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BACKGROUND Recently, there has been much interest in relating domain-domain interactions (DDIs) to protein-protein interactions (PPIs) and vice versa, in an attempt to understand the molecular basis of PPIs. RESULTS Here we map structurally derived DDIs onto the cellular PPI networks of different organisms and demonstrate that there is a catalog of domain(More)
MicroRNAs (miRNAs) are approximately 22 nt-long non-coding RNA molecules, believed to play important roles in gene regulation. We present a comprehensive analysis of the conservation and clustering patterns of known miRNAs in human. We show that human miRNA gene clustering is significantly higher than expected at random. A total of 37% of the known human(More)
Virally encoded microRNAs (miRNAs) have recently been discovered in herpesviruses. However, their biological roles are mostly unknown. We developed an algorithm for the prediction of miRNA targets and applied it to human cytomegalovirus miRNAs, resulting in the identification of the major histocompatibility complex class I-related chain B (MICB) gene as a(More)
MOTIVATION Over the past decade, deciphering the roles of microRNAs (miRNAs) has relied heavily upon the identification of their targets. Most of the targets that were computationally and experimentally characterized were evolutionarily conserved 'seed' targets, containing a perfect 6-8 nt match between the miRNA 5(')-region and the messenger RNA (mRNA).(More)
Computational identification of putative microRNA (miRNA) targets is an important step towards elucidating miRNA functions. Several miRNA target-prediction algorithms have been developed followed by publicly available databases of these predictions. Here we present a new database offering miRNA target predictions of several binding types, identified by our(More)
Micro (mi)RNAs are small non-coding RNAs that regulate the expression of their targets' messenger RNAs through both translational inhibition and regulation of target RNA stability. Recently, a number of viruses, particularly of the herpesvirus family, have been shown to express their own miRNAs to control both viral and cellular transcripts. Although some(More)
1 Acknowledgments First, I would like to thank my advisors: Nati Linial and Tali Tishby of the computer science department and Michal Linial of the life science department at the Hebrew University. Within the last ve years we have come a long way together, and I'm grateful for their guidance, support, warmth and generous help all these years. I would like(More)
Acknowledgments First, I would like to thank my advisors: Nati Linial and Tali Tishby of the computer science department and Michal Linial of the life science department at the Hebrew University. Within the last ve years we have come a long way together, and I'm grateful for their guidance, support, warmth and generous help all these years. I would like to(More)
Cells adapt to environmental changes by efficiently adjusting gene expression programs. Staphylococcus aureus, an opportunistic pathogenic bacterium, switches between defensive and offensive modes in response to quorum sensing signal. We identified and studied the structural characteristics and dynamic properties of the core regulatory circuit governing(More)
permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Conservation of interacting domains <p>Mapping of domain-domain interactions onto the cellular protein-protein interaction networks of different organisms demonstrates that there is a catalogue of domain pairs that is used for mediating(More)
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