Literature
Study questions
We have written down a set of study questions.
List of Papers
Note: This is a preliminary list of articles that is subject to change
| L2 |
Mandatory: Mihai Pop: Genome assembly reborn: recent computational challenges. Paper for student presentation: Vezzi et al on the Feature Response Curve. Paper for student presentation: Bradnam et al: Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species |
| L3 | |
| L5 |
Mandatory: Trapnell and Salzberg: How to map billions of short reads onto genomes Paper for student presentation: Langmead and Salzberg: Fast gapped-read alignment with Bowtie 2 |
| L6 |
Mandatory: RNA-seq analysis methods: Garber et al, Nature Methods 8:469-477 (2011) Optional: Lecture notes on RNA-seq from BB2440 Bioinformatics and biostatistics (fall 2015) (use this to refresh your RNA-seq acquaintance) Optional: RNA-seq: a revolutionary tool for transcriptomics Wang et al. Nat Rev Genet 10:57-63 (2009) Paper for student presentation, STAR: Dobin et al. Bioinformatics 29:15-21 (2013) Paper for student presentation, DEseq: Anders and Huber. Genome Biol 11:r106 (2010) |
| L7 |
Mandatory: ChIP-seq introduction: Furey, Nat Rev Genet 13:840-852 (2012) Paper for student presentation, MACS: Zhang et al Genome Biol 9:r137 (2008) |
| L8 |
Introduction MS-based proteomics: Steen and Mann, Nat Rev Mol Cell Biol. 5:699-711 (2004) [Do not try to read the printable pdf, use the html or readcube versions] Computational MS-based Proteomics: Noble and Maccoss, PLoS Comput Biol 8(1): e1002296 (2012) |
| L9 |
Assigning Significance: Käll et al. J Proteome Res, 7 (01):29–34 (2008) A draft map of the human proteome: Kim et al. Nature 509:575–581 (2014) |
| L10 |
Targeted Proteomics: Picotti et al. Cell. 2009 Aug 21;138(4):795-806. |
| L11 |
Project Organization: Noble PLoS Comput Biol 5(7): e1000424 (2009) |