<br> Paper Reading Class 2009 Fall Term

<br> Suggested Reading list


<br> Wet-lab: More biochemistry

<br> 1. Janet Jansson, et al. (2009) Metabolomics reveals metabolic biomarkers of Crohn's disease. PLoS One 2009, 28;4(7):e6386

<br> 2. J. Sterlling, et al. (2004) Robustness of cellular functions. Cell 2004, 118:675-685.

<br> 3. Samir M. Hanas et al. (2008) Mining the plasma proteome for cancer biomarkers. Nature 2008, 452, 571-579

<br> 4. Jeremy K. Nicholson, et al. (2008) Systems biology: Metabonomics. Nature 2008, 455, 1054-1056

<br> 5. Paula D. Bos, et al. Genes that mediate breast cancer metastasis to the brain. Nature 2009, 459(7249):1005-9.

<br> 6. Kim JI, et al. (2009) A highly annotated whole-genome sequence of a Korean individual. Nature 2009, 20;460(7258):1011-5

<br> 7. He L and Hannon GJ (2004) MicroRNAs: small RNAs with a big role in gene regulation. Nature Reviews Genetics 5, 522-531.


<br> System biology: wet and dry

<br> 1. Beisel, C. L., T. S. Bayer, et al. (2008). "Model-guided design of ligand- regulated RNAi for programmable control of gene expression."

           Mol Syst Biol 4: 224.

<br> 2. Brynildsen, M. P. and J. C. Liao (2009). "An integrated network approach identifies the isobutanol response network of

           Escherichia coli." Mol Syst Biol 5: 277.

<br> 3. Gal-Yam, E. N., G. Egger, et al. (2008). "Frequent switching of Polycomb repressive marks and DNA hypermethylation in the

           PC3 prostate cancer cell line." Proc Natl Acad Sci U S A 105(35): 12979-84.

<br> 4. Hood, L., J. R. Heath, et al. (2004). "Systems biology and new technologies enable predictive and preventative medicine."

           Science 306(5696): 640-3.

<br> 5. Jothi, R., S. Balaji, et al. (2009). "Genomic analysis reveals a tight link between transcription factor dynamics and regulatory

           network architecture." Mol Syst Biol 5: 294.

<br> 6. Kim, P. M., A. Sboner, et al. (2008). "The role of disorder in interaction networks: a structural analysis." Mol Syst Biol 4: 179.

<br> 7. Lamb, J., E. D. Crawford, et al. (2006). "The Connectivity Map: using gene- expression signatures to connect small molecules,

           genes,and disease." Science 313(5795): 1929-35.

<br> 8. Nguyen, D. H. and P. D'Haeseleer (2006). "Deciphering principles of transcription regulation in eukaryotic genomes."

           Mol Syst Biol 2: 2006 0012.

<br> 9. Reuter, J. A., S. Ortiz-Urda, et al. (2009). "Modeling inducible human tissue neoplasia identifies an extracellular matrix interaction

           network involved in cancer progression." Cancer Cell 15(6): 477-88.

<br> 10. Skotheim, J. M., S. Di Talia, et al. (2008). "Positive feedback of G1 cyclins ensures coherent cell cycle entry." Nature 454: 291-296.

<br> 11. Yanai, I., L. R. Baugh, et al. (2008). "Pairing of competitive and topologically distinct regulatory modules enhances patterned

           gene expression." Mol Syst Biol 4: 163.

<br> 12. Lage, K, Hansen NT, et al. (2008) A large-scale analysis of tissue-specific pathology and gene expression of human disease

           genes and complexes. Proc Natl Acad Sci USA 105:20870-20875.

<br> 13. Lehner B & Fraser AG. (2004)  A first-draft human protein-interaction map. Gen Biology 5:R93 pp1-9

<br> 14. Goh KI et al. (2007) The human disease network. PNAS 104:8685-8690.