Weekly Discussion Sections & Readings Group 1: Friday 1:00 - 2:00 PM, BASS 405 Group 2: Monday 12:00 - 1:00 PM, BASS 405 The first discussion section will meet on 1/29/2016 (Group 1) and 2/1/2016 (Group 2).
Format In each section, we will have a discussion of two papers assigned below.
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@gersteinlab.org BEFORE each section).
- Students will give approx. 15 min presentations about each paper. (To sign up for presentations, see the spreadsheet below)
- Students will be graded on a combination of the written summary, presentation, and participation in discussions.
Section Readings
Session 1: Next-Gen Sequencing - Metzker ML. "Sequencing technologies - the next generation” Nature Reviews Genetics. 11 (2010) 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
- T.F. Smith and M.S. Waterman. (1981) Identification of common molecular subsequences. Journal of Molecular Biology,147(1): 195-7. PMID: 7265238. PDF
- Nevan J. Krogan et al (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae Nature 440, 637-643 (30 March 2006) PDF
- Additional readings suggested by Professor Rinehart
Session 3: Sequence Alignment/Machine learning
- 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
- Yip, KY, Cheng, C, Gerstein, M (2013). Machine learning and genome annotation: a match meant to be?. Genome Biol., 14, 5:205. PDF
Session 4: Bioinformatics for Next-Gen Sequencing
- 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 5: Networks
- 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 6: Immunological Modeling/Semantic Web
- Perelson AS. Modelling viral and immune system dynamics. Nat Rev Immunol. 2002 Jan;2(1):28-36. PDF
- Antezana E, Egaña M, Blondé W, Illarramendi A, Bilbao I, De Baets B, Stevens R, Mironov V, Kuiper M. (2009) The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process. Genome Biol. 2009;10(5):R58. Epub 2009 May 29. PDF
Session 7: Protein Simulation 1
- Martin Karplus and J. Andrew McCammon. (2002) Molecular dynamics simulations of biomolecules. Nature Structural Biology,9, 646-52. PMID: 12198485.PDF
- Zhou, AQ, O'Hern, CS, Regan, L (2011). Revisiting the Ramachandran plot from a new angle. Protein Sci., 20, 7:1166-71 PDF
Session 8: Protein Simulation 2
- 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
CBB 752 discussion section sign-up sheet
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