Department of Mathematics

MATH 6770, Fall 2010
TTh 12:25-1:45am, LCB 222 (LeRoy Cowles Building)

Mathematical Biology I:

Mathematical modeling of cancer and other chronic conditions versus the immune system

Instructor:

Peter Kim
Office: LCB 313 (LeRoy Cowles Building)
Phone: 585-1645
(my 3-letter last name)[at symbol]math[dot]utah[dot]edu

Office hours:

I am available right after lecture,
or by appointment via email.


Course Info Recommended Texts Course Outline

Course Info

Date Topic Relevant handouts/papers
Tue, Aug 24 (First day of class) Introduction
Cancer stem cells
Chronic myelogenous leukemia
Syllabus.pdf
Michor et al. (2005) Dynamics of chronic myeloid leukaemia. Nature
Thu, Aug 26 Chronic myelogenous leukemia
Agent-based modeling
Age/maturity-structured modeling
Roeder et al. (2006) Dynamic modeling of imatinib-treated chronic myeloid leukemia: functional insights and clinical implications. Nature Medicine
Tue, Aug 31 Colon cancer
Age/maturity-structured modeling
Johnston et al. (2007) Mathematical modeling of cell population dynamics in the colonic crypt and in colorectal cancer. PNAS
Johnston et al. (supplementary info)
Thu, Sept 2 Colon cancer
Komarova et al. (2007) Initiation of Colorectal Cancer: Where do the Two Hits Hit? Cell Cycle
Michor et al. (2004) Linear Model of Colon Cancer Initiation. Cell Cycle
Tue, Sept 7 Colon cancer
Skin cancer
van Leeuwen et al. (2009) An integrative computational model for intestinal tissue renewal. Cell Prolif.
Eyles et al. (2010)Tumor cells disseminate early, but immunosurveillance limits metastatic outgrowth, in a mouse model of melanoma. J Clin Invest.
Thu, Sept 9 Skin cancer
Eikenberry et al. (2009) Tumor-Immune Interaction, Surgical Treatment, and Cancer Recurrence in a Mathematical Model of Melanoma. PLoS Comput Biol.
Tue, Sept 14 Hallmarks of cancer
HIV, HIV latency
Hanahan and Weinberg (2000) The Hallmarks of Cancer. Cell
Rong and Perelson (2009) Modeling Latently Infected Cell Activation: Viral and Latent Reservoir Persistence, and Viral Blips in HIV-infected Patients on Potent Therapy. PLoS Comput Biol.
Thu, Sept 16 HIV treatment
Memory T cell depletion
Sedaghat et al. (2008) Decay dynamics of HIV-1 depend on the inhibited stages of the viral life cycle. PNAS
Yates et al. (2007) Understanding the Slow Depletion of Memory CD4+ T Cells in HIV Infection. PLoS Medicine
Tue, Sept 21 Hepatitis C
Immune surveillance: NK cells
Dahari et al. (2007) Triphasic Decline of Hepatitis C Virus RNA During Antiviral Therapy. Hepatology
Merrill (1981) A Model of the Role of Natural Killer Cells in Immune Surveillance - I. J Math Biology
Thu, Sept 23 Immune surveillance: NK cells and T cells de Pillis et al. (2005) A Validated Mathematical Model of Cell-Mediated Immune Response to Tumor Growth. Cancer Research
Tue, Sept 28 Epstein-Barr Virus yet-to-be-published sources
Thu, Sept 30 Epstein-Barr Virus yet-to-be-published sources
Tue, Oct 5 Project presentations 1
Thu, Oct 7 Project presentations 1
Oct 12 and 14 Fall break
Tue, Oct 19 No class
Thu, Oct 21 Guest lecture: Cell motility Mark Zajac
Tue, Oct 26 Regulatory T cells Leon et al. (2000) How regulatory CD25(+)CD4(+) T cells impinge on tumor immunobiology? On the existence of two alternative dynamical classes of tumors J Theor Biol.
Thu, Oct 28 Regulatory T cells and cancer Leon et al. (2007) How regulatory CD25(+)CD4(+) T cells impinge on tumor immunobiology? On the existence of two alternative dynamical classes of tumors J Theor Biol.
Tue, Nov 2 Adaptive regulatory T cells Fouchet and Regoes (2008) A Population Dynamics Analysis of the Interaction between Adaptive Regulatory T Cells and Antigen Presenting Cells PLoS ONE
Thu, Nov 4 Cancer therapy Kirschner and Panetta (1998) Modeling immunotherapy of the tumor–immune interaction J. Math. Biol.
Iliadis and Barbolosi (2000) Optimizing Drug Regimens in Cancer Chemotherapy by an Efficacy–Toxicity Mathematical ModelComputers and Biomedical Research
Tue, Nov 9 Project presentations 2
Thu, Nov 11 Project presentations 2
Tue, Nov 16 Tumor invasion & game theory
Overview
Basanta, Hatzikirou, and Deutsch (2008) Studying the emergence of invasiveness in tumours using game theory Eur. Phys. J. B
Bellomo, Li, and Maini (2008) On the foundations of cancer modelling: selected topics, speculations, and perspectives Mathematical Models and Methods in Applied Sciences
Thu, Nov 18 Guest lecture: Risk Assessment for Emerging Infectious Diseases Damon Toth
Tue, Nov 23 Thanksgiving break
Thu, Nov 25 Thanksgiving Day
Tue, Nov 30 No class
Thu, Dec 2 Guest lecture: Deep brain stimulation and Parkinson's disease Stephen Odom
Tue, Dec 7 Project presentations 3
Thu, Dec 9 Project presentations 3

Required Texts

None. You are not required to buy any textbook. I will provide the necessary reading material.

Recommended Texts

How the Immune System Works (Blackwell's How It Works), by Lauren M Sompayrac.

Immunobiology, 6th edition, by Charles Janeway,
or Janeway's Immunobiology, 7th edition.

(These texts should be available in the library or by asking around people in the department.)

Course Outline

The details of the outline and the readings are likely to change based on student interest, but the overall plan will probably not. I will either post the readings on the web page, hand them out, or both.