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Search Results: 1 - 10 of 5239 matches for " Roy Navon "
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GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists
Eran Eden, Roy Navon, Israel Steinfeld, Doron Lipson, Zohar Yakhini
BMC Bioinformatics , 2009, DOI: 10.1186/1471-2105-10-48
Abstract: GOrilla is a web-based application that identifies enriched GO terms in ranked lists of genes, without requiring the user to provide explicit target and background sets. This is particularly useful in many typical cases where genomic data may be naturally represented as a ranked list of genes (e.g. by level of expression or of differential expression). GOrilla employs a flexible threshold statistical approach to discover GO terms that are significantly enriched at the top of a ranked gene list. Building on a complete theoretical characterization of the underlying distribution, called mHG, GOrilla computes an exact p-value for the observed enrichment, taking threshold multiple testing into account without the need for simulations. This enables rigorous statistical analysis of thousand of genes and thousands of GO terms in order of seconds. The output of the enrichment analysis is visualized as a hierarchical structure, providing a clear view of the relations between enriched GO terms.GOrilla is an efficient GO analysis tool with unique features that make a useful addition to the existing repertoire of GO enrichment tools. GOrilla's unique features and advantages over other threshold free enrichment tools include rigorous statistics, fast running time and an effective graphical representation. GOrilla is publicly available at: http://cbl-gorilla.cs.technion.ac.il webciteThe availability of functional genomics data has increased dramatically over the last decade, mostly due to the development of high-throughput microarray-based technologies such as expression profiling. Automatic mining of these data for meaningful biological signals requires systematic annotation of genomic elements at different levels. The Gene Ontology (GO) project [1] is a collaborative effort aimed at providing a controlled vocabulary to describe gene product attributes in all organisms. GO consists of three hierarchically structured vocabularies (ontologies) that describe gene products in terms o
Semi-supervised class discovery using quantitative phenotypes – CVD as a case study
Steinfeld Israel,Navon Roy,Ardigò Diego,Zavaroni Ivana
BMC Bioinformatics , 2007, DOI: 10.1186/1471-2105-8-s8-s6
Abstract:
Novel Rank-Based Statistical Methods Reveal MicroRNAs with Differential Expression in Multiple Cancer Types
Roy Navon,Hui Wang,Israel Steinfeld,Anya Tsalenko,Amir Ben-Dor,Zohar Yakhini
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0008003
Abstract: microRNAs (miRNAs) regulate target genes at the post-transcriptional level and play important roles in cancer pathogenesis and development. Variation amongst individuals is a significant confounding factor in miRNA (or other) expression studies. The true character of biologically or clinically meaningful differential expression can be obscured by inter-patient variation. In this study we aim to identify miRNAs with consistent differential expression in multiple tumor types using a novel data analysis approach.
Silencing of a large microRNA cluster on human chromosome 14q32 in melanoma: biological effects of mir-376a and mir-376c on insulin growth factor 1 receptor
Liron Zehavi, Roi Avraham, Aviv Barzilai, Dalia Bar-Ilan, Roy Navon, Yechezkel Sidi, Dror Avni, Raya Leibowitz-Amit
Molecular Cancer , 2012, DOI: 10.1186/1476-4598-11-44
Abstract: We show that the expression of miRNAs from a large cluster on human chromosome 14q32 is significantly down-regulated in melanoma cell lines, benign nevi and melanoma samples relative to normal melanocytes. This miRNA cluster resides within a parentally imprinted chromosomal region known to be important in development and differentiation. In some melanoma cell lines, a chromosomal deletion or loss-of-heterozygosity was observed in the cis-acting regulatory region of this cluster. In several cell lines we were able to re-express two maternally-induced genes and several miRNAs from the cluster with a combination of de-methylating agents and histone de-acetylase inhibitors, suggesting that epigenetic modifications take part in their silencing. Stable over-expression of mir-376a and mir-376c, two miRNAs from this cluster that could be re-expressed following epigenetic manipulation, led to modest growth retardation and to a significant decrease in migration in-vitro. Bioinformatic analysis predicted that both miRNAs could potentially target the 3'UTR of IGF1R. Indeed, stable expression of mir-376a and mir-376c in melanoma cells led to a decrease in IGF1R mRNA and protein, and a luciferase reporter assay indicated that the 3'UTR of IGF1R is a target of both mir-376a and mir-376c.Our work is the first to show that the large miRNA cluster on chromosome 14q32 is silenced in melanoma. Our results suggest that down-regulation of mir-376a and mir-376c may contribute to IGF1R over-expression and to aberrant negative regulation of this signaling pathway in melanoma, thus promoting tumorigenesis and metastasis.
The role of codon selection in regulation of translation efficiency deduced from synthetic libraries
Sivan Navon, Yitzhak Pilpel
Genome Biology , 2011, DOI: 10.1186/gb-2011-12-2-r12
Abstract: We define the region in a gene that takes the longest time to translate as the bottleneck. We found that localization of the bottleneck at the beginning of a transcript promoted a high level of expression, especially if the computed dwell time of the ribosome within this region was sufficiently long. The location and translation time of the bottleneck were not correlated with the cost of expression, approximated by the fitness of the host cell, yet utilization of specific codons was. Particularly, enhanced usage of the codons UCA and CAU was correlated with increased cost of production, potentially due to sequestration of their corresponding rare tRNAs.The distribution of codons along the genes appears to affect translation efficiency, consistent with analysis of natural genes. This study demonstrates how synthetic biology complements bioinformatics by providing a set-up for well controlled experiments in biology.Understanding the mechanisms that control the efficiency of protein translation is a major challenge for proteomics, computational biology and biotechnology. Efficient translation of proteins, either in their natural biological context or in heterologous expression systems, amounts to maximizing production, while minimizing the costs of the process. Abundant genome sequence data now make it possible to decipher sequence design elements that govern the efficiency of translation. The codon adaptation index (CAI) [1] was the first measure to be introduced for gauging translation efficiency directly from nucleotide sequences of genes. This measure quantifies the extent to which the codon bias of a gene resembles that of highly expressed genes. The tRNA adaptation index (tAI) assesses the extent to which the codons of a gene are biased towards the more abundant tRNAs in the organism [2]. Despite several simplifying assumptions, both tAI and CAI are good measurements for predicting protein abundance from sequence [3,4]. Perhaps the most critical simplification of
Linear programming bounds for codes via a covering argument
Michael Navon,Alex Samorodnitsky
Mathematics , 2007,
Abstract: We recover the first linear programming bound of McEliece, Rodemich, Rumsey, and Welch for binary error-correcting codes and designs via a covering argument. It is possible to show, interpreting the following notions appropriately, that if a code has a large distance, then its dual has a small covering radius and, therefore, is large. This implies the original code to be small. We also point out (in conjunction with further work) that this bound is a natural isoperimetric constant of the Hamming cube, related to its Faber-Krahn minima. While our approach belongs to the general framework of Delsarte's linear programming method, its main technical ingredient is Fourier duality for the Hamming cube. In particular, we do not deal directly with Delsarte's linear program or orthogonal polynomial theory.
POD/DEIM Nonlinear model order reduction of an ADI implicit shallow water equations model
Razvan Stefanescu,Ionel Michael Navon
Physics , 2012, DOI: 10.1016/j.jcp.2012.11.035
Abstract: In the present paper we consider a 2-D shallow-water equations (SWE) model on a $\beta$-plane solved using an alternating direction fully implicit (ADI) finite-difference scheme on a rectangular domain. The scheme was shown to be unconditionally stable for the linearized equations. The discretization yields a number of nonlinear systems of algebraic equations. We then use a proper orthogonal decomposition (POD) to reduce the dimension of the SWE model. Due to the model nonlinearities, the computational complexity of the reduced model still depends on the number of variables of the full shallow - water equations model. By employing the discrete empirical interpolation method (DEIM) we reduce the computational complexity of the reduced order model due to its depending on the nonlinear full dimension model and regain the full model reduction expected from the POD model. To emphasize the CPU gain in performance due to use of POD/DEIM, we also propose testing an explicit Euler finite difference scheme (EE) as an alternative to the ADI implicit scheme for solving the swallow water equations model. We then proceed to assess the efficiency of POD/DEIM as a function of number of spatial discretization points, time steps, and POD basis functions. As was expected, our numerical experiments showed that the CPU time performances of POD/DEIM schemes are proportional to the number of mesh points. Once the number of spatial discretization points exceeded 10000 and for 90 DEIM interpolation points, the CPU time was decreased by a factor of 10 in case of POD/DEIM implicit SWE scheme and by a factor of 15 for the POD/DEIM explicit SWE scheme in comparison with the corresponding POD SWE schemes. Our numerical tests revealed that if the number of points selected by DEIM algorithm reached 50, the approximation errors due to POD/DEIM and POD reduced systems have the same orders of magnitude.
A Novel Translocation Breakpoint within the BPTF Gene Is Associated with a Pre-Malignant Phenotype
Yosef Buganim,Ido Goldstein,Doron Lipson,Michael Milyavsky,Sylvie Polak-Charcon,Corine Mardoukh,Hilla Solomon,Eyal Kalo,Shalom Madar,Ran Brosh,Marina Perelman,Roy Navon,Naomi Goldfinger,Iris Barshack,Zohar Yakhini,Varda Rotter
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0009657
Abstract: Partial gain of chromosome arm 17q is an abundant aberrancy in various cancer types such as lung and prostate cancer with a prominent occurrence and prognostic significance in neuroblastoma – one of the most common embryonic tumors. The specific genetic element/s in 17q responsible for the cancer-promoting effect of these aberrancies is yet to be defined although many genes located in 17q have been proposed to play a role in malignancy. We report here the characterization of a naturally-occurring, non-reciprocal translocation der(X)t(X;17) in human lung embryonal-derived cells following continuous culturing. This aberrancy was strongly correlated with an increased proliferative capacity and with an acquired ability to form colonies in vitro. The breakpoint region was mapped by fluorescence in situ hybridization (FISH) to the 17q24.3 locus. Further characterization by a custom-made comparative genome hybridization array (CGH) localized the breakpoint within the Bromodomain PHD finger Transcription Factor gene (BPTF), a gene involved in transcriptional regulation and chromatin remodeling. Interestingly, this translocation led to elevation in the mRNA levels of the endogenous BPTF. Knock-down of BPTF restricted proliferation suggesting a role for BPTF in promoting cellular growth. Furthermore, the BPTF chromosomal region was found to be amplified in various human tumors, especially in neuroblastomas and lung cancers in which 55% and 27% of the samples showed gain of 17q24.3, respectively. Additionally, 42% percent of the cancer cell lines comprising the NCI-60 had an abnormal BPTF locus copy number. We suggest that deregulation of BPTF resulting from the translocation may confer the cells with the observed cancer-promoting phenotype and that our cellular model can serve to establish causality between 17q aberrations and carcinogenesis.
Tracking of Moving Objects in Video Through Invariant Features in Their Graph Representation
Miller O,Averbuch A,Navon E
EURASIP Journal on Image and Video Processing , 2008,
Abstract: The paper suggests a contour-based algorithm for tracking moving objects in video. The inputs are segmented moving objects. Each segmented frame is transformed into region adjacency graphs (RAGs). The object's contour is divided into subcurves. Contour's junctions are derived. These junctions are the unique a€ signaturea€ of the tracked object. Junctions from two consecutive frames are matched. The junctions' motion is estimated using RAG edges in consecutive frames. Each pair of matched junctions may be connected by several paths (edges) that become candidates that represent a tracked contour. These paths are obtained by the -shortest paths algorithm between two nodes. The RAG is transformed into a weighted directed graph. The final tracked contour construction is derived by a match between edges (subcurves) and candidate paths sets. The RAG constructs the tracked contour that enables an accurate and unique moving object representation. The algorithm tracks multiple objects, partially covered (occluded) objects, compounded object of merge/split such as players in a soccer game and tracking in a crowded area for surveillance applications. We assume that features of topologic signature of the tracked object stay invariant in two consecutive frames. The algorithm's complexity depends on RAG's edges and not on the image's size.
Tracking of Moving Objects in Video Through Invariant Features in Their Graph Representation
O. Miller,A. Averbuch,E. Navon
EURASIP Journal on Image and Video Processing , 2008, DOI: 10.1155/2008/328052
Abstract: The paper suggests a contour-based algorithm for tracking moving objects in video. The inputs are segmented moving objects. Each segmented frame is transformed into region adjacency graphs (RAGs). The object's contour is divided into subcurves. Contour's junctions are derived. These junctions are the unique ¢ € signature ¢ € of the tracked object. Junctions from two consecutive frames are matched. The junctions' motion is estimated using RAG edges in consecutive frames. Each pair of matched junctions may be connected by several paths (edges) that become candidates that represent a tracked contour. These paths are obtained by the k-shortest paths algorithm between two nodes. The RAG is transformed into a weighted directed graph. The final tracked contour construction is derived by a match between edges (subcurves) and candidate paths sets. The RAG constructs the tracked contour that enables an accurate and unique moving object representation. The algorithm tracks multiple objects, partially covered (occluded) objects, compounded object of merge/split such as players in a soccer game and tracking in a crowded area for surveillance applications. We assume that features of topologic signature of the tracked object stay invariant in two consecutive frames. The algorithm's complexity depends on RAG's edges and not on the image's size.
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