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 Storey&Tibshirani

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)

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 Deep Proteomics: Pirmoradian et al., Molecular & Cellular Proteomics, 12, 3330-3338. (2013)

Blind-PTMs: Tsur et al., Nature Biotechnology 23:1562Assigning Significance: Käll et al. J Proteome Res, 7 (01):29–34 (20058)

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)