V. Plano, S. C. Straley, K. A. McDonough, M. L. Nilles, J. S. Matson, F. R. Blattner & R. D. Perry (2002) Genome sequence of Yersinia pestis KIM. J Bacteriol 184(16):4601-4611. doi:10.1128/JB.184.16.4601-4611.2002. [PMID: 12142430] [PMC: PMC135232]

  19. N. T. Perna, G. Plunkett III, V. Burland, B. Mau, J. D. Glasner, J. Kim & F. R. Blattner (2002) Comparative Analyses of Enterobacterial Genomes. pp. 296-301 in: Biology of Plant-Microbe Interactions, Volume 3, S. A. Leong, C. Allen, & E. W. Triplett, eds. International Society for Molecular Plant-Microbe Interactions, St. Paul.
    (proceedings of the “10th International Congress on Molecular Plant-Microbe Interactions” held in Madison, Wisconsin, USA on July 10-14, 2001) [ISBN: 0965462528]

  20. V. Kolisnychenko, G. Plunkett III, C. D. Herring, T. Fehér, J. Pósfai, F. R. Blattner & G. Pósfai (2002) Engineering a reduced Escherichia coli genome. Genome Res 12(4):640-647. doi:10.1101/gr.217202. [PMID: 11932248] [PMC: PMC187512]

  21. A. Lim, E. T. Dimalanta, K. D. Potamousis, G. Yen, J. Apodoca, C. Tao, J. Lin, R. Qi, J. Skiadas, A. Ramanathan, N. T. Perna, G. Plunkett III, V. Burland, B. Mau, J. Hackett, F. R. Blattner, T. S. Anantharaman, B. Mishra & D. C. Schwartz (2001) Shotgun optical maps of the whole Escherichia coli O157:H7 genome. Genome Res 11(9):1584-1593. doi:10.1101/gr.172101. [PMID: 11544203] [PMC: PMC311123]

  22. N. T. Perna, G. Plunkett III, V. Burland, B. Mau, J. D. Glasner, D. J. Rose, G. F. Mayhew, P. S. Evans, J. Gregor, H. A. Kirkpatrick, G. Pósfai, J. Hackett, S. Klink, A. Boutin, Y. Shao, L. Miller, E. J. Grotbeck, N. W. Davis, A. Lim, E. Dimalanta, K. D. Potamousis, J. Apodaca, T. S. Anantharaman, J. Lin, G. Yen, D. C. Schwartz, R. A. Welch, & F. R. Blattner (2001) Genome sequence of enterohemorrhagic Escherichia coli O157:H7. Nature 409(6819):529-533. Erratum in: Nature 410(6825):240. doi:10.1038/35054089. [PMID: 11206551]

  23. G. Plunkett III, D. J. Rose, T. J. Durfee, & F. R. Blattner (1999) Sequence of Shiga toxin 2 phage 933W from Escherichia coli O157:H7: Shiga toxin as a phage late-gene product. J Bacteriol 181(6):1767-1778. [PMID: 10074068] [PMC: PMC93574]

  24. J. Mahillon, H. A. Kirkpatick, H. L. Kijenski, C. A. Bloch, C. K. Rode, G. F. Mayhew, D. J. Rose, G. Plunkett III, V. Burland, & F. R. Blattner (1998) Subdivision of the Escherichia coli K-12 genome for sequencing: manipulation and DNA sequence of transposable elements introducing unique restriction sites. Gene 223(1-2):47-54. doi:10.1016/S0378-1119(98)00365-5. [PMID: 9858680]

  25. V. Burland, Y. Shao, N. T. Perna, G. Plunkett III, H. J. Sofia, & F. R. Blattner (1998) The complete DNA sequence and analysis of the large virulence plasmid of Escherichia coli O157:H7. Nucleic Acids Res 26(18):4196-4204. doi:10.1093/nar/26.18.4196. [PMID: 9722640] [PMC: PMC147824]

  26. M. Masters & G. Plunkett III (1998) Bacterial genomes: the Escherichia coli model. pp. 715-744, in: ICRF Handbook of Genome Analysis, N. K. Spurr, B. D. Young, & S. P. Bryant, eds. Blackwell Science Ltd, Oxford. [ISBN: 0632037288]

  27. F. R. Blattner, G. Plunkett III, C. A. Bloch, N. T. Perna, V. Burland, M. Riley, J. Collado-Vides, J. D. Glasner, C. K. Rode, G. F. Mayhew, J. Gregor, N. W. Davis, H. A. Kirkpatrick, M. A. Goeden, D. J. Rose, B. Mau, & Y. Shao (1997) The complete genome sequence of Escherichia coli K-12. Science 277(5331):1453-1462. doi:10.1126/science.277.5331.1453. [PMID: 9278503]

  28. F. R. Blattner, G. Plunkett III, G. F. Mayhew, J. Gregor, W. Davis, M. Goeden, N. Perna, D. Rose, Y. Shao, H. Kirkpatrick, C. Bloch, G. Pósfai, & C. Rode (1996) E. coli Genome Project. Microb Comp Genomics 1(4):357.
    (abstracts for “Small genomes: sequencing, functional characterization and comparative genomics” held in Hilton Head, South Carolina, USA on January 25-28, 1997) [PMID: 9722406]

  29. J. Reizer, A. Reizer, M. J. Merrick, G. Plunkett III, D. J. Rose, & M. H. Saier, Jr (1996) Novel phosphotransferase-encoding genes revealed by analysis of the Escherichia coli genome: a chimeric gene encoding an Enzyme I homologue that possesses a putative sensory transduction domain. Gene 181(1-2):103-108. doi:10.1016/S0378-1119(96)00481-7. [PMID: 8973315]

  30. K. E. Rudd, H. J. Sofia, E. V. Koonin, G. Plunkett III, S. Lazar, & P. E. Rouviere (1995) A new family of peptidyl-prolyl isomerases. Trends Biochem Sci 20(1):12-14. doi:10.1016/S0968-0004(00)88940-9. [PMID: 7878731]

  31. V. Burland, G. Plunkett III, H. J. Sofia, D. L. Daniels, & F. R. Blattner (1995) Analysis of the Escherichia coli genome VI: DNA sequence of the region from 92.8 through 100 minutes. Nucleic Acids Res 23(12):2105-2119. doi:10.1093/nar/23.12.2105. [PMID: 7610040] [PMC: PMC306997]

  32. H. J. Sofia, V. Burland, D. L. Daniels, G. Plunkett III, & F. R. Blattner (1994) Analysis of the Escherichia coli genome. V. DNA sequence of the region from 76.0 to 81.5 minutes. Nucleic Acids Res 22(13):2576-2586. doi:10.1093/nar/22.13.2576. [PMID: 8041620] [PMC: PMC308212]

  33. F. R. Blattner, V. Burland, G. Plunkett III, H. J. Sofia, & D. L. Daniels (1993) Analysis of the Escherichia coli genome. IV. DNA sequence of the region from 89.2 to 92.8 minutes. Nucleic Acids Res 21(23):5408-5417. doi:10.1093/nar/21.23.5408. [PMID: 8265357] [PMC: PMC310579]

  34. S.-E. Chuang, V. Burland, G. Plunkett III, D. L. Daniels, & F. R. Blattner (1993) Sequence analysis of four new heat-shock genes constituting the hslTS/ibpAB and hslVU operons in Escherichia coli. Gene 134(1):1-6. doi:10.1016/0378-1119(93)90167-2. [PMID: 8244018]

  35. G. Plunkett III, V. Burland, D. L. Daniels, & F. R. Blattner (1993) Analysis of the Escherichia coli genome. III. DNA sequence of the region from 87.2 to 89.2 minutes. Nucleic Acids Res 21(15):3391-3398. doi:10.1093/nar/21.15.3391. [PMID: 8346018] [PMC: PMC331436]

  36. V. Burland, D. L. Daniels, G. Plunkett III, & F. R. Blattner (1993) Genome sequencing on both strands: the Janus strategy. Nucleic Acids Res 21(15):3385-3390. doi:10.1093/nar/21.15.3385. [PMID: 8346017] [PMC: PMC331435]

  37. V. Burland, G. Plunkett III, D. L. Daniels, & F. R. Blattner (1993) DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: organizational symmetry around the origin of replication. Genomics 16(3):551-561. doi:10.1006/geno.1993.1230. [PMID: 7686882]

  38. F. R. Blattner, D. L. Daniels, V. D. Burland, G. Plunkett III, & S.-E. Chuang (1993) The E. coli genome project: towards the first megabase. pp. 43-59, in: The Chromosome, J.S. Heslop-Harrison & R.B. Flavell, eds. Bios Scientific Publishers, Oxford.
    (selected reviews from the “Tenth John Innes Symposium” held in Norwich, England on September 7-10, 1992) [ISBN: 1872748325]

  39. D. L. Daniels, G. Plunkett III, V. Burland, & F. R. Blattner (1992) Analysis of the Escherichia coli genome: DNA sequence of the region from 84.5 to 86.5 minutes. Science 257(5071):771-778. doi:10.1126/science.1379743. [PMID: 1379743]

  40. G. Plunkett III & H. Echols (1989) Retroregulation of the bacteriophage lambda int gene: limited secondary degradation of the RNase III-processed transcript. J Bacteriol 171(1):588-592. [PMID: 2521618] [PMC: PMC209629]

  41. G. Plunkett III, G. P. Mazzara, & W. H. McClain (1981) Characterization of bacteriophage T4 band D RNA, a low-molecular-weight RNA of unknown function. Arch Biochem Biophys 210(1):298-306. doi:10.1016/0003-9861(81)90193-4. [PMID: 6271070]

  42. G. P. Mazzara, G. Plunkett III, & W. H. McClain (1981) DNA sequence of the transfer RNA region of bacteriophage T4: implications for transfer RNA synthesis. Proc Natl Acad Sci USA 78(2):889-892. doi:10.1073/pnas.78.2.889. [PMID: 6262781] [PMC: PMC319909]

  43. G. P. Mazzara, G. Plunkett III, & W. H. McClain (1980) Maturation events leading to transfer RNA and ribosomal RNA. pp. 439-545, in: Cell Biology: A Comprehensive Treatise, Vol. 3 (Gene Expression: The Production of RNAs), L. Goldstein & D. Prescott, eds. Academic Press, New York. [ISBN: 0122895037]

Patents

  1. Blattner, Burland, Perna, Plunkett, & Welch “Sequences of E. coli O157” U.S. Patent 6,365,723 (Apr. 2, 2002)
  2. Blattner, Burland, Perna, Plunkett, & Welch “Sequences of E. coli O157” U.S. Patent 6,855,814 (Feb. 15, 2005)
  3. Blattner, Posfai, Herring, Plunkett, & Glasner “Bacteria with reduced genome” U.S. Patent 6,989,265 (Jan. 24, 2006)
  4. Blattner, Posfai, Herring, Plunkett, Glasner, & Twose “Competent bacteria” U.S. Patent 7,303,906 (Dec. 4, 2007)
  5. Blattner, Campbell, & Plunkett “Plasmid DNA preparations and methods for producing same” U.S. Patent 7,935,505 (May 3, 2011)
  6. Blattner, Campbell, & Plunkett “Methods and compositions for producing recombinant proteins using a gene for TRNA” U.S. Patent 7,989,181 (Aug. 2, 2011)
  7. Blattner, Posfai, Herring, Plunkett, & Glasner “Bacteria with reduced genome” U.S. Patent 8,043,842 (Oct. 25, 2011)
  8. Blattner, Campbell, Frisch, Plunkett, & Posfai “Insertion sequence-free bacteria” U.S. Patent 8,119,365 (Feb. 21, 2012)

Consulting

Last updated November 27, 2012       What's with all this E. coli stuff!? Maybe you were looking for Gregory Plunkett or Greg Plunkett?
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