Publication [1]: "Composite effects of gene determinants on the translation speed and density of ribosomes."
In this work we studied the affect of gene's coding sequence features (tRNA pool, amino acid charge, and mRNA folding energy) on its translation elongation. We found that each of these features has a non-negligible distinct correlation with the speed of translation elongation. In addition, each of these features might contribute independently to slowing down ribosomal speed at the beginning of genes, which was suggested in previous studies to improve ribosomal allocation and the cost of translation, and to decrease ribosomal jamming. A model of ribosomal translation based on these three basic features highly correlated with the genomic profile of ribosomal density. We showed that the robustness to transcription errors in terms of the values of these features is higher at the beginnings of genes, suggesting that this region is important for translation.Publication [2]: "Gene bi-targeting by viral and human miRNAs."
In this paper we developed an efficient filtration algorithm for microRNA target prediction, which is based on tree-to-tree sequence alignment techniques. In addition we developed a new clustering approach, based on an admissible branch-and-bound algorithm, which we call "bi-targeting", to study cross-genome (human and viral) post-transcriptional regulation. This approach allows to efficiently cluster modules consisting of human and viral microRNAs, which share common target genes. We then applied our method to a thorough bioinformatic study, leading to the prediction of some significant microRNA modules consisting of human and viral Epstein Barr virus (EBV) miRNAs and human genes.Publication [3]: "FASH : A web application for nucleotides sequence search."
This paper presents a fast sequence alignment algorithm based on Fast Fourier Transform, called FASH. Given a query sequence and a long text-sequence (e.g, the human genome), FASH detects subsequences within the text that are remotely-similar to the query. FASH offers an alternative approach to Blast/Fasta for querying long RNA/DNA sequences. FASH differs from these other approaches in that it does not depend on the existence of contiguous seed-sequences in its initial detection phase.Publication [4]: "Computational identification of three-way junctions in folded RNAs: A case study in Arabidopsis."
In this work we present an algorithm, based on ideas originating from computational geometry, for detecting three-way junctions in data sets of genes that are related to a metabolic pathway of interest. Three-way junctions in folded RNAs have been investigated both experimentally and computationally, and were shown to have a functional role. Applying the algorithm to the search of three-way junctions in Arabidopsis, resulted in a candidate that was speculated to have an interesting functional role and was verified experimentally.Publication [5]: "A structure based flexible search method for ncRNA motifs."
In this work we developed an RNA motif search tool called STRMS (Structural RNA Motif Search), which takes as input the secondary structure of the query, including local sequence and structure constraints, and a target sequence database. It reports all occurrences of the query in the target, ranked by their similarity to the query. Our tool is flexible and takes into account a large number of sequence options and existence of potential pseudoknots as dictated by specific queries. Our approach combines pre-folding and an RNA pattern matching algorithm based on subtree homeomorphism for ordered, rooted trees. We employed STRMS in search for both new and known RNA motifs (riboswitches and tRNAs) in large target databases. Our results point to a number of additional purine bacterial riboswitch candidates in newly sequenced bacteria, and demonstrate high sensitivity on known riboswitches and tRNAs.