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Results: 1 to 20 of 61

1.

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 Jul 10. pii: AEM.01844-15. [Epub ahead of print]

3.

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 Jan 1;3:e01322. doi: 10.7554/eLife.01322.

4.

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
5.

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.

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 13. [Epub ahead of print]

PMID:
24042552
7.

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.

8.

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.

9.

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.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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
18.

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.

19.

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.

20.

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.

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