Final Project Submission

The form for submitting your final project is here: Final Project Artifact Submission Form You should submit your final project by Tuesday, Dec 6 (AoE), which is 7:00am Eastern Time on Wednesday, Dec 7 (there is a 4 hour grace period on this, so you can submit up to 11:00am Wednesday, Dec 7 without any need to arrange an extension). Note: this is different from the form you should use to submit your presentation: Project Presentation Form (as mentioned here).

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Class 24: Project Presentations and Covid Origins

Slides: Class 24: Project Presentations and Covid Origins Letter organized by Peter Daszak, Statement in support of the scientists, public health professionals, and medical professionals of China combatting COVID-19, The Lancet, 19 February 2020. Addendum on competing interests, 21 June 2021. Kristian G. Andersen, Andrew Rambaut, W. Ian Lipkin, Edward C. Holmes and Robert F. Garry . The proximal origin of SARS-CoV-2. Nature Medicine, 17 March 2020.

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Quiz 3

Quiz 3 is posted here: Quiz 3 The quiz is untimed (no time limit enforced), but is expected to take about 30 minutes. Before taking the quiz, make sure you understand and are confident you are able to follow the honor policy for this quiz: The quiz is closed resources. Once you start the quiz, you are not allowed to use any other materials. You should not switch to other browser tabs or look at any notes.

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Class 23: Protein Structure Prediction

Schedule See the Schedule for Presentations and a Plan for this week on the github discussions site. Slides and Links Slides: Class 23: Protein Structure Prediction (without annotations, will be updated later) Ken A. Dill, S. Banu Ozkan, M. Scott Shell, and Thomas R. Weikl. The Protein Folding Problem. Annual Review of Biophysics, 2008. Bonnie Berger and Tom Leighton. Protein Folding in the Hydrophobic-Hydrophilic Model is NP-Complete.

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Plans for Week and Presentations

I’ve posted the Schedule for Presentations and a Plan for this week on the github discussions site. (Everyone should get email notifications for these from the github site (if not, check that you have the “Watch” selected for the repository), but I’m posting redundantly here in case you are not getting them.)

Class 21: Computational Epidemiology

Class 21 was a guest leacture by Jack Heavey on Computational Epidemiology.

Here are the slides: Computational Epidemiology

Class 20: Death and Cancer

Slides and Links Slides: Class 20: Death and Cancer CDC WONDER Death Statistics Peyton Rous. A Sarcoma of the Fowl Transmissible by an Agent Separable from the Tumor Cells. Journal of Experimental Medicine. April 1911. Kimberly M. Newkirk, Erin M. Brannick, and Donna F. Kusewitt. Neoplasia and Tumor Biology (Chapter 6 from Pathologic Basis of Veterinary Disease). 2017. Robert J. Duronio and Yue Xiong.

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Class 22: Programmable Pharmaceuticals

Slides and Links Slides: Class 22: Programmable Pharmaceuticals Michael Bretthauer, Magnus Løberg, Paulina Wieszczy, Mette Kalager, Louise Emilsson, Kjetil Garborg, Maciej Rupinski, Evelien Dekker, Manon Spaander, Marek Bugajski, Øyvind Holme, Ann G. Zauber, et al., for the NordICC Study Group. Effect of Colonoscopy Screening on Risks of Colorectal Cancer and Related Death. New England Journal of Medicine, October 2022. Zhen Xie, Liliana Wroblewska, Laura Prochazka, Ron Weiss, Yaakov Benenson.

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Class 19: Prime Editing

Schedule Project Reports are due on Monday, 7 November (AoE). Use this form to submit your project: Project Report Form Tuesday, November 8 is Election Day (and a UVA class holiday — no class on Tuesday). Quiz 2 Quiz 2 was today in class. Slides and Links Slides: Class 19: Even Crispyr CRISPR Andrew V. Anzalone, Peyton B. Randolph, Jessie R. Davis, Alexander A. Sousa, Luke W. Koblan, Jonathan M.

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Class 18: Crispyr CRISPR

Schedule (repeated from Class 16) Quiz 2 will be on Thursday, November 3 and will focus on material from Classes 14 – 18 (mostly on editing genomes, but also including most likely one question on the discussion of Quiz 1 from Class 14.) Project reports are due Monday, 7 November. This should be a complete project report, which will be graded. You will receive feedback on it, and have an opportunity to revise and improve.

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