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Articles 1 - 3 of 3
Full-Text Articles in Computational Biology
Semiparametric Regression Of Multi-Dimensional Genetic Pathway Data: Least Squares Kernel Machines And Linear Mixed Models, Dawei Liu, Xihong Lin, Debashis Ghosh
Semiparametric Regression Of Multi-Dimensional Genetic Pathway Data: Least Squares Kernel Machines And Linear Mixed Models, Dawei Liu, Xihong Lin, Debashis Ghosh
Harvard University Biostatistics Working Paper Series
No abstract provided.
Bounded Search For De Novo Identification Of Degenerate Cis-Regulatory Elements, Jonathan M. Carlson, Arijit Chakravarty, Radhika S. Khetani, Robert H. Gross
Bounded Search For De Novo Identification Of Degenerate Cis-Regulatory Elements, Jonathan M. Carlson, Arijit Chakravarty, Radhika S. Khetani, Robert H. Gross
Dartmouth Scholarship
The identification of statistically overrepresented sequences in the upstream regions of coregulated genes should theoretically permit the identification of potential cis-regulatory elements. However, in practice many cis-regulatory elements are highly degenerate, precluding the use of an exhaustive word-counting strategy for their identification. While numerous methods exist for inferring base distributions using a position weight matrix, recent studies suggest that the independence assumptions inherent in the model, as well as the inability to reach a global optimum, limit this approach.
Genome Scanning Methods For Comparing Sequences Between Groups, With Application To Hiv Vaccine Trials, Peter B. Gilbert, Chunyuan Wu, David V. Jobes
Genome Scanning Methods For Comparing Sequences Between Groups, With Application To Hiv Vaccine Trials, Peter B. Gilbert, Chunyuan Wu, David V. Jobes
UW Biostatistics Working Paper Series
Consider a placebo-controlled preventive HIV vaccine efficacy trial. An HIV amino acid sequence is measured from each volunteer who acquires HIV, and these sequences are aligned together with the reference HIV sequence represented in the vaccine. We develop genome scanning methods to identify HIV positions at which the amino acids in sequences from infected vaccine recipients tend to be more divergent from the corresponding reference amino acid than the amino acids in sequences from infected placebo recipients. We consider five two-sample test statistics, based on Euclidean, Mahalanobis, and Kullback-Leibler divergence measures. Weights are incorporated to reflect biological information contained in …