Carl Tony Fakhry

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Small RNAs (sRNAs) constitute an important class of post-transcriptional regulators that control critical cellular processes in bacteria. Recent research using high-throughput transcriptomic approaches has led to a dramatic increase in the discovery of bacterial sRNAs. However, it is generally believed that the currently identified sRNAs constitute a(More)
We propose an unsupervised method for extracting causal relations between biomedical entities using stochastic difference equations (SDE). Our method attempts to generalize the propagation of relevance in medical sentences in order to extract related biomedical terms and the semantic relation between them. We model the propagation of relevance in candidate(More)
Inference of active regulatory cascades under specific molecular and environmental perturbations is a recurring task in transcriptional data analysis. Commercial tools based on large, manually curated networks of causal relationships offering such functionality have been used in thousands of articles in the biomedical literature. The adoption and extension(More)
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