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Full-Text Articles in Life Sciences
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.
Principal Component Analysis For Predicting Transcription-Factor Binding Motifs From Array-Derived Data, Yunlong Liu, Matthew P Vincenti, Hiroki Yokota
Principal Component Analysis For Predicting Transcription-Factor Binding Motifs From Array-Derived Data, Yunlong Liu, Matthew P Vincenti, Hiroki Yokota
Dartmouth Scholarship
The responses to interleukin 1 (IL-1) in human chondrocytes constitute a complex regulatory mechanism, where multiple transcription factors interact combinatorially to transcription-factor binding motifs (TFBMs). In order to select a critical set of TFBMs from genomic DNA information and an array-derived data, an efficient algorithm to solve a combinatorial optimization problem is required. Although computational approaches based on evolutionary algorithms are commonly employed, an analytical algorithm would be useful to predict TFBMs at nearly no computational cost and evaluate varying modelling conditions. Singular value decomposition (SVD) is a powerful method to derive primary components of a given matrix. Applying SVD …
Spermidine-Condensed Phi X174 Dna Cleavage By Micrococcal Nuclease: Torus Cleavage Model And Evidence For Unidirectional Circumferential Dna Wrapping., Kenneth A. Marx, Thomas C. Reynolds
Spermidine-Condensed Phi X174 Dna Cleavage By Micrococcal Nuclease: Torus Cleavage Model And Evidence For Unidirectional Circumferential Dna Wrapping., Kenneth A. Marx, Thomas C. Reynolds
Dartmouth Scholarship
Spermidine-condensed phi X174 replicative form (RF) II DNA was digested with micrococcal nuclease to yield seven identifiable DNA bands forming an arithmetic fragment-length series. The DNA monomer unit length was found to be 780 +/- 80 base pairs. This result is most consistent with a proposed model for micrococcal nuclease cleavage of a DNA torus organized by the unidirectional, circumferential wrapping of B-geometry DNA. By a topological consideration, the blunt-end-rod-fusion model for torus formation [Eickbush, T. H. & Moudrianakis, E. N. (1978) Cell 13, 295-306] is shown to be inconsistent with our empirical solution results. We propose a continuous, circumferential …