Week 5
October 27Next Generation Sequencing
How High-Speed Gene Sequencing Works [via Wired Science] NNGS - 
sr320 Oct 28, 2008
[ http://feeds.delicious.com/v2/rss/sr320/ngs?count=15]
full list from delicious
Papers to Discuss:
- Primer: Sequencing—the next generation
Different sequencing technologies, at a glance. NATURE METHODS | VOL.5 NO.1 | JANUARY 2008 | 15 - Pyrosequence analysis of expressed sequence tags for Manduca sexta hemolymph proteins involved in immune responses. Zou Z, Najar F, Wang Y, Roe B, Jiang H. Insect Biochemistry and Molecular Biology Volume38, Ppg. 677-82
6/1/2008
manduca.pdf - Detection of Large Numbers of Novel Sequences in the Metatranscriptomes of Complex Marine Microbial CommunitiesJack A. Gilbert,1* Dawn Field,2 Ying Huang,3 Rob Edwards,4,5 Weizhong Li,3 Paul Gilna,3 and Ian Joint1
PLoS ONE. 2008; 3(8): e3042.
Special Guest Presentations | Dr. Jim Seeb and Dr. Lisa Seeb
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The Basics: DNA sequencing Traditional (Sanger)
Early DNA sequencing (Sanger)
NGS
Solexa Technology
Two movies from Roche (one hardware, the other on chemistry)
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| The SOLiD™ System is a revolutionary genetic analysis platform that enables massively parallel sequencing of clonally-amplified DNA fragments linked to beads. The SOLiD™ sequencing methodology is based on sequential ligation with dye-labeled oligonucleotides. Each run will produce 40 million reads, totaling 1 billion bases! |
Additional Readings on the topic:
- Next-generation sequencing transforms today’s biology
Stephan C Schuster | 18 | VOL.5 NO.1 | JANUARY 2008 | NATURE METHODS - DNA Technology Posts Dramatic Speed Increases | Wired Science from Wired.com
blog.wired.com/wiredscience/2008/07/british-ins... - Pyrosequence analysis of expressed sequence tags for Manduca sexta hemolymph proteins involved in immune responses. Zou Z, Najar F, Wang Y, Roe B, Jiang H. Insect Biochemistry and Molecular Biology Volume38, Ppg. 677-82
6/1/2008 - Construction of a robust microarray from a non-model species largemouth bass, Micropterus salmoides (Lacèpede), using pyrosequencing technology N. Garcia-Reyero, R. J. Griffitt, L. Liu, K. J. Kroll, W. G. Farmerie, D. S. Barber, N. D. Denslow Journal of Fish Biology Volume72, Ppg. 2354 - 2376
6/28/2008
View Publication - Rapid transcriptome characterization for a non-model organism using 454 pyrosequencing J. C. Vera, C.W. Wheat, H.W. Fescemyer, M.J. Frilander, D.L. Crawford, I. Hanski, J.H. Marden Molecular Ecology Volume17, Ppg. 1636-1647
2/5/2008
View Publication - Microbial community gene expression in ocean surface waters Jorge Frias-Lopez, Yanmei Shi, Gene W. Tyson, Maureen L. Coleman, Stephan C. Schuster, Sallie W. Chisholm, and Edward F. DeLong PNAS Volume105, Ppg. 3805–3810
3/11/2008
View Publication - Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome Urich T, Lanzén A, Qi J, Huson DH, Schleper C, Schuster SC. PloS One Volume3, Ppg.
6/25/2008 - doi:10.1016/j.ygeno.2008.07.001 Genomics Volume 92, Issue 5, November 2008, Pages 255-264> Review Applications of next-generation sequencing technologies in functional genomics