[talks] V Yao generals

Melissa M. Lawson mml at CS.Princeton.EDU
Thu May 16 10:16:40 EDT 2013

Vicky Yao will present her research seminar/general exam on Monday May 20 at 10AM in Room 402. The 
members of her committee are: Olga Troyanskaya (advisor), Mona Singh, and John Storey (MOL). 
Everyone is invited to attend her talk, and those faculty wishing to remain for the oral exam following are 
welcome to do so. Her abstract and reading list follow below. 

----- Original Message -----


Integration of genomics data has already been shown to be helpful in improving our understanding of functional relationships between genes in a wide range of organisms, including yeast, worm, mouse, and human. As the quantity of these datasets increases, we are presented with the opportunity not only in improving functional predictions between genes, but also in attempting to attack this difficult problem of understanding functional relationships in tissue-specific contexts, with the eventual goal of developing a better understanding of alternative splicing and isoform expression in different tissues. We create tissue-specific functional networks in C. elegans by utilizing knowledge of already curated tissue-specific genes in our integration of available genomics data using Bayesian learning methods. By extending our tissue-specific functional predictions in genes to differentially spliced exons and leveraging known protein domain interaction data, we hope to be able to predict potential tissue-specific protein interactions. These predictions would be extremely useful for improving our understanding of tissue-specific processes. 

Reading list: 
Introduction to Machine Learning (second edition) by Ethem Alpaydin 

Ch 1 Introduction 
Ch 2 Supervised Learning 
Ch 3 Bayesian Decision Theory 
Ch 4 Parametric Methods 
Ch 5 Multivariate Methods 
Ch 8 Nonparametric Methods 
Ch 10 Linear Discrimination 
Ch 14 Bayesian Estimation 
Ch 17 Combining Multiple Learners 
Ch 19 Design and Analysis of Machine Learning Experiments 

Anders S, Huber W (2010) Differential expression analysis for sequence count data. Genome Biology 11:R106. 

Anders S, Reyes A, Huber W (2012) Detecting differential usage of exons from RNA-seq data. Genome Research 22: 2008-2017. 

Bossi A, Lehner B (2009) Tissue specificity and the human protein interaction network. Mol Syst Biol 5: 260. 

Buljan M, Chalancon G, Eustermann S, Wagner GP, Fuxreiter M, Bateman A, Babu MM (2012) Tissue-specific splicing of disordered segments that embed binding motifs rewires protein interaction networks. Mol Cell 46(6): 871-83. 

Chikina MD, Huttenhower C, Murphy CT, Troyanskaya OG (2009) Global Prediction of Tissue-Specific Gene Expression and Context-Dependent Gene Networks in Caenorhabditis elegans. PLoS Comput Biol 5(6): e1000417. 

Guan Y, Gorenshteyn D, Burmeister M, Wong AK, Schimenti JC, Handel MA, Bult CJ, Hibbs MA, Troyanskaya OG (2012) Tissue-specific functional networks for prioritizing phenotype and disease genes. PLoS Comput Biol 8(9): e1002694. 

Kim D, Pertea G, Trapnell C, Pimentel H, Kelley H, Salzberg SL (2013) TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biology 14:R36. 

Li Y, Breitling R, Snoek BL, van der Velde KJ, Swertz MA, Riksen J, Jansen RC, Kammenga JE (2010) Global Genetic Robustness of the Alternative Splicing Machinery in Caenorhabditis elegans . Genetics 186: 405-410. 

Merkin J, Russel C, Chen P, Burge CB (2012) Evolutionary Dynamics of Gene and Isoform Regulation in Mammalian Tissues. Science 338(6114): 1593-9. 

Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schorth GP, Burge CB (2008) Alternative isoform regulation in human tissue transcriptomes. Nature 456: 470-476. 

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