Difference between revisions of "CANB 610:Materials"

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#Science_Photo_Library 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 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
 
</biblio>
 
</biblio>
 +
===Lecture Slides===
 +
*[http://openwetware.org/images/6/6a/Widespread_RNA_and_DNA.pptx Widespread RNA and DNA differences]
  
 
==Week 4: Functional Genomics==
 
==Week 4: Functional Genomics==
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===Lecture slides===
 
===Lecture slides===
 +
[http://openwetware.org/images/a/aa/Tim_Butler_Intro-Functional_genomics_reveal_that_the_serine_synthesis.pptx Introduction: Cancer Metabolism, Functional Genomics, and Breast Cancer]
 +
<br>
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[http://openwetware.org/images/3/32/FunctionalGenomics_SerinePathway_BreastCancer.pdf Results: Functional Genomics Reveal that the Serine Synthesis Pathway is Essential in Breast Cancer]
  
==Week 5: TBA==
+
==Week 5: No Class==
===Papers===
+
==General Background for Genomic Instability and Cancer==
===Bonus Materials===
+
*The DNA damage response and cancer therapy http://www.ncbi.nlm.nih.gov/pubmed/22258607
 
+
*Defining 'chromosomal instability'. http://www.ncbi.nlm.nih.gov/pubmed/18192061
===Lecture slides===
 
  
 
==Week 6: Chromothripsis==
 
==Week 6: Chromothripsis==
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===Lecture Slides===
 
===Lecture Slides===
  
==Week 7: Circadian ==
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==Week 7: Circadian rhythm and cancer ==
 
===Papers===
 
===Papers===
 
*Control of skin cancer by the circadian rhythm http://www.ncbi.nlm.nih.gov/pubmed/22025708
 
*Control of skin cancer by the circadian rhythm http://www.ncbi.nlm.nih.gov/pubmed/22025708
 
===Bonus Materials===
 
===Bonus Materials===
*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
 
*Circadian clock control of the cellular response to DNA damage http://www.ncbi.nlm.nih.gov/pubmed/20227409
*Circadian rhythms and tumor growth http://www.ncbi.nlm.nih.gov/pubmed/20227409
+
*Circadian rhythms and tumor growth http://www.ncbi.nlm.nih.gov/pubmed/22252116
 
*Circadian Integration of Metabolism and Energetics http://www.ncbi.nlm.nih.gov/pubmed/21127246
 
*Circadian Integration of Metabolism and Energetics http://www.ncbi.nlm.nih.gov/pubmed/21127246
*The genetics of mammalian circadian order and disorder: implications for physiology and disease http://www.ncbi.nlm.nih.gov/pubmed/18802415
+
*The genetics of mammalian circadian order and disorder: implications for physiology and disease http://www.ncbi.nlm.nih.gov/pubmed/18802415<br>
 +
*Circadian timing in cancer treatment http://www.ncbi.nlm.nih.gov/pubmed/20055686
 +
 
 +
===Presentations===
 +
*[http://openwetware.org/images/1/10/Control_of_skin_cancer_by_the_circadian_rhythm.pptx Introduction:Control of skin cancer by the circadian rhythm]
 +
*[http://openwetware.org/images/b/b7/Tim_Butler_-_Control_of_skin_cancer_by_the_circadian_rhythm.pptx Results: Control of skin cancer by the circadian rhythm]
  
==Week 8: TBA==
+
==Week 8: Inflammation and cancer==
 
===Papers===
 
===Papers===
<biblio>
+
*The Mutyh Base Excision Repair Gene Influences the Inflammatory Response in a Mouse Model of Ulcerative Colitis http://www.ncbi.nlm.nih.gov/pubmed/20706593
# pmid=
+
*DNA damage induced by chronic inflammation contributes to colon carcinogenesis in mice. http://www.ncbi.nlm.nih.gov/pubmed/18521188
</biblio>
 
 
===Bonus Materials===
 
===Bonus Materials===
 +
*Base Excision Repair and Lesion-Dependent Subpathways for Repair of Oxidative DNA Damage http://www.ncbi.nlm.nih.gov/pubmed/20649466
 +
*Intestinal Inflammation and Cancer http://www.ncbi.nlm.nih.gov/pubmed/21530747
 +
===Lecture Slides===
 +
*[http://openwetware.org/images/d/de/Inflammation_and_Cancer_background.pdf Background: Inflammation and Cancer]
  
==Week 9: TBA==
+
==Week 9: Drug Development part 1 GIST==
 
===Papers===
 
===Papers===
<biblio>
+
*ETV1 is a lineage survival factor that cooperates with KIT in gastrointestinal stromal tumours http://www.nature.com/nature/journal/v467/n7317/full/nature09409.html
# pmid=
+
 
</biblio>
 
 
===Bonus Materials===
 
===Bonus Materials===
 +
; See supplemental materials including excel spreadsheets and movies that accompany the main paper
 +
*Cancer: Oncogenes in context. http://www.nature.com/nature/journal/v467/n7317/full/467796a.html
  
 +
===Lecture Slides===
 +
*[http://openwetware.org/images/4/4c/ETV1_and_GIST_intro.pptx Introduction: GI Stromal Tumors and ETV1]
 +
*[http://openwetware.org/images/a/a4/GIST-_3-8-2012%281%29.pptx Results: GIST and ETV1]
  
==Week 10: TBA==
+
==Week 10: No Class==
 
===Papers===
 
===Papers===
<biblio>
+
 
# pmid=
 
</biblio>
 
 
===Bonus Materials===
 
===Bonus Materials===
  
==Week 11: TBA==
+
==Week 11: Drug Development part 2==
 
===Papers===
 
===Papers===
<biblio>
+
*The secret ally: immunostimulation by anticancer drugs. http://www.ncbi.nlm.nih.gov/pubmed/22301798
# pmid=
+
 
</biblio>
 
 
===Bonus Materials===
 
===Bonus Materials===

Latest revision as of 15:31, 4 April 2012

CANB 610 Advanced Topics in Cancer Biology

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Home        People        Materials        Schedule        Help        Discussion       

    • IN PROGRESS**

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. Frequent mutations of genes encoding ubiquitin-mediated proteolysis pathway components in clear cell renal cell carcinoma. Nat Genet. 2011 Dec 4;44(1):17-9. DOI:10.1038/ng.1014 | PubMed ID:22138691 | 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. Tumour evolution inferred by single-cell sequencing. Nature. 2011 Apr 7;472(7341):90-4. DOI:10.1038/nature09807 | PubMed ID:21399628 | 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. Widespread RNA and DNA sequence differences in the human transcriptome. Science. 2011 Jul 1;333(6038):53-8. DOI:10.1126/science.1207018 | PubMed ID:21596952 | 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. Altered adenosine-to-inosine RNA editing in human cancer. Genome Res. 2007 Nov;17(11):1586-95. DOI:10.1101/gr.6493107 | PubMed ID:17908822 | HubMed [RNA_Editing_in_cancer]
  3. Langmead B, Trapnell C, Pop M, and Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10(3):R25. DOI:10.1186/gb-2009-10-3-r25 | PubMed ID:19261174 | HubMed [bowtie]
  4. Trapnell C, Pachter L, and Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009 May 1;25(9):1105-11. DOI:10.1093/bioinformatics/btp120 | PubMed ID:19289445 | 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]

Lecture Slides

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. Functional genomics reveal that the serine synthesis pathway is essential in breast cancer. Nature. 2011 Aug 18;476(7360):346-50. DOI:10.1038/nature10350 | PubMed ID:21760589 | 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. A rapid and scalable system for studying gene function in mice using conditional RNA interference. Cell. 2011 Apr 1;145(1):145-58. DOI:10.1016/j.cell.2011.03.012 | PubMed ID:21458673 | 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

Introduction: Cancer Metabolism, Functional Genomics, and Breast Cancer
Results: Functional Genomics Reveal that the Serine Synthesis Pathway is Essential in Breast Cancer

Week 5: No Class

General Background for Genomic Instability and Cancer

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. Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell. 2011 Jan 7;144(1):27-40. DOI:10.1016/j.cell.2010.11.055 | PubMed ID:21215367 | HubMed [Stephens-2011]

Bonus Materials

link to Cell podcast by the author

Lecture Slides

Week 7: Circadian rhythm and cancer

Papers

Bonus Materials

Presentations

Week 8: Inflammation and cancer

Papers

Bonus Materials

Lecture Slides

Week 9: Drug Development part 1 GIST

Papers

Bonus Materials

See supplemental materials including excel spreadsheets and movies that accompany the main paper

Lecture Slides

Week 10: No Class

Papers

Bonus Materials

Week 11: Drug Development part 2

Papers

Bonus Materials