CANB 610:Materials

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*Base excision repair and lesion-dependent subpathways for repair of oxidative DNA damage. http://www.ncbi.nlm.nih.gov/pubmed/20649466
*Base excision repair and lesion-dependent subpathways for repair of oxidative DNA damage. http://www.ncbi.nlm.nih.gov/pubmed/20649466
*Does evening sun increase the risk of skin cancer? http://www.ncbi.nlm.nih.gov/pubmed/22084098
*Does evening sun increase the risk of skin cancer? http://www.ncbi.nlm.nih.gov/pubmed/22084098
 +
*Circadian clock control of the cellular response to DNA damage http://www.ncbi.nlm.nih.gov/pubmed/20227409
==Week 8: TBA==
==Week 8: TBA==

Revision as of 22:47, 2 February 2012

CANB 610 Advanced Topics in Cancer Biology

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    • IN PROGRESS**

Contents

Class Focus, Winter 2012

  1. Organization Meeting and Rules of Engagement
  2. Genomics and Cancer
  3. Genomic instability and Cancer
  4. Drug Discovery

Organizational Meeting: Introduction and Scheduling

Presentation Zen

  1. Slide Zen
  2. Delivery Zen
  3. Feel free to add links that help you

Evaluation Forms

Week 1: Tumor Sequencing, part 1

Papers

  1. Guo G, Gui Y, Gao S, Tang A, Hu X, Huang Y, Jia W, Li Z, He M, Sun L, Song P, Sun X, Zhao X, Yang S, Liang C, Wan S, Zhou F, Chen C, Zhu J, Li X, Jian M, Zhou L, Ye R, Huang P, Chen J, Jiang T, Liu X, Wang Y, Zou J, Jiang Z, Wu R, Wu S, Fan F, Zhang Z, Liu L, Yang R, Liu X, Wu H, Yin W, Zhao X, Liu Y, Peng H, Jiang B, Feng Q, Li C, Xie J, Lu J, Kristiansen K, Li Y, Zhang X, Li S, Wang J, Yang H, Cai Z, and Wang J. . pmid:22138691. PubMed HubMed [Guo]

Bonus Materials

and then a bit of a leap:

Lecture Slides

Week 2: Tumor Sequencing, part 2

Papers

  1. Navin N, Kendall J, Troge J, Andrews P, Rodgers L, McIndoo J, Cook K, Stepansky A, Levy D, Esposito D, Muthuswamy L, Krasnitz A, McCombie WR, Hicks J, and Wigler M. . pmid:21399628. PubMed HubMed [Navin]

Bonus Materials

Lecture slides

Week 3: RNA sequencing

Papers

  1. Li M, Wang IX, Li Y, Bruzel A, Richards AL, Toung JM, and Cheung VG. . pmid:21596952. PubMed HubMed [Li-2011]
  2. Paz N, Levanon EY, Amariglio N, Heimberger AB, Ram Z, Constantini S, Barbash ZS, Adamsky K, Safran M, Hirschberg A, Krupsky M, Ben-Dov I, Cazacu S, Mikkelsen T, Brodie C, Eisenberg E, and Rechavi G. . pmid:17908822. PubMed HubMed [RNA_Editing_in_cancer]
  3. Langmead B, Trapnell C, Pop M, and Salzberg SL. . pmid:19261174. PubMed HubMed [bowtie]
  4. Trapnell C, Pachter L, and Salzberg SL. . pmid:19289445. PubMed HubMed [tophat]
All Medline abstracts: PubMed HubMed

Bonus Materials

  1. Very Few RNA and DNA Sequence Differences in the Human Transcriptome http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0025842 [Schrider-2011]
  2. Post on Paralogs and Splice Junctions http://www.genomesunzipped.org/2011/05/notes-on-the-evidence-for-extensive-rna-editing-in-humans.php [GenomesUnzipped]
  3. nice pictures for presentations http://www.sciencephoto.com/search?subtype=keywords&searchstring=transcription&oldsearchstring=ribosome&matchtype=&sort_results=&media_type=images&license=all&channel=all&Search.x=0&Search.y=0 [Science_Photo_Library]

Week 4: Functional Genomics

Papers

  1. Possemato R, Marks KM, Shaul YD, Pacold ME, Kim D, Birsoy K, Sethumadhavan S, Woo HK, Jang HG, Jha AK, Chen WW, Barrett FG, Stransky N, Tsun ZY, Cowley GS, Barretina J, Kalaany NY, Hsu PP, Ottina K, Chan AM, Yuan B, Garraway LA, Root DE, Mino-Kenudson M, Brachtel EF, Driggers EM, and Sabatini DM. . pmid:21760589. PubMed HubMed [possemato-2011]
  2. Premsrirut PK, Dow LE, Kim SY, Camiolo M, Malone CD, Miething C, Scuoppo C, Zuber J, Dickins RA, Kogan SC, Shroyer KR, Sordella R, Hannon GJ, and Lowe SW. . pmid:21458673. PubMed HubMed [background]
All Medline abstracts: PubMed HubMed

http://www.nature.com/nrc/journal/v11/n9/full/nrc3128.html Jones, R. G. & Thompson, C. B. Tumor suppressors and cell metabolism: a recipe for cancer growth.Genes Dev. 23, 537–548 (2009)

Bonus Materials

Lecture slides

Week 5: TBA

Papers

Bonus Materials

Lecture slides

Week 6: Chromothripsis

Papers

  1. Stephens PJ, Greenman CD, Fu B, Yang F, Bignell GR, Mudie LJ, Pleasance ED, Lau KW, Beare D, Stebbings LA, McLaren S, Lin ML, McBride DJ, Varela I, Nik-Zainal S, Leroy C, Jia M, Menzies A, Butler AP, Teague JW, Quail MA, Burton J, Swerdlow H, Carter NP, Morsberger LA, Iacobuzio-Donahue C, Follows GA, Green AR, Flanagan AM, Stratton MR, Futreal PA, and Campbell PJ. . pmid:21215367. PubMed HubMed [Stephens-2011]

Bonus Materials

link to Cell podcast by the author

Lecture Slides

Week 7: Circadian

Papers

Bonus Materials

Week 8: TBA

Papers

  1. = [pmid]

Bonus Materials

Week 9: TBA

Papers

  1. = [pmid]

Bonus Materials

Week 10: TBA

Papers

  1. = [pmid]

Bonus Materials

Week 11: TBA

Papers

  1. = [pmid]

Bonus Materials

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