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Bioinformatics 2

Notes

Where possible I shall post lecture notes the evening after the lecture. Additional reading will be posted before or after the lecture as appropriate.

2006 notes are available for reference
Note that there is a considerable change is emphasis and order this year.

Lecture Notes

Lecture 1 (Jan 10 2007) Introduction and Proteomics I
Introduction to Bioinformatics; Proteomics Data and Concepts, Guest speaker, Juri Rappsilber.
Note: Juri is adding some text notes to his slides before posting so there wil be a short delay. his lecture will be concluded next week.
Introduction lecture Notes p1
Proteomics 1 (UofE access only
Wikipedia: Peptide sequence
IonSource - lots of links to info and tutorials on Mass Spec
MASCOT Sequest

Lecture 2 (Jan 17 2007) Proteomics II
Overview of Bioinformatics and Central Dogma of Molecular Biology.
Protemics II, Juri Rappsilber cont'd; Protein Interactions and Networks pdf
OMSSA
Geer LY, Markey SP, Kowalak JA, Wagner L, Xu M, Maynard DM, Yang X, Shi W, Bryant SH.Open mass spectrometry search algorithm. J Proteome Res. 2004 Sep-Oct;3(5):958-64
Good introduction/tutorial: Steen H, Mann M. "The ABC's (and XYZ's) of peptide sequencing." Nat Rev Mol Cell Biol. 2004 Sep;5(9):699-711

Lecture 3 (Jan 24 2007) CANCELLED

Lecture 3 (Jan 31 2007) Gene Expression Arrays, Guest speaker, Donald Dunbar.
Lecture notes

Lecture 4 (Feb 7 2007) From genomes and proteomics to biological networks.
Slides. (2up)
Milo et al 2002 paper on Network Motifs
H. Jeong, B. Tombor, R. Albert, Z.N. Oltvai, and A.-L. Barabási The large-scale organization of metabolic networks Nature 407, 651-654 (2000). PDF

Lecture 5 (Feb 14 2007) Protein Networks
Lecture notes (draft) [2 up]
Rual et al 2005
Han et al 2004
Pocklington et al 2006

Lecture 6 (Feb 21 2007) Sequence Alignment
Lecture notes [2_up]
alignment exercise

Lecture 7 (Feb 28 2007) Databases, Multiple Alignments, Gene and Protein Features
Lecture notes part 1 [2_up]
Lecture notes part 2 [2_up]

Lecture 8 (Mar 7 2007) Perspectives on Bioinformatics.
Malcolm Walkinshaw Ribosome movie
Philippe Sanseau slides [2_up]

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