07/20/2016 @ 15:15-16:00 Tutorial by Ben Raphael Computational Analysis of Somatic Mutations in Cancer 1. Ding, L., Wendl, M.C., McMichael, J.F. and Raphael, B.J., 2014. Expanding the computational toolbox for mining cancer genomes. Nature Reviews Genetics, 15(8), pp.556-570. 2. Raphael, B.J., Dobson, J.R., Oesper, L. and Vandin, F., 2014. Identifying driver mutations in sequenced cancer…
07/20/2016 @ 09:15-10:00 Tutorial by Fereydoun Hormozdiari Detecting Structural Variation 1. Hormozdiari, F., Alkan, C., Eichler, E.E. and Sahinalp, S.C., 2009. Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes. Genome research, 19(7), pp.1270-1278. 2. Alkan, C., Coe, B.P. and Eichler, E.E., 2011. Genome structural variation discovery and genotyping. Nature Reviews Genetics, 12(5), pp.363-376….
07/19/2016 @ 15:15-16:00 Tutorial by Alex Zelikovsky High-Throughput Sequencing Applications to Molecular Epidemiology 1. Wertheim, J.O., Brown, A.J.L., Hepler, N.L., Mehta, S.R., Richman, D.D., Smith, D.M. and Pond, S.L.K., 2014. The global transmission network of HIV-1. Journal of Infectious Diseases, 209(2), pp.304-313. 2. Jombart, T., Cori, A., Didelot, X., Cauchemez, S., Fraser, C. and Ferguson,…
07/19/2016 @ 14:00-14:45 Tutorial by Sohini Ramachandran Genomic Reconstructions of Deep Human History 1. Palacios, J.A., Wakeley, J. and Ramachandran, S., 2015. Bayesian nonparametric inference of population size changes from sequential genealogies. Genetics, pp.genetics-115. 2. Rasmussen, M.D., Hubisz, M.J., Gronau, I. and Siepel, A., 2014. Genome-wide inference of ancestral recombination graphs. PLoS Genet, 10(5), p.e1004342….
07/19/2016 @ 10:00-10:45 Tutorial by Jo Hardin Tutorial on RNASeq Normalization and Differential Expression 1. Wang, Z., Gerstein, M. and Snyder, M., 2009. RNA-Seq: a revolutionary tool for transcriptomics. Nature reviews genetics, 10(1), pp.57-63. 2. Bullard, J.H., Purdom, E., Hansen, K.D. and Dudoit, S., 2010. Evaluation of statistical methods for normalization and differential expression in…
07/19/16 @ 09:15-10:00 Tutorial by Alexander Schönhuth Snakemake: Reproducible and Scalable Data Analysis 1. Köster, J. and Rahmann, S., 2012. Snakemake—a scalable bioinformatics workflow engine. Bioinformatics, 28(19), pp.2520-2522. 2. Köster, J., 2014. Parallelization, scalability, and reproducibility in next generation sequencing analysis (Doctoral dissertation).
07/18/16 @ 09:15-10:00 Tutorial by Brian Browning An Introduction to Genotype Imputation 1. Marchini, J. and Howie, B., 2010. Genotype imputation for genome-wide association studies. Nature Reviews Genetics, 11(7), pp.499-511. 2. Howie, B., Fuchsberger, C., Stephens, M., Marchini, J. and Abecasis, G.R., 2012. Fast and accurate genotype imputation in genome-wide association studies through pre-phasing. Nature…
07/18/2016 @ 10:00-10:45 Tutorial by William (Xiaoquan) Wen Bayesian Statistics and its Application to Integrative Statistical Genomics 1. Stephens, M. and Balding, D.J., 2009. Bayesian statistical methods for genetic association studies. Nature Reviews Genetics, 10(10), pp.681-690. 2. Wakefield, J., 2009. Bayes factors for genome‐wide association studies: comparison with P‐values. Genetic epidemiology, 33(1), pp.79-86. 3. Wen,…