Weekly Discussion Sections & Readings
Time and Location
| Session | Time | Location | Note |
|---|---|---|---|
| Section 1 | 9:30-10:30 AM | BASS 405 | |
| Section 2 | 1:00-2:00 PM | BASS 405 | Room Change: BASS 434 for 2/21 |
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 (There will be a class instead of discussion session on 1/17/2020)
- How to (seriously) read a scientific paper, on your own. [Link]
Session 1, 1/24, BASS 405 for both Sessions (First Discussion Sessions)
Topic
- Next-Gen Sequencing and database
Reading Assignment
- Goodwin S. et al. “Coming of age: ten years of next-generation sequencing technologies” Nature Reviews Genetics. 17 (2016) [PDF]
- Wheeler DA et al. “The complete genome of an individual by massively parallel DNA sequencing,” Nature. 452:872-876 (2008) [PDF]
Session 2, 1/31, BASS 405 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, 2/7, BASS 405 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, 2/14, BASS 405 for both Sessions
Topic
- Help session on Quiz 1 - TFs prepare materials on SW alignments and Q&A session
- 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, 2/21, BASS 405 for Session 1, BASS 434 for Session 2 (Note Room Change)
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. [PDF]
- 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 [PDF]
Session 6, 2/28, BASS 405 for both Sessions
Topic
Debate III - Cancer incidence
Reading Assignment
- 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, 3/6, BASS 405 for both Sessions
Topic
- Deep learning for genomics
Reading Assignment
(spring recess)
Session 8, 3/27, Zoom meeting
Topic
- Immune system modelling and dynamics
Reading Assignment
- Perelson AS. Modelling viral and immune system dynamics. Nat Rev Immunol. 2002 Jan;2(1):28-36. [PDF]
- Modeling the Spread of Ebola [PDF]
Session 9, 4/3, Zoom meeting
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, 4/17, Zoom meeting
Topic
- Help session on HW 2 / final project
Reading Assignment
- (no reading assignment this week)