Section Readings
Weekly Discussion Sections & Readings
Group 1: Friday 1:00pm - 2:00pm
Group 2: Tuesday 6:00pm - 7:00pm
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. 20 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
Introduction to Personalized Medicine:
Carl Zimmer's Game of Genomes: https://www.statnews.com/feature/game-of-genomes/season-one/
Carl Zimmer additional reading: https://www.statnews.com/2016/08/17/genetic-variants-ex-ac-sequence/
Ashley EA. "Towards precision medicine" Nature Reviews Genetics. 17 (2016) PDF
Chen R. "Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes" Cell 148 (2012) PDF
Session 1: Next-Gen Sequencing
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
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: 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
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 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
Session 9: CRISPR off target prediction
Shengdar Q. Tsai and J. Keith Joung (2016) Defining and improving the genomewide specificities of CRISPR–Cas9 nucleases PDF
Alexendar R Perez et al. (2017) GuideScan software for improved single and paired CRISPR guide RNA design PDF
