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Cenk Sahinalp | HIT’nDRIVE | Patient-Specific Multi-Driver Gene Prioritization for Precision Oncology | CGSI 2017

07/14/2017 @ 14:45-15:30 Research Talk by Cenk Sahinalp HIT’nDRIVE: Patient-Specific Multi-Driver Gene Prioritization for Precision Oncology 1. El-Kebir, M., Satas, G., Oesper, L. and Raphael, B.J., 2016. Inferring the mutational history of a tumor using multi-state perfect phylogeny mixtures. Cell Systems, 3(1), pp.43-53. 2. El-Kebir, M., Oesper, L., Acheson-Field, H. and Raphael, B.J., 2015. Reconstruction…

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Alex Zelikovsky | Inference of metabolic pathway activity from metatranscriptomic reads | CGSI 2017

07/14/2017 @ 13:30-14:15 Research Talk by Alex Zelikovsky Inference of metabolic pathway activity from metatranscriptomic reads 1. Temate-Tiagueu, Y., Al Seesi, S., Mathew, M., Mandric, I., Rodriguez, A., Bean, K., Cheng, Q., Glebova, O., Măndoiu, I., Lopanik, N.B. and Zelikovsky, A., 2016. Inferring metabolic pathway activity levels from RNA-Seq data. BMC genomics, 17(5), p.542. 2….

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Jason Ernst | Computational approaches for deciphering the non-coding human genome | CGSI 2017

07/14/2017 @ 10:00-10:45 Research Talk by Jason Ernst Computational approaches for deciphering the non-coding human genome 1. Ernst, J. and Kellis, M., 2010. Discovery and characterization of chromatin states for systematic annotation of the human genome. Nature biotechnology, 28(8), pp.817-825. 2. Ernst, J., Kheradpour, P., Mikkelsen, T.S., Shoresh, N., Ward, L.D., Epstein, C.B., Zhang, X.,…

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Elhanan Borenstein | Multi-omic and model-based analysis of the human microbiome | CGSI 2017

07/13/2017 @ 15:45-16:30 Research Talk by Elhanan Borenstein Multi-omic and model-based analysis of the human microbiome 1. Manor, O. and Borenstein, E., 2017. Systematic Characterization and Analysis of the Taxonomic Drivers of Functional Shifts in the Human Microbiome. Cell Host & Microbe, 21(2), pp.254-267. 2. Noecker, C., Eng, A., Srinivasan, S., Theriot, C.M., Young, V.B.,…

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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…

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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,…

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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,…

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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.,…

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Can Alkan | Next-generation sequence characterization of complex genome structural variation | CGSI 2017

07/11/2017 @ 12:00-12:45 Research Talk by Can Alkan Next-generation sequence characterization of complex genome structural variation 1. Alkan, C., Coe, B.P. and Eichler, E.E., 2011. Genome structural variation discovery and genotyping. Nature Reviews Genetics, 12(5), pp.363-376. 2. Alkan, C., Kidd, J.M., Marques-Bonet, T., Aksay, G., Antonacci, F., Hormozdiari, F., Kitzman, J.O., Baker, C., Malig, M.,…

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