BIOST/STAT 578A • Winter 2009

Analytic Methods in Infectious Diseases

Course Readings

1. January 6th, 2009


• Introduction
• Readings: Halloran, Longini, Struchiner (2009) Introduction
• Further: Ross (1916); Fraser et al (2004)
• Software: http://www.berkeleymadonna.com


2. January 8th, 2009


• Reed-Frost model, Greenwood model, chain-binomial model
• Readings: Halloran, Longini, Struchiner (2009) Chapter 4; Longini (1998)
• Further: Fox and Elveback (1975); Bailey (1975); Becker (1989)
• Software: small simulator


3. January 13th, 2009


• Dependent happenings; direct, indirect, total and overall effects of interventions;
  VE_SVE_I, VE_P; overview of study designs for different effects; herd immunity
• Readings: Chapter 2 and Chapter 6, Halloran, Longini, Struchiner (2009)
• Further: Greenwood and Yule (1915); Rhodes, Halloran, Longini (1996); Halloran (2001b);
  Halloran and Struchiner (1991); Halloran et al (1997); Basta et al (2008) and Fine (1993)


4. January 15th, 2009


• Deterministic models I; simple insights from R₀; SIR, SEIR, SIS and SI models
• Readings: Halloran (2001a)
• Further: Fraser et al (2004); Anderson and May (1991)


5. January 20th, 2009


• Vaccine efficacy and models of vaccine mechanisms; time-to-event and final value data
• Readings: Halloran, Longini, Struchiner (2009) Chapter 7
• Further: Smith, Rodrigues, Fine (1984); Longini and Halloran (1996); Durham et al (1999);
  Halloran, Longini, Struchiner (1999); Durham et al (1998)


6. January 22nd, 2009


• Estimating R₀ for emerging infectious diseases in real time
• Readings: Wallinga and Teunis (2004); Yang et al (2007a); Yang et al (2007b)
• Further: Cauchemez et al (2006)


7. January 27th, 2009


• 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
• Readings: Halloran, Longini, Struchiner (2009) Chapters 10-12
• Further: Longini et al (1988); Halloran, Preziosi, Chu (2003); Longini and Koopman (1982);
  Becker (1989); O'Neill et al (2000); Longini, Datta, Halloran (1996); Preziosi and Halloran (2003);
  Fine et al (1988); Halloran et al (2006)


8. January 29th, 2009


• Stochastic epidemic models: Pandemic influenza I
  
• Readings: Halloran, Longini, Struchiner (2009) Chapter 4
• Further: Longini et al (2005); Germann et al (2006); Ferguson et al (2005); Ferguson et al (2006); Halloran and Longini (2006);
  Longini et al (2004); Halloran et al (2002); Patel et al (2005)


9. February 3rd, 2009


• Stochastic epidemic models: Pandemic influenza II
  
• Readings: (See previous class)


10. February 5th, 2009


• Households within a community II; estimating (A)VE_I and (A)VE_S from time of onset data
• Readings: Halloran, Longini, Struchiner (2009) Chapters 10-12
• Further: Yang et al (2007a); Yang et al (2007b) Rampey et al (1992) and Cauchemez et al (2006)


11. February 10th, 2009


• Evaluating indirect, total, and overall effects before and after vaccination, mini-community design
  
• Readings: Halloran, Longini, Struchiner (2009) Chapter 13
• Further: Halloran and Struchiner (1991)


12. February 12th, 2009


• Deterministic model II: Rubella Vaccination Strategies in China
  
• Readings: TBN


13. February 17th, 2009


• Community trials for estimating vaccine effects
• Reading: Halloran, Longini, Struchiner (2009) Chapter 13
• Further: Longini et al (2002); Struchiner and Halloran (2007); Hayes and Moulton (2009); Hayes et al (1995);
  Moulton et al (2004); Gambia Hepatitis Study Group (1987)


14. February 19th, 2009


• Evaluating immunological surrogates of protection
• Reading: Chapter 15 and Chapter 3, Halloran, Longini, Struchiner (2009)
• Further: Gilbert and Hudgens (2008); Qin et al (2007)


15. February 24th, 2009


• What exactly is R₀ anyway? Theory of heterogeneous mixing; critical vaccination fraction;
  R₀ as the eigenvalue of the next generation matrix; flu optimization
• Readings: Hill and Longini (2002)
• Further: Dieckmann et al (1990)


16. February 26th, 2009


• Cholera: ecologic determinants and vaccination
  
• Reading: Halloran, Longini, Struchiner (2009) Chapter 4
• Further: Hartley et al (2006); Longini et al (2002); Huq et al (2005)


17. Tuesday, March 3rd 2009


• Estimating efficacy of vaccination on post-infection outcomes, VE_P
• Reading: Halloran, Longini, Struchiner (2009) Chapter 9
• Further: Gilbert et al (2003a); Hudgens and Halloran (2006); Preziosi and Halloran (2003a)


18. Thursday, March 5th, 2009


• Estimation of subtype-specific infectiousness of HIV
• Reading: Hudgens et al (2002)
• Further: Hudgens et al (2001)


19. Tuesday, March 10th, 2009


• Validation sets for outcomes in vaccine studies
• Reading: Halloran, Longini, Struchiner (2009) Chapter 8
• Further: Halloran et al (2003); Halloran and Longini (2001); Scharfstein et al (2006)


20. Thursday, March 12th, 2009


• How do we discover contact structures and what do they tell us about epidemic outcomes?
  Network-based analysis of stochastic SIR models
• Readings: Wallinga et al (2006); Halloran (2006); Keeling and Eames (2005); Newman et al (2001)
• Further: Kenah and Robins (2007a); Kenah and Robins (2007b); Andersson (1998)


21. 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)