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  • Authors: Zaslavsky, Elena (2006)

  • A major objective in molecular biology is to understand how a genome encodes the information that speci es when and where a gene will be transcribed into its protein product. Mediating proteins, known as transcription factors, facilitate this process by interacting with the cell 's sDNA and the transcription machinery. It is of central importance to identify all sequence-speci c DNA binding sites of transcription factors. In this thesis, we consider two relevant computational problems. The first problem is to develop a representation for a group of known binding sites of a particular transcription factor, in order to facilitate recognition of other binding sites of the same protein. ...

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  • Authors: Puma, Michael Joseph (2006)

  • The spatial and temporal scaling properties of soil moisture and evapotranspiration in water-limited ecosystems are investigated. These scaling properties are critical for efforts to measure, model, and predict fundamental ecohydrologic processes. Simulation studies yield insight into the dependence of space-time scaling on soil, vegetation, and climate characteristics. Soil moisture and transpiration are first examined at the plant scale to improve predictions through a better understanding of the temporal scaling of rainfall. Simulation results demonstrate that rainfall data resolved at the daily level allow accurate prediction of soil moisture and transpiration dynamics for smaller...

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  • Authors: Ailon, Nir (2006)

  • This work is comprised of three separate parts: (1) Lower bounds for linear degeneracy testing (based on joint work with Bernard Chazelle [5]); (2) Aggregating inconsistent information (based on joint work with Moses Charikar and Alantha Newman [3]); and (3) The fast Johnson-Lindenstrauss transform and approximate nearest neighbor searching (based on joint work with Bernard Chazelle [6]). The first part discusses a fundamental computational geometric problem called rSUM: given n real numbers, do any r of them sum up to 0? It is the simplest case of a more general family of problems called degeneracy testing. This seemingly naive problem is in the core of the di cult y in designing al...