TRAC in high-content gene expression analysis: applications in microbial population studies, process biotechnology and biomedical research

References

• Lamb J, Crawford ED, Peck D et al. The connectivity map: using gene-expression signatures to connect small molecules, genes, and disease. Science313(5795), 1929–1935 (2006).
   PubMed Web of Science ®Google Scholar
• Hieronymus H, Lamb J, Ross KN et al. Gene expression signature-based chemical genomic prediction identifies a novel class of HSP90 pathway modulators. Cancer Cell10(4), 321–330 (2006).
   PubMed Web of Science ®Google Scholar
• Glas AM, Floore A, Delahaye LJ et al. Converting a breast cancer microarray signature into a high-throughput diagnostic test. BMC Genomics7, 7278–330 (2006).
   Google Scholar
• Marchionni L, Wilson RF, Wolff AC et al. Systematic review: gene expression profiling assays in early-stage breast cancer. Ann. Intern. Med.148(5), 358–369 (2008).
   PubMed Web of Science ®Google Scholar
• TriMark Publications. Gene Expression Reagents Markets – Trends, Industry Participants, Product Overviews and Market Drivers. TMRGER07–0401 (2007).
   Google Scholar
• Bookout AL, Cummins CL, Mangelsdorf DJ, Pesola JM, Kramer MF. High-throughput real-time quantitative reverse transcription PCR. Curr. Protoc. Mol. Biol. Chapter 15, Unit 15.8 (2006).
   PubMedGoogle Scholar
• Ning B, Dial S, Sun Y et al. Systematic and simultaneous gene profiling of 84 drug-metabolizing genes in primary human hepatocytes. J. Biomol. Screen. (In Press) (2008).
   PubMedGoogle Scholar
• Zhang A, Pastor L, Nguyen Q et al. Small interfering RNA and gene expression analysis using a multiplex branched DNA assay without RNA purification. J. Biomol. Screen.10(6), 549–556 (2005).
   PubMed Web of Science ®Google Scholar
• Yang L, Tran DK, Wang X. BADGE, beads array for the detection of gene expression, a high-throughput diagnostic bioassay. Genome Res.11(11), 1888–1898 (2001).
   PubMed Web of Science ®Google Scholar
• Tian H, Cao L, Tan Y et al. Multiplex mRNA assay using electrophoretic tags for high-throughput gene expression analysis. Nucleic Acids Res.32(16), E126 (2004).
   Google Scholar
• Rautio JJ, Kataja K, Satokari R et al. Rapid and multiplexed transcript analysis of microbial cultures using capillary electophoresis-detectable oligonucleotide probe pools. J. Microbiol. Methods65(3), 404–416 (2006).
   PubMedGoogle Scholar
• Satokari RM, Kataja K, Söderlund H. Multiplexed quantification of bacterial 16S rRNA by solution hybridization with oligonucleotide probes and affinity capture. Microb. Ecol.50(1), 120–127 (2005).
   PubMedGoogle Scholar
• Kataja K, Satokari RM, Arvas M, Takkinen K, Söderlund H. A highly sensitive and multiplexed method for focused transcript analysis. J. Microbiol. Methods67(1), 102–113 (2006).
   PubMedGoogle Scholar
• Kivioja T, Arvas M, Kataja K et al. Assigning probes into a small number of pools separable by electrophoresis. Bioinformatics18 (1), 199–206 (2002).
   Google Scholar
• Rautio JJ, Huuskonen A, Vuokko H, Vidgren V, Londesborough J. Monitoring yeast physiology during very high gravity wort fermentations by frequent analysis of gene expression. Yeast24(9), 741–760 (2007).
   PubMed Web of Science ®Google Scholar
• Maukonen J, Mätto J, Satokari R et al. PCR DGGE and RT-PCR DGGE show diversity and short-term temporal stability in the Clostridium coccoides–Eubacterium rectale group in the human intestinal microbiota. FEMS Microbiol. Ecol.58(3), 517–528 (2006).
   PubMed Web of Science ®Google Scholar
• Maukonen J, Satokari R, Mätto J et al. Prevalence and temporal stability of selected clostridial groups in irritable bowel syndrome in relation to predominant faecal bacteria. J. Med. Microbiol.55(5), 625–633 (2006).
   PubMed Web of Science ®Google Scholar
• Rautio JJ, Smit BA, Wiebe M, Penttilä M, Saloheimo M. Transcriptional monitoring of steady state and effects of anaerobic phases in chemostat cultures of the filamentous fungus Trichoderma reesei. BMC Genomics7, 247 (2006).
   PubMed Web of Science ®Google Scholar
• Wiebe MG, Rintala E, Tamminen A et al. Central carbon metabolism of Saccharomyces cerevisiae in anaerobic, oxygen-limited and fully aerobic steady-state conditions and following a shift to anaerobic conditions. FEMS Yeast Res.8(1), 140–154 (2008).
   PubMedGoogle Scholar
• Rautio JJ, Bailey M, Kivioja T et al. Physiological evaluation of the filamentous fungus Trichoderma reesei in production processes by marker gene expression analysis. BMC Biotechnol.7, 28 (2007).
   PubMed Web of Science ®Google Scholar
• Gasser G, Maurer M, Rautio M et al. Monitoring of transcriptional regulation in Pichia pastoris under protein production conditions. BMC Genomics8, 179 (2007).
   PubMedGoogle Scholar
• Glas AM, Kersten MJ, Delahaye LJ et al. Gene expression profiling in follicular lymphoma to assess clinical aggressiveness and to guide the choice of treatment. Blood105(1), 301–307 (2005).
   PubMed Web of Science ®Google Scholar
• Johnson JJ, Mukhtar H. Curcumin for chemoprevention of colon cancer. Cancer Lett.255(2), 170–181 (2007).
   PubMed Web of Science ®Google Scholar
• Stenman J, Paju A, Rissanen O et al. Targeted gene-expression analysis by genome-controlled reverse transcription-PCR. Clin. Chem.52(11), 1988–1996 (2006).
   PubMedGoogle Scholar
• Fire A, Xu S, Montgomery MK et al. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans.Nature391(6669), 806–811 (1998).
   PubMed Web of Science ®Google Scholar
• Perrimon N, Mathey-Prevot B. Applications of high-throughput RNA interference screens to problems in cell and developmental biology. Genetics175(1), 7–16 (2007).
   PubMed Web of Science ®Google Scholar
• Pappas TC, Bader AG, Andruss BF, Brown D, Ford LP. Applying small RNA molecules to the directed treatment of human diseases: realizing the potential. Expert Opin. Ther. Targets12(1), 115–127 (2008).
   PubMed Web of Science ®Google Scholar
• Krueger U, Bergauer T, Kaufmann B et al. Insights into effective RNAi gained from large-scale siRNA validation screening. Oligonucleotides17(2), 237–250 (2007).
   PubMedGoogle Scholar
• Zidek N, Hellmann J, Kramer PJ, Hewitt PG. Acute hepatotoxicity: a predictive model based on focused illumina microarrays. Toxicol. Sci.99(1), 289–302 (2007).
   PubMed Web of Science ®Google Scholar