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Items: 1 to 20 of 95

1.

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.

2.

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.

3.

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.

4.

Integrated minimum-set primers and unique probe design algorithms for differential detection on symptom-related pathogens.

Huang YC, Chang CF, Chan CH, Yeh TJ, Chang YC, Chen CC, Kao CY.

Bioinformatics. 2005 Dec 15;21(24):4330-7. Epub 2005 Oct 25.

PMID:
16249263
6.

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.

7.

PRIMEGENS: robust and efficient design of gene-specific probes for microarray analysis.

Xu D, Li G, Wu L, Zhou J, Xu Y.

Bioinformatics. 2002 Nov;18(11):1432-7.

PMID:
12424113
8.

AutoDimer: a screening tool for primer-dimer and hairpin structures.

Vallone PM, Butler JM.

Biotechniques. 2004 Aug;37(2):226-31.

PMID:
15335214
9.

Degenerate primer design via clustering.

Wei X, Kuhn DN, Narasimhan G.

Proc IEEE Comput Soc Bioinform Conf. 2003;2:75-83.

PMID:
16452781
10.

Computing TaqMan probes for multiplex PCR detection of E. coli O157 serotypes in water.

Ram S, Shanker R.

In Silico Biol. 2005;5(5-6):499-504.

PMID:
16268792
11.

Dual-genome primer design for construction of DNA microarrays.

Andersson A, Bernander R, Nilsson P.

Bioinformatics. 2005 Feb 1;21(3):325-32. Epub 2004 Aug 27.

PMID:
15333463
12.

CEMAsuite: open source degenerate PCR primer design.

Lane CE, Hulgan D, O'Quinn K, Benton MG.

Bioinformatics. 2015 Nov 15;31(22):3688-90. doi: 10.1093/bioinformatics/btv420. Epub 2015 Jul 20.

PMID:
26198106
13.

Biosensor for dengue virus detection: sensitive, rapid, and serotype specific.

Baeumner AJ, Schlesinger NA, Slutzki NS, Romano J, Lee EM, Montagna RA.

Anal Chem. 2002 Mar 15;74(6):1442-8.

PMID:
11922316
14.

matchprobes: a Bioconductor package for the sequence-matching of microarray probe elements.

Huber W, Gentleman R.

Bioinformatics. 2004 Jul 10;20(10):1651-2. Epub 2004 Feb 26.

PMID:
14988118
15.

Detection and identification of Rift Valley fever virus in mosquito vectors by quantitative real-time PCR.

Mwaengo D, Lorenzo G, Iglesias J, Warigia M, Sang R, Bishop RP, Brun A.

Virus Res. 2012 Oct;169(1):137-43. doi: 10.1016/j.virusres.2012.07.019. Epub 2012 Jul 25.

PMID:
22841800
16.

Genome-scale probe and primer design with PRIMEGENS.

Srivastava GP, Xu D.

Methods Mol Biol. 2007;402:159-76. Review.

PMID:
17951795
17.

Non-infectious plasmid engineered to simulate multiple viral threat agents.

Carrera M, Sagripanti JL.

J Virol Methods. 2009 Jul;159(1):29-33. doi: 10.1016/j.jviromet.2009.02.021. Epub 2009 Mar 3.

PMID:
19442841
18.

Primer and probe sets for group-specific quantification of the genera Nitrosomonas and Nitrosospira using real-time PCR.

Lim J, Do H, Shin SG, Hwang S.

Biotechnol Bioeng. 2008 Apr 15;99(6):1374-83.

PMID:
18023051
19.

Human-blind probes and primers for dengue virus identification.

Putonti C, Chumakov S, Mitra R, Fox GE, Willson RC, Fofanov Y.

FEBS J. 2006 Jan;273(2):398-408.

20.

Java web tools for PCR, in silico PCR, and oligonucleotide assembly and analysis.

Kalendar R, Lee D, Schulman AH.

Genomics. 2011 Aug;98(2):137-44. doi: 10.1016/j.ygeno.2011.04.009. Epub 2011 May 3.

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