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Full-Text Articles in Life Sciences
A Novel Topology For Representing Protein Folds, Mark R. Segal
A Novel Topology For Representing Protein Folds, Mark R. Segal
Mark R Segal
Various topologies for representing three dimensional protein structures have been advanced for purposes ranging from prediction of folding rates to ab initio structure prediction. Examples include relative contact order, Delaunay tessellations, and backbone torsion angle distributions. Here we introduce a new topology based on a novel means for operationalizing three dimensional proximities with respect to the underlying chain. The measure involves first interpreting a rank-based representation of the nearest neighbors of each residue as a permutation, then determining how perturbed this permutation is relative to an unfolded chain. We show that the resultant topology provides improved association with folding and …
Clustering With Exclusion Zones: Genomic Applications, Mark Segal, Yuanyuan Xiao, Fred Huffer
Clustering With Exclusion Zones: Genomic Applications, Mark Segal, Yuanyuan Xiao, Fred Huffer
Mark R Segal
Methods for formally evaluating the clustering of events in space or time, notably the scan statistic, have been richly developed and widely applied. In order to utilize the scan statistic and related approaches, it is necessary to know the extent of the spatial or temporal domains wherein the events arise. Implicit in their usage is that these domains have no “holes”—hereafter “exclusion zones”—regions in which events a priori cannot occur. However, in many contexts, this requirement is not met. When the exclusion zones are known, it is straightforward to correct the scan statistic for their occurrence by simply adjusting the …
Identification Of Yeast Transcriptional Regulation Networks Using Multivariate Random Forests, Yuanyuan Xiao, Mark Segal
Identification Of Yeast Transcriptional Regulation Networks Using Multivariate Random Forests, Yuanyuan Xiao, Mark Segal
Mark R Segal
The recent availability of whole-genome scale data sets that investigate complementary and diverse aspects of transcriptional regulation has spawned an increased need for new and effective computational approaches to analyze and integrate these large scale assays. Here, we propose a novel algorithm, based on random forest methodology, to relate gene expression (as derived from expression microarrays) to sequence features residing in gene promoters (as derived from DNA motif data) and transcription factor binding to gene promoters (as derived from tiling microarrays). We extend the random forest approach to model a multivariate response as represented, for example, by time-course gene expression …
Chess, Chance And Conspiracy, Mark Segal
Chess, Chance And Conspiracy, Mark Segal
Mark R Segal
Chess and chance are seemingly strange bedfellows. Luck and/or randomness have no apparent role in move selection when the game is played at the highest levels. However, when competition is at the ultimate level, that of the World Chess Championship (WCC), chess and conspiracy are not strange bedfellows, there being a long and colorful history of accusations levied between participants. One such accusation, frequently repeated, was that all the games in the 1985 WCC (Karpov vs Kasparov) were fixed and prearranged move by move. That this claim was advanced by a former World Champion, Bobby Fischer, argues that it ought …