Recommanded background reading for all:

•   Kwok, Biochem Soc Trans (2016) 44(5):1395-1410. Dawn of the in vivo RNA structurome and interactome. (paper: kwok_2016.pdf)
• Eddy, Annu Rev Biophys. (2014) 43:433-56 Computational analysis of conserved RNA secondary structure in transcriptomes and genomes. (paper: eddy_2014.pdf)

List of seminar papers:

In case you have any questions regarding your paper(s), please be in touch with Stefan or Peter, see the details below for each paper. Note that some presentations cover more than one paper. Every presentation should take 45 minutes plus 15-20 minutes of discussion. Be sure to include one or two slides with your own ideas/questions at the end to chair the discussion.

All pdf-files for papers can be found in this folder.

(1) Reautschnig et al., RNA Biol. (2017) 14(5):651-66 The notorious R.N.A. in the spotlight - drug or target for the treatment of disease. (paper: reautschnig_2017.pdf, contact: Stefan)

(2) Havens et al., Nucleic Acids Res. (2016) 44(14):6549-63 Splice-switching antisense oligonucleotides as therapeutic drugs.  
 (paper: havens_2016.pdf, contact: Stefan),  see also info on Spinraza (Nusinersen), Fomivirsen and other FDA-approved antisense oligonucleotide drugs.

(3) Watts et al. Nature (2009), 460(7256) Architecture and secondary structure of an entire HIV-1 RNA genome. (paper: watts_2009.pdf, SI: watts_2009_supplementary_data.pdf, contact: Stefan)

(4) Siegfried et al., Nat Methods. (2014) 11(9):959-65. RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP). (paper: siegfried_2014.pdf, contact: Stefan)

(5) Rausch et al., Front Microbiol. (2018) 8:2634, Probing the Structures of Viral RNA Regulatory Elements with SHAPE and Related Methodologies. (paper: rausch_2018_review.pdf, contact: Stefan)

(6) Deigan et al., PNAS (2009) 106(1):97--102, Accurate SHAPE-directed RNA structure determination. (paper: deigan_2009.pdf) and Lorenz et al. Bioinformatics (2016) 32(1):145-147, SHAPE directed RNA folding. (paper: lorenz_2016.pdf, contact: Peter)

(7) Sükösd et al, Bioinformatics (2012) 28(20):2691-2. PPfold 3.0: fast RNA secondary structure prediction using phylogeny and auxiliary data. (paper: suekoesd_2012_ppfold.pdf) and Sahoo et al., Bioinformatics. (2016) 32(17):2626-35. ProbFold: a probabilistic method for integration of probing data in RNA secondary structure prediction. (paper: sahoo_2016_probfold.pdf,
SI: sahoo_2016_probfold_SI.pdf, contact: Peter)

(8) Pervouchine, RNA (2014), 20(10):1519-31. IRBIS: a systematic search for conserved complementarity. (paper: pervouchine_2014_irbis.pdf, contact: Peter)

(9) Pervouchine, RNA (2012), 18(1):1-15. Evidence for widespread association of mammalian splicing and conserved long-range RNA structures. (paper: pervouchine_2012.pdf, contact: Peter)

(10) Mazloomian et al, RNA Biology (2015) 12(12):1391-401. Genome-wide identification and characterization of tissue-specific RNA editing events in D. melanogaster and their potential role in regulating alternative splicing. (paper: mazloomian_2015.pdf, SI: mazloomian_2015.tar.bz2, contact: Peter)

(11) Lai et al, Nucleic Acids Research (2016) 44(7): e61, A comprehensive comparison of general RNA-RNA interaction prediction methods. (paper: lai_2016.pdf, contact: Peter)

(12)  Fukunaga et al., Bioinformatics (2017) 33(17):2666-2674 RIblast: an ultrafast RNA-RNA interaction prediction system based on a seed-and-extension approach (paper: fukunaga_2017.pdf) and Mann et al. Nucleic Acids Research (2017) 45:W435-W439 IntaRNA 2.0: enhanced and customizable prediction of RNA-RNA interactions (paper: mann_2017.pdf, contact: Peter)

(13) Melamed et al, Mol Cell. (2016) 63(5):884-97. Global Mapping of Small RNA-Target Interactions in Bacteria. (paper: melamed_2016.pdf, contact: Stefan)

(14) Lu et al., Cell (2016) 165(5):1267-79, RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure. (paper: lu_2016_paris.pdf, paper and SI: lu_2016.tar.bz2, contact: Stefan)

(15) Sharma et al., Mol Cell. (2016) 62(4):618-26, Global Mapping of Human RNA-RNA Interactions. (paper: sharma_2016_LIGR_seq.pdf, paper and SI: sharma_2016.tar.bz2) and Aw et al., Mol Cell. (2016) 62(4):603-17, In Vivo Mapping of Eukaryotic RNA Interactomes Reveals Principles of Higher-Order Organization and Regulation. (paper: aw_2016_SPLASH.pdf, paper and SI: aw_2016.tar.bz2, contact: Stefan)