Leonid Kruglyak | Complex Traits and Simple Systems | CGSI 2017
07/13/2017 @ 15:00-15:45 Research Talk by Leonid Kruglyak Complex Traits and Simple Systems
Melissa Gymrek | Analyzing complex repeat variation from high throughput sequencing data | CGSI 2017
07/13/2017 @ 13:45-14:30 Research Talk by Melissa Gymrek Analyzing complex repeat variation from high throughput sequencing data 1. Gymrek, M., Golan, D., Rosset, S. and Erlich, Y., 2012. lobSTR: a short tandem repeat profiler for personal genomes. Genome research, 22(6), pp.1154-1162. 2. Willems, T., Zielinski, D., Gordon, A., Gymrek, M. and Erlich, Y., 2016. Genome-wide…
Lior Pachter | Differential analysis of count data in genomics | CGSI 2017
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.,…
Itsik Pe’er | Identity by descent in medical and population genomics | CGSI 2017
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…
Or Zuk | Co-evolution analysis | Methods and applications | CGSI 2017
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…
Brian Browning | Genotype phasing with large sample sizes | CGSI 2017
07/12/2017 @ 16:00-16:45 Research Talk by Brian Browning Genotype phasing with large sample sizes 1. Kong, A., Masson, G., Frigge, M.L., Gylfason, A., Zusmanovich, P., Thorleifsson, G., Olason, P.I., Ingason, A., Steinberg, S., Rafnar, T. and Sulem, P., 2008. Detection of sharing by descent, long-range phasing and haplotype imputation. Nature genetics, 40(9), pp.1068-1075. 2. Browning,…
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….
David Tse | How to solve NP-hard assembly problems in linear time | CGSI 2017
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,…
Ran Blekhman | Human genomic control of the microbiome | CGSI 2017
07/12/2017 @ 13:30-14:15 Research Talk by Ran Blekhman Human genomic control of the microbiome 1. Goodrich, J.K., Waters, J.L., Poole, A.C., Sutter, J.L., Koren, O., Blekhman, R., Beaumont, M., Van Treuren, W., Knight, R., Bell, J.T. and Spector, T.D., 2014. Human genetics shape the gut microbiome. Cell, 159(4), pp.789-799. 2. Blekhman, R., Goodrich, J.K., Huang,…
Daniel Wegmann | Tracing the spread of farming using ancient DNA | Bioinformatic challenges and population genetic insights | CGSI 2017
07/12/2017 @ 14:45-15:30 Research Talk by Daniel Wegmann Tracing the spread of farming using ancient DNA: Bioinformatic challenges and population genetic insights 1. Kousathanas, A., Leuenberger, C., Link, V., Sell, C., Burger, J. and Wegmann, D., 2017. Inferring heterozygosity from ancient and low coverage genomes. Genetics, 205(1), pp.317-332. 2. Broushaki, F., Thomas, M.G., Link, V.,…