Undergraduate Research Project Description Spring 2009
Statistical modeling of DNA selection protocols
(CLOSED: Not accepting applications for this position)
Professor Rasmus Nielsen We are collaborating with biological researchers on developing methods and strategies for filtering out certain parts of a DNA molecule. The experimental methods we are developing will be particularly useful in biological research which uses DNA to investigate the history and ecology of natural populations of different species of animals.
We need a student to test out different strategies computationally before the biological researchers conduct their experiments. The student will participate in establishing statistical models describing the experimental designs and implementing and applying computer programs for testing different strategies. No prior knowledge of biology is needed, but the student needs to have good computational skills.
Student Researcher for ENCODE and the Berkeley Drosophila Transcription Network Project
(Closed: Not accepting applications for this position)
Professor Peter BickelPostdoc Ben Brown
This student will work on a variety of projects in the general area of Systems Biology, with a focus on the Genomics of Humans and Drosophila. Responsibilities will involve extensive programming in Python and C. Opportunities for scientific contribution and publication will exist throughout.
The successful applicant will have extensive experience in the Python programming language, and preferably also in C. At least some background in statistics will be needed.
Simulating Models of Speciation
(CLOSED: Not accepting applications for this position)
Grad Student Peter RalphFrom 1929 to 1962, Sewall Wright and Sir R A Fisher, two of the primary driving forces behind the then-emerging field of population genetics, engaged in an often heated debate over the nature of evolution that profoundly shaped how the discipline, and our understanding of the theory of evolution, has evolved. The question: Does most evolutionary change arise from a gradual, inexorable improvement of genes in large populations, or is it necessary to have a constellation of smaller populations, tossed about on the winds of chance, to gain an evoluationary breakthrough? This controversy (known as the Wright-Fisher Controversy) extends to the modern day.
We will develop a few simple models of speciation or genetic isolation, simulate them with existing software (simuPOP), and compare the results in the context above. Some knowledge of R, and possibly python, is desired.
Counting Civilian Casualties in Times of War and Conflict
(CLOSED: Not accepting applications for this position)
Professor Nicholas P. JewellEstimates of civilian casualties associated with the current war in Iraq have proven to be extremely controversial. The statistical techniques used to date are all subject to various biases and suffer from differing levels of precision. Currently I am researching historical approaches to counting civilian casualties, focusing on the US Civil War, World Wars I and II, and the Vietnam War, in order to give perspective on, and contrast with, methods used in Iraq. This project would involve historical research in addition to statistical investigation.