James Zou | Deep learning in genomics | Introduction and examples | CGSI 2017
07/11/2017 @ 11:15-12:00 Research Talk by James Zou Deep learning in genomics: Introduction and examples
William (Xiaoquan) Wen | Bayesian approaches for integrative genetic association analysis | Data integration and scalable computation | CGSI 2017
07/11/2017 @ 10:00-10:45 Research Talk by William (Xiaoquan) Wen Bayesian approaches for integrative genetic association analysis: Data integration and scalable computation 1. Wen, X., Lee, Y., Luca, F. and Pique-Regi, R., 2016. Efficient integrative multi-SNP association analysis via Deterministic Approximation of Posteriors. The American Journal of Human Genetics, 98(6), pp.1114-1129. 2. Wen, X., Pique-Regi, R….
Dana Pe’er | Imputation in Single Cell RNA-seq Data | CGSI 2017
07/10/2017 @ 14:45-15:30 Research Talk by Dana Pe’er Imputation in Single Cell RNA-seq Data 1. van Dijk, D., Nainys, J., Sharma, R., Kathail, P., Carr, A.J., Moon, K.R., Mazutis, L., Wolf, G., Krishnaswamy, S. and Pe’er, D., 2017. MAGIC: A diffusion-based imputation method reveals gene-gene interactions in single-cell RNA-sequencing data. bioRxiv, p.111591. 2. Prabhakaran, S.,…
Jennifer Listgarten | Machine learning for CRISPR gene editing | CGSI 2017
07/10/2017 @ 13:30-14:15 Research Talk by Jennifer Listgarten Machine learning for CRISPR gene editing 1. Fusi, N., Smith, I., Doench, J. and Listgarten, J., 2015. In silico predictive modeling of CRISPR/Cas9 guide efficiency. bioRxiv, p.021568. 2. Listgarten, J., Weinstein, M., Elibol, M., Hoang, L., Doench, J. and Fusi, N., 2016. Predicting off-target effects for end-to-end…
Lior Pachter | An introduction to pseudoalignment | CGSI 2017
07/10/2017 @ 09:15-10:00 Research Talk by Lior Pachter An introduction to pseudoalignment 1. Bray, N.L., Pimentel, H., Melsted, P. and Pachter, L., 2016. Near-optimal probabilistic RNA-seq quantification. Nature biotechnology, 34(5), pp.525-527.
Joel Mefford | Linear Mixed Models – and their Equivalents | CGSI 2016
08/12/2016 @ 10:00-11:00 Research Talk by Joel Mefford Linear Mixed Models – and their Equivalents
Kin Fai Au (External, non-CGSI Event)
08/10/2016 @ 16:00-17:00 External (non-CGSI) Event presented by Kin Fai Au UCLA Bioinformatics Lecture: Transcriptome Analysis by 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…
Jo Hardin | Assumptions in Normalizing RNASeq Data | CGSI 2016
08/10/2016 @ 09:30-10:30< Research Talk by Jo Hardin Assumptions in Normalizing RNASeq Data 1. Wang, Z., Gerstein, M. and Snyder, M., 2009. RNA-Seq: a revolutionary tool for transcriptomics. Nature reviews genetics, 10(1), pp.57-63. 2. Bullard, J.H., Purdom, E., Hansen, K.D. and Dudoit, S., 2010. Evaluation of statistical methods for normalization and differential expression in mRNA-Seq...
Barbara Engelhardt | Exploring Covariation in Gene Expression Data | CGSI 2016
08/09/2016 @ 09:30-10:30 Research Talk by Barbara Engelhardt Exploring Covariation in Gene Expression Data
Sriram Sankararaman | Inferring the Structure of Archaic Admixture in Modern Humans | CGSI 2016
08/05/2016 @ 11:15-12:00 Research Talk by Sriram Sankararaman Inferring the Structure of Archaic Admixture in Modern Humans 1. Patterson, N., Moorjani, P., Luo, Y., Mallick, S., Rohland, N., Zhan, Y., Genschoreck, T., Webster, T. and Reich, D., 2012. Ancient admixture in human history. Genetics, 192(3), pp.1065-1093. 2. Sankararaman, S., Patterson, N., Li, H., Pääbo, S….