Schedule: Spring 2013

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DateTopic

Slides/Notes

Reading

(Some available only from Brown IP addresses)

January 24

Lecture: Overview and Biology Outline

 Slides
  • Molecular Biology Primer (Chapter 3 of Jones & Pevzner)
  • Stratton, M. R. Exploring the genomes of cancer cells: progress and promise. Science (2011)
  • Stratton, M. R.,Campbell, P.J., Futreal, P.A. The cancer genome Nature (2009)
    • January 29 Lecture: Mutation Detection from Sequencing Data Slides
  • Sequencing technologies -- the next generation
  • Advances in understanding cancer genomes through second-generation sequencing

    • Additional reading:

  • Genome Sequencing Technology and Algorithms [Ch. 6]
  • The impact of next-generation sequencing technology on genetics. E. Mardis

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    January 31 Lecture: Mutation Detection and Recurrent Somatic Mutations Slides
  • Genome structural variation discovery and genotyping
  • Developing Algorithms to Discover Novel Cancer Genes

    • Additional reading:

  • Genome Sequencing Technology and Algorithms [Ch. 7]

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    February 5 Lecture: Recurrent Somatic Mutations: Slides
    February 7 Lecture: Recurrent Combinations of Somatic Mutations:
  • Slides
  • Computer Assignment
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  • Vandin, Upfal, and Raphael Algorithms and Genome Sequencing: Identifying Driver Pathways in Cancer. IEEE Computer (2012)
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    February 12 Lecture/Discussion: Tools for Identifying Somatic Mutations    
    February 14 Lecture: Intra-Tumor Heterogeneity and Mixture Models Slides  
    February 19 HOLIDAY: NO CLASS    
    February 21 Lecture:Combinations of Somatic Mutations: Networks Slides
  • Vandin, Upfal, and Raphael Algorithms for Detecting Significantly Mutated Pathways in Cancer.Journal of Computational Biology (2011)
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    February 26 Lecture:Combinations of Somatic Mutations: Exclusivity Slides
  • Vandin, Upfal, and Raphael De novo discovery of mutated driver pathways in cancer Genome Research (2012)
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    February 28 Lecture:Tumor Evolution 1: Perfect Phylogeny Slides Dan Gusfield Book Chapter (distributed in class)
    March 5 Lecture:Tumor Evolution 2: Coalescent Models Coalescent simulator
    March 7 Lecture:Tumor Evolution 3: Coalesecent Models and Selection Coalescent simulator
    March 12 Paper Presentation and Discussion: Layla
  • Goya, et al. SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors.Bioinformatics (2010) 26 (6): 730-736.
  • Additional reading: Roth, et al. JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data.Bioinformatics (2012) 28(7):907-13.
    • March 14 Paper Presentation and Discussion: Vishesh Rausch, et al. DELLY: structural variant discovery by integrated paired-end and split-read analysis.Bioinformatics (2012) 28(18):i333-i339.
    March 19 Paper Presentation and Discussion: Eirini  
  • Greenman, et al. Statistical Analysis of Pathogenicity of Somatic Mutations in Cancer.Genetics (2006)
  • Getz, et al. Comment on "The Consensus Coding Sequences of Human Breast and Colorectal Cancers" [Supporting Information] Science (2007).
    • March 21 Paper Presentation and Discussion: Hanxiang Diskin et al. STAC: A method for testing the significance of DNA copy number aberrations across multiple array-CGH experiments. Genome Research (2006)
    March 22 Initial Project Proposal DUE  
    March 26 NO CLASS: Spring break    
    March 28 NO CLASS: Spring break    
    April 2 Paper Presentation and Discussion:Connor Glaab, et al. EnrichNet: network-based gene set enrichment analysis. Bioinformatics (2012)
    April 4 Paper Presentation and Discussion: Akshay I Bozic, et al. Accumulation of driver and passenger mutations during tumor progression Proceedings of the National Academy of Sciences 107, 18545-18550 (2010)
    April 9 Paper Presentation and Discussion: Vishesh Ciriello, et al. Mutual exclusivity analysis identifies oncogenic network modulesGenome Research (2012)
    April 11 Work on Projects    
    April 16 Paper Presentation and Discussion: Hanxiang Ye et al. Statistical method on nonrandom clustering with application to somatic mutations in cancer BMC Bioinformatics (2010)[Sections 1.1 and 1.2 in Methods are optional]
    April 18 Paper Presentation and Discussion: Eirini   Kim et al. Identifying Causal Genes and Dysregulated Pathways in Complex Diseases PLOS Computational Biology (2011)
    April 19 Midterm Project Proposal DUE  
    April 23 Paper Presentation and Discussion: Layla   Nik-Zainal et al. The Life History of 21 Breast Cancers Cell (2012)
    April 25 Work on Projects    
    April 30 Paper Presentation and Discussion: Connor  
  • J. Dutkowski and T. Ideker Protein Networks as Logic Functions in Development and Cancer PLOS Computational Biology (2011)
  • Background reading: Kingsford and Salzberg What are decision trees? Nature Biotechnology (2008)
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    May 2 Paper Presentation and Discussion: Akshay Gerlinger M, et al. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N Engl J Med 2012;366:883-892
    May 3 Cancer Symposium: Please attend! Schedule of talks
    May 7    

    PROJECT PRESENTATIONS

    		 
    May 17 FINAL PROJECT REPORT DUE Final Project Proposal DUE