07/26/2017 @ 09:00-10:00 Tutorial by Noah Zaitlen Covariate adjustment in genetics and genomics 1. Zaitlen, N., Lindström, S., Pasaniuc, B., Cornelis, M., Genovese, G., Pollack, S., Barton, A., Bickeböller, H., Bowden, D.W., Eyre, S. and Freedman, B.I., 2012. Informed conditioning on clinical covariates increases power in case-control association studies. PLoS Genet, 8(11), p.e1003032. 2. Aschard,…
07/24/2017 @ 09:15-10:00 Tutorial by Bogdan Pasaniuc Genetic correlations to gain insights into relations between traits 1. Mancuso, N., Shi, H., Goddard, P., Kichaev, G., Gusev, A. and Pasaniuc, B., 2017. Integrating Gene Expression with Summary Association Statistics to Identify Genes Associated with 30 Complex Traits. The American Journal of Human Genetics, 100(3), pp.473-487. 2….
07/20/2017 @ 10:30-11:15 Tutorial by Fabio Vandin Computational discovery of significantly mutated genes and pathways in cancer 1. Vandin, F., Upfal, E. and Raphael, B.J., 2011. Algorithms for detecting significantly mutated pathways in cancer. Journal of Computational Biology, 18(3), pp.507-522. 2. Raphael, B.J., Dobson, J.R., Oesper, L. and Vandin, F., 2014. Identifying driver mutations in…
07/19/2017 @ 10:30-11:15 Tutorial by Ben Raphael Inferring tumor evolution
07/19/2017 @ 09:15-10:00 Tutorial by John Novembre Computational tools for understanding population structure in genetic variation data 1. Novembre, J. and Stephens, M., 2008. Interpreting principal component analyses of spatial population genetic variation. Nature genetics, 40(5), pp.646-649. 2. Alexander, D.H., Novembre, J. and Lange, K., 2009. Fast model-based estimation of ancestry in unrelated individuals. Genome…
07/14/2017 @ 09:15-10:00 Tutorial by Saharon Rosset Stochastic process models for mutations, their estimation from data, and their uses 1. Huelsenbeck, J.P. and Crandall, K.A., 1997. Phylogeny estimation and hypothesis testing using maximum likelihood. Annual Review of Ecology and Systematics, 28(1), pp.437-466. 2. Tamura, K. and Nei, M., 1993. Estimation of the number of nucleotide…
07/13/2017 @ 09:00-09:45 Tutorial by Or Zuk Co-evolution analysis: Methods and applications 1. Felsenstein, J., 1985. Phylogenies and the comparative method. The American Naturalist, 125(1), pp.1-15. 2. Pellegrini, M., Marcotte, E.M., Thompson, M.J., Eisenberg, D. and Yeates, T.O., 1999. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proceedings of the National Academy of…
07/13/2017 @ 09:45-10:30 Tutorial by Itsik Pe’er Identity by descent in medical and population genomics 1. Palamara, P.F., Francioli, L.C., Wilton, P.R., Genovese, G., Gusev, A., Finucane, H.K., Sankararaman, S., Sunyaev, S.R., de Bakker, P.I., Wakeley, J. and Pe’er, I., 2015. Leveraging distant relatedness to quantify human mutation and gene-conversion rates. The American Journal of…
07/13/2017 @ 13:00-13:45 Tutorial by Lior Pachter Differential analysis of count data in genomics 1. Anders, S. and Huber, W., 2010. Differential expression analysis for sequence count data. Genome biology, 11(10), p.R106. 2. Soneson, C., Love, M.I. and Robinson, M.D., 2015. Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences. F1000Research, 4. 3. Pimentel, H.,…
07/12/2017 @ 10:00-10:45 Tutorial by David Tse How to solve NP-hard assembly problems in linear time 1. Bresler, G., Bresler, M.A. and Tse, D., 2013. Optimal assembly for high throughput shotgun sequencing. BMC bioinformatics, 14(5), p.S18. 2. Shomorony, I., Kim, S.H., Courtade, T.A. and David, N.C., 2016. Information-optimal genome assembly via sparse read-overlap graphs. Bioinformatics,…