Friday, 11:00 AM - 12:00 PM
110 Barker Hall
NOTE: The first course meeting will be Friday, September 7. Professor Alber will email the paper to enrolled students.
| Week | Date | Instructor | Method | Assigned Paper |
|---|---|---|---|---|
| 2 | Sept 7 | Alber | DNA polymerase editing mechanism | Hsu GW, Ober M, Carell T, Beese LS (2004) Error-prone replication of oxidatively damaged DNA by a high-fidelity DNA polymerase. Nature 431: 217-221. Supplementary Figure 1 Supplementary Figure 2 Supplementary Figure 3 Supplementary Figure 4 Supplementary Figure Legends |
| 3 | Sept 14 | Alber | Genome sequencing | Mwangi MM, Wu SW, Zhou Y, Sieradzki K, de Lencastre H, Richardson P, Bruce D, Rubin E, Myers E, Siggia ED, Tomasz A (2007). Tracking the in vivo evolution of multidrug resistance in Staphylococcus aureus by whole-genome sequencing.
Proc Natl Acad Sci USA 104: 9451-6. Background: Shendure J, Mitra RD, Varma C, Church GM 2004. Advanced sequencing technologies: methods and goals. Nat Rev Genet 5: 335-44. |
| 4 | Sept 21 | Alber | Computational analysis of genome sequences | Stedman HH, Kozyak BW, Nelson A, Thesier DM, Su LT, Low DW, Bridges CR, Shrager JB, Minugh-Purvis N, Mitchell MA (2004) Myosin gene mutation correlates with anatomical changes in the human lineage. Nature 428: 415-418. |
| 5 | Sept 28 | Alber | Gene finding and linkage | Lamason R.L., et al. (2005). SLC24A5, a putative cation exchanger, affects pigmentation in zebrafish and humans.
Science 310, 1782-6. |
| Week | Date | Instructor | Method | Assigned Paper |
|---|---|---|---|---|
| 6 | Oct 5 | Zhou | DNA microarrays | Iyer VR, Eisen MB, Ross T, Schuler G, et al. (1999) The transcriptional program in the response of human fibroblasts to serum. Science 283: 83-87. |
| 7 | Oct 12 | Zhou | RNA interference | Zamore PD, Tuschl T, Sharp PA, Bartel DP (2000) RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell 101: 25-33. |
| 8 | Oct 19 | Zhou | Nucleic acid modification and retroviral infection | Harris RS, Bishop KN, Sheehy AM, Craig HM, Petersen-Mahrt SK, Watt IN, Neuberger MS, Malim MH (2003) DNA deamination mediates innate immunity to retroviral infection. Cell 113: 803-809. [Erratum Cell 116: 629 (2004] |
| 9 | Oct 26 | Zhou | DNA footprinting and ChIP analysis | Espinosa JM, Emerson BM (2001) Transcriptional regulation by p53 through intrinsic DNA/chromatin binding and site-directed cofactor recruitment. Mol. Cell 8: 57-69. |
| Week | Date | Instructor | Method | Assigned Paper |
|---|---|---|---|---|
| 10 | Nov 2 | Nogales | Gel electrophoresis and its applications | Brewer BJ, Fangman W (1987) The localization of replication origins on ARS plasmids in S. cerevisiae. Cell 51: 463-471. |
| 11 | Nov 9 | Nogales | Methods for analyzing protein-nucleic acid interactions | Velankar SS, Soultanas P, Dillingham MS, Subramanya HS, Wigley DB (1999) Crystal structures of complexes of PcrA DNA helicase with a DNA substrate indicate an inchworm mechanism. Cell 97: 75-84. |
| 12 | Nov 16 | Nogales | Single-molecule methods | Spies M, Bianco PR, Dillingham MS, Handa N, Baskin RJ, Kowalczykowski SC (2003) A molecular throttle: the recombination hotspot chi controls DNA translocation by the RecBCD helicase. Cell 114: 647-654. |
| 13 | Nov 23 | Thanksgiving Holiday | ||
| 14 | Nov 30 | Nogales | Biological applications of electron microscopy | Halic M, Becker T, Pool MR, Spahn CM,Grassucci RA, Frank J, Beckmann R (2004) Structure of the signal recognition particle interacting with the elongation-arrested ribosome. Nature 427: 808-814. |