Weekly Discussion Sections & Readings
Mondays, Bass 405 2:20 pm - 3:20 pm; or 6:00 - 7:00 pm
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, tentatively, we require the following
Students are expected to bring approx. a half page (2-3 paragraph) summaries of each paper to the section. (we will collect a hard copy during each session, but if you'd like to save some trees, we will accept electronic submission. Please submit PDF to cbb752 (at) gersteinlab.org BEFORE each section).
Students will give approx. 20 min presentations about each paper.
Students will be graded on a combination of the written summary, presentation, and participation in discussions.
Section Readings
Reading assignments for discussion sessions are listed below.
Session 0: Introductory Matters; Monday, 1/22/18, Bass 405 2:30 pm - 3:30 pm; 5:00 - 6:00 pm
No required reading
Come to either the 2:30 or 5:00 pm session depending on what is most convenient for you
These may not be the semester-long days and times
Email the TAs at cbb752@gersteinlab.org if you cannot attend either session
Session 1: Next-Gen Sequencing; Monday, 1/29/18, Bass 405 2:20 pm - 3:20 pm; 6:00 - 7:00 pm
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: Proteomics/Sequence Alignment; 2/5/18
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: Midterm Review: Needleman-Wunsch Alignment; 2/12/18
Session 4: Sequence Alignment/Machine learning; 2/19/18
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
Yip, KY, Cheng, C, Gerstein, M (2013). Machine learning and genome annotation: a match meant to be?. Genome Biol., 14, 5:205. PDF
Session 5: Hands-On Demo on Alignment and Variant Calling; 2/26/18
https://software.broadinstitute.org/gatk/best-practices/
https://software.broadinstitute.org/gatk/best-practices/workflow?id=11165
https://software.broadinstitute.org/gatk/best-practices/workflow?id=11145
https://docs.google.com/spreadsheets/d/1nXrk3rXAvI_U8-Fps2rMdK3G-JOhnYzQcX1KRVmFTnk/edit?usp=sharing
Session 6: Bioinformatics for Next-Gen Sequencing; 3/5/18
Rozowsky, J, Euskirchen, G, Auerbach, RK, Zhang, ZD, Gibson, T, Bjornson, R, Carriero, N, Snyder, M, Gerstein, MB (2009). PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat. Biotechnol., 27, 1:66-75 PDF
Cooper, GM, Shendure, J (2011). Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data. Nat. Rev. Genet., 12, 9:628-40 PDF
Session 7: Final Project Planning; 3/26/18
Session 8: Networks; 4/2/18
Ekman D, Light S, Björklund AK, Elofsson A. (2006) What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae? Genome Biol. 2006;7(6):R45. PDF
Barabási, AL, Oltvai, ZN (2004). Network biology: understanding the cell's functional organization. Nat. Rev. Genet., 5, 2:101-13. PDF
Session 9: Workshop on Detecting Cancer Driver Genes; 4/09/18
*NO READING RESPONSE NECESSARY*
https://docs.google.com/spreadsheets/d/10d179MOVXX3S826YtXwPVNjr32HgXSV0lgcgZYjrSAE/edit#gid=0
http://www.cancergenomicscloud.org/
http://www.cell.com/cell/fulltext/S0092-8674(18)30237-X?utm_campaign=STMJ_1522958526_SC&utm_channel=WEB&utm_source=WEB&dgcid=STMJ_1522958526_SC
https://www.nature.com/articles/nature12213
Session 10: Protein Simulation; 4/16/18
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 11: Final Project Presentations; 4/23/18