O. Paliy and B. Foy
Mathematical modeling of 16S ribosomal DNA amplification reveals optimal conditions for the interrogation of complex microbial communities with phylogenetic microarrays (2011) Bioinformatics, 27(15): 213440.
Full text (pdf)
Supplementary material:
 Supplementary figure S1 (png): Agarose gel electrophoresis of gDNA samples amplified with different number of PCR cycles
 Supplementary figure S2 (png): Simulation results  average sample amplification rate vs PCR cycle number
 Supplementary figure S3 (png): Simulation results  fraction of 16S rDNA in amplified sample vs PCR cycle number
 Supplementary figure S4 (png): Simulation results  deviation of relative 16S rDNA abundances with PCR cycle number [graphs are shown for most abundant gDNA species in the original sample {rank 1}, midabundant {rank 200}, and least abundant {rank 400}]
 Supplementary figure S5 (png): Simulation results  yield of PCR reaction as a function of PCR cycle number and amount of starting gDNA [no loss due to PCR reaction purification is assumed]
 Supplementary figure S6 (png): Simulation results  number of PCRamplified samples needed to becombined to obtain 1500 bp microarray load [we assume 50% loss of DNA during PCR purification]
 Supplementary table S1 (pdf): Comparison of simulated and experimental results
 Detailed model description (pdf)
 Matlab files used to run simulation (zip)
