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Computational
Genomics
BME 230, Spring 2006

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Schedule of Lectures

  • Week 1: Tue, Apr 4: (Stuart) Genes to genomes: introduction to computational genomics
  • Week 1: Thu, Apr 6: (Baertsch) Programming Libraries for Computational Genomics at UCSC
    • Lecture slides [pdf] [ppt]
    • Required reading: The Sordid Details by Jim Kent [html] [pdf]
  • Week 2: Tue, Apr 11: (Kent) Genome resources at UCSC
    • Lecture slides [ppt] [pdf]
    • Scribed notes from last year by Galt Barber [pdf]
    • Required reading: The UCSC Genome Browser [pdf] and The UCSC GeneSorter [pdf]
  • Week 2: Thu, Apr 13: (Stuart) Functional Genomics I
    • Lecture Slides [ppt] [pdf]
    • Scribed notes from last year by Ron Chao [pdf]
    • Topics: Systems biology & Exploratory algorithms, High-throughput biology, Microarrays, protein-protein interactions, chromatin-IP, synthetic lethal analysis, unsupervised analysis (hierarchical clustering, K-means)
    • Required Reading:
      • "From molecular to modular cell biology" LH Hartwell et al Nature 1999. [pdf]
      • "Cluster analysis and display of genome-wide expression patterns" MB Eisen et al. PNAS 1998. [pdf]
      • "A probabilistic view of gene function" AG Fraser and EM Marcotte Nature Genetics 2004. [pdf]
    • Suggested Reading:
      • "Use of a cDNA microarray to analyze gene expression patterns in human cancer" J DeRisi et al. Nature 1996. [pdf]
      • "Genome-wide high-throughput screens in functional genomics." A Friedman and N Perrimon Curr Opinions in Gen. & Dev [pdf]
      • "Global Mapping of the Yeast Genetic Interaction Network" AH Tong et al. Science 2004. [pdf]
  • Week 3: Tue, Apr 18: (Stuart) Functional Genomics II
    • Lecture slides [pdf] [ppt]
    • Scribe notes from last year by Chi To [pdf]
    • Topics: Cluster evaluatiown. Curated ontologies. Hypothesis guided algorithms, Feature selection, Separating hyperplanes, Recommender systems.
  • Week 3: Thu, Apr 20: (Haussler) Mathematical Background
    • Scribed notes from last year by Courtney Onodera [pdf]
    • Topics: Probability, conditional probability, P-values, E-values, Sensitivity/Specificity, Cross-validation
    • Required Reading: Durbin, chapters 1-2.
  • Week 4: Tue, Apr 25: (Haussler) Motif discovery
    • Scribed notes from last year by Rachel Harte and David Bernick [pdf]
    • Topics: Profiles, motif discovery, Gibbs sampling
    • Suggested Reading: Mount Ch 4.
    • Required Reading: Durbin Appendices Pages 299-313, 319-325.
  • Week 4: Thu, Apr 27: (Haussler) HMMs I
    • Scribed notes from last year by David Bernick [pdf]
    • Topics: Principles of HMMs, HMMs models for gene finding
    • Required Reading: Durbin Chap 3 & 5.
    • Required Reading: Chap 4 in Computational Methods in Molecular Biology, SL Salzberg, DB Searls, and S Kasif (Eds), Elsevier Science, 1998.
    • Required Reading: "An introduction to Hidden markov models for biological sequences" by Anders Krogh
  • Week 5: Tue, May 2: (Haussler) HMMs II
    • Scribed notes from last year by Wing Wong [pdf]
    • Topics: Training HMMs, Viterbi algorithm, Forward & backward algorithm, Higher-order markov chains
    • Required reading: Durbin chap 6 pp 149-159 (skip the  first part of chap 6
  • Week 5: Thu, May 4: (Haussler) HMMs III
    • Scribed notes from last year by Nathan Bahr [pdf]
    • Topics: HMMs for pairwise & multiple sequence alignment, learning HMM parameters from observations, Expectation-Maximization with Baum-Welch, pair-HMMs for comparative genomics
  • Week 6: Tues, May 9: (Haussler) Evolutionary reconstruction I
    • Scribed notes from last year, set 1 by Sol Katzman [pdf]
    • Scribed notes from last year, set 2 by Maria Deleke [pdf]
    • Topics: Parsimony, Stationary markov processes, Rate matrices, Maximum Likelihood, Maximum a posteriori, Felsenstein’s Post-order traversal
  • Week 6: Thu, May 11: (Brosius) The genomes through major evolutionary transitions: From the RNA world to "inorganic" carriers.
    • Lecture slides [pdf] [ppt]
    • Required Reading: "Gene duplication and other evolutionary strategies: from the RNA world to the future." Brosius, 2003[pdf]
    • Optional Reading
      • "The contribution of RNAs and retrotransposition to evolutionary novelties." Brosius, 2003 [pdf]
      • "Transmutation of tRNA over time." Brosius, 1999 [pdf]
      • "tRNAs in the spotlight during protein biosynthesis." Brosius, 2001 [pdf]
      • "Echoes from the past -- are we still in an RNP world?" Brosius, 2005 [pdf]
      • "Waste not, want not -- transcript excess in multicellular eukaryotes." Brosius, 2006 [pdf]
  • Week 7: Tue, May 16: (Haussler) Evolutionary reconstruction II
    • Scribed notes from last year by Neema Bhukhan [pdf]
    • Lecture Slides [ppt] [pdf]
    • Topics: PhyloHMMs
    • Required Reading: Phylogenetic Hidden Markov Models book chapter by Siepel and Haussler [pdf].
    • Suggested Reading: Manual on the conservation track. [pdf]
  • Week 7: Thu, May 18: (Stuart) Gene Networks I
    • Lecture slides [pdf] [ppt]
    • Topics: Graphical models of gene function. Boolean networks. Attractors. Bayesian networks
    • Scribed notes from last year by Alex Williams [pdf] and by David Ng [pdf]
    • Topics: Inference with probabilistic graphical models
  • Week 8: Tue, May 23: (Haussler) RNA Genomics, RNA folding
    • Scribed notes from last year by Tim Dreszer [pdf]
    • RNA structure and function, Minimum free energy structures
  • Week 8: Thu, May 25: (Stuart) Gene Networks II
    • Topics: Learning probabilistic graphical models
    • Lecture slides [pdf] [ppt]
    • Scribed notes from last year by Jes Frellsen [pdf] or by Grant Thiltgen [pdf]
    • Required Reading
      • "Genome-wide discovery of transcriptional modules from DNA sequence and gene expression" E Segal et al Bioinformatics 2003 [pdf]
      Topics: Probabilistic relational models, joint learning
  • Week 9: Tue, May 30: (Haussler) Grammars for RNA recognition
    • Scribed notes by Craig Lowe [pdf]
    • Topics: SCFGs
  • Week 9: Thu, Jun 1: (Haussler) Whole-genome comparative genomics
  • Week 10: Tue, Jun 6: (Stuart) Gene Networks III0
  • Week 10: Thu, Jun 8: Guest lectures
    • (Bejarano) Ultra-conserved elements.
    • (Kern) Human genome variation.
  • Finals Week: Jun 12-15: Final Project Presentations (Time and Data TBA)