Paper Reading Class 2010 Spring Term

Suggested Reading list



1.         Metzker, M.L., Sequencing technologies - the next generation. Nat Rev Genet, 2010. 11(1): p. 31-46. (PDF) (HTML)

2.         Ozsolak, F., et al., Direct RNA sequencing. Nature, 2009. 461(7265): p. 814-8. (PDF) (HTML)


3.         Taylor, B.S., et al., Functional copy-number alterations in cancer. PLoS One, 2008. 3(9): p. e3179. (PDF) (HTML)

4.         Walther, A., et al., Genetic prognostic and predictive markers in colorectal cancer. Nat Rev Cancer, 2009. 9(7): p. 489-99. (PDF) (HTML)

5.         Dahan, L., et al., Modulation of cellular redox state underlies antagonism between oxaliplatin and cetuximab in human colorectal cancer cell lines. Br J Pharmacol, 2009. 158(2): p. 610-20. (PDF) (HTML)

6.         Bignell, G.R., et al., Signatures of mutation and selection in the cancer genome. Nature, 2010. 463(7283): p. 893-8. (PDF) (HTML)

7.         Pece, S., et al., Biological and molecular heterogeneity of breast cancers correlates with their cancer stem cell content. Cell. 140(1): p. 62-73. (PDF) (HTML)

8.         Yeang, C.H., F. McCormick, and A. Levine, Combinatorial patterns of somatic gene mutations in cancer. Faseb J, 2008. 22(8): p. 2605-22. (PDF) (HTML)

Development, evolution, immunology, and epigenetics

9.         Christodoulou, F., et al., Ancient animal microRNAs and the evolution of tissue identity. Nature, 2010. 463(7284): p. 1084-8. (PDF) (HTML)

10.       Zhou, R., et al., Thioredoxin-interacting protein links oxidative stress to inflammasome activation. Nat Immunol, 2009. 11(2): p. 136-40. (PDF) (HTML)

11.       Marques-Bonet, T., et al., A burst of segmental duplications in the genome of the African great ape ancestor. Nature, 2009. 457(7231): p. 877-881. (PDF) (HTML)

12.       Hittinger, C.T. and S.B. Carroll, Gene duplication and the adaptive evolution of a classic genetic switch. Nature, 2007. 449(7163): p. 677-681. (PDF) (HTML)

13.      Levenson, J.M. and J.D. Sweatt, Epigenetic mechanisms in memory formation. Nat Rev Neurosci, 2005. 6(2): p. 108-18. (PDF) (HTML)

Systems biology

14.       Olsen, S.K., et al., Active site remodelling accompanies thioester bond formation in the SUMO E1. Nature, 2009. 463(7283): p. 906-12. (PDF) (HTML)

15.       Nicholson, J.K. and J.C. Lindon, Systems biology: Metabonomics. Nature, 2008. 455(7216): p. 1054-6. (PDF) (HTML)

16.       Beisel, C.L., et al., Model-guided design of ligand-regulated RNAi for programmable control of gene expression. Mol Syst Biol, 2008. 4: p. 224. (PDF) (HTML)

17.       Brynildsen, M.P. and J.C. Liao, An integrated network approach identifies the isobutanol response network of Escherichia coli. Mol Syst Biol, 2009. 5: p. 277. (PDF) (HTML)

18.       Jothi, R., et al., Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture. Mol Syst Biol, 2009. 5: p. 294. (PDF) (HTML)

19.       Nguyen, D.H. and P. D'Haeseleer, Deciphering principles of transcription regulation in eukaryotic genomes. Mol Syst Biol, 2006. 2: p. 2006 0012. (PDF) (HTML)

20.       Skotheim, J.M., et al., Positive feedback of G1 cyclins ensures coherent cell cycle entry. Nature, 2008. 454(7202): p. 291-6. (PDF) (HTML)

21.       Lage, K., et al., A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes. Proc Natl Acad Sci U S A, 2008. 105(52): p. 20870-5. (PDF) (HTML)

22.       Segal, E., et al., A genomic code for nucleosome positioning. Nature, 2006. 442(7104): p. 772-8. (PDF) (HTML)

23.       Ishii, N., et al., Multiple high-throughput analyses monitor the response of E. coli to perturbations. Science, 2007. 316(5824): p. 593-7. (PDF) (HTML)


24.       Schlitt, T. and A. Brazma, Current approaches to gene regulatory network modelling. BMC Bioinformatics, 2007. 8(Suppl 6): p. S9. (PDF) (HTML)

25.       Friedman, R. and A.L. Hughes, Gene duplication and the structure of eukaryotic genomes. Genome Res, 2001. 11(3): p. 373-81. (PDF) (HTML)

26.       Alon, U., Network motifs: theory and experimental approaches. Nat Rev Genet, 2007. 8(6): p. 450-61. (PDF) (HTML)

27.       Ideker, T., et al., Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science, 2001. 292(5518): p. 929-34. (PDF) (HTML)

28.       Buchler, N.E., U. Gerland, and T. Hwa, On schemes of combinatorial transcription logic. Proc Natl Acad Sci U S A, 2003. 100(9): p. 5136-41. (PDF) (HTML)

Newly Added

29.       Michael Costanzo, et al., The Genetic Landscape of a Cell. Science, 2010. 327(5964): p. 425-31. (PDF) (HTML)

30.       Masato Kanemaki, Alberto Sanchez-Diaz, Agnieszka Gambus & Karim Labib, Functional proteomic identification of DNA replication proteins by induced proteolysis in vivo. Nature, 2003. 423: p. 720-5. (PDF) (HTML)

31.       Alexander Marson, et al., Connecting microRNA Genes to the Core Transcriptional Regulatory Circuitry of Embryonic Stem Cells. Cell, 2008. 134(3): p. 521-33. (PDF) (HTML)