SynBERC:MIT/Calendar/2007-1-17

Anyone in the synthetic biology community is welcome to attend.

Wednesday at 1pm

56-614, MIT

Topic of discussion

This week's lunch will be a journal club on papers covering the algorithms and validation testing of RNA folding programs like UNAfold, Sfold and Vienna fold.

Papers:

1. Do CB, Woods DA, and Batzoglou S. CONTRAfold: RNA secondary structure prediction without physics-based models. Bioinformatics. 2006 Jul 15;22(14):e90-8. DOI:10.1093/bioinformatics/btl246 |

   Results section only, especially Fig. 4 and Tables 3-4

2. Mathews DH. Revolutions in RNA secondary structure prediction. J Mol Biol. 2006 Jun 9;359(3):526-32. DOI:10.1016/j.jmb.2006.01.067 |
3. Shao Y, Wu Y, Chan CY, McDonough K, and Ding Y. Rational design and rapid screening of antisense oligonucleotides for prokaryotic gene modulation. Nucleic Acids Res. 2006;34(19):5660-9. DOI:10.1093/nar/gkl715 |

For more information see papers recommended by Chase in the Smolke lab.