2011 Summer Program in Mathematical Biology for Undergraduates (June 20-July 1, 2011)
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.
Topics
- Statistical Phylogenetics
- Mathematical Neuroscience
- Bioinformatics
- Chemogenomics
- Environmental Statistics
Week 1: June 21 - 25, 2010 |
|||
| Monday 6/20: Statistical Phylogenetics | |||
| 8:30am | Registration and welcome | ||
| 9:00am-10:00am | Dennis Pearl: Background, alignment, and parsimony | ||
| 10:00am-10:30am | Coffee break | ||
| 10:30am-11:30am | Dennis Pearl: Maximum likelihood and Bayesian approaches | ||
| 11:30am-2:00pm | Lunch break | ||
| 2:00pm-4:00pm | Computer lab: David Gerard - Hands-on use of sequence alignment and phylogenetics software | ||
| Tuesday 6/21: Bioinformatics | |||
| 9:00am-10:00am | Victor Jin | ||
| 10:00am-10:30am | Coffee break | ||
| 10:30am-11:30am | Victor Jin | ||
| 11:30pm-2:00pm | Lunch break | ||
| 2:00pm-4:00pm | Computer lab: Xun Lan | ||
| Wednesday 6/22: Mathematical Neuroscience | |||
| 9:00am-10:00am | Janet Best: Neuroscience, Neural rhythms | ||
| 10:00am-10:30am | Coffee break | ||
| 10:30am-11:30am | Janet Best: Mathematical models, Dynamical systems | ||
| 11:30pm-2:00pm | Lunch break | ||
| 2:00pm-4:00pm | Computer lab: Jung Eun Kim - XPPAUT and Matlab | ||
| Thursday 6/23: Chemogenomics | |||
| 9:00am-10:00am | Joe Verducci: Gene Expression: sources of variation and hypothesis testing | ||
| 10:00am-10:30am | Coffee break | ||
| 10:30am-11:30am | Joe Verducci: Genes in Concert: SCOOP method of selection | ||
| 11:30am-2:00pm | Lunch break | ||
| 2:00pm-4:00pm | Computer lab: Katie Thompson - Introduction to R, Bioconductor, and SCOOP | ||
| Friday 6/24: Environmental Statistics | |||
| 9:00am-10:00am | Tao Shi: Introduction to environmental statistics, exploratory data analysis | ||
| 10:00am-10:30am | Coffee break | ||
| 10:30am-11:30am | Tao Shi: Statistical modeling, classification, project introduction | ||
| 11:30am-2:00pm | Lunch break | ||
| 2:00pm-4:00pm | Computer lab: Jinguo Gao - Introduction to R | ||
Week 2: Lab Tours and Team Projects |
|||
| Tuesday 6/28 | |||
| 1:00pm | Tour of Joe Traver's Neuroscience Lab | ||
| 2:00pm | Tour of Lumina Next Generation Sequencing Lab | ||
| Wednesday 6/29 | |||
| 1:00pm | Tour of Libby Marschall's Aquatics Lab | ||
| Friday 7/1 | |||
| 12:00-12:30pm | Students set up posters and prepare for presentations | ||
| 12:30-1:00pm | Poster viewing | ||
| 1:00-3:30pm | Oral presentations | ||
Team Projects: June 28 - July 1, 2009
Nitish Aggarwal, Hong Tran, Brian Kinney (Chemogenomics) - A comparison of different classification methods for Breast Cancer prediction
Yan Lu and Xuan Zhu (Statistical Phylogenetics) - Where did penguins originate? Phylogenetic relationships
Alice Shen and Dinesh Manandhar (Bioinformatics) - Computational elucidation of the GATA1 and GATA2 regulatory protein networks in the K562 cell model line
Kiah Hardcastle, Junfei Huang, and Jesus A. O'neill Rodriguez (Mathematical Neuroscience) -
Jamie Prezioso and Hanna Chakoian (Environmental Statistics) - Temperature Anomalies, Methane, and Climate Change
REU Presentations: August 12, 2011
Junfei Huang - Insomnia in the two-process model: EEG, serotonin, and neurofeedback
Yan Lu and Xuan Zhu - Phylogenetic analysis of HIV-1 in AIDS Reference Centre in Ghent, Belgium
Dinesh Manandhar - A Computational Approach For Genome-wide Analysis of Combinatorial Epigenetic Marks in H1, Gm12878 and K562 Cell lines
Jesus A. O'Neill - A mathematical investigation of the link between depression and insomnia
Hong Tran - A comparison of different gene selection methods and classification methods for breast cancer prediction
