If you use mathFISH for any type of probe evaluation please cite:

 

Yilmaz, L. S., Parkernar, S., and Noguera, D. R. (2011) “mathFISH, a Web Tool That Uses Thermodynamics-Based Mathematical Models for In Silico Evalulation of Oligonucleotide Probes for Fluorescence In Situ Hybridization”, Applied and Environmental Microbiology, 77: 1118-1122.

 

If you use free energy and hybridization efficiency calculations please also cite:

 

Yilmaz, L. S., Okten, H. E., and Noguera, D. R. (2006) “All Regions of the 16S rRNA of Escherichia coli are Accessible in situ to DNA Oligonucleotides with Sufficient Thermodynamic Affinity”, Applied and Environmental Microbiology, 72: 733-744.

 

Yilmaz, L. S. and Noguera, D. R. (2004) “Mechanistic Approach to the Problem of Hybridization Efficiency in Fluorescent in situ Hybridization”, Applied and Environmental Microbiology, 70: 7126-7139.

 

If you use formamide curves please also cite:

 

Yilmaz, L. S. and Noguera, D. R. (2007) “Development of Thermodynamic Models for Simulating Probe Dissociation Profiles in Fluorescence in situ Hybridization”, Biotechnology and Bioengineering, 96 (2): 349-363.

 

If you use mismatch analysis tool please also cite:

 

Yilmaz, L. S., Bergsven, L., and Noguera, D. R. (2008) “Systematic Evaluation of Single Mismatch Stability Predictors for Fluorescence in situ Hybridization”, Environmental Microbiology, 10(10):2872-2085.

 

If you use competitor model please also cite:

 

Hoshino, T., Yilmaz , L. S., Noguera, D. R., Daims, H., and Wagner, M. (2008) “Quantification of Target Molecules Needed to Detect Microorganisms by Fluorescence in situ Hybridization (FISH) and Catalyzed Reporter Deposition-FISH”, Applied and Environmental Microbiology, 74(16):5068-5077.