07/18/2017 @ 09:15-10:00 Research Talk by Jo Hardin Prediction intervals for random forests with applications to high throughput data 1. Chen, X. and Ishwaran, H., 2012. Random forests for genomic data analysis. Genomics, 99(6), pp.323-329. 2. Pang, H., Lin, A., Holford, M., Enerson, B.E., Lu, B., Lawton, M.P., Floyd, E. and Zhao, H., 2006. Pathway…
07/17/2017 @ 09:15-10:00 Research Talk by David Tse Maximally correlation and principal component analysis 1. Rényi, A., 1959. On measures of dependence. Acta mathematica hungarica, 10(3-4), pp.441-451. 2. Feizi, S. and Tse, D., 2017. Maximally Correlated Principle Component Analysis. arXiv preprint arXiv:1702.05471.
07/17/2017 @ 14:30-15:15 Research Talk by Kin Fai Au Transcriptome analysis at the gene isoform level using hybrid sequencing 1. Au, K.F., Sebastiano, V., Afshar, P.T., Durruthy, J.D., Lee, L., Williams, B.A., van Bakel, H., Schadt, E.E., Reijo-Pera, R.A., Underwood, J.G. and Wong, W.H., 2013. Characterization of the human ESC transcriptome by hybrid sequencing. Proceedings…
07/17/2017 @ 10:30-11:15 Research Talk by Saharon Rosset Quality preserving databases for statistically sound “big data” analysis on public databases 1. Rosset, S., Aharoni, E. and Neuvirth, H., 2014. Novel Statistical Tools for Management of Public Databases Facilitate Community‐Wide Replicability and Control of False Discovery. Genetic epidemiology, 38(5), pp.477-481. 2. Aharoni, E. and Rosset, S.,…
07/14/2017 @ 16:00-16:45 Research Talk by Sagi Snir A universal PaceMaker as a better explanation of evolution and aging 1. Snir, S., Wolf, Y.I. and Koonin, E.V., 2012. Universal pacemaker of genome evolution. PLoS Comput Biol, 8(11), p.e1002785. 2. Snir, S. and Pellegrini, M., 2016. A Statistical Framework to Identify Deviation from Time Linearity in…
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…
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….
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.,…
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 @ 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.,…