Research projects

Studying the functional relationship between transcription factors and non-coding RNAs
Transcription factors (TFs) as well as chromatin associated protein complexes, activate and repress transcription by binding to regulatory regions of the DNA and recruiting the transcriptional machinery. To-date there are increasing evidence that in addition to the TFs, long intergenic non-coding RNAs (lincRNAs) play an important role in gene regulation.
Read more >>
Exploring the world of dual RNA and DNA binding proteins in human embryonic stem cells
We are currently developing a proteomic-based methodology to uncover the repertoire of dual binding DNA and RNA binding proteins (DRBPs) in human embryonic stem cells (hESCs), motivated by recent evidence demonstrating the ability of transcription factors to bind diverse types of RNA.
Read more >>
Exploring the co-regulatory network between RNA binding proteins and miRNAs
We study the functional relationships between RNA binding proteins (RBPs) and microRNAs. Our recent analysis revealed a high percentage of shared microRNA targets among different RBPs. Among the shared targets of eight RBPs we observed an unexpected high number of microRNAs that are significantly enriched in specific cellular processes.
Read more >>
A combined sequence and structure based approach for discovering enriched motifs in RNA from in vivo binding data
RNA binding proteins (RBPs) play an important role in regulating many processes in the cell. RBPs often recognize their RNA targets in a specific manner. In addition to the RNA primary sequence, the structure of the RNA has been shown to play a central role in RNA recognition by RBPs. SMARTIV is a novel computational tool for discovering combined sequence and structure binding motifs from in vivo RNA binding data relying on the sequences of the target sites, the ranking of their binding scores and their predicted secondary structure.
Read more >>
PatchBag - a novel approach for quick detection of interface similarity and complementarity
With the growing amount of protein structures, new methods for identifying functional similarities are critically needed. We developed PatchBag, a vector representation of the protein surface that enables rapid and accurate identification of surface similarity and interface complementarity on large datasets, based on a ‘bag-of-words’ approach.
Read more >>
Widespread evidence to the role of flanking regions on transcription factor binding preferences
Recent studies suggest that on average 99.8% of transcription factor binding motifs in the human genome are unbound by the respective transcription factor. In our study we investigate what distinguishes a “binding motif” from another similar motif which does not bind protein within the same genomic environment. We show that DNA features far beyond the core motif contribute to DNA recognition by transcription factors. Interestingly, these features are characteristic of the transcription factor family.
Read more >>
RBPmap: mapping binding sites of RNA-binding proteins
Regulation of gene expression is executed in many cases by RNA-binding proteins (RBPs) that bind to mRNAs as well as to non-coding RNAs. RBPs recognize their RNA target via specific binding sites on the RNA. Predicting the binding sites of RBPs is known to be a major challenge. RBPmap is a webserver for accurate prediction and mapping of RBP binding sites.
Read more >>
The role of RNA conformations in RNA-protein recognition
In this project we studied protein-RNA structures from 9 RNA binding protein families extracted from the PDB and characterized the structural properties of RNA within the interfaces. In addition, we looked on RNA-protein interactions and examined the sequences binding the RRM domain.
Read more >>
An epigenetic signature at intragenic exons with implication for expression
While the role of CpG methylation at the gene promoter is well characterized, the function of DNA methylation and histone modifications within the gene, specifically at intragenic exons, remains unclear. In this study we investigated the relationship between DNA methylation and histone modifications at intragenic exons and the exon expression in Human tissue culture and primary cells. Consistent with previous work we found that DNA methylation within the gene is positively correlated with its expression. Moreover we identified a set of hypo-methylated exons widespread in the genome that have a unique epigenetic signature positively correlated with expression.
Read more >>
An integrated regulatory network reveals pervasive cross-regulation among transcription and splicing factors
To date there is increasing evidence of coupling between transcription and splicing regulation. In this study, we modeled a network integrating the two regulations. Analysis of the network indicated that splicing factors were more often regulated by alternative splicing while transcription factors were more extensively controlled by transcriptional regulation. Overall, we postulate that regulatory proteins in the cell are controlled preferentially by the specific regulation they conduct.
Read more >>
Comparative metagenomic analyses reveal viral-induced shifts of host metabolism towards nucleotide biosynthesis
Viral genomes often contain metabolic genes that were acquired from host genomes (auxiliary genes). It is assumed that these genes are fixed in viral genomes as a result of a selective force, favoring viruses that acquire specific metabolic functions. In this study, we identify a set of statistically enriched auxiliary genes in marine viral metagenomes. These genes are assigned to a global metabolism network we created. Our analysis suggests that many of the metabolic functions enriched in the viral metagenomes induce shift in the host metabolism, upon infection, towards nucleotide recycling and deoxynucleotide synthesis.
Read more >>