Morning Sessions
 
**Session 1** 
**7:25-7:50** HIV-Haplotype Inference using a Constraint-based Dirichlet Process Mixture Model *Sandhya Prabhakaran* - 
**7:50-8:15** De novo RNA-seq-based Genome Annotation *Jonas Behr* 
**8:15-8:40** Inferring exon junction expression from RNA-Seq data *Boyko Kakaradov*  
**8:40-09:05** Predicting Tissue-Dependent Alternative Splicing Using Bayesian Neural Networks *Hui Xiong*  
**09:05-09:20** Coffee  
 
**Session 2**,  
**9:20-10:05** Invited Talk: Orienting physical networks * Roded Sharan, Tel-Aviv University* In a network orientation problem one is given a mixed graph, consisting of directed and undirected edges, and a set of source-target vertex pairs. The goal is to orient the undirected edges so that a maximum number of pairs admit a directed path from the source to the target. This problem arises in the context of analyzing physical networks of protein-protein and protein- DNA interactions. While the latter are naturally directed from a transcription factor to a gene, the direction of signal flow in protein-protein interactions is often unknown or cannot even be measured en masse. One then tries to infer this information by using causality data on pairs of genes such that the perturbation of one gene changes the expression level of the other gene. In my talk I will discuss the complexity of the problem, show approximation algorithms for several variants of it and present an efficient ILP solution for it. I will then describe the application of this algorithm to orient protein-protein interactions in yeast, improving our understanding of the structure and function of the network.  
**10:05-10:35** Regularized Output Kernel Regression for protein-protein interaction prediction: application to link transfer and transduction *Florence d'Alché-Buc*  
 
Afternoon Sessions 
 
**Session 3**  
**3:45-4:10** Inferring Multiple Regulation Networks *Julien Chiquet* 
**4:10-4:35** A probabilistic topic model for the analysis of blood diseases *Gerald Quon* 
**4:35-5:00** JigPheno: Semantic Feature Extraction from biological images *Theofanis Karaletsos* 
**05:00-05:15** Coffee  
 
**Session 4** 
**5:15-5:40** A joint genotypic/phenotypic mixture model for GWAS *Anna Goldenberg*  
**5:40-6:00** Correction for Hidden Confounders in the Genetic Analysis of Gene Expression *Jennifer Listgarten*  
**6:00-6:20** Explaining Confounding Factors in eQTL Studies using a Dictionary of Latent Variables *Nicolò Fusi* 
**6:20-6:30** Discussion