Algorithms for Cancer Genomics: Spring 2015 : Schedule

1 | Date | Topic | Readings (Restricted to Brown) | Slides | Assignments |
---|---|---|---|---|---|

2 | 1/22/2015 | Lecture 1: Introduction | Cancer Evolution: Mathematical Models and Computational Inference | Lecture1 PDF | |

3 | 1/27/2015 | NO CLASS: Blizzard | |||

4 | 1/29/2015 | Lecture 2: Perfect Phylogeny | Gusfield Book Chapter | Lecture2 PDF | |

5 | Section 2.1 | ||||

6 | 2/3/2015 | Lecture 3: Cancer Sequencing and Detecting Somatic Mutations | Lecture3 PDF | ||

7 | 2/5/2015 | Lecture 4: Perfect Phylogeny 2 | Gusfield Book Chapter | Lecture4 PDF | |

8 | Sections 2.2-2.4 | ||||

9 | 2/10/2015 | Paper Discussion: Andrew | TrAp: a tree approach for fingerprinting subclonal tumor composition | Review Form | |

10 | Paper Discussion: Ben | A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data | |||

11 | 2/12/2015 | Paper Discussion: Gryte | Inferring clonal evolution of tumors from single nucleotide somatic mutations; Jiao et al. BMC Bioinf. (2014) | Review Form | |

12 | 2/17/2015 | NO CLASS: Holiday | |||

13 | 2/19/2015 | Paper Discussion and Lecture 5 | Clonality Inference in Multiple Tumor Samples using Phylogeny | Lecture5 PDF | Review Form |

14 | Reconstruction of clonal trees and tumor composition from multi-sample cancer sequencing data | Sections 1-2 and accompanying material in supplement ONLY | |||

15 | 2/24/2015 | Lecture 6: Random Walks on Graphs | Lecture 6 Notes | Lecture6 PDF | |

16 | 2/26/2015 | Lecture 7: Diffusions on Graphs | Lecture 7 Notes | ||

17 | 3/3/2015 | Lecture 8: PageRank | Lecture 8 Notes | ||

18 | 3/5/2015 | Paper Discussion: Vidur | Semi-Supervised Learning Using Gaussian Fields and Harmonic Functions | Additional information in notes from Dan Spielman (Yale): http://www.cs.yale.edu/homes/spielman/462/lect12-13.pdf | |

19 | Walking the Interactome for Prioritization of Candidate Disease Genes | ||||

20 | 3/10/2015 | Paper Discussion: Max | Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes | Read: Second ("HotNet2") and third sections ("HotNet2 parameters") of the methods. | |

21 | 3/12/2015 | Paper Discussion: Max | Supplement for "Pan-cancer network..." | Read: Sections S1.1-1.5; S5.3 | |

22 | Lecture 8 Part 2: Continuous-time PageRank | Lecture 9 Notes | |||

23 | 3/17/2015 | Lecture 9: Introduction to Spectral Theory and Convergene of Random Walk | Lecture 10 Notes | Vertex Neighborhoods, Low Conductance Cuts, ... | |

24 | 3/19/2015 | Lecture 10: Spectral Graph Partition and Graph Drawing | |||

25 | 3/24/2015 | NO CLASS: Spring Break | |||

26 | 3/26/2015 | NO CLASS: Spring Break | |||

27 | 3/31/2015 | Lecture 11:Normalized Laplacian and Graph Partitioning | |||

28 | 4/2/2015 | Lecture 12: Cheeger's Inequality | |||

29 | 4/7/2015 | Paper Discussion: Stephanie | Local Partitioning for Directed Graphs Using PageRank | You may skip Section 7 | |

30 | Presentation and Discussion: Will | Aaron Clausen Lecture Notes on Stochastic Block Model | |||

31 | 4/9/2015 | Work on Projects | |||

32 | 4/13/2014 | DUE: Project Proposal | Project Proposal Instructions | ||

33 | 4/14/2015 | Paper Discussion: Will | Mixed Membership Stochastic Blockmodels | Read: Section 1; Section 2.0 (stop at 2.1); Sections 2.3, 4.2, 4.3 | |

34 | 4/16/2015 | Paper Discussion: Alexis | Background on branching processes | ||

35 | The allele distribution in next-generation sequencing data sets is accurately described as the result of a stochastic branching process | Read: Introduction, first section ection "Fragment amplification... " in Results, and Supplement | |||

36 | Supplement for "The allele distribution..." | ||||

37 | 4/21/2015 | Lecture 13: Network Modularity. | Community detection in graphs | Sections 3.3.2, 6.1 | |

38 | Introduction to Multi-state perfect phylogeny | Perfect Phylogeny Problem | Sections 2-4 | ||

39 | 4/23/2015 | Lecture 14: Multi-state Perfect Phylogeny | Perfect Phylogeny Problem -- Sections 6-7 | Lecture14.pdf | Lecture14 Notes |

40 | 4/27/2015 | DUE: Project Proposal, Part 2 | Project Proposal Instructions | ||

41 | 4/28/2015 | Paper Discussion: Nick | Reducing Multi-state to Binary Perfect Phylogeny with Applications to Missing, Removable, Inserted, and Deleted Data | ||

42 | 5/14/2015 | 2PM: Final Project Presentations | |||

43 | Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps |