Date | Topic | Papers | Presenter | Notes and related papers |
1/20 | Course overview, introduction to basics of cancer biology | Hanahan2011, Vogelstein2013, Ding2014 | Lecture | Slides (pptx, pdf) |
1/22 | Types of “omic” data, resources and databases | | Lecture | Slides (pptx, pdf) |
1/27 | DNA mutation significance, correcting for confounders | MutSigCV (Lawrence2013) | Chris M. | MutSig (Getz2007), MuSiC (Dees2012) Slides (pptx, pdf) |
1/29 | Copy number variation significance | GISTIC 2.0 (Mermel2011) | Erkin O. | GISTIC (Beroukhim2007), RAIG (Wu2014) Slides (pdf) |
2/3 | Mutational signatures, topic models for mutations | Alexandrov2013a | Taylor J. | Lee1999, Lee2001, Nik-Zainal2012, Alexandrov2013b Slides (pptx, pdf) |
2/5 | Identifying mutually exclusive genomic events | MEMo (Ciriello2012) | Haixiang L. | Szczurek2014 Slides (ppt, pdf) |
2/10 | Identifying mutually exclusive genomic events | Multi-Dendrix (Leiserson2013) | Jiayue L. | Dendrix (Vandin2012) Slides (pptx, pdf) |
2/12 | Classification | Golub1999 | Vee V. | PAM (Tibshirani2002), Parker2009 Slides (pptx, pdf) |
2/17 | Clustering and gene signatures | van'tVeer2002 | Tyler H. | Slides (pdf) Present project ideas (pptx, pdf) |
2/19 | Random gene expression signatures | Venet2011 | Molly C. | Ein-Dor2005, Tofigh2014 Slides (pptx, pdf) |
2/24 | Matching tumors and cell lines | Domcke2013 | Anita S. | Dudley2011, Sun2015 Slides (pptx, pdf) |
2/26 | Drug response | CCLE (Barretina2012) | Chris M. | Elastic net (Zou2005), Garnett2012, Haibe-Kains2013 Slides (pdf) |
3/3 | Gene essentiality | ATARiS (Shao2013) | Erkin O. | Achilles (Cheung2011), Marcotte2012 Slides (pdf) |
3/5 | Integrating RNAi screens and tumor data | Helios (Sanchez-Garcia2014) | Taylor J. | Slides (pptx, pdf) |
3/10 | Integrated modeling of transcriptional drivers | Setty2012 | Jiayue L. | Project proposals due Kim2010, Verhaak2010 Slides (pptx, pdf) |
3/12 | Integrating ENCODE and TCGA data | RACER (Li2014) | Haixiang L. | GenMiR++ (Huang2007) Slides (pdf) |
3/17 | Integrating phosphorylation and transcription | Osmanbeyoglu2014 | Vee V. | Slides (pdf) |
3/19 | Pan-cancer clustering | Hoadley2014 | Anita S. | ConsensusClusterPlus (Wilkerson2010), TCGA pan-cancer Slides (pptx, pdf) |
3/24 | Pathway and gene set enrichment analysis | Subramanian2005 | Chris M. | DAVID (Huang2008), Irizarry2009, PathScan (Wendl2011) Slides (pdf) |
3/26 | Probabilistic graphical models for pathway inference | PARADIGM (Vaske2010) | Erkin O. | PARADIGM-SHIFT (Ng2010), Sedgewick2013 Slides (pdf) |
3/31 | Spring break | | No class | |
4/2 | Spring break | | No class | |
4/7 | Network diffusion and hot spot identification | HotNet (Vandin2011) | Taylor J. | Qi2008, TieDIE (Paull2013), HotNet2 (Leiserson2014) Slides (pptx, pdf) |
4/9 | Network-based stratification | NBS (Hofree2013) | Jiayue L. | Project status report due Cai2008 Slides (pptx, pdf) |
4/14 | Mutations’ impact on phosphorylation signaling | ActiveDriver (Reimand2013) | Haixiang L. | |
4/16 | Finding connections in protein interaction networks | PCST (Huang2013) | Professor Gitter | msgsteiner (Bailly-Bechet2011), Multi-PCSF (Gitter2014) Slides (pptx, pdf) |
4/21 | Prioritizing drivers with regulatory networks | DIGGIT (Chen 2014) | Vee V. | Slides (pdf) |
4/23 | Intra-tumor heterogeneity, tumor phylogenetics | PhyloSub (Jiao2014) | Anita S. | Clomial (Zare2014), Theta2 (Oesper2014) Slides (pptx, pdf) |
4/28 | Predicting the functional impact of mutations | CHASM (Carter2009) | Taylor J. | SIFT (Ng2001), PolyPhen (Ramensky2002), MutationAssessor (Reva2011) Slides (pdf) |
4/30 | Drug repurposing | CMapBatch (Fortney2015) | Erkin O. | Connectivity Map (Lamb2006) Slides (pdf) |
5/5 | Probabilistic subtyping | Cho2013 | Professor Gitter | Relational topic model (Chang2010), Patel2014 Slides (pptx, pdf) |
5/7 | Project presentations | | Groups | Last class |
5/11 | No class | | No class | Project reports due |