Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 29

1.

Phylogenomic Pipeline Validation for Foodborne Pathogen Disease Surveillance.

Timme RE, Strain E, Baugher JD, Davis S, Gonzalez-Escalona N, Sanchez Leon M, Allard MW, Brown EW, Tallent S, Rand H.

J Clin Microbiol. 2019 Apr 26;57(5). pii: e01816-18. doi: 10.1128/JCM.01816-18. Print 2019 May. Review.

2.

Utilizing the Public GenomeTrakr Database for Foodborne Pathogen Traceback.

Timme RE, Sanchez Leon M, Allard MW.

Methods Mol Biol. 2019;1918:201-212. doi: 10.1007/978-1-4939-9000-9_17.

PMID:
30580411
3.

Salmonella enterica Phylogeny Based on Whole-Genome Sequencing Reveals Two New Clades and Novel Patterns of Horizontally Acquired Genetic Elements.

Worley J, Meng J, Allard MW, Brown EW, Timme RE.

MBio. 2018 Nov 27;9(6). pii: e02303-18. doi: 10.1128/mBio.02303-18.

4.

GenomeTrakr proficiency testing for foodborne pathogen surveillance: an exercise from 2015.

Timme RE, Rand H, Sanchez Leon M, Hoffmann M, Strain E, Allard M, Roberson D, Baugher JD.

Microb Genom. 2018 Jul;4(7). doi: 10.1099/mgen.0.000185. Epub 2018 Jun 15.

5.

Resistome of carbapenem- and colistin-resistant Klebsiella pneumoniae clinical isolates.

Lomonaco S, Crawford MA, Lascols C, Timme RE, Anderson K, Hodge DR, Fisher DJ, Pillai SP, Morse SA, Khan E, Hughes MA, Allard MW, Sharma SK.

PLoS One. 2018 Jun 8;13(6):e0198526. doi: 10.1371/journal.pone.0198526. eCollection 2018.

6.

Benchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance.

Timme RE, Rand H, Shumway M, Trees EK, Simmons M, Agarwala R, Davis S, Tillman GE, Defibaugh-Chavez S, Carleton HA, Klimke WA, Katz LS.

PeerJ. 2017 Oct 6;5:e3893. doi: 10.7717/peerj.3893. eCollection 2017.

7.

Development of a Reference Standard Library of Chloroplast Genome Sequences, GenomeTrakrCP.

Zhang N, Ramachandran P, Wen J, Duke JA, Metzman H, McLaughlin W, Ottesen AR, Timme RE, Handy SM.

Planta Med. 2017 Dec;83(18):1420-1430. doi: 10.1055/s-0043-113449. Epub 2017 Jun 26.

PMID:
28651291
8.

TreeToReads - a pipeline for simulating raw reads from phylogenies.

McTavish EJ, Pettengill J, Davis S, Rand H, Strain E, Allard M, Timme RE.

BMC Bioinformatics. 2017 Mar 20;18(1):178. doi: 10.1186/s12859-017-1592-1.

9.

An analysis of Echinacea chloroplast genomes: Implications for future botanical identification.

Zhang N, Erickson DL, Ramachandran P, Ottesen AR, Timme RE, Funk VA, Luo Y, Handy SM.

Sci Rep. 2017 Mar 16;7(1):216. doi: 10.1038/s41598-017-00321-6.

10.

Draft Genome Sequences of 40 Salmonella enterica Serovar Typhimurium Strains Isolated from Humans and Food in Brazil.

Almeida F, Medeiros MI, Rodrigues DP, Payne J, Timme RE, Allard MW, Falcão JP.

Genome Announc. 2016 Sep 22;4(5). pii: e00892-16. doi: 10.1128/genomeA.00892-16.

11.

Draft Genome Sequences of Histamine-Producing Photobacterium kishitanii and Photobacterium angustum, Isolated from Albacore (Thunnus alalunga) and Yellowfin (Thunnus albacares) Tuna.

Bjornsdottir-Butler K, McCarthy SA, Dunlap PV, Timme RE, Benner RA Jr.

Genome Announc. 2015 Apr 30;3(2). pii: e00400-15. doi: 10.1128/genomeA.00400-15.

12.

Genome-wide methylation patterns in Salmonella enterica Subsp. enterica Serovars.

Pirone-Davies C, Hoffmann M, Roberts RJ, Muruvanda T, Timme RE, Strain E, Luo Y, Payne J, Luong K, Song Y, Tsai YC, Boitano M, Clark TA, Korlach J, Evans PS, Allard MW.

PLoS One. 2015 Apr 10;10(4):e0123639. doi: 10.1371/journal.pone.0123639. eCollection 2015.

13.

Characterization and evolution of Salmonella CRISPR-Cas systems.

Shariat N, Timme RE, Pettengill JB, Barrangou R, Dudley EG.

Microbiology. 2015 Feb;161(2):374-386. doi: 10.1099/mic.0.000005.

PMID:
28206902
14.

Characterization and evolution of Salmonella CRISPR-Cas systems.

Shariat N, Timme RE, Pettengill JB, Barrangou R, Dudley EG.

Microbiology. 2015 Feb;161(Pt 2):374-86. doi: 10.1099/mic.0.000005. Epub 2014 Dec 5.

PMID:
25479838
15.

The evolutionary history and diagnostic utility of the CRISPR-Cas system within Salmonella enterica ssp. enterica.

Pettengill JB, Timme RE, Barrangou R, Toro M, Allard MW, Strain E, Musser SM, Brown EW.

PeerJ. 2014 Apr 17;2:e340. doi: 10.7717/peerj.340. eCollection 2014.

16.

Phylogenetic diversity of the enteric pathogen Salmonella enterica subsp. enterica inferred from genome-wide reference-free SNP characters.

Timme RE, Pettengill JB, Allard MW, Strain E, Barrangou R, Wehnes C, Van Kessel JS, Karns JS, Musser SM, Brown EW.

Genome Biol Evol. 2013;5(11):2109-23. doi: 10.1093/gbe/evt159.

17.

Development of a locked nucleic acid real-time polymerase chain reaction assay for the detection of Pinus armandii in mixed species pine nut samples associated with dysgeusia.

Handy SM, Timme RE, Jacob SM, Deeds JR.

J Agric Food Chem. 2013 Feb 6;61(5):1060-6. doi: 10.1021/jf304223a. Epub 2013 Jan 23.

PMID:
23311709
18.

Erratum: Multigene phylogeny of the green lineage reveals the origin and diversification of land plants.

Finet C, Timme RE, Delwiche CF, Marletaz F.

Curr Biol. 2012 Aug 7;22(15):1456-7. No abstract available.

19.

Draft genome sequences of 21 Salmonella enterica serovar enteritidis strains.

Timme RE, Allard MW, Luo Y, Strain E, Pettengill J, Wang C, Li C, Keys CE, Zheng J, Stones R, Wilson MR, Musser SM, Brown EW.

J Bacteriol. 2012 Nov;194(21):5994-5. doi: 10.1128/JB.01289-12.

20.

Origin of strigolactones in the green lineage.

Delaux PM, Xie X, Timme RE, Puech-Pages V, Dunand C, Lecompte E, Delwiche CF, Yoneyama K, Bécard G, Séjalon-Delmas N.

New Phytol. 2012 Sep;195(4):857-71. doi: 10.1111/j.1469-8137.2012.04209.x. Epub 2012 Jun 27.

21.

Broad phylogenomic sampling and the sister lineage of land plants.

Timme RE, Bachvaroff TR, Delwiche CF.

PLoS One. 2012;7(1):e29696. doi: 10.1371/journal.pone.0029696. Epub 2012 Jan 13.

22.

Plants.

Delwiche CF, Timme RE.

Curr Biol. 2011 Jun 7;21(11):R417-22. doi: 10.1016/j.cub.2011.04.021. Review. No abstract available.

23.

Multigene phylogeny of the green lineage reveals the origin and diversification of land plants.

Finet C, Timme RE, Delwiche CF, Marlétaz F.

Curr Biol. 2010 Dec 21;20(24):2217-22. doi: 10.1016/j.cub.2010.11.035. Epub 2010 Dec 9. Erratum in: Curr Biol. 2012 Aug 7;22(15):1456-7.

24.

Unraveling the evolution of auxin signaling.

De Smet I, Voss U, Lau S, Wilson M, Shao N, Timme RE, Swarup R, Kerr I, Hodgman C, Bock R, Bennett M, Jürgens G, Beeckman T.

Plant Physiol. 2011 Jan;155(1):209-21. doi: 10.1104/pp.110.168161. Epub 2010 Nov 16.

25.
26.

PHYLOGENY OF FOUR DINOPHYSIACEAN GENERA (DINOPHYCEAE, DINOPHYSIALES) BASED ON rDNA SEQUENCES FROM SINGLE CELLS AND ENVIRONMENTAL SAMPLES(1).

Handy SM, Bachvaroff TR, Timme RE, Wayne Coats D, Kim S, Delwiche CF.

J Phycol. 2009 Oct;45(5):1163-74. doi: 10.1111/j.1529-8817.2009.00738.x. Epub 2009 Sep 10.

PMID:
27032361
27.

High-resolution phylogeny for Helianthus (Asteraceae) using the 18S-26S ribosomal DNA external transcribed spacer.

Timme RE, Simpson BB, Linder CR.

Am J Bot. 2007 Nov;94(11):1837-52. doi: 10.3732/ajb.94.11.1837.

28.
29.

Using MoBIoS' scalable genome join to find conserved primer pair candidates between two genomes.

Xu W, Briggs WJ, Padolina J, Timme RE, Liu W, Linder CR, Miranker DP.

Bioinformatics. 2004 Aug 4;20 Suppl 1:i355-62.

PMID:
15262820

Supplemental Content

Loading ...
Support Center