Last updated

Last updated: Friday, September 02, 2011 12:08 AM

External Links and References

Topic 1

CSH site (restriction enzymes, ligation, sequencing, cloning, PCR)

Plasmid DNA prep.

Promega DNA/RNA purification

Qiagen protocols

Oligonucleotide synthesis

PNA

Morpholinos

Electrophoresis

Pulsed-field gel electrophoresis 1

Pulsed-field gel electrophoresis 2

Non-isotopic nucleic acid detection

Indirect labeling (ABC method)

(Biotin-Avidin)

FISH

Microarrays

Topic 2: DNA cloning

2-1 Zhou & Gomez-Sanchez. Universal TA cloning. Curr. Issues Mol. Biol (2000) 2, 1-7

2-2 Albertis, Gitler, Lindquist.A suite of Gateway® cloning vectors for high-throughput genetic analysis in Saccharomyces cerevisiae (pages 913–919) Yeast (07) 24,913-919

2-3 Li & Elledge. Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC. Nature Methods (07)4, 251-6

Topic 3: Physical Genome Mapping:

3-1 Eric Green. Strategies for the systematic sequencing of complex genomes. Nat. Rev. Genetics 2001. 2(8):573-83.

3-2 The C. elegans Genome Consortium & Richard Wilson. How the worm was won: the C. elegans genome sequencing project. Trends in Genetics 1992. 15(2):51-8.

3-3 R. Hoskins, et. al. A BAC-based physical map of the major autosomes of Drosophlia melanogaster. Science 2000. 287(5461):2271-4.

3-4 E. Myers, et. al. A whole-genome assembly of Drosophila. Science 2000. 287(5461):2196-204.

3-5 The International Human Genome Mapping Consortium, et. al. A physical map of the human genome. Nature 2001. 409(6822):934-41.

3-6 S. Celniker et. al. Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequence. Genome Biol, Jan 2002; 3(12) 1-14.

3-7 BC Meyers et al., Mapping and sequencing complex genomes: let's get physical! Nat Rev Genet, Aug 2004; 5(8): 578-88.

Sequence assembly software

3-8 J. Rothberg, et al. The development and impact of 454 sequencing. Nature Biotechnology 2008. 26:1117-24.

3-9 J. Shendure, et al. Next generation DNA sequencing. Nature Biotechnology 2008. 26:1135-45.

3-10 M. Margulies, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005. 437:376-80.

3-11a J. Shendure, et al. Accurate multiplex polony sequencing of an evolved bacterial genome. Science 2005. 309:1728-32.

3-11b Shendure et al Supplementary data- See figure 7

3-12 SOLiD System Brochure This is a large file (25MB), so only open it if you have a high speed connection.

3-13 J. Shendure, et al. Advanced sequencing technologies: Methods and Goals. Nature Reviews 2004. 5:335-44.

3-14 D Wheeler, et al. The complete genome of an individual by massively parallel DNA sequencing. Nature 2008. 452:872-76.

3-15 Mardis ER. Next-generation DNA sequencing methods. (2008) Ann Rev. Gen. Hum. Gen. 9, 387-402

3-16 Ansorge WJ. Next-generation DNA sequencing techniques. (2009) New Biotech. 25, 195-203

3-17 Snyder, Du, Gerstein. Personal genome sequencing: current approaches and challenges. (2010) Genes Dev. 24, 423-431

3-18 Nagalakshmi, waern, Snyder. RNA-Seq: a method for comprehensive transcriptome analysis. (2010) Curr. Prot. Mol. biol. 4.11.1-13

3-19 Blencowe Lee. Current-generation high-throughput sequencing: deepening insights into mammalian transcriptomes. (2009) Genes Dev. 23, 1379-1386

Topic 4: Gene Characterization:

4-1 P. Carninci, et. al. Normalization and subtraction of cap-trapper-selected cDNAs to prepare full-lenght cDNA libraries for rapid discovery of new genes. Genome Research 2000. 10(10):1617-30.

4-2 M. Stapleton, et. al. The Drosophila gene collection: Identification of putative full length cDNAs for 70% of D. melanogaster genes. Genome Research 2002. 12(8):1294-00.

4-3 M. Zhang. Computational prediction of eukaryotic protein-coding genes. Nat Rev Genetics 2002. 3(9):698-709.

4-4 P. Flicek. Gene prediction: compare and CONTRAST. Genome Biology 2007. 8(12):233

4-5 S. Maas & A. Rich. Changing genetic information through RNA editing. BioEssays 2000. 22(9):790-802.

4-6 F. Perler. A natural example of protein trans-splicing. Trends Biochem Sci 1999. 24(6):209-11.

4-7 RB Stoughton. Applications of DNA microarrays in biology. Annu Rev Biochem, Jan 2005; 74: 53-82.

4-8 F Bier et al. DNA microarrays.Adv Biochem Engin/Biotechnol (2008) 109: 433–453

4-9 Roberts PC. Gene expression microarray data analysis demystified. (08) Biotech Ann. Rev. 14, 29-61 PDF

4-10 Kurimoto. Global single-cell cDNA amplification to provide a template for representative high-density oligonucleotide microarray analysis.(2007) Nat. protocols 2, 739-752

4-11 Kurimoto & Saitou. Single-cell cDNA microarray profiling of complex biological processes of differentiation. (2010) Curr Op. Gen. Dev. 20, 1-8

Topic 5: Cloning DIsease Genes & Genetic Testing:

5-1 D. Botstein & N. Risch. Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease. Nat Genetics 2003. 33(Suppl):228-37.

5-2 T Manolio et al. A HapMap harvest of insights into the genetics of common disease. The Journal of Clinical Investigation 2008. 5:1590-1604.

5-3 The International HapMap Consortium. A haplotype map of the human genome. Nature 2005. 437:1299-1320.

Coming:

Weedon et al 2008 Genome-wide association analysis identifies 20 loci that influence adult height

Wellcome Trust Consortium 2007 Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls

Topic 6: Studying Protein Function:

6-1 F. Tanious et al. Biosensor-surface plasmon resonance methods for quantitative analysis of biomolecular interactions. Methods in Cell Biology 2008. 84: 53-77.

6-2 Structural Genomics Consortium. Protein Production and Purification. Nature Methods 2008. 5: 135-45.

6-3 F. Katzen et al. The past, present and future of cell-free protein synthesis. Trends in Biotechnology 2005. 23: 150-6.

6-4 D. Shin, et. al. Combinatorial Solid Phase Peptide Synthesis and Bioassays. Biochem. and Mol. Bio. 2005. 38: 517-25.

6-5 V. Muralidharan et al. Protein Ligation: an Enabling Technology for the Biophysical Analysis of Proteins. Nature Methods 2006. 3: 429-38.

6-6 M. Xu et al. Recent Advances in Protein Splicing: Manipulating Proteins in vitro and in vivo. Curr. Opin. Biotechnol. 2005. 16: 440-6.

Coming:

Suter et al 2008 Two hybrid technologies in proteomics research