Genome Sequencing Papers



Paper 1:

Chan, E. Y. (2005). "Advances in sequencing technology." Mutation Research-Fundamental and Molecular Mechanisms of Mutagenesis 573(1-2): 13-40.


Paper 2: One of the papers below:

Bayley, H. (2006). "Sequencing single molecules of DNA." Current Opinion in Chemical Biology 10(6): 628-637.

Shendure, J., R. D. Mitra, et al. (2004). "Advanced sequencing technologies: Methods and goals." Nature Reviews Genetics 5(5): 335-344.

Bentley, D. R. (2006). "Whole-genome re-sequencing." Current Opinion in Genetics & Development 16: 545-552.

Metzker, M. L. (2005). "Emerging technologies in DNA sequencing." Genome Research 15(12): 1767-1776.

Fredlake, C. P., D. G. Hert, et al. (2006). "What is the future of electrophoresis in large-scale genomic sequencing?" Electrophoresis 27(19): 3689-3702.

Ryan, D., M. Rahimi, et al. (2007). "Toward nanoscale genome sequencing." Trends in Biotechnology 25(9): 385-389.


Sanger sequencing methodology:

Paper 3: Sanger, F., S. Nicklen, et al. (1977). "DNA Sequencing with Chain-Terminating Inhibitors."Proceedings of the National Academy of Sciences USA 74(12): 5463-5467.

Capillary Electrophoresis Separation of DNA

Paper 4: Stellwagen, E., Y. J. Lu, et al. (2003). "Unified Description of Electrophoresis and Diffusion for DNA and Other Polyions." Biochemistry 42(40): 11745-11750.

Capillary Electrophoresis DNA Sequencing with Fluorescence Detection

Paper 5: Zhou, H., A. W. Miller, et al. (2000). "DNA Sequencing up to 1300 Bases in Two Hours by Capillary Electrophoresis with Mixed Replaceable Linear Polyacrylamide Solutions." Analytical Chemistry, 72(5): 1045-1052.


For Monday 3/2:

Capillary Electrophoresis DNA Sequencing with Electrochemical Detection

Paper 6: Brazill, S. A., P. H. Kim, et al. (2001). "Capillary Gel Electrophoresis with Sinusoidal Voltammetric Detection: A Strategy To Allow Four-"Color" DNA Sequencing." Analytical Chemistry 73(20): 4882-4890.

Mass Spectrometry DNA Sequencing

Paper 7: Edwards, J. R., H. Ruparel, et al. (2005). "Mass-spectrometry DNA sequencing." Mutation Research-Fundamental and Molecular Mechanisms of Mutagenesis 573(1-2): 3-12.


For Tuesday 3/3:

High sensitivity fluorescence detection

Paper 7: Peck, K., L. Stryer, et al. (1989). "Single-molecule fluorescence detection: autocorrelation criterion and experimental realization with phycoerythrin."Proceedings of the National Academy of Sciences USA 86(11): 4087-4091.



Possible Topics and Papers

Nanopore Sequencing

Rhee, M. and M. A. Burns (2006). "Nanopore sequencing technology: research trends and applications." Trends in Biotechnology 24(12): 580-586.

Soni, G. V. and A. Meller (2007). "Progress toward ultrafast DNA sequencing using solid-state nanopores." Clinical Chemistry 53(11): 1996-2001.



Ronaghi, M. (2001). "Pyrosequencing Sheds Light on DNA Sequencing." Genome Research 11: 3-11.

Zhou, G., T. Kajiyama, et al. (2006). "Enzyme system for improving the detection limit in pyrosequencing." Analytical Chemistry 78(13): 4482-4489.


Single Molecule Sequencing by Synthesis & Fluorescence Detection

Eid, J., A. Fehr, et al. (2009). "Real-Time DNA Sequencing from Single Polymerase Molecules." Science 323(5910): 133-138.

Seo, T. S., X. Bai, et al. (2005). "Four-color DNA sequencing by synthesis on a chip using photocleavable fluorescent nucleotides." Proceedings of the National Academy of Sciences USA 102(17): 5926-5931.


Polymerase Colonies

Mitra, R. D., J. Shendure, et al. (2003). "Fluorescent in situ sequencing on polymerase colonies." Analytical Biochemistry 320: 55-65.

Shendure, J., G. J. Porreca, et al. (2005). "Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome." Science 309: 1728-1732.


Sequencing by Hybridization

Drmanac, R., I. Labat, et al. (1989). "Sequencing of Megabase Plus DNA by Hybridization - Theory of the Method." Genomics 4(2): 114-128.

Drmanac, R., S. Drmanac, et al. (2002). "Sequencing by Hybridization (SBH): Advantages, Achievements, and Opportunities." Advances in Biochemical Engineering/Biotechnology 77: 75-101.

Chee, M., R. Yang, et al. (1996). "Accessing Genetic Information with High-Density DNA Arrays." Science 274(5287): 610-614.


Single Molecule Sequencing by Synthesis & Electrical Detection

Sakata, T. and Y. Miyahara (2006). "DNA Sequencing Based on Intrinsic Molecular Charges." Angewandte Chemie International Edition 45(14): 2225-2228.



Other references

Church, G. M. (2006). "Genomes for all." Scientific American 294(1): 46-54.

Werner, J. H., H. Cai, et al. (2003). "Progress towards single-molecule DNA sequencing: a one color demonstration." Journal of Biotechnology 102(1): 1-14.

Lloyd Davis, et. al, (1991) Rapid DNA Sequencing Based Upon Single Molecule Detection, GATA, 8(1), 1-7.