MATH 5355 Biomathematics II

• Textbook: An introduction to stochastic processes with applications to biology, Linda Allen 2011
• Syllabus
• Office Hours: MW 12:30-2:00, or by appointment

Homework:

• Homework 1: Chapter 1, #1c, 2,4,11,12,19,34. Due Wednesday Feb. 1
• Homework 2: Chapter 2, #1, 2a, 10, 13. Due Monday Feb. 13
• Homework 3: Chapter 2, #14, 17, 20, 23. Due Wednesday Feb. 22
• Homework 4: Chapter 3, #2, 3, 12, 19. Find manuscript on biological application. Due Wednesday March. 8
• Homework 5: Chapter 5, #2, 3, 6, 7,13, 13, 14, 15, 18 Due Monday April. 3
• Homework 6: Chapter 6, #1, 2, Matlab Lab Exercises (below) Due Wednesday April. 19
• Homework 7: Chapter 8, #9a, 16a, Chapter 9, #13a, 15a Due Thursday May 11

Project:

• Project Proposal: Due Monday March. 20
• Written Project, Monday May 8
• Oral Presentation, Friday May 12 (1:30 pm-4:00 pm)
• Project Rubric

Slides:

• Chp.1 Probability Review
• Chp.1 Intro to Stochastic Processes
• Chp.2 Intro to DTMC
• Chp.3 Applications of DTMC
• Chp.5 Intro to CTMC
• Chp.6 CTMC Birth and Death Processes
• Chp.7 Applications of CTMC
• Chp.8 SDE

Matlab Lab:

• Matlab Lab Exercises
• SIR.m code
• Competition.m Code

Papers:

• Common Patterns of Nature: Frank 2009
• DTMC Application: Caswell 2009
• DTMC Application: Etterson 2009
• Gene Expression Models: Paulsson 2005
• Forest Succession Models: Shugart 1980
• SIR: O'Regan 2013
• SIR, Influenze: Xu 2006
• Bayesian Parameter Estimation: Huang 2005