Grape MPSS: Publications
The following lists contain publications from our lab and other labs that have utilized MPSS. The list may not be complete or up to date when you read this. We apologize but please use PubMed for the latest papers. We will try to update the page periodically. Suggestions for additions are also welcome.

The Original MPSS Publications by Illumina, Inc.
  1. Brenner, S., Williams, S.R., Vermaas, E.H., Storck, T., Moon, K., McCollum, C., Mao, J.I., Luo, S., Kirchner, J.J., Eletr, S., DuBridge, R.B., Burcham, T., and Albrecht, G. (2000). In vitro cloning of complex mixtures of DNA on microbeads: physical separation of differentially expressed cDNAs. Proc Natl Acad Sci USA 97, 1665-1670.

  2. Brenner, S., Johnson, M., Bridgham, J., Golda, G., Lloyd, D.H., Johnson, D., Luo, S., McCurdy, S., Foy, M., Ewan, M., Roth, R., George, D., Eletr, S., Albrecht, G., Vermaas, E., Williams, S.R., Moon, K., Burcham, T., Pallas, M., DuBridge, R.B., Kirchner, J., Fearon, K., Mao, J., and Corcoran, K. (2000). Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nature Biotechnology 18, 630-634.

The Original 454 Publications
  1. Margulies M., Egholm M., Altman W.E., Attiya S., Bader J.S., Bemben L.A.,Berka J., Braverman M.S., Chen Y.J., Chen Z., et. al. (2005). Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376-380.

MPSS- or 454-Related Papers from the Meyers Laboratory
The following papers describe the contents of this website, the methods we use, or other aspects of our work on gene expression analyses.
  1. Meyers, B.C., Tej, S.S., Vu, T.H., Haudenschild, C.D., Agrawal, V., Edberg, S.B., Ghazal, H. and S. Decola. (2004). The use of MPSS for whole- genome transcriptional analysis in Arabidopsis. Genome Research. 14, 1641-1653.

  2. Meyers, B.C., Vu, T.H., Tej, S.S., Matvienko, M., Ghazal, H., Agrawal, V., C.D. Haudenschild. (2004). Analysis of the transcriptional complexity of Arabidopsis by massively parallel signature sequencing. Nature Biotechnology. 22, 1006-1011.

  3. Meyers, B.C., Lee, D.K., Vu, T.H., Tej, S.S., Edberg, S.B., Matvienko, M., and L.D. Tindell. (2004) Arabidopsis MPSS: an online resource for quantitative expression analysis. Plant Physiology. 135, 801-813.

  4. Meyers, B.C., Galbraith, D.W., Nelson, T., and V. Agrawal. (2004). Methods for transcriptional profiling in plants: be fruitful and replicate. Plant Physiology. 135, 637-652.

  5. Coughlan, S., Agrawal, V. and B.C. Meyers. (2004). A comparison of global gene expression measurement technologies in Arabidopsis thaliana. Comparative and Functional Genomics 5, 245-252.

  6. Lu, C., Tej, S.S., Luo, S., Haudenschild, C.D., Meyers, B.C., and P.J. Green. (2005). Elucidation of the small RNA component of the transcriptome. Science 309, 1567-1569.

  7. Nakano, M., Nobuta, K., Vemaraju, K., Tej, S.S., Skogen, J.W., and B.C. Meyers. (2006). Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA. Nucleic Acids Research 34, D731-D735.

  8. Meyers B.C., Souret F.F., Lu C., and P.J. Green (2006). Sweating the small stuff: microRNA discovery in plants. Current Opinion in Biotechnology 17(2), 139-146.

  9. Henderson I.R., Zhang X., Lu C., Johnson L., Meyers B.C., Green P.J., and S.E. Jacobsen. (2006). Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning. Nature Genetics 38(6), 721-725.

  10. Yan H., Ito H., Nobuta K., Ouyang S., Jin W., Tian S., Lu C., Venu R.C., Wang G.L., Green P.J., Wing R.A., Buell C.R., Meyers B.C., and J. Jiang. (2006). Genomic and Genetic Characterization of Rice Cen3 Reveals Extensive Transcription and Evolutionary Implications of a Complex Centromere. Plant Cell 18, 2123-33.

  11. Burnside J., Bernberg E., Anderson A., Lu C., Meyers B.C., Green P.J., Jain N., Isaacs G., R.W. Morgan. (2006). Marek's disease virus encodes MicroRNAs that map to meq and the latency-associated transcript. Journal of Virology 80(17), 878-886.

  12. Lu C., Kulkarni K., Souret F.F., Muthuvalliappan R., Tej S.S., Poethig R.S., Henderson I.R., Jacobsen S.E., Wang W., Green P.J., and B.C. Meyers. (2006). MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutan. Genome Research 16, 1276-1288.

  13. Nobuta K., Venu R.C., Lu C., Belo A., Vemaraju K., Kulkarni K., Wang W., Pillay M., Green P.J., Wang G.L., B.C. Meyers. (2007). An expression atlas of rice mRNAs and small RNAs. Nature Biotechnology.



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