Compulsory background reading for the PhD summer school:
For each of the sessions, we have compiled some background literature, which should read by the participants before attending the PhD Course in order to obtain full ECTS credit for the course. Moreover, being familiar with this literature will improve the participants’ learning outcome of the course.
General tools/software
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Galaxy |
http://www.ncbi.nlm.nih.gov/pubmed/20738864 Make this exercise: https://main.g2.bx.psu.edu/galaxy101 (Be sure to make and remember your Galaxy login.)See more about Galaxy here: |
Day 1: Sequencing methods
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Sequencing Technologies |
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Mapping of sequencing reads |
To be announced |
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RNA-seq, using Galaxy pipeline (Tophat, Cufflinks) |
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Protein-RNA interactions |
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UCSC Cancer Genomics Browser |
Day 2: Applied RNA structure prediction
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RNA structure intro |
Mailed pdf: Chapter 6: An Introduction to RNA Databases. Hoeppner et al. To appear in “RNA Bioinformatics”. (background) |
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Single sequence folding |
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Comparative RNA folding |
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RNA structure discovery: homology methods |
Mailed pdf: Building non-coding RNA families. Barquist et al. To appear in “RNA Structure Determination” (core) Mailed pdf: Annotating functional RNAs in genomes using Infernal, Eric P. Nawrocki. To appear in “RNA Bioinformatics” (background) |
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RNA structure discovery: de novo methods |
Day 3: miRNA, miRNA targets and small RNA sequencing
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miRNA introduction (miBase) |
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miRNA targets (TScan) |
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Viral interactions with cellular miRNAs |
http://www.ncbi.nlm.nih.gov/pubmed/15118162 |
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miRNA target site enrichment |
To be announced |
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Cwords / Sylamer exercise |
To be announced |
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Experimental RNA structure probing. |
http://www.ncbi.nlm.nih.gov/pubmed/21057495http://www.ncbi.nlm.nih.gov/pubmed/21615079 |
Day 4: Antisense Oligonucleotide drugs
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RNA-RNA Interactions |
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RNA as a drug target |
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Targeting RNA |
Exploring the RNAiTherapeuticsBlog is a very good way to get into both the science and the business challenges |
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The world’s first microRNA medicine |