BIOST/STAT 578A • Winter 2009

Analytic Methods in Infectious Diseases

1. Tuesday, January 6th, 2009 –Lecturer: M Elizabeth Halloran


• Introduction
• Lecture slides: Lecture 1


2. Thursday, January 8th, 2009 –Lecturer: Ira Longini


• Reed-Frost model, Greenwood model, chain-binomial model
• Lecture slides: Lecture 2
• Lecture program: (see Programs web-page for small simulation)


3. Tuesday, January 13th, 2009 –Lecturer: M Elizabeth Halloran


• Dependent happenings; direct, indirect, total and overall effects of interventions;
  VE_SVE_I, VE_P; overview of study designs for different effects; herd immunity
• Lecture slides (two sets): Lecture 3a, and Lecture 3b


4. Thursday, January 15th, 2009 –Lecturer: M Elizabeth Halloran


• Deterministic models I; simple insights from R₀; SIR, SEIR, SIS and SI models
• Lecture slides: Lecture 4


5. Tuesday, January 20th, 2009 –Lecturer: Ira Longini


• Vaccine efficacy and models of vaccine mechanisms; time-to-event and final value data
• Lecture slides: Lecture 5


6. Thursday, January 22nd, 2009 –Lecturer: Ira Longini


• Estimating R₀ for emerging infectious diseases in real time
• Lecture slides: Lecture 6


7. Tuesday, January 27th, 2009 –Lecturer: M Elizabeth Halloran


• Household Studies I; dynamics, study designs, and estimation; secondary attack rate,
  community probability of infection, estimating VE_S and VE_I, households within
  communities and independent households
• Lecture slides follow in three sets: Lecture 7A; Lecture 7B and Lecture 7C


8. Thursday, January 29th, 2009 –Lecturer: Ira Longini


• Stochastic epidemic models: Pandemic influenza I
  
• Lecture slides: Lecture 8


9. Tuesday, February 3rd, 2009 –Lecturer: Ira Longini


• Stochastic epidemic models: Pandemic influenza II
  
• Lecture slides: Lecture 9


10. Thursday, February 5th, 2009 -Guest Lecture: Dr. Yang Yang


• Households within a community II; estimating (A)VE_I and (A)VE_S from time of onset data
• Lecture slides: Lecture 10

Tuesday, February 10th, 2009 –Lecturer: M Elizabeth Halloran

• Evaluating indirect, total, and overall effects before and after vaccination, mini-community design
  
• Lecture slides (two sets): Lecture 11a and Lecture 11b


11. Thursday, February 12th, 2009 –Guest Lecture: Professor Herb Hethecote


• Deterministic models II; Rubella Vaccination Strategies in China
• Lecture slides: Lecture 12


12. Tuesday, February 17th, 2009 –Lecturer: M Elizabeth Halloran


• Community trials for estimating vaccine effects
• Lecture slides: Lecture 13


13. Thursday, February 19th, 2009 –Lecturer: M Elizabeth Halloran


• Evaluating immunological surrogates of protection
• Lecture slides: Lecture 14


14. Tuesday, February 24th, 2009 –Lecturer: Ira Longini


• What exactly is R₀ anyway? Theory of heterogeneous mixing; critical vaccination fraction;
  R₀ as the eigenvalue of the next generation matrix; flu optimization
• Lecture slides: Lecture 15


15. Thursday, February 26th, 2009 –Lecturer: Ira Longini


• Cholera: ecologic determinants and vaccination
  
• Lecture slides: Lecture 16


16. Tuesday, March 3rd 2009 –Lecturer: M Elizabeth Halloran


• Estimating efficacy of vaccination on post-infection outcomes, VE_P
• Lecture slides: Lecture 17


17. Thursday, March 5th, 2009 –Lecturer: Ira Longini


• Estimation of subtype-specific infectiousness of HIV
• Lecture slides: Lecture 18


18. Tuesday, March 10th, 2009 –Lecturer: M Elizabeth Halloran


• Validation sets for outcomes in vaccine studies
• Lecture slides: Lecture 19


19. Thursday, March 12th, 2009 –Guest Lecturer: Dr. Eben Kenah: last class


• How do we discover contact structures and what do they tell us about epidemic outcomes?
  Network-based analysis of stochastic SIR models
• Lecture slides: Lecture 20


20. March 16th – 20th, 2009


• Exam week: best wishes and break a pencil



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NOTICES - Student Project: due on Thursday March 19, 2009 by 5:00PM (please send to: Rebecca Allen, email listed on course index page)