CANB 610:Materials

From OpenWetWare

(Difference between revisions)
Jump to: navigation, search
(Bonus Materials)
Current revision (19:31, 4 April 2012) (view source)
(Lecture Slides)
 
(36 intermediate revisions not shown.)
Line 76: Line 76:
#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==
Line 88: Line 90:
===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>
 +
[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==
Line 105: Line 109:
===Lecture Slides===
===Lecture Slides===
-
==Week 7: Circadian ==
+
==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/22252116
 +
*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<br>
 +
*Circadian timing in cancer treatment http://www.ncbi.nlm.nih.gov/pubmed/20055686
-
==Week 8: TBA==
+
===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: 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===

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

  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]

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. . 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

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. . pmid:21215367. PubMed 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

Personal tools