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Results: 1 to 20 of 39

1.

Simulate_PCR for amplicon prediction and annotation from multiplex, degenerate primers and probes.

Gardner SN, Slezak T.

BMC Bioinformatics. 2014 Jul 9;15:237. doi: 10.1186/1471-2105-15-237.

PMID:
25005023
[PubMed - in process]
Free Article
2.

The microbial detection array for detection of emerging viruses in clinical samples - a useful panmicrobial diagnostic tool.

Rosenstierne MW, McLoughlin KS, Olesen ML, Papa A, Gardner SN, Engler O, Plumet S, Mirazimi A, Weidmann M, Niedrig M, Fomsgaard A, Erlandsson L.

PLoS One. 2014 Jun 25;9(6):e100813. doi: 10.1371/journal.pone.0100813. eCollection 2014.

PMID:
24963710
[PubMed - in process]
Free PMC Article
3.

Current Strategic Thinking for the Development of a Trivalent Alphavirus Vaccine for Human Use.

Wolfe DN, Heppner DG, Gardner SN, Jaing C, Dupuy LC, Schmaljohn CS, Carlton K.

Am J Trop Med Hyg. 2014 May 19. pii: 14-0055. [Epub ahead of print]

PMID:
24842880
[PubMed - as supplied by publisher]
4.

Microbial Profiling of Combat Wound Infection through Detection Microarray and Next-Generation Sequencing.

Be NA, Allen JE, Brown TS, Gardner SN, McLoughlin KS, Forsberg JA, Kirkup BC, Chromy BA, Luciw PA, Elster EA, Jaing CJ.

J Clin Microbiol. 2014 Jul;52(7):2583-94. doi: 10.1128/JCM.00556-14. Epub 2014 May 14.

PMID:
24829242
[PubMed - in process]
5.

Screening of viral pathogens from pediatric ileal tissue samples after vaccination.

Hewitson L, Thissen JB, Gardner SN, McLoughlin KS, Glausser MK, Jaing CJ.

Adv Virol. 2014;2014:720585. doi: 10.1155/2014/720585. Epub 2014 Mar 23.

PMID:
24778651
[PubMed]
Free PMC Article
6.

When whole-genome alignments just won't work: kSNP v2 software for alignment-free SNP discovery and phylogenetics of hundreds of microbial genomes.

Gardner SN, Hall BG.

PLoS One. 2013 Dec 9;8(12):e81760. doi: 10.1371/journal.pone.0081760. eCollection 2013.

PMID:
24349125
[PubMed - in process]
Free PMC Article
7.

Detection of Bacillus anthracis DNA in complex soil and air samples using next-generation sequencing.

Be NA, Thissen JB, Gardner SN, McLoughlin KS, Fofanov VY, Koshinsky H, Ellingson SR, Brettin TS, Jackson PJ, Jaing CJ.

PLoS One. 2013 Sep 9;8(9):e73455. doi: 10.1371/journal.pone.0073455. eCollection 2013.

PMID:
24039948
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Optimizing SNP microarray probe design for high accuracy microbial genotyping.

Gardner SN, Thissen JB, McLoughlin KS, Slezak T, Jaing CJ.

J Microbiol Methods. 2013 Sep;94(3):303-10. doi: 10.1016/j.mimet.2013.07.006. Epub 2013 Jul 17.

PMID:
23871857
[PubMed - indexed for MEDLINE]
Free Article
9.

Scalable metagenomic taxonomy classification using a reference genome database.

Ames SK, Hysom DA, Gardner SN, Lloyd GS, Gokhale MB, Allen JE.

Bioinformatics. 2013 Sep 15;29(18):2253-60. doi: 10.1093/bioinformatics/btt389. Epub 2013 Jul 4.

PMID:
23828782
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Bioinformatics for microbial genotyping of equine encephalitis viruses, orthopoxviruses, and hantaviruses.

Gardner SN, Jaing CJ.

J Virol Methods. 2013 Oct;193(1):112-20. doi: 10.1016/j.jviromet.2013.04.019. Epub 2013 May 25.

PMID:
23714768
[PubMed - indexed for MEDLINE]
Free Article
11.

Identification of SNPs associated with variola virus virulence.

Hoen AG, Gardner SN, Moore JH.

BioData Min. 2013 Feb 14;6(1):3. doi: 10.1186/1756-0381-6-3.

PMID:
23410064
[PubMed]
Free PMC Article
12.

Skip the alignment: degenerate, multiplex primer and probe design using K-mer matching instead of alignments.

Hysom DA, Naraghi-Arani P, Elsheikh M, Carrillo AC, Williams PL, Gardner SN.

PLoS One. 2012;7(4):e34560. doi: 10.1371/journal.pone.0034560. Epub 2012 Apr 2.

PMID:
22485178
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

LAVA: an open-source approach to designing LAMP (loop-mediated isothermal amplification) DNA signatures.

Torres C, Vitalis EA, Baker BR, Gardner SN, Torres MW, Dzenitis JM.

BMC Bioinformatics. 2011 Jun 16;12:240. doi: 10.1186/1471-2105-12-240.

PMID:
21679460
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

A microbial detection array (MDA) for viral and bacterial detection.

Gardner SN, Jaing CJ, McLoughlin KS, Slezak TR.

BMC Genomics. 2010 Nov 25;11:668. doi: 10.1186/1471-2164-11-668.

PMID:
21108826
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Multiplex primer prediction software for divergent targets.

Gardner SN, Hiddessen AL, Williams PL, Hara C, Wagner MC, Colston BW Jr.

Nucleic Acids Res. 2009 Oct;37(19):6291-304. doi: 10.1093/nar/gkp659. Epub 2009 Sep 16.

PMID:
19759213
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Conserved amino acid markers from past influenza pandemic strains.

Allen JE, Gardner SN, Vitalis EA, Slezak TR.

BMC Microbiol. 2009 Apr 22;9:77. doi: 10.1186/1471-2180-9-77.

PMID:
19386124
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Predicting the sensitivity and specificity of published real-time PCR assays.

Lemmon GH, Gardner SN.

Ann Clin Microbiol Antimicrob. 2008 Sep 25;7:18. doi: 10.1186/1476-0711-7-18.

PMID:
18817537
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

When can a clonal organism escape senescence?

Gardner SN, Mangel M.

Am Nat. 1997 Oct;150(4):462-90. doi: 10.1086/286076.

PMID:
18811287
[PubMed]
19.

DNA signatures for detecting genetic engineering in bacteria.

Allen JE, Gardner SN, Slezak TR.

Genome Biol. 2008;9(3):R56. doi: 10.1186/gb-2008-9-3-r56. Epub 2008 Mar 18.

PMID:
18348716
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

On the origin of smallpox: correlating variola phylogenics with historical smallpox records.

Li Y, Carroll DS, Gardner SN, Walsh MC, Vitalis EA, Damon IK.

Proc Natl Acad Sci U S A. 2007 Oct 2;104(40):15787-92. Epub 2007 Sep 27.

PMID:
17901212
[PubMed - indexed for MEDLINE]
Free PMC Article

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