The agreement with other genetic based methods suggests genomic indexing using microarrays could be an effective method of typing Group II C. botulinum.
One of our conclusions is that in genome-wide association studies of related individuals genomic background based methods such as genomic GRAMMAR-GC should be preferred over the ones exploiting known pedigree structure, such as pedigree GRAMMAR-GC or MG approach.
In fact, genomic signatures based methods reveal prokaryotic plasmid-host similarity to correlate with genomic GC content, i.e. the more GC rich an organism is the more compositionally similar it tends to be with its plasmid(s) [ 9].
Comparisons were made at the level of genomic DNA using oligonucleotide based methods (Markov chain based genomic signatures, genomic codon and amino acid frequencies based comparisons) and proteomes (all-against-all BLAST protein comparisons and pan-genomic analyses).
A genomic background based method for association analysis in related individuals.
To some extent, our genomic feature based method can complement traditional microarray methods and uncover lowly expressed cell cycle genes.
Genomic feature based method exempts us from the drawbacks of microarray and helps us to reveal the regulatory machinery.
The concept of genomic feature based method can be readily extended to human cell cycle process and other transcriptionally regulated processes, such as tissue-specific expression.
The Johnson Lab has expertise in genomic, lipidomic, and molecular biology based methods for understanding how bioactive lipids shape host-microbe interactions.
The more biased a genome is said to be, the more difficult it is to approximate the genomic tetranucleotide frequencies using random walk based methods such as Markov chains.
Studies were performed using blastocyst biopsy [ 14] and either fluorescence in situ hybridization (FISH) [ 15], comparative genomic hybridization (CGH) [ 16– 18] or array based methods, such as array-CGH [ 13, 19, 20] and single-nucleotide polymorphism array (SNP array) [ 21– 24] for sample analysis.
