Wilson WJ, Strout CL, DeSantis TZ, Stilwell JL, Carrano AV, Andersen GL: Sequence-specific identification of 18 pathogenic microorganisms using microarray technology. Mol Cell Probes. 2002, 16: 119-127. 10.1006/mcpr.2001.0397.
Article
CAS
Google Scholar
Guschin DY, Mobarry BK, Proudnikov D, Stahl DA, Rittmann BE, Mirzabekov AD: Oligonucleotide microchips as genosensors for determinative and environmental studies in microbiology. Appl Environ Microbiol. 1997, 63: 2397-2402.
CAS
Google Scholar
Baeumner AJ: Biosensors for environmental pollutants and food contaminants. Anal Bioanal Chem. 2003, 377: 434-445. 10.1007/s00216-003-2158-9.
Article
CAS
Google Scholar
Teles FRR, Fonseca LR: Trends in DNA biosensors. Talanta. 2008, 77: 606-623. 10.1016/j.talanta.2008.07.024.
Article
CAS
Google Scholar
Woese CR, Fox GE: Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci USA. 1977, 74: 5088-5090. 10.1073/pnas.74.11.5088.
Article
CAS
Google Scholar
Desantis TZ, Stone CE, Murray SR, Moberg JP, Andersen GL: Rapid quantification and taxonomic classification of environmental DNA from both prokaryotic and eukaryotic origins using a microarray. FEMS Microbiol Lett. 2005, 245: 271-278. 10.1016/j.femsle.2005.03.016.
Article
CAS
Google Scholar
Amann R, Fuchs BM, Behrens S: The identification of microorganisms by fluorescence in situ hybridisation. Curr Opin Biotechnol. 2001, 12: 231-236. 10.1016/S0958-1669(00)00204-4.
Article
CAS
Google Scholar
Woese CR: Whither microbiology? Phylogenetic trees. Curr Biol. 1996, 6: 1060-1063. 10.1016/S0960-9822(02)70664-7.
Article
CAS
Google Scholar
Anthony RM, Brown TJ, French GL: Rapid diagnosis of bacteremia by universal amplification of 23S ribosomal DNA followed by hybridization to an oligonucleotide array. J Clin Microbiol. 2000, 38: 781-788.
CAS
Google Scholar
Fukushima M, Kakinuma K, Kawaguchi R: Phylogenetic analysis of Salmonella, Shigella, and Escherichia coli strains on the basis of the gyrB gene sequence. J Clin Microbiol. 2002, 40: 2779-2785. 10.1128/JCM.40.8.2779-2785.2002.
Article
CAS
Google Scholar
Kobayashi M, Urata T, Ikezoe T, Hakoda E, Uemura Y, Sonobe H, Ohtsuki Y, Manabe T, Miyagi S, Miyoshi I: Simple detection of the 5S ribosomal RNA of Pneumocystis carinii using in situ hybridisation. J Clin Pathol. 1996, 49: 712-716. 10.1136/jcp.49.9.712.
Article
CAS
Google Scholar
Roth SB, Jalava J, Ruuskanen O, Ruohola A, Nikkari S: Use of an oligonucleotide array for laboratory diagnosis of bacteria responsible for acute upper respiratory infections. J Clin Microbiol. 2004, 42: 4268-4274. 10.1128/JCM.42.9.4268-4274.2004.
Article
CAS
Google Scholar
Yamamoto S, Harayama S: PCR amplification and direct sequencing of gyrB genes with universal primers and their application to the detection and taxonomic analysis of Pseudomonas putida strains. Appl Environ Microbiol. 1995, 61: 1104-1109.
CAS
Google Scholar
Chauhan AK, Spirion D: The gene for a small stable RNA (10Sa RNA) of Escherichia coli. Mol Microbiol. 1989, 3: 1481-1485. 10.1111/j.1365-2958.1989.tb00133.x.
Article
CAS
Google Scholar
Lee SY, Bailey SC, Apirion D: Small stable RNAs from Escherichia coli: Evidence for the Existence of New Molecules and for a New Ribonucleoprotein Particle Containing 6S RNA. J Bacteriol. 1978, 133: 1015-1023.
CAS
Google Scholar
O'Grady J, Sedano-Balbas S, Maher M, Smith T, Barry T: Rapid real-time PCR detection of Listeria monocytogenes in enriched food samples based on the ssrA gene, a novel diagnostic target. Food Microbiol. 2008, 25: 75-84. 10.1016/j.fm.2007.07.007.
Article
Google Scholar
Schönhuber W, Le Bourhis G, Tremblay J, Amann R, Kulakauskas S: Utilization of tmRNA sequences for bacterial identification. BMC Microbiol. 2001, 1: 20-10.1186/1471-2180-1-20.
Article
Google Scholar
Peplies J, Glockner FO, Amann R: Optimization strategies for DNA microarray-based detection of bacteria with 16S rRNA-targeting oligonucleotide probes. Appl Environ Microbiol. 2003, 69: 1397-1407. 10.1128/AEM.69.3.1397-1407.2003.
Article
CAS
Google Scholar
Fuchs BM, Wallner G, Beisker W, Schwippl I, Ludwid W, Amann R: Flow Cytometric Analysis of the In Situ Accessibility of Escherichia Coli 16S rRNA for Fluorescently Labeled Oligonucleotide Probes. Appl Environ Microbiol. 1998, 64: 4973-4982.
CAS
Google Scholar
Ratushna VG, Weller JW, Gibas CJ: Secondary structure in the target as a confounding factor in synthetic oligomer microarray design. BMC Genomics. 2005, 6: 31-10.1186/1471-2164-6-31.
Article
Google Scholar
Yilmaz LS, Ökten HE, Noguera DR: Making All Parts of the 16S rRNA of Escherichia coli Accessible In Situ to Single DNA Oligonucleotides. Appl Environ Microbiol. 2006, 72: 733-744. 10.1128/AEM.72.1.733-744.2006.
Article
CAS
Google Scholar
Xia T, SantaLucia J, Burkard ME, Kierzek R, Schroeder SJ, Jiao X, Cox C, Turner DH: Thermodynamic Parameters for an Expanded Nearest-Neighbor Model for Formation of RNA Duplexes with Watson-Crick Base Pairs. Biochemistry. 1998, 37: 14719-14735. 10.1021/bi9809425.
Article
CAS
Google Scholar
Small J, Call DR, Brockman FJ, Straub TM, Chandler DP: Direct detection of 16S rRNA in soil extracts by using oligonucleotide microarrays. Appl Environ Microbiol. 2001, 67: 4708-4716. 10.1128/AEM.67.10.4708-4716.2001.
Article
CAS
Google Scholar
Chandler DP, Newton GJ, Small JA, Daly DS: Sequence versus Structure for the Direct Detection of 16S rRNA on Planar Oligonucleotide Microarrays. Appl Environ Microbiol. 2003, 69: 2950-2958. 10.1128/AEM.69.5.2950-2958.2003.
Article
CAS
Google Scholar
Pozhitkov A, Noble PA, Domazet-Loso T, Nolte AW, Sonnenberg R, Staehler P, Beier M, Tautz D: Tests of rRNA hybridization to microarrays suggest that hybridization characteristics of oligonucleotide probes for species discrimination cannot be predicted. Nucleic Acids Res. 2006, 34: e66-10.1093/nar/gkl133.
Article
Google Scholar
Yilmaz LS, Noguera DR: Mechanistic Approach to the Problem of Hybridization Efficiency in Fluorescent In Situ Hybridization. Appl Environ Microbiol. 2004, 70: 7126-7139. 10.1128/AEM.70.12.7126-7139.2004.
Article
CAS
Google Scholar
Liao JC, Mastali M, Li Y, Gau V, Suchard MA, Babbitt J, Gornbein J, Landaw EM, McCabe ER, Churchill BM, Haake DA: Development of an advanced electrochemical DNA biosensor for bacterial pathogen detection. J Mol Diagn. 2997, 9: 158-168. 10.2353/jmoldx.2007.060052.
Article
Google Scholar
Fuchs BM, Glöckner FO, Wulf J, Amann R: Unlabeled Helper Oligonucleotides Increase the In Situ Accessibility to 16S rRNA of Fluorescently Labeled Oligonucleotide Probes. Appl Environ Microbiol. 2000, 66: 3603-3607. 10.1128/AEM.66.8.3603-3607.2000.
Article
CAS
Google Scholar
Mathews DH, Sabina J, Zuker M, Turner DH: Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol. 1999, 288: 911-940. 10.1006/jmbi.1999.2700.
Article
CAS
Google Scholar
Zuker M: Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003, 31: 3406-3415. 10.1093/nar/gkg595.
Article
CAS
Google Scholar
Zhang Z, Schwartz S, Wagner L, Miller W: A greedy algorithm for aligning DNA sequences. J Comput Biol. 2000, 7: 203-214. 10.1089/10665270050081478.
Article
CAS
Google Scholar
Ding Y, Chan CY, Lawrence CE: RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble. Rna. 2005, 11: 1157-1166. 10.1261/rna.2500605.
Article
CAS
Google Scholar
Ding Y, Lawrence CE: A statistical sampling algorithm for RNA secondary structure prediction. Nucleic Acids Res. 2003, 31: 7280-301. 10.1093/nar/gkg938.
Article
CAS
Google Scholar
Williams KP: The tmRNA Website: invasion by an intron. Nucleic Acids Res. 2002, 30: 179-182. 10.1093/nar/30.1.179.
Article
CAS
Google Scholar
Burks J, Zwieb C, Muller F, Wower I, Wower J: Comparative 3-D modeling of tmRNA. BMC Mol Biol. 2005, 6: 14-10.1186/1471-2199-6-14.
Article
Google Scholar