Last updated: 09/24/11 11:47

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  




Pulsed-field gel electrophoresis genomics/method/pulse_field.html

Non-isotopic nucleic acid detection

Indirect labeling (ABC method)





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


Protocol online

PCR papers

Long PCR

Real-time PCR

Gateway cloning

TOPO cloning  

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


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.



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.