Weekly Discussion Sections & Readings
Time and Location
| Session | Time | Location | Note |
|---|---|---|---|
| Section 1 | 10:00-11:00 AM | BASS405 | |
| Section 2 | 1:00-2:00 PM | BASS405 |
Format
The standard discussion section involves student presentations on 1 or 2 papers. Some discussion sections will involve hands-on skill-building demos taught by the teaching fellows, such as the use of R, High Performance Computing, and GitHub. The exact format will be determined based on the size of the class. However, we generally require the following:
- Each week, students should read the assigned papers and write at a minimum of 200 words (half a page, single-spaced, per paper) summaries of each paper (two articles = approx. 1 page). We would like to encourage electronic submission, via Canvas. For those who have trouble accessing canvas, we will also accept submission over email to cbb752 (at) gersteinlab.org BEFORE the start of each section.
- Each student will give one presentation about a selected paper (approx. 20 min) in one of the sessions.
- Students will be graded on a combination of the written summary, presentation, and participation in discussions.
- If you are presenting, you are exempt from writing a summary.
- Please notify TFs in advance if you cannot come to the discussion session. Student can miss up to one discussion section without a penalty.
For write-ups and presentation, think about the following:
- What was missing in the field? (introduction/background)
- What were the questions the paper aim to address? (hypothesis)
- What they did and what was the breakthrough? (method/results)
- Conclusion and future direction (discussion/conclusion)
Section Readings
Reading assignments for discussion sessions are listed below:
(Optional) Suggested Reading for Week 1
- How to (seriously) read a scientific paper, on your own. [Link]
Session 1, 2/4, Virtual (Zoom) for both sessions (First Discussion Sessions)
Topic
- Next-Gen Sequencing and database
Reading Assignment
- Wheeler DA et al. “The complete genome of an individual by massively parallel DNA sequencing,” Nature. 452:872-876 (2008) [PDF]
- Logsdon GA et al. “Long-read human genome sequencing and its applications” Nature Reviews Genetics. 21:597-614 (2020) [PDF]
Session 2, 2/11, BASS405 for both sessions
Topic
- Proteomics
Reading Assignment
- A draft map of the human proteome. Nature 509,575–581 (29 May 2014) [PDF]
- Mass-spectrometry-based draft of the human proteome. Nature 509, 582–587 (29 May 2014) [PDF]
Session 3, 2/18, BASS405 for both sessions
Topic
- Debate I
Reading Assignment
- Gencode vs Salzberg et al. debate
- (Main paper) Salzberg et al. CHESS paper using GTEx [PDF]
- (Main paper) GENCODE’s rebuttal [PDF]
- (Optional) New human gene tally reignites debate [News Article]
- (Optional) Why most published research finding are false [PDF]
Session 4, 2/25, BASS405 for both sessions
Topic
- Sequence and Alignments
Reading Assignment
- Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. (1990) Basic local alignment search tool. Journal of Molecular Biology, 215(3):403-10. PMID: 2231712. [PDF]
- T.F. Smith and M.S. Waterman. (1981) Identification of common molecular subsequences. Journal of Molecular Biology,147(1): 195-7. PMID: 7265238. [PDF]
Session 5, 3/4, BASS405 for both sessions
Topic
- Debate II - Phylogenetics
Reading Assignment
- Jarvis ED et al. (2014) Whole-genome analyses resolve early branches in the tree of life of modern birds. Science, 346(6215), 1320-1331. [Link]
- Mitchel KJ, Cooper A, Philips MJ (2015) Comment on “Whole-genome analyses resolve early branches in the tree of life of modern birds.” Science, 349(6255) 1460 [Link]
Session 6, 3/11, BASS405 for both sessions
Topic
Debate III - Cancer incidence
Reading Assignment
- Variation in cancer risk among tissues can be explained by the number of stem cell divisions [Link]
- Stem cell divisions, somatic mutations, cancer etiology, and cancer prevention [Link]
The following two are short comments on the above paper. You should read these comments as well.
- Debate reignites over the contributions of ‘bad luck’ mutations to cancer [Link]
- The simple math that explains why you may (or may not) get cancer [Link]
Session 7, 4/1, BASS405 for both sessions
Topic
- Deep learning for genomics
Reading Assignment
Session 8, 4/8, BASS405 for both sessions
Topic
- Deep learning II
Reading Assignment
- Artificial intelligence powers protein-folding predictions [Link]
- Computed structures of core eukaryotic protein complexes [Link]
Session 9, 4/15, BASS405 for both sessions
Topic
- Protein structure and biophysics
Reading Assignment
- Zhou, AQ, O’Hern, CS, Regan, L (2011). Revisiting the Ramachandran plot from a new angle. Protein Sci., 20, 7:1166-71 [PDF]
- Dill KA, Ozkan SB, Shell MS, Weikl TR. (2008) The Protein Folding Problem. Annu Rev Biophys,9, 37:289-316. PMID: 2443096. [PDF]
- Bowman GR, Beauchamp KA, Boxer G, Pande VS. “Progress and challenges in the automated construction of Markov state models for full protein systems,” J. Chem. Phys. 131 (2009) 124101 [PDF]
Session 10, 4/22, BASS405 for both sessions
Topic
- Help session on HW 2 / final project
Reading Assignment
- (no reading assignment this week)