CONJ606:Materials
Class Focus, Fall 2017
- Organization Meeting and Rules of Engagement
- Genomic instability
- Data Science
- Drug Discovery
Organizational Meeting: Introduction and Scheduling
Evaluation Forms
- Evaluation forms for MC and DL
- Evaluation Form MC
- Evaluation Form Presenter 1(Intro)
- Evaluation Form Presenter 2
Week 1: Data Science & Cancer Biology
Papers
- First Read, Annotated by Alyssa Chamberlain 2015
- Second Read, Article by Cristian Tomasetti & Bert Vogelstein 2017
Bonus Materials
- WHO Press Release in response to First Read
- Is Bad Luck the Main Cause of Cancer?, Critique of the First Read, Weinberg & Zaykin 2015
- A Science Journalist's Reflection, Jennifer Couzin-Frankel 2015
- Intrinsic Risk Factors for Cancer, Response Article, Song Wu & Yusuf Hannun 2016
- Article Commentary on Bad Luck Cancer Debate, Jennifer Couzin-Frankel 2017
- Genes, Environment and "Bad Luck" perspective on Second Read, Article, Martin A. Nowak & Bartlomiej Waclaw 2017
- Most Cancer Cases Arise from "Bad Luck", Comparison of the First and Second Read, Sharon Begley 2017
Lecture Slides
Bad Luck and Cancer: R as a Third Variable
Week 2: Me Myself and I-dentifiers, The Key To Immortality (Persistence)
Papers
Bonus Materials
- Identifiers: Potholes on Information Superhighway
- Some Figures and Info in the blog post may be useful for perspective
- A fun example of identifiers, perhaps, going awry
- Slides by Melissa Haendel
- Rubric for identifiers
- The FAIR Guiding Principles for scientific data management and stewardship, Nature 2017
Lecture Slides
What should we, as life science researchers, pay attention to with identifier use?
Every lesson of the paper will apply to all of us at one point or another, except perhaps for lesson 10. The point is that even though identifier use may be minimal for some individuals, good identifier practice should be observed. Examples of how life scientists use identifiers include citing sources and generating papers and figures. Good identifier practice could be as simple as using DOI to create an identifier for you paper, or could be as complex as using all of the lessons to generate a database that many people can easily use and add to. It depends on what people are doing.
Week 3: TZAP, The Tonsorial Telomere Protein
Papers
- First Main Paper by Julia Su Zhou Li, Javier Miralles Fuste, Tatevik Simavorian, Cristina Bartocci, Jill Tsai, Jan Karlseder, Eros Lazzerini Denchi 2017
- News&Views by Gérald Lossaint, Joachim Lingner 2017 **this is a perspective on the main article
Bonus Materials
Lecture Slides
Week 4: Moonshiner drives piRNA transcription
Papers
- First Main Paper by Peter Refsing Andersen, Laszlo Tirian, Milica Vunjak & Julius Brennecke 2017
- News&Views by Phillip D. Zamore 2017, Containing overview of the main article
Bonus Materials
- Rhino in the news: How cells hack their own genes
- Useful review discussing quantitative mass spec in biological systems
- 2016 Review of piRNA - with theories on how it is transcribed and avoids degradation
Lecture Slides
Revealing transcription in heterochromatin via PIWI RNA
Week 5
Bonus Materials
- “We don’t know which human variations will be advantages and which will be disadvantages in the long arc of our struggle to prevail in an ever-changing environment.”
CTCF Binding Polarity Determines Chromatin Looping*[1]
Gene expression: The coherent Mediator*[2]
Cell division errors: infertility, disorders, and cancers*[3]
Chromosomal Loop Domains Direct the Recombination of Antigen Receptor Genes*[4]
Cohesin Codes*[5]
Three-Dimensional Genome Organization and Function in Drosophila*[6]
Regulation of disease-associated gene expression in the 3D genome*[7]
Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture*[8]
Lecture Slides
Part 1: *https://ohsu.app.box.com/file/256478474798
Part 2: *https://ohsu.app.box.com/file/247445475386
Week 8: Mitogens and p53 battle for cell cycle control entry
Papers
- Competing memories of mitogen and p53 signalling control cell-cycle entry
- Cell biology: The persistence of memory
