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Discussion Section
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Weekly Discussion Sections & Readings

Time and Location

Session Time Location Note
Section 1 Mon 11am-12am YSB 352 ZC
Section 2 Thur 12-1pm YSB 352 SZ
Section 3 Thur 1-2pm YSB 352 MY
Section 4 Fri 10-11am YSB 352 DB

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)
  • Questions you have about the paper, can be either elucidatory or critical

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, 1/23(Thur), 1/24(Fri), 1/27(Mon)

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 2, 1/30(Thur), 1/31(Fri), 2/3(Mon)

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 3, 2/6(Thur), 2/7(Fri), 2/10(Mon)

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]
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