Cancer Bioinformatics (Spring 2015)
Biostatistics & Medical Informatics 826
Computer Sciences 838

Course information
Course overview
Syllabus
Schedule
Project
Pan cancer omics
Image source: TCGA Research Network et al. Nature Genetics 2013

Schedule

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

Presentations were scheduled randomly for all students enrolled during the first class. Students who enrolled after the first class were added to the next available slot.