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
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| L3 |
Storey&Tibshirani
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| 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
Paper for student presentation: Heng Li: Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM
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| L6 |
Mandatory: RNA-seq analysis methods: Garber et al, Nature Methods 8:469-477 (2011)
Optional: RNA-seq introduction: Wang et al, Nat Rev Genet 10:57-63 (2009)
Optional: Lecture notes on RNA-seq from BB2440 Bioinformatics and biostatistics (fall 2015)
Paper for student presentation, TopHat2: Kim et al. Genome Biol 14:r36 (2013)
Paper for student presentation, DEseq: Anders and Huber. Genome Biol 11:r106 (2010)
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| L7 |
Mandatory: ChIP-seq introduction: Park, Nat Rev Genet 10:669-680 (2009)
Paper for student presentation, Macs: Zhang et al Genome Biol 9:r137 (2008)(not required reading)
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| 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)
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| L9 |
Deep Proteomics: Pirmoradian et al., Molecular & Cellular Proteomics, 12, 3330-3338. (2013)
Blind-PTMs: Tsur et al., Nature Biotechnology 23:1562 (2005)
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| L10 |
Targeted Proteomics: Picotti et al. Cell. 2009 Aug 21;138(4):795-806.
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| L11 |
Project Organization: Noble PLoS Comput Biol 5(7): e1000424 (2009)
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