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Items: 1 to 20 of 45


Characterization of Genetic Variability of Venezuelan Equine Encephalitis Viruses.

Gardner SN, McLoughlin K, Be NA, Allen J, Weaver SC, Forrester N, Guerbois M, Jaing C.

PLoS One. 2016 Apr 7;11(4):e0152604. doi: 10.1371/journal.pone.0152604. eCollection 2016.


Targeted amplification for enhanced detection of biothreat agents by next-generation sequencing.

Gardner SN, Frey KG, Redden CL, Thissen JB, Allen JE, Allred AF, Dyer MD, Mokashi VP, Slezak TR.

BMC Res Notes. 2015 Nov 16;8:682. doi: 10.1186/s13104-015-1530-0.


Using populations of human and microbial genomes for organism detection in metagenomes.

Ames SK, Gardner SN, Marti JM, Slezak TR, Gokhale MB, Allen JE.

Genome Res. 2015 Jul;25(7):1056-67. doi: 10.1101/gr.184879.114. Epub 2015 Apr 29.


kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome.

Gardner SN, Slezak T, Hall BG.

Bioinformatics. 2015 Sep 1;31(17):2877-8. doi: 10.1093/bioinformatics/btv271. Epub 2015 Apr 25.


Application of a pathogen microarray for the analysis of viruses and bacteria in clinical diagnostic samples from pigs.

Jaing CJ, Thissen JB, Gardner SN, McLoughlin KS, Hullinger PJ, Monday NA, Niederwerder MC, Rowland RR.

J Vet Diagn Invest. 2015 May;27(3):313-25. doi: 10.1177/1040638715578484. Epub 2015 Apr 8.


Multiplex degenerate primer design for targeted whole genome amplification of many viral genomes.

Gardner SN, Jaing CJ, Elsheikh MM, Peña J, Hysom DA, Borucki MK.

Adv Bioinformatics. 2014;2014:101894. doi: 10.1155/2014/101894. Epub 2014 Aug 3.


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.


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.


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 Sep;91(3):442-50. doi: 10.4269/ajtmh.14-0055. Epub 2014 May 19.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.

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