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Items: 1 to 50 of 62

1.

Complete Genome Sequence of Dickeya dianthicola ME23, a Pathogen Causing Blackleg and Soft Rot Diseases of Potato.

Ma X, Perna NT, Glasner JD, Hao J, Johnson S, Nasaruddin AS, Charkowski AO, Wu S, Fei Z, Perry KL, Stodghill P, Swingle B.

Microbiol Resour Announc. 2019 Feb 14;8(7). pii: e01526-18. doi: 10.1128/MRA.01526-18. eCollection 2019 Feb.

2.

Sepsis and Hemocyte Loss in Honey Bees (Apis mellifera) Infected with Serratia marcescens Strain Sicaria.

Burritt NL, Foss NJ, Neeno-Eckwall EC, Church JO, Hilger AM, Hildebrand JA, Warshauer DM, Perna NT, Burritt JB.

PLoS One. 2016 Dec 21;11(12):e0167752. doi: 10.1371/journal.pone.0167752. eCollection 2016.

3.

The Enterobacterium Trabulsiella odontotermitis Presents Novel Adaptations Related to Its Association with Fungus-Growing Termites.

Sapountzis P, Gruntjes T, Otani S, Estevez J, da Costa RR, Plunkett G 3rd, Perna NT, Poulsen M.

Appl Environ Microbiol. 2015 Oct;81(19):6577-88. doi: 10.1128/AEM.01844-15. Epub 2015 Jul 10.

5.

Evolution of extreme resistance to ionizing radiation via genetic adaptation of DNA repair.

Byrne RT, Klingele AJ, Cabot EL, Schackwitz WS, Martin JA, Martin J, Wang Z, Wood EA, Pennacchio C, Pennacchio LA, Perna NT, Battista JR, Cox MM.

Elife. 2014 Mar 4;3:e01322. doi: 10.7554/eLife.01322.

6.

Computing the joint distribution of tree shape and tree distance for gene tree inference and recombination detection.

Chung Y, Perna NT, Ané C.

IEEE/ACM Trans Comput Biol Bioinform. 2013 Sep-Oct;10(5):1263-74. doi: 10.1109/TCBB.2013.109.

PMID:
24384712
7.

Transcriptome changes associated with anaerobic growth in Yersinia intermedia (ATCC29909).

Babujee L, Balakrishnan V, Kiley PJ, Glasner JD, Perna NT.

PLoS One. 2013 Oct 7;8(10):e76567. doi: 10.1371/journal.pone.0076567. eCollection 2013.

8.

Inferring ancient metabolism using ancestral core metabolic models of enterobacteria.

Baumler DJ, Ma B, Reed JL, Perna NT.

BMC Syst Biol. 2013 Jun 11;7:46. doi: 10.1186/1752-0509-7-46.

9.

Analysis of the Lactobacillus casei supragenome and its influence in species evolution and lifestyle adaptation.

Broadbent JR, Neeno-Eckwall EC, Stahl B, Tandee K, Cai H, Morovic W, Horvath P, Heidenreich J, Perna NT, Barrangou R, Steele JL.

BMC Genomics. 2012 Oct 5;13:533. doi: 10.1186/1471-2164-13-533.

10.

Evolution of the metabolic and regulatory networks associated with oxygen availability in two phytopathogenic enterobacteria.

Babujee L, Apodaca J, Balakrishnan V, Liss P, Kiley PJ, Charkowski AO, Glasner JD, Perna NT.

BMC Genomics. 2012 Mar 22;13:110. doi: 10.1186/1471-2164-13-110.

11.

Using comparative genomics for inquiry-based learning to dissect virulence of Escherichia coli O157:H7 and Yersinia pestis.

Baumler DJ, Banta LM, Hung KF, Schwarz JA, Cabot EL, Glasner JD, Perna NT.

CBE Life Sci Educ. 2012 Spring;11(1):81-93. doi: 10.1187/cbe.10-04-0057.

12.

Insight into the transmission biology and species-specific functional capabilities of tsetse (Diptera: glossinidae) obligate symbiont Wigglesworthia.

Rio RV, Symula RE, Wang J, Lohs C, Wu YN, Snyder AK, Bjornson RD, Oshima K, Biehl BS, Perna NT, Hattori M, Aksoy S.

MBio. 2012 Feb 14;3(1). pii: e00240-11. doi: 10.1128/mBio.00240-11. Print 2012.

13.

The Comprehensive Phytopathogen Genomics Resource: a web-based resource for data-mining plant pathogen genomes.

Hamilton JP, Neeno-Eckwall EC, Adhikari BN, Perna NT, Tisserat N, Leach JE, Lévesque CA, Buell CR.

Database (Oxford). 2011 Nov 26;2011:bar053. doi: 10.1093/database/bar053. Print 2011.

14.

The evolution of metabolic networks of E. coli.

Baumler DJ, Peplinski RG, Reed JL, Glasner JD, Perna NT.

BMC Syst Biol. 2011 Nov 1;5:182. doi: 10.1186/1752-0509-5-182.

15.

Genome sequence of the plant-pathogenic bacterium Dickeya dadantii 3937.

Glasner JD, Yang CH, Reverchon S, Hugouvieux-Cotte-Pattat N, Condemine G, Bohin JP, Van Gijsegem F, Yang S, Franza T, Expert D, Plunkett G 3rd, San Francisco MJ, Charkowski AO, Py B, Bell K, Rauscher L, Rodriguez-Palenzuela P, Toussaint A, Holeva MC, He SY, Douet V, Boccara M, Blanco C, Toth I, Anderson BD, Biehl BS, Mau B, Flynn SM, Barras F, Lindeberg M, Birch PR, Tsuyumu S, Shi X, Hibbing M, Yap MN, Carpentier M, Dassa E, Umehara M, Kim JF, Rusch M, Soni P, Mayhew GF, Fouts DE, Gill SR, Blattner FR, Keen NT, Perna NT.

J Bacteriol. 2011 Apr;193(8):2076-7. doi: 10.1128/JB.01513-10. Epub 2011 Jan 7.

16.

progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement.

Darling AE, Mau B, Perna NT.

PLoS One. 2010 Jun 25;5(6):e11147. doi: 10.1371/journal.pone.0011147.

17.

chipD: a web tool to design oligonucleotide probes for high-density tiling arrays.

Dufour YS, Wesenberg GE, Tritt AJ, Glasner JD, Perna NT, Mitchell JC, Donohue TJ.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W321-5. doi: 10.1093/nar/gkq517. Epub 2010 Jun 6.

18.

Annotation and overview of the Pseudomonas savastanoi pv. savastanoi NCPPB 3335 draft genome reveals the virulence gene complement of a tumour-inducing pathogen of woody hosts.

Rodríguez-Palenzuela P, Matas IM, Murillo J, López-Solanilla E, Bardaji L, Pérez-Martínez I, Rodríguez-Moskera ME, Penyalver R, López MM, Quesada JM, Biehl BS, Perna NT, Glasner JD, Cabot EL, Neeno-Eckwall E, Ramos C.

Environ Microbiol. 2010 Jun;12(6):1604-20. doi: 10.1111/j.1462-2920.2010.02207.x. Epub 2010 Apr 1.

PMID:
20370821
19.

Complete genome sequence of the plant pathogen Erwinia amylovora strain ATCC 49946.

Sebaihia M, Bocsanczy AM, Biehl BS, Quail MA, Perna NT, Glasner JD, DeClerck GA, Cartinhour S, Schneider DJ, Bentley SD, Parkhill J, Beer SV.

J Bacteriol. 2010 Apr;192(7):2020-1. doi: 10.1128/JB.00022-10. Epub 2010 Jan 29.

20.

Reordering contigs of draft genomes using the Mauve aligner.

Rissman AI, Mau B, Biehl BS, Darling AE, Glasner JD, Perna NT.

Bioinformatics. 2009 Aug 15;25(16):2071-3. doi: 10.1093/bioinformatics/btp356. Epub 2009 Jun 10.

21.

Text-mining of PubMed abstracts by natural language processing to create a public knowledge base on molecular mechanisms of bacterial enteropathogens.

Zaremba S, Ramos-Santacruz M, Hampton T, Shetty P, Fedorko J, Whitmore J, Greene JM, Perna NT, Glasner JD, Plunkett G 3rd, Shaker M, Pot D.

BMC Bioinformatics. 2009 Jun 10;10:177. doi: 10.1186/1471-2105-10-177.

22.

Directed evolution of ionizing radiation resistance in Escherichia coli.

Harris DR, Pollock SV, Wood EA, Goiffon RJ, Klingele AJ, Cabot EL, Schackwitz W, Martin J, Eggington J, Durfee TJ, Middle CM, Norton JE, Popelars MC, Li H, Klugman SA, Hamilton LL, Bane LB, Pennacchio LA, Albert TJ, Perna NT, Cox MM, Battista JR.

J Bacteriol. 2009 Aug;191(16):5240-52. doi: 10.1128/JB.00502-09. Epub 2009 Jun 5.

23.

Phylogeny and virulence of naturally occurring type III secretion system-deficient Pectobacterium strains.

Kim HS, Ma B, Perna NT, Charkowski AO.

Appl Environ Microbiol. 2009 Jul;75(13):4539-49. doi: 10.1128/AEM.01336-08. Epub 2009 May 1.

24.
25.

Niche-specificity and the variable fraction of the Pectobacterium pan-genome.

Glasner JD, Marquez-Villavicencio M, Kim HS, Jahn CE, Ma B, Biehl BS, Rissman AI, Mole B, Yi X, Yang CH, Dangl JL, Grant SR, Perna NT, Charkowski AO.

Mol Plant Microbe Interact. 2008 Dec;21(12):1549-60. doi: 10.1094/MPMI-21-12-1549.

26.

Host range and molecular phylogenies of the soft rot enterobacterial genera pectobacterium and dickeya.

Ma B, Hibbing ME, Kim HS, Reedy RM, Yedidia I, Breuer J, Breuer J, Glasner JD, Perna NT, Kelman A, Charkowski AO.

Phytopathology. 2007 Sep;97(9):1150-63. doi: 10.1094/PHYTO-97-9-1150.

27.

Construction and characterization of an expressed sequenced tag library for the mosquito vector Armigeres subalbatus.

Mayhew GF, Bartholomay LC, Kou HY, Rocheleau TA, Fuchs JF, Aliota MT, Tsao IY, Huang CY, Liu TT, Hsiao KJ, Tsai SF, Yang UC, Perna NT, Cho WL, Christensen BM, Chen CC.

BMC Genomics. 2007 Dec 18;8:462.

28.

Analyzing patterns of microbial evolution using the mauve genome alignment system.

Darling AE, Treangen TJ, Messeguer X, Perna NT.

Methods Mol Biol. 2007;396:135-52.

PMID:
18025691
29.

Enteropathogen Resource Integration Center (ERIC): bioinformatics support for research on biodefense-relevant enterobacteria.

Glasner JD, Plunkett G 3rd, Anderson BD, Baumler DJ, Biehl BS, Burland V, Cabot EL, Darling AE, Mau B, Neeno-Eckwall EC, Pot D, Qiu Y, Rissman AI, Worzella S, Zaremba S, Fedorko J, Hampton T, Liss P, Rusch M, Shaker M, Shaull L, Shetty P, Thotakura S, Whitmore J, Blattner FR, Greene JM, Perna NT.

Nucleic Acids Res. 2008 Jan;36(Database issue):D519-23. Epub 2007 Nov 13.

30.

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.

Greene JM, Plunkett G 3rd, Burland V, Glasner J, Cabot E, Anderson B, Neeno-Eckwall E, Qiu Y, Mau B, Rusch M, Liss P, Hampton T, Pot D, Shaker M, Shaull L, Shetty P, Shi C, Whitmore J, Wong M, Zaremba S, Blattner FR, Perna NT.

Adv Exp Med Biol. 2007;603:28-42.

PMID:
17966403
31.

Genome-wide detection and analysis of homologous recombination among sequenced strains of Escherichia coli.

Mau B, Glasner JD, Darling AE, Perna NT.

Genome Biol. 2006;7(5):R44. Epub 2006 May 31.

32.

CGHScan: finding variable regions using high-density microarray comparative genomic hybridization data.

Anderson BD, Gilson MC, Scott AA, Biehl BS, Glasner JD, Rajashekara G, Splitter GA, Perna NT.

BMC Genomics. 2006 Apr 25;7:91.

33.

Escherichia coli K-12: a cooperatively developed annotation snapshot--2005.

Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G 3rd, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL.

Nucleic Acids Res. 2006 Jan 5;34(1):1-9. Print 2006.

34.

ASAP: a resource for annotating, curating, comparing, and disseminating genomic data.

Glasner JD, Rusch M, Liss P, Plunkett G 3rd, Cabot EL, Darling A, Anderson BD, Infield-Harm P, Gilson MC, Perna NT.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D41-5.

35.

Genome-wide identification of plant-upregulated genes of Erwinia chrysanthemi 3937 using a GFP-based IVET leaf array.

Yang S, Perna NT, Cooksey DA, Okinaka Y, Lindow SE, Ibekwe AM, Keen NT, Yang CH.

Mol Plant Microbe Interact. 2004 Sep;17(9):999-1008.

36.

Mauve: multiple alignment of conserved genomic sequence with rearrangements.

Darling AC, Mau B, Blattner FR, Perna NT.

Genome Res. 2004 Jul;14(7):1394-403.

37.

Description of the transcriptomes of immune response-activated hemocytes from the mosquito vectors Aedes aegypti and Armigeres subalbatus.

Bartholomay LC, Cho WL, Rocheleau TA, Boyle JP, Beck ET, Fuchs JF, Liss P, Rusch M, Butler KM, Wu RC, Lin SP, Kuo HY, Tsao IY, Huang CY, Liu TT, Hsiao KJ, Tsai SF, Yang UC, Nappi AJ, Perna NT, Chen CC, Christensen BM.

Infect Immun. 2004 Jul;72(7):4114-26.

39.

GRIL: genome rearrangement and inversion locator.

Darling AE, Mau B, Blattner FR, Perna NT.

Bioinformatics. 2004 Jan 1;20(1):122-4.

PMID:
14693819
40.

Acquisition of stcE, a C1 esterase inhibitor-specific metalloprotease, during the evolution of Escherichia coli O157:H7.

Lathem WW, Bergsbaken T, Witowski SE, Perna NT, Welch RA.

J Infect Dis. 2003 Jun 15;187(12):1907-14. Epub 2003 Jun 4.

PMID:
12792867
41.

Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T.

Wei J, Goldberg MB, Burland V, Venkatesan MM, Deng W, Fournier G, Mayhew GF, Plunkett G 3rd, Rose DJ, Darling A, Mau B, Perna NT, Payne SM, Runyen-Janecky LJ, Zhou S, Schwartz DC, Blattner FR.

Infect Immun. 2003 May;71(5):2775-86. Erratum in: Infect Immun. 2003 Jul;71(7):4223.

42.

ASAP, a systematic annotation package for community analysis of genomes.

Glasner JD, Liss P, Plunkett G 3rd, Darling A, Prasad T, Rusch M, Byrnes A, Gilson M, Biehl B, Blattner FR, Perna NT.

Nucleic Acids Res. 2003 Jan 1;31(1):147-51.

43.

Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli.

Welch RA, Burland V, Plunkett G 3rd, Redford P, Roesch P, Rasko D, Buckles EL, Liou SR, Boutin A, Hackett J, Stroud D, Mayhew GF, Rose DJ, Zhou S, Schwartz DC, Perna NT, Mobley HL, Donnenberg MS, Blattner FR.

Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):17020-4. Epub 2002 Dec 5.

44.

A whole-genome shotgun optical map of Yersinia pestis strain KIM.

Zhou S, Deng W, Anantharaman TS, Lim A, Dimalanta ET, Wang J, Wu T, Chunhong T, Creighton R, Kile A, Kvikstad E, Bechner M, Yen G, Garic-Stankovic A, Severin J, Forrest D, Runnheim R, Churas C, Lamers C, Perna NT, Burland V, Blattner FR, Mishra B, Schwartz DC.

Appl Environ Microbiol. 2002 Dec;68(12):6321-31.

45.

Identification and characterization of lpfABCC'DE, a fimbrial operon of enterohemorrhagic Escherichia coli O157:H7.

Torres AG, Giron JA, Perna NT, Burland V, Blattner FR, Avelino-Flores F, Kaper JB.

Infect Immun. 2002 Oct;70(10):5416-27.

46.

Characterization of Cah, a calcium-binding and heat-extractable autotransporter protein of enterohaemorrhagic Escherichia coli.

Torres AG, Perna NT, Burland V, Ruknudin A, Blattner FR, Kaper JB.

Mol Microbiol. 2002 Aug;45(4):951-66.

47.

Genomic variability of O islands encoding tellurite resistance in enterohemorrhagic Escherichia coli O157:H7 isolates.

Taylor DE, Rooker M, Keelan M, Ng LK, Martin I, Perna NT, Burland NT, Blattner FR.

J Bacteriol. 2002 Sep;184(17):4690-8.

48.

Genome sequence of Yersinia pestis KIM.

Deng W, Burland V, Plunkett G 3rd, Boutin A, Mayhew GF, Liss P, Perna NT, Rose DJ, Mau B, Zhou S, Schwartz DC, Fetherston JD, Lindler LE, Brubaker RR, Plano GV, Straley SC, McDonough KA, Nilles ML, Matson JS, Blattner FR, Perry RD.

J Bacteriol. 2002 Aug;184(16):4601-11.

49.

Microarray profiling of Erwinia chrysanthemi 3937 genes that are regulated during plant infection.

Okinaka Y, Yang CH, Perna NT, Keen NT.

Mol Plant Microbe Interact. 2002 Jul;15(7):619-29.

50.

hrp genes of Erwinia chrysanthemi 3937 are important virulence factors.

Yang CH, Gavilanes-Ruiz M, Okinaka Y, Vedel R, Berthuy I, Boccara M, Chen JW, Perna NT, Keen NT.

Mol Plant Microbe Interact. 2002 May;15(5):472-80.

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