WHERE
Takustr. 9, Room 005


WHEN
Wednesday, 12 am-14 pm


CONTENT
Non-coding RNAs have been recognized as an abundant class of genes with a wide spectrum of functions, often performed through their structure. Given their involvement in almost every biological process, in the last 10 years increasing attention has been given to RNA bioinformatics, the discipline devoted to the development of computational tools and methodologies for the analysis of RNA sequence, structure and function.
This seminar is meant for master students and the goal is to look deeper at some selected papers describing algorithms or statistical methods for ncRNA promoter and gene finding, RNA structure prediction, ncRNA functional analysis, RNA motif discovery and RNA-protein interaction prediction. In addition, the aim will be to use the articles as a starting point to critically assess the methodologies, and understand how they can be improved or extended to other contexts. The proposed journal articles are listed below and this list can be extended or changed depending on the number of participants. The number of participants will be limited to 14.

    

Non-coding RNA Gene finding methods

   

1) A statistical model for prediction and scoring of novel microRNA genes from deep sequencing data
http://www.ncbi.nlm.nih.gov/pubmed/18392026

presentation_miRDeep ...by Valentin

2) Prediction of non-coding RNA genes using comparative genomics (RNAz)
http://www.ncbi.nlm.nih.gov/pubmed/15665081 

presentation_RNAz ..by Marcel

3) Computational discovery of transcripts with conserved splice sites
http://www.ncbi.nlm.nih.gov/pubmed/21622663

presentation_phylogenSVM ..by Adrian


Analysis of RNA sequence and structure

    

4) RNA consensus secondary structure prediction from multiple sequence alignments (RNAalifold)
http://www.ncbi.nlm.nih.gov/pubmed/19014431

presentation_RNAalifold ..by Moritz

5) Analysis of RNA secondary structure in vivo - PARS
http://www.ncbi.nlm.nih.gov/pubmed/24476892

presentation_PARSscores ..by Fritz

6) Analysis of Secondary Structure in vivo - DMS

http://www.ncbi.nlm.nih.gov/pubmed/24270811

presentation_DMSscores ..by Arsene

7) An overview on the analysis of RNA-seq data

presentation_RNAseq ..by Matthias

  

Discovery of RNA motifs

    

8) De Novo discovery of functional motifs in mRNAs using context-free grammars
http://www.ncbi.nlm.nih.gov/pubmed/22495308

presentation_TEISER ..by Timo

9) Prediction of RNA motifs using a covariance model
http://www.ncbi.nlm.nih.gov/pubmed/16357030

presentation_CMfinder ..by Annkatrin

    

RNA-binding site predictions

   

10) Probabilistic model for the prediction of protein binding sites for RNA sequences and structures
http://www.ncbi.nlm.nih.gov/pubmed/20617199

presentation_RNAcontext ..by Ria

11) A method to identify differential RNA binding proteins from iCLIP data using a Hidden Markov Model
http://www.ncbi.nlm.nih.gov/pubmed/24398258

presentation_dCLIP ..by Jakob

12) Overview on the analysis of CLIP-seq data (mainly iCLIP)

presentation_iCLIP ..by Sabrina

  

Functional analysis of non-coding RNA targets

   

13) A machine learning method (regression model)  to rank microRNA target genes
http://www.ncbi.nlm.nih.gov/pubmed/20799968

presentation_miRSVR ..by Stefan

14) Combinatorial miRNA target prediction
http://www.ncbi.nlm.nih.gov/pubmed/15806104

presentation_picTar ..by Herbert

 
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