Polony technology menu

Haplonies thin-sections

What is it? : Polymerase-colony (pronounced "Pahl'ahnee" at Hahvahd, and "Pole own' ee" at the Deli).

How to get it?
Software : Image analysis for haplotyping, exon-typing and sequencing.
Hardware : Slide amplifiers, Auto-Grunt, Scanners.
Wetware : Protocols. Cleavable Fluor-dNTPs
Vaporware : Public discussion forum & wish-list-Wiki.

Brought to you by: Advanced Sequencing Technology NHGRI grants CEGS , 2004 & 2005
Ancient History of Nucleic Acid Cloning and Sequencing by Synthesis.

More details?

Shendure, J, Porreca, GJ, Reppas, NB, Lin, X, McCutcheon, JP, Rosenbaum, AM, Wang, MD , Zhang, K, Mitra, RD, Church, GM (2005) Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome (Science 4-Aug)

12. Shendure J, Mitra R, Varma C, Church GM (2004) Advanced Sequencing Technologies: Methods and Goals. Nature Reviews of Genetics May;5(5):335-44.

11. Mikkilineni, V, Mitra, RD, Merritt, J, DiTonno, JR, Church, GM, Ogunnaike, B, and Edwards, JS. (2004) Digital Quantitative Measurements Of Gene Expression. Biotechnology and Bioengineering 86(2):117-24.

10. Dressman D, Yan H, Traverso G, Kinzler KW, and Vogelstein B. (2003) Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations. Proc Natl Acad Sci U S A. 2003 Jul 22;100(15):8817-22.

9. Butz J, Wickstrom E, and Edwards J. Characterization of mutations and loss of heterozygosity of p53 and K-ras2 in pancreatic cancer cell lines by immobilized polymerase chain reaction. BMC Biotechnol. 2003 Jul 23;3(1):11.

8. Constans, A (2003) Beyond Sanger: Toward the $1000 genome. The Scientist 17: 36.

7. Aach, J and Church, GM (2004) Mathematical models of diffusion-constrained polymerase chain reactions: basis of high-throughput nucleic acid assays and simple self-organizing systems. J. Theoret. Biol. May 7;228(1):31-46.

6. Buhler, J., Souvenir, R., Zhang, W, and Mitra, R. (2004) Design of a high-throughput assay for alternative splicing using polymerase colonies. PSB 2004.

5. Zhu,J, Shendure,J, Mitra, RD, and Church, GM (2003) Single Molecule Profiling of Alternative Pre-mRNA Splicing. Science. 2003 Aug 8;301(5634):836-8.

4. Mitra,RD, Shendure,J, Olejnik,J, Olejnik,EK, and Church,GM (2003) Fluorescent in situ Sequencing on Polymerase Colonies. Analyt. Biochem. 320:55-65.

3. Merritt J, DiTonno JR, Mitra RD, Church GM, and Edwards JS. (2003) Parallel competition analysis of Saccharomyces cerevisiae strains differing by a single base using polymerase colonies. . Nucleic Acids Res. Aug 1;31(15):e84.

2. Mitra, RD, Butty, V, Shendure, J, Williams, BR, Housman, DE, and Church, GM (2003) Digital Genotyping and Haplotyping with Polymerase Colonies. Proc Natl Acad Sci USA. May 13;100(10):5926-31.

1. Mitra, R. and Church, G.M. (1999) In situ localized amplification and contact replication of many individual DNA molecules. Nucleic Acids Res. 27(24):e34; pp.1-6.

Last update 15-Apr-2004 by GMC from Arep.