Publications
Leparc, GG and Mitra RD. A Sensitive Procedure to Detect
Alternatively Spliced mRNA in Pooled-Tissue Samples. Submitted
Wang, H, Johnston, M, Mitra, RD. Calling Cards for DNA-binding
Proteins. In Press, Genome Research.
Leparc, GG and Mitra RD. Non-EST-based prediction of novel
alternatively spliced cassette exons with cell signaling function in
Caenorhabditis elegans and human. Nucleic Acids Research 2007;35(10):
3192-202.
Zhang K, Zhu J, Shendure J, Porreca GJ, Aach JD, Mitra RD, Church GM.
Long-range polony haplotyping of individual human chromosome
molecules. Nature Genetics 2006; 38(3):382-7.
Shendure J, Porreca GJ, Reppas NB, Lin X, McCutcheon JP, Rosenbaum AM,
Wang MD, Zhang K, Mitra RD, Church GM. Accurate multiplex polony
sequencing of an evolved bacterial genome. Science, 2005;
309:1728-32.
Shendure J, Mitra R, Varma C, Church GM (2004) Advanced Sequencing Technologies: Methods and Goals. Nature Reviews of Genetics, 5, 335 –344
Mikkilineni V, Mitra RD, Merritt J, DiTonno JR, Church GM, Ogunnaike B, Edwards JS. Digital quantitative measurements of gene expression. Biotechnol Bioeng. 2004 Apr 20;86(2):117-24.
Buhler, J., Souvenir, R., Zhang, W, and Mitra, R. (2004) Design of a high-throughput assay for alternative splicing using polymerase colonies. Pac Symp Biocomput. 5-16.
Zhu, J., Shendure, J., Mitra, R.D., and Church, G.M. (2003) Single Molecule Profiling of Alternative Pre-mRNA Splicing. Science. 301(5634):836-8.
Merritt, J, DiTonno, JR, Mitra,
RD, Church, GM, Edwards, JS (2003) Functional
characterization of mutant yeast PGK1 within the context of the whole
cell. Nucleic Acids Research 2003 Aug 1;31(15):e84. .
Mitra, R.D., Shendure,
J., Olejnik, J., Edyta-Krzymansk-Olejnik, and Church, G.M. (2003) Fluorescent
in situ Sequencing on Polymerase Colonies. Anal Biochem. 320(1):55-65.
Mitra, R.D., Butty, V., Shendure, J., Housman, D., and Church, G.M. (2003) Digital Genotyping and Haplotyping with Polymerase Colonies. Supplementary Text. Supplementary Figure 6. Supplementary Table 3. Proc Natl Acad Sci. 100(10):5926-31.
Cohen, B.A., Pilpel, Y., Mitra, R.D., and Church, G.M. (2002) Discrimination Between Paralogs Using Microarray Analysis: Application to the Yap1p and Yap2p Transcriptional Networks. Mol. Biol. Cell, 13:1608-1614.
Cohen, B.A.*, Mitra,
R.D.*, Hughes, J.D., and Church, G.M. (2000) A
computational analysis of whole-genome expression data reveals chromosomal
domains of gene expression. Nature Genetics 26(2):183-186.
(*these authors contributed equally)
Mitra R.D. and Church, G.M. (1999) In situ localized amplification and contact replication of many individual DNA molecules. Nucleic Acids Res 1999 Dec 15;27(24):e34; pp.1-6.
Mitra, R.D., Silva, C.M., Youvan, D.C. (1996) Fluorescence resonance energy transfer between blue-emitting and red-shifted excitation derivatives of the green fluorescent protein. Gene 173: 13-17.
Jones, H.L.J., Mitra, R.D., Silva, C.M. (1995) Using GFP expressing E.coli to measure ingestion rates in mixotrophic algae and ciliates. European Journal of Protistology 31: 437.
