External Links and References

Last updated: 09/24/11 11:47

External Links and References

Topic 1

CSH site (restriction enzymes, ligation, sequencing, cloning, PCR) http://www.dnai.org/b/index.html

Plasmid DNA prep. http://www.cores.utah.edu/DNASequencing/plasmid.html

Promega DNA/RNA purification http://www.promega.com/tbs/dna_rna.htm

Qiagen protocols http://www1.qiagen.com/literature/Default.aspx?Term=&Language=EN&LiteratureType=4%3b8%3b9%3b10&ProductCategory=235

Oligonucleotide synthesis http://www.bio.davidson.edu/Courses/Molbio/MolStudents/spring2003/Holmberg/oligonucleotide_synthesis.htm

PNA http://en.wikipedia.org/wiki/Peptide_nucleic_acid

Morpholinos http://files.gene-tools.com/Biocompare/

Electrophoresis http://learn.genetics.utah.edu/units/biotech/gel/

Pulsed-field gel electrophoresis http://www.nal.usda.gov/pgdic/Probe/v2n3/puls.html

http://www.bio.davidson.edu/Courses/ genomics/method/pulse_field.html

Non-isotopic nucleic acid detection http://www.kpl.com/docs/techdocs/TECHGUID.PDF

Indirect labeling (ABC method) http://www.vectorlabs.com/infopage.asp?dpID=4&locID=609308

(Biotin-Avidin) http://www.vectorlabs.com/products.asp?catID=28&locID=0

FISH http://www.pasteur.fr/recherche/unites/biophyadn/e-fish.html

FISH http://members.aol.com/chrominfo/fishinfo.htm

Microarrays http://www.highveld.com/pages/microarray-resources.html

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

2-4 Quikchange Manual

2-5 Gateway Seminar

Electroporation http://www.bio.davidson.edu/Courses/Molbio/MolStudents/spring2003/McCord/electroporation.htm

Protocol online http://www.protocol-online.org/prot/Molecular_Biology/index.html

PCR papers http://www.open-access-biology.com/

Long PCR http://arep.med.harvard.edu/labgc/estep/longPCR_protocol.html

Real-time PCR http://www.premierbiosoft.com/tech_notes/real_time_PCR.html http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction

http://marketing.appliedbiosystems.com/mk/get/GEMINI_landing?isource=fr_E_Keyword_Google_7500Fast_05_0105_1231

Gateway cloning http://tools.invitrogen.com/content.cfm?pageid=11905

TOPO cloning http://www.invitrogen.com/content.cfm?pageid=4073&CID=KNC-GOOGLE

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 http://www.phrap.org

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

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.

Topic 6: High throughput DNA sequencing

6-1 J. Rothberg, et al. The development and impact of 454 sequencing. Nature Biotechnology 2008. 26:1117-24.

6-2 J. Shendure, et al. Next generation DNA sequencing. Nature Biotechnology 2008. 26:1135-45.

6-3 M. Margulies, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005. 437:376-80.

6-4a J. Shendure, et al. Accurate multiplex polony sequencing of an evolved bacterial genome. Science 2005. 309:1728-32.

6-4b Shendure et al Supplementary data- See figure 7

6-5 SOLiD System Brochure This is a large file (25MB), so only open it if you have a high speed connection.

6-6 J. Shendure, et al. Advanced sequencing technologies: Methods and Goals. Nature Reviews 2004. 5:335-44.

6-7 D Wheeler, et al. The complete genome of an individual by massively parallel DNA sequencing. Nature 2008. 452:872-76.

6-8 P Carninci, et al. Noncoding RNA transcription beyond annotated genes. Current Opinion in Genetics and Development 2007. 17:139-44.

6-9 J Cheng, et al. Transcriptional Maps of 10 human chromosomes at 5-nucleotide resolution. Science 2005. 308:1149-54.

6-10 P Kapranov, et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 2007. 316:1484-88.

6-11 The ENCODE Project Consortium. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007. 447:799-816.

6-12 Mardis ER. Next-generation DNA sequencing methods. (2008) Ann Rev. Gen. Hum. Gen. 9, 387-402

6-13 Ansorge WJ. Next-generation DNA sequencing techniques. (2009) New Biotech. 25, 195-203

6-14 Snyder, Du, Gerstein. Personal genome sequencing: current approaches and challenges. (2010) Genes Dev. 24, 423-431

6-15 Nagalakshmi, waern, Snyder. RNA-Seq: a method for comprehensive transcriptome analysis. (2010) Curr. Prot. Mol. biol. 4.11.1-13

6-16 Blencowe Lee. Current-generation high-throughput sequencing: deepening insights into mammalian transcriptomes. (2009) Genes Dev. 23, 1379-1386

6-17 van der Brug. Deep sequencing of coding and non-coding RNA in the CNS. Cookson (10) Brain Res. 1338, 146-154

Additional Topics covered in previous years

Topic 8: Investigating Gene Function:

8-1 M. Lewandoski. Conditional control of gene expression in the mouse. Nature Reviews Genetics 2002. 2:743-55.

8-2 A. Perkins. Functionaql genomics in the mouse. Functional & Integrative Genomics 2002. 2:81-91.

8-3 J. Rossant & A. Spence. Chimeras and mosiacs in mouse mutant analysis. Trends in Genetics 1998. 14(9).

8-4 C-T. Chien, et. al. The two-hybrid system: A method to identify and clone genes for proteins that interact with a protein of interest. PNAS USA 1991. 88:9578-82.

8-5 M. Vidal & H. Endoh. Prospects for drug screening using the reverse two-hybrid system. Trends in Biotechnology 1999. 17:374-81.

8-6 D. SenGupta, et. al. A three-hybrid system to detect RNA-protein interactions in vitro. PNAS USA 1996. 93:8496-501.

Topic 9: Studying Protein Function:

9-1 F. Tanious et al. Biosensor-surface plasmon resonance methods for quantitative analysis of biomolecular interactions. Methods in Cell Biology 2008. 84: 53-77.

9-2 Structural Genomics Consortium. Protein Production and Purification. Nature Methods 2008. 5: 135-45.

9-3 F. Katzen et al. The past, present and future of cell-free protein synthesis. Trends in Biotechnology 2005. 23: 150-6.

9-4 D. Shin, et. al. Combinatorial Solid Phase Peptide Synthesis and Bioassays. Biochem. and Mol. Bio. 2005. 38: 517-25.

9-5 V. Muralidharan et al. Protein Ligation: an Enabling Technology for the Biophysical Analysis of Proteins. Nature Methods 2006. 3: 429-38.

9-6 M. Xu et al. Recent Advances in Protein Splicing: Manipulating Proteins in vitro and in vivo. Curr. Opin. Biotechnol. 2005. 16: 440-6.

Topic 10: Proteomics

10-1 R Aebersold & M Mann. Mass spectrometry-based proteomics. Nature 2003. 422:198-207.

10-2 H Zhu et al. Proteomics. Annual Reviews Biochemistry 2003. 72:783-812.

10-3 S Charbonnier et al. The social network of a cell: Recent advance in interactome mapping. Biotechnology Annual Reviews 2008. 14:1-28.

10-4 W Yang et al. Proteomic approaches to the analysis of multiprotein signaling complexes. Proteomics 2008. 8:832-851.

10-5 B Boeckmann et al. Protein variety and functional diversity: Swiss-Prot annotation in its biological context. C.R. Biologies 2005. 328:882-99.

Topic 11: SNPs, HAPLOTYPES, DISEASE, & EVOLUTION

11-1 P Sabeti et al. Genome-wide detection and characterization of positive selection in human populations. Nature 2007. 449:913-18.

11-2 T Manolio et al. A HapMap harvest of insights into the genetics of common disease. The Journal of Clinical Investigation 2008. 5:1590-1604.

11-3 The International HapMap Consortium. A haplotype map of the human genome. Nature 2005. 437:1299-1320.