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640:338, Spring 2010; Home Page

640:338 Discrete and Probabilistic Methods in Biology
Spring 2010

  • Class schedule: TTH6 (5:00pm--6:20pm), SEC 220, Busch
  • Text: Available (free!) on line at
  • Instructor: Daniel Ocone; ocone-at-math-dot-rutgers-dot-edu.
  • Office Hours: Hill 518: Monday 3:30-5:30, Tuesday 3:30-4:30
  • Click here for SYLLABUS, NOTES, and PROBLEM SETS.
  • Tests, homework, grades: There will be weekly, graded problem sets, two midterms, and a final. The final grade will be computed from an average of the final grade (200 points), the midterm grades (100 points each), and the homework grades (100 points). The midterms are tentatively scheduled for March 2 and April 8. All exams are open book and open notes.
  • Prerequisites: Linear Algebra (640:250), Multivariable Calculus (640:251), Probability (640:477 or one of 198:206, 960:381, 14:332:321, 14:540:210. The probability prerequisite is particularly important. The course assumes a good working knowledge of undergraduate probability at the level of 640:477
  • Spring 2010 Course Summary:
    • Population genetics for large populations; difference equations.
    • Population genetics for small populations; Markov chain models.
    • Coverage analysis for shotgun sequencing.
    • Poisson processes and applications to restriction enzyme digests.
    • Likelihood functions, Maximum Likelihood Estimation, hypothesis testing, and application to models for biological sequences.
    • Dynamic Programming and sequence alignment.
    • Hidden Markov models for sequence evolution and applications to alignment.