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SessionTopicsPapersSession 1
(Tue)
Presenter
(write your name here)
Session 2
(Fri)
Presenter
(write your name here)
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0Introduction/Basics of R, GitHub, and PythonSession 1 slidesJanuary 24thTAsJanuary 27thTAs
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1Next-Gen SequencingGoodwin S. "Coming of age: ten years of next generation sequencing technologies” Nature Reviews Genetics. 17 (2016) PDFJanuary 31stFebruary 3rd
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Wheeler DA et al. "The complete genome of an individual by massively parallel DNA sequencing,” Nature. 452:872-876 (2008) PDF
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2Proteomics/Sequence AlignmentKim et al. A draft map of the human proteome. Nature 509,575–581 (29 May 2014)February 7thFebruary 10thJay Stanley
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Wilhelm et al. Mass-spectrometry-based draft of the human proteome. Nature 509, 582–587 (29 May 2014)Ramya Prathuri
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3Sequence Alignment/Machine learningAltschul 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. PDFFebruary 14thHussein MohsenFebruary 17th
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T.F. Smith and M.S. Waterman. (1981) Identification of common molecular subsequences. Journal of Molecular Biology,147(1): 195-7. PMID: 7265238.PDF
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Yip, KY, Cheng, C, Gerstein, M (2013). Machine learning and genome annotation: a match meant to be?. Genome Biol., 14, 5:205. PDFJames Diao
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4Bioinformatics for Next-Gen SequencingRozowsky, 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 PDFFebruary 21stAcer XuFebruary 24th
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Cooper, GM, Shendure, J (2011). Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data. Nat. Rev. Genet., 12, 9:628-40PDF
Megan BradyZhaolong Yu
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5NetworksEkman 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. PDFFebruary 28thJiawei WangMarch 3rdDingjue Ji
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Barabási, AL, Oltvai, ZN (2004). Network biology: understanding the cell's functional organization. Nat. Rev. Genet., 5, 2:101-13. PDFYuyang Liu
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6Immunological Modeling/Semantic WebPerelson AS. Modelling viral and immune system dynamics. Nat Rev Immunol. 2002 Jan;2(1):28-36. PDFMarch 7thAmy ZhaoMarch 10th
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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. PDFOlivia Justynski
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7Protein Simulation 1Martin Karplus and J. Andrew McCammon. (2002) Molecular dynamics simulations of biomolecules. Nature Structural Biology,9, 646-52. PMID: 12198485.PDFMarch 28thKrystle ReissMarch 31stAmber Jessop
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Zhou, AQ, O'Hern, CS, Regan, L (2011). Revisiting the Ramachandran plot from a new angle. Protein Sci., 20, 7:1166-71 PDFDaniel Chawla
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8Protein Simulation 2Dill KA, Ozkan SB, Shell MS, Weikl TR. (2008) The Protein Folding Problem.Annu Rev Biophys,9, 37:289-316. PMID: 2443096.PDFApril 4thYekaterina KovalyovaApril 7th
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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
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9CRISPR off target predictionDefining and improving the genomewide specificities of CRISPR–Cas9 nucleasesApril 11thApril 14th
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GuideScan software for improved single and paired CRISPR guide RNA design
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10eQTL identificationThe role of regulatory variation in complex traits and diseaseApril 18thApril 21st
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Matrix eQTL: ultra fast eQTL analysis via large matrix operations
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