Genome analyses

M Schena, D Shalon, R Heller, A Chai, PO Brown, RW Davis. Parallel human genome analysis Microairay-based expression monitoring of 1000 genes. Pi oc Natl Acad Sci USA 93 10614-10619, 1996. 

Oda Y, SK Samanta, FE Rey, L Wu, X Liu, T Yan, J Zhou, CS Harwood (2005) Functional genomic analysis of three nitrogenase isoenzymes in the photosynthetic bacterium Rhodopseudomonas palustris. J Bacterial 187 7784-7794. 

It should be possible to extend the DNA microarray-binding experiment to whole-genome analysis of transcription factor binding sites. The authors suggest that a microarray spotted with 12,000 one-kilobase sequences would span the entire Saccharomyces cerevisiae genome (Bulyk et al., 2001). Such an array could be used to characterize the sequence specificity of S. cerevisiae transcription factors. These experiments would be useful for predicting functions of previously uncharacterized transcription... 

Pellegrini, M., Marcotte, E. M., Thompson, M. J., Eisenberg, D., and Yeates, T. O. (1999). Assigning protein functions by comparative genome analysis Protein phylogenetic profiles. Proc. Natl. Acad. Sci. USA 96, 4285-4288. 

GATC Biotech is the evolved company resulted from Gene Alliance, which was previously known by their large-scale genome analysis projects, particularly from its 2001 results on the genome project Aspergillus funded by DSM (the Netherlands). 

ERGO (Genome Analysis Suite) by Integrated Genomics. 

In summary, the system among many other things, enables to (i) assign primary functions based on cross-genome analysis, (ii) assert metabolic pathways and function... 

Subramanian G, Koonin EV, Aravind L. Comparative genome analysis of the pathogenic spirochetes Borrelia burgdorferi and Treponema pallidum. Infect Im-mun 2000 68(3] 1633-1648. 

Aravind L. Guilt by association contextual information in genome analysis. Genome Res 2000 10[8] 1074-1077. 

Hacker J, Kaper JB. Pathogenicity islands and the evolution of microbes. Annu Rev Microbiol 2000 54 641-679. Wren BW. Microbial genome analysis insights into virulence, host adaptation and evolution. Nature Rev Genet 2000 l[l] 30-39. 

Hynes RO. Genomic analysis of metastasis reveals an essential role for RhoC. Nature 2000 403 532-535. 

Array-based comparative genomic hybridization (a-CGH) is a genomic analysis system that allows identification of alterations in DNA sequence and copy number, with a potential goal of individualized diagnosis and targeted cancer therapy.35,36 A number of reports have described application of a-CGH to DNA extracted from FFPE tissues, with variable results.35,37 38... 

Thompson, A., Prescott, M., Chelebi, N., Smith, J., Brown, T., and Schmidt, G. (2007) Electrospray ionisation-cleavable tandem nucleic acid mass tag-peptide nucleic acid conjugates Synthesis and applications to quantitative genomic analysis using electrospray ionisation-MS/MS. Nucleic Acids Res. 35(4), e28. 

SHIRLEY, B.W., HANLEY, S., GOODMAN, H.M., Effects of ionizing radiation on a plant genome analysis of two Arabidopsis transparent testa mutations, Plant Cell, 1992, 4, 333-347. 

Emtestam, L., Zetterquist, H., and Olerup, O., HLA-DR, -DQ and -DP alleles in nickel, chromium, and/or cobalt-sensitive individuals genomic analysis based on restriction fragment length polymorphisms, J. Invest. Dermatol., 100, 271, 1993. 

The statement that genomic analysis is sufficient for disease-related research has long been proven wrong. In contrast, the translation products, the proteins, are the exe-cuters of cell functions and are of major interest. The example of the caterpillar and the butterfly that have the same genotype, but a quite different phenotype, is often used to exemplify the need for proteomics. However, the study of proteins is complicated by a number of facts ... 

Meyer B. STD NMR to screen libraries and characterize binding, in NMR drug discovery and design - Post-genomic analysis. 2000. McLean, Virginia Cambridge Healthtech Institute. 

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