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Information for Current Students:
BIOL 285/485;Quantitaive Biology Seminar;
Mon: 5:30p - 6:45pm
Blocker 628

Randy Gil, email:
Christine Schwartz, email


Later talks will be updated as soon as schedules are confirmed.

Course Requirements:
The focus of this class is to discuss recent approaches to answering biological questions and the role that computational methods, if applicable, might play in this process. For the class, you will be grouped either according to classification or research interest and each group will be required to lead a discussion on one paper. Alternatively, those groups that are currently doing research may discuss their work and relevant data.

Those groups that lead discussions must divide the work evenly among the group members. You will be responsible for knowing the material covered in the paper, but you will also be responsible for asking questions to the audience, with the aim of discussing the research aims presented, and the rationale behind the research.

Each presenter, regardless of whether a paper or personal research is presented, will be evaluated by 2 independent peers. These evaluations are for the benefit of the presenter and will not affect your grade in the class, but they will help you in becoming a better presenter. Writing an evaluation will be part of your completion grade, so it is important to come to the meetings every week.

Useful Links:

McGraw-Hill Online Scientific Encyclopedia (good for getting definitions of terms)

Mathworld (Also good for Mathematical terms/concepts)

Guides to reading scientific articles (supplemental to what you were given in class (PDF)

Recommended Papers : Please Note - the hyperlinks below can only be accessed by computers ON CAMPUS.

1.Fumihiko Miyoshi, Yoichi Nakayama, Kazunari Kaizu, Hideo Iwasaki, and Masaru Tomita
A Mathematical Model for the Kai-Protein-Based Chemical Oscillator and Clock Gene Expression Rhythms in Cyanobacteria.
Journal of Biological Rhythms. 2007 Feb;22(1):69-80

2. Gilioli G, Pasquali S, Ruggeri F.
Bayesian Inference for Functional Response in a Stochastic Predator-Prey System.
Bulletin of Mathematical Biology. 2007 Aug 16

3. Michael J. Ryan, Craig M. Pease, Molly R. Morris
A Genetic Polymorphism in the Swordtail Xiphophorus nigrensis: Testing the Prediction of Equal Fitnesses
The American Naturalist, Vol. 139, No. 1. (Jan., 1992), pp. 21-31.

4. Hoelzel AR, Hey J, Dahlheim ME, Nicholson C, Burkanov V, Black N.
Evolution of population structure in a highly social top predator, the killer whale.
Mol Biol Evol. 2007 Jun;24(6):1407-15

5. Kovac H, Stabentheiner A, Hetz SK, Petz M, Crailsheim K.
Respiration of resting honeybees.
J Insect Physiology. 2007 Jul 13;

6. Pandolfi JM, Bradbury RH, Sala E, Hughes TP, Bjorndal KA, Cooke RG, McArdle D, McClenachan L, Newman MJ, Paredes G, Warner RR, Jackson JB.
Global trajectories of the long-term decline of coral reef ecosystems.
Science. 2003 Aug 15;301(5635):955-8.

7. Maquet J, Letellier C, Aguirre LA.
Global models from the Canadian lynx cycles as a direct evidence for chaos in real ecosystems
J Mathematical Biology. 2007 Jul;55(1):21-39.

8. Nijhout HF, Emlen DJ.
Competition among body parts in the development and evolution of insect morphology
Proc Natl Acad Sci U S A. 1998 Mar 31;95(7):3685-9

9. Schwartz MW, Iverson LR, Prasad AM, Matthews SN, O'Connor RJ
Predicting extinctions as a result of climate change.
Ecology. 2006 Jul;87(7):1611-5

10. Lourdes Esteva, Gerardo Rivas and Hyun Mo Yang
Modelling parasitism and predation of mosquitoes by water mites
Journal of Mathematical Biology. Volume 53, Number 4 / October, 2006: 540-555

11. Flexas J, Bota J, Loreto F, Cornic G, Sharkey TD.
Diffusive and metabolic limitations to photosynthesis under drought and salinity in C(3) plants.
Plant Biol (Stuttg). 2004 May;6(3):269-79.

12. Ph. Getto, O. Diekmann and A.M. de Roos
On the (dis) advantages of cannibalism
Journal of Mathematical Biology.Volume 51, Number 6 / December, 2005: 695-712.

13. M. James C. Crabbe
Global warming and coral reefs: Modelling the effect of temperature on Acropora palmata colony growth
Computational Biology and Chemistry 31 (2007) 294-297.

14. Buhl J, Gautrais J, Louis Deneubourg J, Kuntz P, Theraulaz G.
The growth and form of tunnelling networks in ants.
J Theoretical Biology. 2006 Dec 7;243(3):287-98.

15. Raman, B.; Sun, P.A.; Gutierrez-Galvez, A.; Gutierrez-Osuna, R.
Processing of chemical sensor arrays with a biologically inspired model of olfactory coding

16. Grozinger CM, Robinson GE
Endocrine modulation of a pheromone-responsive gene in the honey bee brain
J Comp Physiol A Neuroethol Sens Neural Behav Physiol. 2006 Dec 28

17. Xu Y, Wang LV, Ambartsoumian G, Kuchment P
Reconstructions in limited-view thermoacoustic tomography
Med Phys. 2004 Apr;31(4):724-33.

18. Goll MG, Kirpekar F, Maggert KA, Yoder JA, Hsieh CL, Zhang X, Golic KG,Jacobsen SE, Bestor TH.
Methylation of tRNAAsp by the DNA methyltransferase homolog Dnmt2
Science. 2006 Jan 20;311(5759):395-8.

19. Huyghues-Despointes BM, Qu X, Tsai J, Scholtz JM
Terminal ion pairs stabilize the second beta-hairpin of the B1 domain of protein G
Proteins. 2006 Jun 1;63(4):1005-17.

20. Niell CM
Theoretical analysis of a synaptotropic dendrite growth mechanism.
J Theor Biol. 2006 Jul 7;241(1):39-48.

Presentation Schedule:


Dr. Jay Walton - Dept. of Mathematics
Intro/Organizational Meeting
Dr. Rodolfo Amaroyo - Dept. of Biology
Faculty Talk
Drew - Dr. Walton
Student Presentation
Cara - Dr. Walton and Shana - Dr. Qin
Student Presentation
Dr. Susan Golden - Dept. Of Biology
Faculty Talk
Dr. Jay Walton - Dept. of Mathematics
Faculty Talk
Ryan and Philip - Dr. Cassone
Student Talk
Spring Break
Study at home
Aaron and Sean - Dr. Rosenthal
Student Talk
Brad Johnson - Dr. Rosenthal
Graduate Student Talk
David and Alexis
Student Talk
Dr. Deb Bell-Pederson - Dept. of Biology
Faculty Talk
Dr. Michael Longnecker - Dept. of Statistics
Faculty Talk
Dead Week - No Class
Study for finals