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David Koslicki | The CAMI Project | Assessment of computational techniques in metagenomics | CGSI 2017

07/12/2017 @ 09:15-10:00 Tutorial by David Koslicki The CAMI Project: Assessment of computational techniques in metagenomics 1. Sczyrba, A., Hofmann, P., Belmann, P., Koslicki, D., Janssen, S., Droege, J., Gregor, I., Majda, S., Fiedler, J., Dahms, E. and Bremges, A., 2017. Critical Assessment of Metagenome Interpretation− a benchmark of computational metagenomics software. Biorxiv, p.099127. 2….

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Alexander Schönhuth | Assembling polyploid genomes | CGSI 2017

We apologize that this video is currently unavailable. 07/11/2017 @ 09:15-10:00 Tutorial by Alexander Schönhuth Assembling polyploid genomes 1. Baaijens, J.A., El Aabidine, A.Z., Rivals, E. and Schönhuth, A., 2017. De novo assembly of viral quasispecies using overlap graphs. Genome Research, 27(5), pp.835-848. 2. Välimäki, N., Ladra, S. and Mäkinen, V., 2012. Approximate all-pairs suffix/prefix…

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Ilan Gronau | Demography inference | From parameter estimation to model selection | CGSI 2017

07/10/2017 @ 10:00-10:45 Tutorial by Ilan Gronau Demography inference: From parameter estimation to model selection 1. Gronau, I., Hubisz, M.J., Gulko, B., Danko, C.G. and Siepel, A., 2011. Bayesian inference of ancient human demography from individual genome sequences. Nature genetics, 43(10), pp.1031-1034. 2. Hey, J. and Nielsen, R., 2007. Integration within the Felsenstein equation for…

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Jason Ernst | Functional Genomics Time-series Analysis | CGSI 2016

08/11/2016 @ 10:30-11:30 Tutorial by Jason Ernst Functional Genomics Time-series Analysis 1. Ernst, J., Nau, G.J. and Bar-Joseph, Z., 2005. Clustering short time series gene expression data. Bioinformatics, 21(suppl 1), pp.i159-i168. 2. Ernst, J. and Bar-Joseph, Z., 2006. STEM: a tool for the analysis of short time series gene expression data. BMC bioinformatics, 7(1), p.191….

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David Koslicki | Bacterial Community Reconstruction via Compressed Sensing | CGSI 2016

08/11/2016 @ 09:30-10:30 Tutorial by David Koslicki Bacterial Community Reconstruction via Compressed Sensing 1. Candès, E.J. and Wakin, M.B., 2008. An introduction to compressive sampling. IEEE signal processing magazine, 25(2), pp.21-30. 2. Koslicki, D., Foucart, S. and Rosen, G., 2013. Quikr: a method for rapid reconstruction of bacterial communities via compressive sensing. Bioinformatics, p.btt336. 3….

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Kenneth Lange | Next Generation Statistical Genetics: Modeling, Penalization, and Optimization in High-dimensional Data | CGSI 2016

08/09/2016 @ 10:30-11:30 Tutorial by Kenneth Lange Next Generation Statistical Genetics: Modeling, Penalization, and Optimization in High-dimensional Data 1. Lange, K., Papp, J.C., Sinsheimer, J.S. and Sobel, E.M., 2014. Next-generation statistical genetics: modeling, penalization, and optimization in high-dimensional data. Annual review of statistics and its application, 1, pp.279-300.

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Sriram Sankararaman | Challenges in Genomic Privacy | CGSI 2016

08/08/2016 @ 10:30-11:30 Tutorial by Sriram Sankararaman Challenges in Genomic Privacy 1. Erlich, Y. and Narayanan, A., 2014. Routes for breaching and protecting genetic privacy. Nature Reviews Genetics, 15(6), pp.409-421. 2. Gymrek, M., McGuire, A.L., Golan, D., Halperin, E. and Erlich, Y., 2013. Identifying personal genomes by surname inference. Science, 339(6117), pp.321-324. 3. Sankararaman, S.,…

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Sagi Snir | Tutorial on reconstructing Evolution from the Tiniest Fractions | CGSI 2016

08/03/2016 @ 10:30-11:30 Tutorial by Sagi Snir Tutorial on reconstructing Evolution from the Tiniest Fractions: Basics, Challenges, and Application 1. Hinchliff, C.E., Smith, S.A., Allman, J.F., Burleigh, J.G., Chaudhary, R., Coghill, L.M., Crandall, K.A., Deng, J., Drew, B.T., Gazis, R. and Gude, K., 2015. Synthesis of phylogeny and taxonomy into a comprehensive tree of life….

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