M. Bittner

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Current gene-expression microarrays carry an enormous amount of information. This paper examines lossy SPIHT and JPEG 2000 compression of oligo microarray images and addresses the accuracy of differential expression detection with compressed images. Experiments show that the identification disagreement rate for all genes monotonically increases with the(More)
Intervention in a gene regulatory network is used to avoid undesirable states, such as those associated with a disease. Several types of intervention have been studied in the framework of a probabilistic Boolean network (PBN), which is obtained by joining several Boolean networks (BN) using a probabilistic structure. In this work we treat a case in which we(More)
The long-run characteristics of a dynamical system are critical and their determination is a primary aspect of system analysis. In the other direction, system synthesis involves constructing a network possessing a given set of properties. This constitutes the inverse problem. This paper addresses the long-run inverse problem pertaining to Boolean networks(More)
A set of predictor genes is said to be intrinsically multi-variate predictive (IMP) for a target gene if all properly contained subsets of the predictor set are bad predictors of the target but the full predictor set predicts the target with great accuracy. A basic measure of the predictive power of a set of genes with respect to the target is the(More)
Several classification studies have been conducted to relate molecular expression to disease progression, outcome and vulnerability. These studies have failed except in simple situations. A reason for this has been that classification schemes have in general ignored the heterogeneity of underlying cellular contexts. In this work we conduct a model based(More)
Cell adjusts its regulatory machinery in response to environmental changes to maintain its basic functionality. Different cellular conditions require different regulatory mechanisms that tightly regulate genes. Due to this tightly coordinated regulation, the expression of those genes should show consistent patterns within the same cellular contexts while(More)
When using cDNA microarrays, normalization to correct biases is a common preliminary step before carrying out any data analysis, its objective being to reduce the systematic variations between the arrays. The biases are due to various systematic factors - scanner setting, amount of mRNA in the sample pool, and dye response characteristics between the(More)
RNA interference has been widely used to identify genes involved in the production of particular biological phenotypes. This type of gene silencing technology has been used in plants, invertebrates and mammalian systems [1]. The availability of the sequences of large numbers of genes has allowed large libraries of siRNAs to be produced. To effectively use(More)
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