CANB 610:Materials: Difference between revisions

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{{Template:CANB_610_Advanced_Topics_in_Cancer_Biology}}
{{Template:CANB_610_Advanced_Topics_in_Cancer_Biology}}
**IN PROGRESS**


==Class Focus, Winter 2012==
==Class Focus, Winter 2012==
Line 25: Line 26:


===Bonus Materials===
===Bonus Materials===
*Kidney cancer http://www.ncbi.nlm.nih.gov/pubmed/20368728
*Mutations in cancer http://www.ncbi.nlm.nih.gov/pubmed/17932254
*Hallmarks of cancer http://www.ncbi.nlm.nih.gov/pubmed/21376230
*Sequencing technologies http://www.ncbi.nlm.nih.gov/pubmed/20847746
and then a bit of a leap:
*Application to clinic http://www.ncbi.nlm.nih.gov/pubmed/22133722


===Lecture Slides===
===Lecture Slides===
 
*[http://lifetech-it.hosted.jivesoftware.com/videos/1016 ion torrent video]
*[[Image:Frequent_mutations_of_genes_encoding_ubiquitin-mediated_proteolysis_pathway.pptx]]
*[http://www.youtube.com/watch?v=GLwCs370IGI Lectures on genomics] 13 week Series on Genomics 2012 on YouTube
*[http://cancergenome.nih.gov/newsevents/multimedialibrary/videos/spectralawrence Spectra of Somatic Mutations] Michael Lawrence lecture from 2011 TCGA conference on somatic mutation heterogeneity


==Week 2: Tumor Sequencing, part 2==
==Week 2: Tumor Sequencing, part 2==
Line 34: Line 46:
Navin pmid=21399628
Navin pmid=21399628
</biblio>
</biblio>
===Bonus Materials===
===Bonus Materials===
*Previous work from Wigler on progression http://www.ncbi.nlm.nih.gov/pubmed/19903760
*Old work on heterogeneity http://www.ncbi.nlm.nih.gov/pubmed/9108466
*Evolution by serial sampling http://www.ncbi.nlm.nih.gov/pubmed/20393555
*Evolution in pancreatic cancer http://www.ncbi.nlm.nih.gov/pubmed/20981101
*Mathematical treatment of rearrangement phylogeny (suggested by Paul) http://www.ncbi.nlm.nih.gov/pubmed/21994251
*Michor (suggested by Paul) http://www.ncbi.nlm.nih.gov/pubmed/20864632
* Taniguchi paper on BRCA2 compensatory mutations following cisplatin  http://www.ncbi.nlm.nih.gov/pubmed/18264087
*Ashworth paper on BRCA2 compensatory mutations in Ovarian cancer following PARPi  http://www.ncbi.nlm.nih.gov/pubmed/18264088


===Lecture slides===
===Lecture slides===
[[Media:CMGcomplex-intro-17apr07clp.ppt|Chayne's Intro slides (ppt) ]]


[[Media:Moyer.ppt|Larry's slides on Moyer (ppt)]]
==Week 3: RNA sequencing==
 
==Week 4:non-coding RNAs==
===Papers===
===Papers===
<biblio>
<biblio>
#Chaumeil-GD-2006 pmid=16912274
#Li-2011 pmid=21596952
#Pollard-Nature-2006 pmid=16915236
#RNA_Editing_in_cancer pmid=17908822
</biblio>
#bowtie pmid=19261174
===Bonus Materials===
#tophat pmid=19289445
<biblio>
#cufflinks pmid=20436464
#news-n-views pmid=16915234
#cell-review pmid=17320512
#reference pmid=8954732
#GenesDev-review pmid=16847345
#ncRNAreview pmid=15809263
#Nature-Review pmid=11253071
#NatStrucBiol-Jarid1C pmid=17310255
#Genetics pmid=16980402
#Annualreview pmid=16124854
</biblio>
</biblio>
[http://www.nature.com/nature/podcast/v443/n7108/nature-2006-09-14.mp3 Nature podcast on Pollard paper]
[[Media:bcmb625-XistPaper-26apr07clp.ppt|Summary ppt of Chaumeil, et al]]
[[Media:X_Chromosome_Inactivation_and_ncRNA_Intro.ppt|X Inactivation Intro Slides]]
==Week 5: Consolidating weeks 2, 3 and 4 (Wed May 2 10AM)==
Review of Methods/papers, answering questions from non-coding RNA and DNA Replication papers
==Week 6: Student Research Forum==
[http://www.ohsu.edu/gso/SRF07/index.html SRF 2007]
==Week 7: Nucleosome positioning and Chromatin Structure==
===Papers===


===Bonus Materials===
===Bonus Materials===
<biblio>
<biblio>
#Chromatin-code-NewsViews pmid=16915272
#Schrider-2011 Very Few RNA and DNA Sequence Differences in the Human Transcriptome http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0025842
#What-Positions_Nucleosomes pmid=12123795
#GenomesUnzipped Post on Paralogs and Splice Junctions http://www.genomesunzipped.org/2011/05/notes-on-the-evidence-for-extensive-rna-editing-in-humans.php
 
#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>
*link to [http://genie.weizmann.ac.il/pubs/nucleosomes06/ Eran Segal's Lab page] where you can test your favorite sequence for predicted nucleosome occupancy
===Lecture Slides===
===Lecture Slides===
[[BMCB625:Nucl Code Intro | Nucleosome Coding Introduction]]
*[http://openwetware.org/images/6/6a/Widespread_RNA_and_DNA.pptx Widespread RNA and DNA differences]


[[Media:BMCM625Genomic code.ppt  | Nucleosome Coding Paper]]
==Week 4: Functional Genomics==
 
 
----
[[BMCB625:Nucleosome Coding | Nucleosome Coding- student Q&A]]
 
==Week 8: Structure function of DNA Helicases==
===Papers===
===Papers===
<biblio>
<biblio>
#Enemark  pmid=16855583
#possemato-2011 pmid=21760589
#background pmid=21458673
</biblio>
</biblio>
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===
===Bonus Materials===
<biblio>
Power-Pump pmid=15454074
#Gai pmid=15454080


#AAA-type-ATPase-review pmid=16072036
===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]
#Review
<br>
:PCNA, the Maestro of the Replication Fork [[http://www.cell.com/content/article/abstract?uid=PIIS0092867407005946]]
[http://openwetware.org/images/3/32/FunctionalGenomics_SerinePathway_BreastCancer.pdf Results: Functional Genomics Reveal that the Serine Synthesis Pathway is Essential in Breast Cancer]
A recent addition to Cell that looks at a critical component of the replication fork.
--~~~~
 
#Gorillas---proteins-that-move-DNA_Maureen-suggested-reading pmid=16936698
 
 
----
</biblio>
 
----
[[BMCB625:Helicases]]


[[Media:Helicase_DNA_Replication.ppt | Helicase_DNA_Replication.ppt]]
==Week 5: No Class==
==General Background for Genomic Instability and Cancer==
*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


==Week 9: A gripping story about the RNA exon junction complex==
==Week 6: Chromothripsis==
===Papers===
===Papers===
<biblio>
<biblio>
#Bono pmid=16923391
#Stephens-2011 pmid=21215367
</biblio>
</biblio>
===Bonus Materials===
===Bonus Materials===
*Link to Schedule Page and Questions/Comments[[http://openwetware.org/wiki/BMCB625:Exon_Jxn_Complex]]
[http://download.cell.com/images/edimages/podcasts/cell144i1paperclip.mp3 link to Cell podcast by the author]
<biblio>
#GREAT-EJC-REVIEW pmid=15145352
#Science-crystal-structure pmid=16931718
#3D-EJC pmid=16797590
#eIF4AIII pmid=15034551
#EJC-eIF4AIII pmid=16170325
#Mago-Y14 pmid=12704080
#DEADbox pmid=16337753
</biblio>


----
===Lecture Slides===
Presentations:
*Introduction:[[Image:053107_EJC.ppt]]
*Paper: [[Image:EJC_Presentation_May2007.ppt]] (Note: 33MB File)


Link to Schedule page:
==Week 7: Circadian rhythm and cancer ==
[[BMCB625:Exon Jxn Complex]]
===Papers===
*Control of skin cancer by the circadian rhythm http://www.ncbi.nlm.nih.gov/pubmed/22025708
===Bonus Materials===
*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 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


----
===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 10: Individual Presentations==
==Week 8: Inflammation and cancer==
===Papers===
*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
*DNA damage induced by chronic inflammation contributes to colon carcinogenesis in mice. http://www.ncbi.nlm.nih.gov/pubmed/18521188
===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]


===Chris - Papers===
==Week 9: Drug Development part 1 GIST==
Outline of Talk and Discussion
===Papers===
#Introduction: Perspectives between disciplines and establishing common languages
*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
#"Classic Paper" (as reference): Luria and Delbruck Fluctuation Test, trends via statistical arguements
#"Main Paper" : Lactose Utilization as a model for Bistability
#Discussion


PAPERS:
===Bonus Materials===
*MAIN PAPER: "Multistability in the lactose utilization network of Escherichia coli"
; See supplemental materials including excel spreadsheets and movies that accompany the main paper
EM Ozbudak, et al,
*Cancer: Oncogenes in context. http://www.nature.com/nature/journal/v467/n7317/full/467796a.html
Nature 427, 737-740 (19 February 2004)
[http://www.nature.com/nature/journal/v427/n6976/abs/nature02298.html Main Paper]
*CLASSIC: "Mutations of Bacteria from Virus Sensitivity to Virus Resistance"
S. E. Luria and M. Delbrück,
Genetics. 1943 November; 28(6): 491–511
[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17247100 Classic Paper]
*See Below: "Biologists Fixing Radios"
* Presentation: [http://openwetware.org/wiki/Image:7June2007_Math_in_Bio.ppt Presentation]


===Chris - Bonus Materials===
===Lecture Slides===
A good primer on how biologists and engineers look at a problem in different ways; while many comments do not address the complexity of biochemistry and genetics, it does provide an interesting perspective on what we consider "important."  Also, of importance, in my opinion, is developing a common language by which numerous disciplines can communicate. I'll touch more on this particular topic during my talk.
*[http://openwetware.org/images/4/4c/ETV1_and_GIST_intro.pptx Introduction: GI Stromal Tumors and ETV1]
Y. Lazebnik, "Can a Biologist Fix a Radio? or, What I Learned while Studying Apoptosis"
*[http://openwetware.org/images/a/a4/GIST-_3-8-2012%281%29.pptx Results: GIST and ETV1]
[http://www.protein.bio.msu.ru/biokhimiya/contents/v69/pdf/bcm_1403.pdf Bio fixing Radios]


----
==Week 10: No Class==
===Papers===


===Chayne - Papers===
===Bonus Materials===


*Presentation slides:
==Week 11: Drug Development part 2==
[[Media:Bcmb625-7jun07-DNAGyrase-piscitelli.ppt | DNA Gyrase ppt lecture (Nollmann, et al.)]]
===Papers===
*The secret ally: immunostimulation by anticancer drugs. http://www.ncbi.nlm.nih.gov/pubmed/22301798


<biblio>
===Bonus Materials===
#Nollman pmid=17334374
</biblio>
===Chayne - Bonus Materials===
*A good "News & Views" on the [[http://www.nature.com/nsmb/journal/v14/n4/full/nsmb0407-256.html |DNA Gyrase Article]]
 
<biblio>
#TopoII_review pmid=16246146
#TopoII_review pmid=16246147
#Great_overview_of_Topos pmid=15139806
#The_original_gyrase_paper pmid=186775
#single_molecule_plus_topology_review pmid=15130115
#DNA_topology_review pmid=3010458
#New_Review pmid=17397985
</biblio>
:Nicholas Cozzarelli (1938-2006) [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-4JW6SX8-5&_user=1072900&_coverDate=05%2F05%2F2006&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000048262&_version=1&_urlVersion=0&_userid=1072900&md5=626a0163005dad4f93625597bf5e0d0d  obituary in Cell]----
 
==Week 11: Individual Presentations==
===Mahta - Papers===
<biblio>
#Christov-MCB-2006 pmid=16943439
</biblio>
===Mahta -Bonus Materials===
<biblio>
#Ro60-autoimmunity pmid=15168680
#Ro-binding-Y pmid=9671049
#Y-RNA_conservation pmid=7505620
#hY-structure pmid=8041611
</biblio>
 
----
 
[[Image:BMCB625_Y_RNA_061307.ppt]]
 
[[BMCB625:Noncoding Y RNA]]
 
----
 
===Jeremy - Papers===
<biblio>
#Zalfa pmid=12581522
</biblio>
 
[[Media:FMRP_and_BC1_RNA.ppt|FMRP and BC1 RNA Slides]]
 
===Jeremy-Bonus Materials===
<biblio>
#Zalfa pmid=16707258
</biblio>
 
<biblio>
#Bagni pmid=15861180
</biblio>
 
<biblio>
#Klann pmid=15550948
</biblio>
 
<biblio>
#Martignetti pmid=8265590
</biblio>
 
<biblio>
#Tiedge pmid=7684772
</biblio>
 
<biblio>
#Dendritic_spine_shape_in_learning_and_memory pmid=17498943
</biblio>
 
<biblio>
#lit_review pmid=14994288
</biblio>
 
===Larry - Papers===
<biblio>
#Ogi-NCB-2006 pmid=16738703
</biblio>
===Larry-Bonus Materials===
[http://www.nature.com/ncb/journal/v8/n6/abs/ncb0606-547.html News and Views]
 
<biblio>
#review pmid=17188030
#polk_kinetics pmid=12444249
#poldelta_kinetics pmid=10748013
#pol-eta_structure pmid=11545743
#Function_of_DNA_Polymerases_Review pmid=15588842
</biblio>
 
[[Media:Final.ppt|Pol Kappa Presentation]]
 
===Jon - Papers===
<biblio>
#2 pmid=17293872
</biblio>
<br>
Evidence that two smaller subunits of RPA bind weakly and preferentially to telomeric DNA. These telomere capping proteins have functional similarities (OB fold) with ssDNA binding proteins and may be involved in the recruitment of telomere maintenance proteins.
 
 
[[Media:Telomere.ppt| Telomere Presentation]]
 
===Jon - Bonus Materials===
<biblio>
#1 pmid=16598261
#2 pmid=17334404 
#3 pmid=9164449
#4 pmid=10655599
</biblio>
[http://biology.kenyon.edu/BMB/Chime2/2006/RPA/index.htm cool RPA discussion]
 
[http://www.pnas.org/cgi/content/full/98/15/8572 G4_Antibody]
 
[http://www.nature.com/embor/journal/v7/n4/full/7400661.html EMBO REPORTS]
 
===So many papers, so little time: Papers we would have liked to cover (note podcast link below)===
<biblio>
#Olaussen-NEJM-2006 pmid=16957145
#Kumagai-Cell-2006 pmid=16530042
#Zegerman pmid=17167417
#comment-Zegerman pmid=17230184
#Kitamura pmid=16814716,
#comment-Kitamura pmid=16814710
</biblio>
===Overlapping coverage but Podcast is interesting===
<biblio>
#Zhou pmid=17301785 (see podcast link below)
</biblio>
[http://www.nature.com/nature/podcast/v445/n7129/nature-2007-02-15.mp3 Nature podcast on Zhou paper]

Latest revision as of 16:31, 4 April 2012

CANB 610 Advanced Topics in Cancer Biology

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

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