Homework (Seminar summary reports)
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- Raivo Kolde
Q1. Why are methylation values obtained from whole genome bisulfite sequencing inaccurate?
Q2. What do we gain from smoothing the methylation measurements?
- Sten Ilmjärv
Q1. How does epigenetics regulate gene expression?
Q2. What are the two epigenetic indicators measured by the NOMe-seq method?
- Priit Adler (deadline 8.Apr)
Q1. What are the two prerequisites for the proposed method to work properly ?
Q2. From the point of differential expression: why would be looking whole pathways more interesting than individual genes ?
- Tauno Metsalu
Q1. What is the difference between basespace and colorspace read format? Convert the following sequence into colorspace format: AGCGACCGTA ?
Q2. What is phasing (in genomic context)? Describe which situations can arise when trying to phase a child SNP based on his/her mother and father SNP?
- Vijayachitra Modhukur
Q1. Does the model predicting gene expression based on chromatin features worked well in different cell lines ? was there major difference in prediction across multiple cell lines?
Q2. Describe bestbin? Can you list any disadvantages of this method.
- Kristjan Korjus
Q1. Sum up the diffusion distance in the simplest possible way for a non-technical person.
Q2. Think about your last high-demnsional data. How non-linear is the "information" in the data? Could the diffusion maps be useful for your work?
- Elena Nikolaeva
Q1. Describe the difference between regular Boolean network and Probabilistic Boolean network?
Q2. Look at the general modular structure of the model. Think why it was needed to introduce reprogramming module E to the system containing only modules A,B and P?
- Aleksei Panarin