2008 Summer Program in Mathematical Biology for Undergraduates
This program consists of two parts: (a) two weeks of introductory lectures plus short projects and a computer lab, and (b) a summer long research experience (6 weeks to be followed immediately after the 2 weeks) devoted to projects in the interface of mathematics, statistics, and biological sciences.
The 2008 Summer Program dates are June 23 - July 3
Program Leaders:
- David Terman (Department of Mathematics): Mathematical Neuroscience
- Dennis Pearl (Department of Statistics): Statistical Phylogenetics
- Joseph Verducci (Department of Statistics) and Paul Blower (Department of Pharmacology): Chemogenomics
- Mark Berliner (Department of Statistics): Climate Change
- Greg Singer (Center of Integrative Cancer Biology): Bioinformatics
Week 1 |
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| Monday 6/23: Statistical Phylogenetics | |||
| 8:30am | Registration and welcome | ||
| 9:00am-10:00am | Dennis Pearl: Background, Sequence Alignment, Parsimony, Maximum Likelihood | ||
| 10:00am-10:30am | Coffee break | ||
| 10:30am-11:30am | Dennis Pearl: Optimization algorithms, the Bootstrap, Bayesian Phylogenetics | ||
| 11:30am-2:00pm | Lunch break | ||
| 2:00pm-4:00pm | Computer lab: Jeff Pan Software: Clustal, Phylip, MrBayes |
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| Tuesday 6/24: Chemogenomics | |||
| 9:00am-10:00am | Joe Verducci: Chemogenomics-Testing for Monotone Association in Subpopulations | ||
| 10:00am-10:30am | Coffee break | ||
| 10:30am-11:30am | Paul Blower: Chemogenomics Methods | ||
| 11:30am-2:00pm | Lunch break | ||
| 2:00pm-4:00pm | Computer lab: Li Yu Software: R |
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| Wednesday 6/25: Mathematical Neuroscience (Sleep Rhythms) | |||
| 9:00am-10:00am | Dave Terman: Background, Neuroscience and sleep rhythms | ||
| 10:00am-10:30am | Coffee break | ||
| 10:30am-11:30am | Dave Terman: Mathematical methods: dynamical systems theory | ||
| 11:30pm-2:00pm | Lunch break | ||
| 2:00pm-4:00pm | Computer lab: Hyejin Park and Michael Rempe Software: xppaut, MatLab |
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| Thursday 6/26: Climate Change | |||
| 9:00am-10:00am | Tao Shi: Climate Change I | ||
| 10:00am-10:30am | Coffee break | ||
| 10:30am-11:30am | Tao Shi: Climate Change II | ||
| 11:30pm-2:00pm | Lunch break | ||
| 2:00pm-4:00pm | Computer lab: Jenny Brynjarsdottir
Software: MatLab |
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| Friday 6/27: Bioinformatics | |||
| 9:00am-10:00am | Greg Singer: Bioinformatics I | ||
| 10:00am-10:30am | Coffee break | ||
| 10:30am-11:30am | Francisco Agosto-Perez: Bioinformatics II | ||
| 11:30am-2:00pm | Lunch break | ||
| 2:00pm-4:00pm | Computer lab: Greg Singer & Francisco Agosto-Perez
Software: web browser |
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Team Projects: June 30 - July 3
David Terman: We will explore mathematical models for mechanisms underlying sleep rhythms and the human sleep/wake cycle.
Group 3: Kyle Lyman, Xiaoge Clare Tao, Brittny Major, and Harika Rayala
Dennis Pearl: The phylogenetics project will explore the evolution and global spread of the bird flu (H5N1) virus and how this evolution may be related to the clinical course of the disease.
Group 1: Amrish Deshmukh, Stephanie Hayes, Ryan Starski, and Tim Wang
Tao Shi: The climate change project will concentrate on exploring the statistical relationship between the record of global average temperature and human and non-human factors driving climate changes.
Group 4: Arjun Dasgupta, Mark Hilkert, and Lyda Urresta
Greg Singer: We will use database techniques to find human genes that are not present in other mammalian genomes. We will then attempt to characterize these human-specific genes.
Group 5: Vikas Choudhary, Valerie Tiu, Michael Sharpnack, and Adam Jones
Joe Verducci: Correlational methods will be used to relate mRNA expression to drug activity over the NCI-60 panel of cancer cell lines.
Group 2: Jack Enyeart, Mike Martin, and Hunter Rhodes.
Lab Tours and Presentations: June 30 - July 3
| Monday 6/30 (Lab tours) | |||
| 9:45 am | Meet at MBI for walk to campus labs | ||
| 10:00 - 10:45am | Joe Travers: Neuroscience Lab | ||
| 10:50 - 11:35am | Pearlly Yan: Epigenomics Lab | ||
| Tuesday 7/1 (Lab tours) | |||
| 1:15pm | Meet at MBI for drive to Kinnear Road labs | ||
| 1:30 - 2:15pm | John Wenzel: Biodiversity Museum | ||
| 2:25 - 3:10pm | Libby Marschall: Aquatics Lab | ||
| Wednesday 7/2 (Lab tour) | |||
| 10:15am | Meet at MBI for walk to Byrd Polar Research Center | ||
| 10:30 - 11:15am | Lijia Wei: Ice-core paleoclimatology lab | ||
| Thursday 7/3 | |||
| 1:00-1:30pm | Students set up posters and prepare for presentations | ||
| 1:30-1:50pm | Poster viewing | ||
| 1:50-3:30pm | Oral presentations | ||
REU Presentations
Ryan Starski and Amrish Deshmukh: Statistical Phylogenetics: An Application to Corbiculate Bees and Geography
