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Date	Presenter	Respondent	Paper
16-Sep Tuesday 9:30-12:30 Dr. Steffany Bennett Dr Daniel Figeys	All students		2 min Introduction using 1 Powerpoint slide On the first day of class, please bring a brief abstract introducing yourself (see below) and a single powerpoint slide you can use to introduce yourself to the group. Please include the following information in your abstract: a) who you work for b) where you are in your program (M.Sc. or Ph.D, what year) c) whether this your first graduate course d) your thesis topic and areas of expertise Maximum 100 words. Each student will introduce themselves with a slide on the first day of class (2 min presentation in which you tell us a-d above). Background reading for class: Glass DJ and Hall N (2008) A brief history of the hypothesis. Cell 134:378-381 (PDF)
23-Sep Tuesday 9:30-12:30 Dr Daniel Figeys	Proteomics		Background reading: Kocher T, Superti-Furga G (2007) Mass spectrometry-based functional proteomics: from molecular machines to protein networks. Nat Methods 4:807-815. (PDF) Smith JC, Lambert JP, Elisma F, Figeys D (2007) Proteomics in 2005/2006: developments, applications and challenges. Anal Chem 79:4325-4343. (PDF)
	Presenter Katy Morin	Respondent Luke Wu	Kruger M, Moser M, Ussar S, Thievessen I, Luber CA, Forner F, Schmidt S, Zanivan S, Fassler R, Mann M (2008) SILAC mouse for quantitative proteomics uncovers kindlin-3 as an essential factor for red blood cell function. Cell 134:353-364. (PDF)
30-Sept Tuesday 9:30-12:30 Dr Robert Screaton Coordinator: Dr. Daniel Figeys	Delineating signaling pathways using functional genomics		Background reading: Echeverri CJ, Perrimon N (2006) High-throughput RNAi screening in cultured cells: a user's guide. Nat Rev Genet 7:373-384. (PDF)
	Presenter James Butcher	Respondent Yubing Liu	Pick one of the following or compare and contrast both papers (email Drs Bennett and Figeys your choice): Kittler R, Pelletier L, Heninger AK, Slabicki M, Theis M, Miroslaw L, Poser I, Lawo S, Grabner H, Kozak K, Wagner J, Surendranath V, Richter C, Bowen W, Jackson AL, Habermann B, Hyman AA, Buchholz F (2007) Genome-scale RNAi profiling of cell division in human tissue culture cells. Nat Cell Biol 9:1401-1412 (PDF) Pelkmans L, Fava E, Grabner H, Hannus M, Habermann B, Krausz E, Zerial M (2005) Genome-wide analysis of human kinases in clathrin- and caveolae/raft-mediated endocytosis. Nature 436:78-86. (PDF)
7-Oct Tuesday 9:30-12:30 Dr Kristin Baetz Coordinator: Dr. Steffany Bennett	Functional and chemical genomics		Background reading: Armour CD, Lum PY (2005) From drug to protein: using yeast genetics for high-throughput target discovery. Curr Opin Chem Biol 9:20-24. (PDF)
	Presenter Maryam Zaid	Respondent All students	Hoon S, Smith AM, Wallace IM, Suresh S, Miranda M, Fung E, Proctor M, Shokat KM, Zhang C, Davis RW, Giaever G, StOnge RP, Nislow C (2008) An integrated platform of genomic assays reveals small-molecule bioactivities. Nat Chem Biol 4:498-506 (PDF)
14-Oct Tuesday 9:30-12:30 Dr Alexandre Blais Coordinator: Dr. Daniel Figeys	Functional genomics: ChIP-on-chip, RNA interference and expression profiling Background reading		Background reading: Baylin SB, Schuebel KE (2007) Genomic biology: the epigenomic era opens. Nature 448:548-549. (PDF) Bernstein BE, Meissner A, Lander ES (2007) The mammalian epigenome. Cell 128:669-681. (PDF)
	Presenter Yubing Liu	Respondent Houssein Salem Abdou	Mikkelsen TS et al. (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448:553-560. (PDF) Supplementary material (PDF)
21-Oct Tuesday 9:30-12:30 Dr Steffany Bennett Dr Daniel Figeys	All students		Writing Workshop Topic: How to write a scholarly review of a published paper Resources: 1. What is plagiarism (PDF)? 2. How to plan write and prepare a biomedical paper for publication: Online writing course (Inter-Biotec) 3. Westbrook G and Cooper L. Say it Simply: Tips for Clear Writing. (published online) 4. Westbrook G and Cooper L. Techniques for Clear Scientific Writing and Editing. (published online) First paper for scholarly review: A systems level analysis of transcriptional changes in Alzheimer's disease and normal aging. J Neurosci 28:1410-1420. (PDF)
28-Oct Tuesday 9:30-12:30 Dr. Mads Kaern Coordinator: Dr. Daniel Figeys	Computational Biology		Background reading: Muzzey D, van Oudenaarden A (2006) When it comes to decisions, myeloid progenitors crave positive feedback. Cell 126:650-652. (PDF)
	Presenter Luke Wu	Respondent Maryam Zaid	Laslo P, Spooner CJ, Warmflash A, Lancki DW, Lee HJ, Sciammas R, Gantner BN, Dinner AR, Singh H (2006) Multilineage transcriptional priming and determination of alternate hematopoietic cell fates. Cell 126:755-766. (PDF)
4-Nov Tuesday 9:30-12:30 Dr Marjorie Brand Coordinator: Dr. Steffany Bennett	The proteomics of differentiation		Background reading: Panchaud A, Affolter M, Moreillon P, Kussmann M (2008) Experimental and computational approaches to quantitative proteomics: status quo and outlook. J Proteomics 71:19-33. (PDF)
	Presenter All students General Discussion	Respondent Josh Chan opens discussion	Williamson AJ, Smith DL, Blinco D, Unwin RD, Pearson S, Wilson C, Miller C, Lancashire L, Lacaud G, Kouskoff V, Whetton AD (2008) Quantitative proteomics analysis demonstrates post-transcriptional regulation of embryonic stem cell differentiation to hematopoiesis. Mol Cell Proteomics 7:459-472. (PDF)
11-Nov Tuesday 9:30-12:30 Dr Jean-François Couture Coordinator: Dr. Steffany Bennett Coordinator Evaluation	Metabolomics: Applying structural biology to the study of gene regulation Background reading
	Presenter Houssein Salem Abdou	Respondent James Butcher	Compare both papers in your presentation (they are tightly linked): Sims RJ, 3rd, Chen CF, Santos-Rosa H, Kouzarides T, Patel SS, Reinberg D (2005) Human but not yeast CHD1 binds directly and selectively to histone H3 methylated at lysine 4 via its tandem chromodomains. J Biol Chem 280:41789-41792. (PDF) Flanagan JF, Mi LZ, Chruszcz M, Cymborowski M, Clines KL, Kim Y, Minor W, Rastinejad F, Khorasanizadeh S (2005) Double chromodomains cooperate to recognize the methylated histone H3 tail. Nature 438:1181-1185. (PDF)
18-Nov Tuesday 9:30-12:30 Dr Steffany Bennett Dr Daniel Figeys Coordinator Evaluation	All students		Writing Workshop Topic: Improving an article by responding to peer review Improving peer-review critique 2nd paper for scholarly review handed out
25-Nov Tuesday 9:30-12:30 Dr Hai-Ying Mary Cheng Coordinator: Dr. Daniel Figeys	Metabolomics: Cellular Mechanisms of Biological Timing		Background reading: Green CB, Takahashi JS, Bass J (2008) The meter of metabolism. Cell 134:728-742. (PDF)
	Presenter Tara Seibert	Respondent Katy Morin	Compare both papers in your presentation (they are tightly linked): Asher G, Gatfield D, Stratmann M, Reinke H, Dibner C, Kreppel F, Mostoslavsky R, Alt FW, Schibler U (2008) SIRT1 regulates circadian clock gene expression through PER2 deacetylation. Cell 134:317-328. (PDF) Nakahata Y, Kaluzova M, Grimaldi B, Sahar S, Hirayama J, Chen D, Guarente LP, Sassone-Corsi P (2008) The NAD+-dependent deacetylase SIRT1 modulates CLOCK-mediated chromatin remodeling and circadian control. Cell 134:329-340. (PDF)
2-Dec Tuesday 9:30-12:30 Dr. Steffany Bennett	Lipidomics Background reading		Background reading: Piomelli D, Astarita G, Rapaka R (2007) A neuroscientist's guide to lipidomics. Nat Rev Neurosci 8:743-754. (PDF)
	Presenter Josh Chan	Respondent Tara Seibert	Kiebish MA, Han X, Cheng H, Chuang JH, Seyfried TN (2008) Cardiolipin and electron transport chain abnormalities in mouse brain tumor mitochondria: Lipidomic evidence supporting the Warburg theory of cancer. J Lipid Res. (epub ahead of print) (PDF)
9-Dec Tuesday (9:30-12:30) Dr. Steffany Bennett Dr Daniel Figeys	All students		Writing Workshop Topic: How to co-author a paper. What is the role of the corresponding author?
16-Dec Tuesday (9:30-12:30) Dr. Steffany Bennett Dr Daniel Figeys	Final paper due. Designated corresponding author submits the paper online