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.
2007 notes are available for reference
Lecture Notes
Lecture 1 (09 Jan 2008) Introduction to Bioinformatics
BBSRC grant search page (enter bioinformatics as keyword)
Bioinformatics Journal
BMC Bioinformatics
Molecular Systems Biology
Notes in
pdf format (
2_up)
Lecture 2 (16 Jan 2008) Proteomics
Guest lecture from Juri Rappsilber
Notes
OPTIONAL: Web resources
IonSource - lots of links to info and tutorials on Mass Spec http://www.ionsource.com/
Proteome Commons - Repository of online tools for proteomics http://www.proteomecommons.org/tools.jsp
OPTIONAL
Further reading
General introduction: Steen H, Mann M. "The ABC's (and XYZ's) of peptide sequencing." Nat Rev Mol Cell Biol. 2004 Sep;5(9):699-711
Target-Decoy approach: Elias JE, Gygi SP. "Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry." Nat Methods. 2007 Mar;4(3):207-14.
SVM approach: Käll L, Canterbury JD, Weston J, Noble WS, MacCoss MJ. "Semi-supervised learning for peptide identification from shotgun proteomics datasets." Nat Methods. 2007 Nov;4(11):923-5. Epub 2007 Oct 21.
Cross-linking: Maiolica A, Cittaro D, Borsotti D, Sennels L, Ciferri C, Tarricone C, Musacchio A, Rappsilber J. "Structural analysis of multi-protein complexes by cross-linking, mass spectrometry and database searching." Mol Cell Proteomics. 2007 Dec;6(12):2200-11.
Protein vs peptide identification: Rappsilber J, Mann M. "What does it mean to identify a protein in proteomics?" Trends Biochem Sci. 2002 Feb;27(2):74-8.
Lecture 3 (21 Jan 2008) Protein Interaction Networks
Preparatory Review (internal access only)
Lecture
notes (
2_up)
Rual et al 2005
Han et al 2004
Pocklington et al 2006
Lecture 4 (30 Jan 2008) Microarray Technologies
Guest lecture from Donald Dunbar
Prep material:
Animated array tutorial (simple) at Davidson College
Detailed tutorial from UCL
Lecture
notes (
2_up)
February 6th - study week, no lecture
Lecture 5 (13 Feb 2008) Gene networks
Notes
Lecture 6 (20 Feb 2008) Gene sequences
Notes(
2_up)
Alignment exercise
Question: How does PAM250 work if it means a 250% substitution rate? I think the following description covers it, slides from
Golding and Morton's course at McMaster
Lecture 7 (27 Feb 2008) Bioinformatics in Industry
Slides, 6up, edinburgh access only
Slides, 2up colour, edinburgh access only
Lecture 8 (5 Mar 2008) Databases, Multiple Alignments, Gene and Protein Features
Slides, 6up
Slides 2up, colour
