Syllabus [PDF]
New place and time: Biotech 202, Mon 1:00-2:00
| Date | Paper | Presenter |
|---|---|---|
| 1/28 | Bernal et al. Global discriminative learning for higher-accuracy computational gene prediction. PLoS Comput Biol (2007) vol. 3 (3) pp. e54 [link] | Abra |
| 2/04 | Krogh et al. Hidden neural networks. Neural computation (1999) vol. 11 (2) pp. 541-63 [link] | Ben |
| 2/11 | DeCaprio et al. Conrad: gene prediction using conditional random fields. Genome Res (2007) vol. 17 (9) pp. 1389-98 [link] | Andre |
| 2/18 | Huelsenbeck et al. A nonparametric method for accommodating and testing across-site rate variation. Syst Biol (2007) vol. 56 (6) pp. 975-87 [link] | Carolin |
| 2/25 | Rodrigue et al. Uniformization for sampling realizations of Markov processes: applications to Bayesian implementations of codon substitution models. Bioinformatics (2008) vol. 24 (1) pp. 56-62 [link] | Fang |
| 3/03 | No class (ACS on travel) | ----- |
| 3/10 | Rasmussen et al. Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes. Genome Res (2007) [link] | Tristan |
| 3/17 | Spring break | ----- |
| 3/24 | Tang et al. Reconstructing genetic ancestry blocks in admixed individuals. Am J Hum Genet (2006) vol. 79 (1) pp. 1-12 [link] | Tomas |
| 3/31 | Luedi et al. Computational and experimental identification of novel human imprinted genes. Genome Res (2007) vol. 17 (12) pp. 1723-30 [link] | Gabe |
| 4/07 | Stark et al. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature (2007) vol. 450 (7167) pp. 219-32 [link] | Brona |
| 4/14 | Drosophila 12 Genomes Consortium et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) vol. 450 (7167) pp. 203-218 [link] | Kathryn |
| 4/21 | Raijman et al. Evolution and Selection in Yeast Promoters: Analyzing the Combined Effect of Diverse Transcription Factor Binding Sites. PLoS Comput Biol (2008) vol. 4 (1) pp. e7 [link] | Patrick |
| 4/28 | Frith et al. A code for transcription initiation in mammalian genomes. Genome Res (2008) vol. 18 (1) pp. 1-12 [link] | Lalit |
Original list of possible papers [link]