Mitra Lab Publications

Tessler, L. A. and Mitra, R. D. (2011), Sensitive single-molecule protein quantification and protein complex detection in a microarray format. PROTEOMICS, 11: 4731–4735.

Tessler LA, Donahoe CD, Garcia DJ, Jun YS, Elbert DL, Mitra RD, Nanogel coatings for improved single-molecule detection substrates. Journal of the Royal Society, Interface, 2011 Epub Feb 16. PMID: 21325313

Francesco L.M. Vallania, Todd E. Druley, Enrique Ramos, et al. High-throughput discovery of rare insertions and deletions in large discovery of rare insertions and deletions in large cohorts. Genome Res. (2010) Epub November 1, 2010

Varley KE, Mitra RD.  (2010)  Bisulfite Patch PCR enables multiplexed sequencing of promoter methylation across cancer samples.  Genome Res. Sep;20(9):1279-87. Epub 2010 Jul 13.PMID: 20627893

• Related news piece:  Hager, M Wash U Researchers Develop Sample-Prep Technique for Multiplexed Bisulfite Sequencing In Sequence, July 20, 2010

Mogno I, Vallania F, Mitra RD, Cohen BA. (2010)  TATA is a modular component of synthetic promoters. Genome Res. Oct;20(10):1391-7. Epub 2010 Jul 13.PMID: 20627890

Varley KE, Mitra RD.  (2009) Nested Patch PCR for highly multiplexed amplification of genomic loci.  Cold Spring Harb Protoc. Jul;2009(7):pdb.prot5252.PMID: 20147217

Matkovich SJ, Van Booven DJ, Hindes A, Kang MY, Druley TE, Vallania FL, Mitra RD, Reilly MP, Cappola TP, Dorn GW 2nd.  (2010)  Cardiac signaling genes exhibit unexpected sequence diversity in sporadic cardiomyopathy, revealing HSPB7 polymorphisms associated with disease.  J Clin Invest. 2010 Jan 4;120(1):280-9.  PMID: 20038796

Goodman AL, McNulty NP, Zhao Y, Leip D, Mitra RD, Lozupone CA, Knight R, Gordon JI.  (2009)  Identifying genetic determinants needed to establish a human gut symbiont in its habitat.  Cell Host Microbe. 2009 Sep 17;6(3):279-89.PMID: 19748469

Tessler, L.A., Reifenberger, J.G. and Mitra, R.D. (2009) Protein quantification in complex mixtures by solid phase single-molecule counting. Analytical Chemistry, 81, 7141-7148.

• Related news piece:  Gebel, E.  (2009)  *Molecule Counting Made Easy.  Analytical Chemistry, 81(17), pp 7130–7131

Varley, K.E., Mutch, D.G., Edmonston, T.B., Goodfellow, P.J. and Mitra, R.D. (2009) Intra-tumor heterogeneity of MLH1 promoter methylation revealed by deep single molecule bisulfite sequencing. Nucleic acids research, 37, 4603-4612.

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.

• Related news piece:  Pentimalli, F(2007)  Technology:  On the trail of transcription factors. Nature Review Genetics 8, 655 (September)

• Related news piece:  Rusk, N. (2007)  Transcription factors come to call.  Nature Methods, 4, 690

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.

• Related news piece:  Flintoff, L  Nature: Milestones in DNA Technology.  Milestone 18  The next generation arrives.
• Related Review:  Shendure, J and Ji,H. (2008)  Next Generation DNA Sequencing.  Nature Biotechnology, 26(10)  1135-1145.

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.

• Related news piece:  Flintoff, L  (2007) Nature: Milestones in DNA Technology. Milestone 18  The next generation arrives.
• Related Review:  Shendure, J and Ji,H. (2008)  Next Generation DNA Sequencing.  Nature Biotechnology, 26(10)  1135-1145.
• Related Review:  Church, G. (2006) Genomes for All. Scientific American. January, 2006

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.