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>
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===Lecture Slides===
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*[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===
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[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]
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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]
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==Week 5: TBA==
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==Week 5: No Class==
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===Papers===
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==General Background for Genomic Instability and Cancer==
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===Bonus Materials===
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*The DNA damage response and cancer therapy http://www.ncbi.nlm.nih.gov/pubmed/22258607
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*Defining 'chromosomal instability'. http://www.ncbi.nlm.nih.gov/pubmed/18192061
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===Lecture slides===
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==Week 6: Chromothripsis==
==Week 6: Chromothripsis==
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*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===
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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
 
*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/22252116
*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
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*The genetics of mammalian circadian order and disorder: implications for physiology and disease http://www.ncbi.nlm.nih.gov/pubmed/18802415
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*The genetics of mammalian circadian order and disorder: implications for physiology and disease http://www.ncbi.nlm.nih.gov/pubmed/18802415<br>
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*Circadian timing in cancer treatment http://www.ncbi.nlm.nih.gov/pubmed/20055686
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===Presentations===
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*[http://openwetware.org/images/1/10/Control_of_skin_cancer_by_the_circadian_rhythm.pptx Introduction:Control of skin cancer by the circadian rhythm]
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*[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: Inflammation and cancer==
==Week 8: Inflammation and cancer==
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*DNA damage induced by chronic inflammation contributes to colon carcinogenesis in mice. http://www.ncbi.nlm.nih.gov/pubmed/18521188
*DNA damage induced by chronic inflammation contributes to colon carcinogenesis in mice. http://www.ncbi.nlm.nih.gov/pubmed/18521188
===Bonus Materials===
===Bonus 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
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*Intestinal Inflammation and Cancer http://www.ncbi.nlm.nih.gov/pubmed/21530747
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===Lecture Slides===
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*[http://openwetware.org/images/d/de/Inflammation_and_Cancer_background.pdf Background: Inflammation and Cancer]
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==Week 9: TBA==
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==Week 9: Drug Development part 1 GIST==
===Papers===
===Papers===
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<biblio>
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*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
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# pmid=
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</biblio>
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===Bonus Materials===
===Bonus Materials===
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; See supplemental materials including excel spreadsheets and movies that accompany the main paper
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*Cancer: Oncogenes in context. http://www.nature.com/nature/journal/v467/n7317/full/467796a.html
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===Lecture Slides===
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*[http://openwetware.org/images/4/4c/ETV1_and_GIST_intro.pptx Introduction: GI Stromal Tumors and ETV1]
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*[http://openwetware.org/images/a/a4/GIST-_3-8-2012%281%29.pptx Results: GIST and ETV1]
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==Week 10: TBA==
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==Week 10: No Class==
===Papers===
===Papers===
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<biblio>
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# pmid=
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</biblio>
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===Bonus Materials===
===Bonus Materials===
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==Week 11: TBA==
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==Week 11: Drug Development part 2==
===Papers===
===Papers===
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<biblio>
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*The secret ally: immunostimulation by anticancer drugs. http://www.ncbi.nlm.nih.gov/pubmed/22301798
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# pmid=
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</biblio>
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===Bonus Materials===
===Bonus Materials===

Current revision

CANB 610 Advanced Topics in Cancer Biology

Home        People        Materials        Schedule        Help        Discussion       

    • 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

Error fetching PMID 22138691:
  1. Error fetching PMID 22138691: [Guo]

Bonus Materials

and then a bit of a leap:

Lecture Slides

Week 2: Tumor Sequencing, part 2

Papers

Error fetching PMID 21399628:
  1. Error fetching PMID 21399628: [Navin]

Bonus Materials

Lecture slides

Week 3: RNA sequencing

Papers

Error fetching PMID 21596952:
Error fetching PMID 17908822:
Error fetching PMID 19261174:
Error fetching PMID 19289445:
Error fetching PMID 20436464:
  1. Error fetching PMID 21596952: [Li-2011]
  2. Error fetching PMID 17908822: [RNA_Editing_in_cancer]
  3. Error fetching PMID 19261174: [bowtie]
  4. Error fetching PMID 19289445: [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

Error fetching PMID 21760589:
Error fetching PMID 21458673:
  1. Error fetching PMID 21760589: [possemato-2011]
  2. Error fetching PMID 21458673: [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

Error fetching PMID 21215367:
  1. Error fetching PMID 21215367: [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

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