Mitra Lab Publications

Todd E Druley, Francesco L M Vallania, Daniel J Wegner, Katherine E Varley, Olivia L Knowles, Jacqueline A Bonds, Sarah W Robison, Scott W Doniger, Aaron Hamvas, F Sessions Cole, Justin C Fay, Robi D Mitra. Quantification of rare allelic variants from pooled genomic DNA. Nature Methods, 2009, 6: 263-265.

Varley, K., Mitra, RD. Nested patch PCR enables highly multiplexed mutation discovery in candidate genes. Genome Research, 2008, 18: 1844-1850.

Wang, H, Heinz, M, Crosby, S, Johnston, M, Mitra, RD. ‘Calling cards’ method for high-throughput identification of targets of yeast DNA-binding proteins. Nature Protocols, 2008, 3(10):1569-1577.

Rieger, C, Poppino, R, Sheridan, R, Moley, K, Mitra, RD, Gottlieb, D. Polony analysis of gene expression in ES cells and blastocysts. Nucleic Acids Research, 2007, 35(22):e151.

Leparc, GG, Mitra RD. A sensitive procedure to detect alternatively spliced mRNA in pooled-tissue samples. Nucleic Acids Research, 2007; 35(21):e146.

Rawls, A, Schultz, S, Mitra, RD, Wolff, T. Bedraggled, a putative transporter, influences the tissue polarity complex during the R3/R4 fate decision in the drosophila eye. Genetics, 2007, 177:313-328.

Wang, H, Johnston, M, Mitra, RD. Calling cards for DNA-binding proteins. Genome Research, 2007, 17:1202-1209.

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.