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Search Results: 1 - 10 of 388 matches for " Zakharia Frenkel "
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Hierarchy of Protein Loop-Lock Structures: A New Server for the Decomposition of a Protein Structure into a Set of Closed Loops  [PDF]
Simon Kogan, Zakharia Frenkel, Oleg Kupervasser, Zeev Volkovich
Computational Molecular Bioscience (CMB) , 2013, DOI: 10.4236/cmb.2013.31001
Abstract:

HoPLLS (Hierarchy of protein loop-lock structures) (http://leah.haifa.ac.il/~skogan/Apache/mydata1/main.html) is a web server that identifies closed loops-a structural basis for protein domain hierarchy. The server is based on the loop-and-lock theory for structural organisation of natural proteins. We describe this web server, the algorithms for the decomposition of a 3D protein into loops and the results of scientific investigations into a structural “alphabet” of loops and locks.

Human nucleosomes: special role of CG dinucleotides and Alu-nucleosomes
Thomas Bettecken, Zakharia M Frenkel, Edward N Trifonov
BMC Genomics , 2011, DOI: 10.1186/1471-2164-12-273
Abstract: When analyzing the human genome sequence with the positional autocorrelation method, we found that only the dinucleotide CG shows the 10.4 base periodicity, which is indicative of the presence of nucleosomes. There is a high occurrence of CG dinucleotides that are either 31 (10.4 × 3) or 62 (10.4 × 6) base pairs apart from one another - a sequence bias known to be characteristic of Alu-sequences. In a similar analysis with repetitive sequences removed, peaks of repeating CG motifs can be seen at positions 10, 21 and 31, the nearest integers of multiples of 10.4.Although the CG dinucleotides are dominant, other elements of the standard nucleosome positioning pattern are present in the human genome as well.The positional autocorrelation analysis of the human genome demonstrates that the CG dinucleotide is, indeed, one visible element of the human nucleosome positioning pattern, which appears both in Alu sequences and in sequences without repeats. The dominant role that CG dinucleotides play in organizing human chromatin is to indicate the involvement of human nucleosomes in tuning the regulation of gene expression and chromatin structure, which is very likely due to cytosine-methylation/-demethylation in CG dinucleotides contained in the human nucleosomes. This is further confirmed by the positions of CG-periodical nucleosomes on Alu sequences. Alu repeats appear as monomers, dimers and trimers, harboring two to six nucleosomes in a run. Considering the exceptional role CG dinucleotides play in the nucleosome positioning, we hypothesize that Alu-nucleosomes, especially, those that form tightly positioned runs, could serve as "anchors" in organizing the chromatin in human cells.The periodical distribution of various dinucleotides along eukaryotic DNA sequences with a period of 10-11 bases is commonly considered as the manifestation of a nucleosome positioning signal present in the sequences [1-8]. The period, the more accurate value of which is 10.4 bases [9-12], corre
Nucleosome DNA sequence structure of isochores
Zakharia M Frenkel, Thomas Bettecken, Edward N Trifonov
BMC Genomics , 2011, DOI: 10.1186/1471-2164-12-203
Abstract: Extraction of the patterns from the isochore DNA sequences by Shannon N-gram extension reveals that while the general motif YRRRRRYYYYYR is characteristic for all isochore types, the dominant positioning patterns of the isochores vary between TAAAAATTTTTA and CGGGGGCCCCCG due to the large differences in G+C composition. This is observed in human, mouse and chicken isochores, demonstrating that the variations of the positioning patterns are largely G+C dependent rather than species-specific. The species-specificity of nucleosome positioning patterns is revealed by dinucleotide periodicity analyses in isochore sequences. While human sequences are showing CG periodicity, chicken isochores display AG (CT) periodicity. Mouse isochores show very weak CG periodicity only.Nucleosome positioning pattern as revealed by Shannon N-gram extension is strongly dependent on G+C content and different in different isochores. Species-specificity of the pattern is subtle. It is reflected in the choice of preferentially periodical dinucleotides.The nucleosome positioning signal in human genome sequences is rather weak. It lacks the periodical AA and TT dinucleotides, the main component of the nucleosome positioning pattern in most of other genomes [1,2]. Similarly, the mouse genome is featureless in terms of dinucleotide periodicities [2]. This lack of periodicities, diagnostic of the presence of a nucleosome positioning signal, makes the extraction of a nucleosome signal from such "silent" genomes problematic. One possible way to tackle this problem is to analyze the oligonucleotide composition of DNA sequences, which may reflect to some degree the hidden positioning patterns. The pattern-specific short oligonucleotides would be expected to appear more often in the overall vocabularies of the oligonucleotides, which then may be used for detection of the pattern. Indeed, recent Shannon N-gram extension analysis [3] of eukaryotic genomes [4] revealed that the majority of the genomes are
Improved haplotyping of rare variants using next-generation sequence data
Fouad Zakharia,Carlos Bustamante
Quantitative Biology , 2012,
Abstract: Accurate identification of haplotypes in sequenced human genomes can provide invaluable information about population demography and fine-scale correlations along the genome, thus empowering both population genomic and medical association studies. Yet phasing unrelated individuals remains a challenging problem. Incorporating available data from high throughput sequencing into traditional statistical phasing approaches is a promising avenue to alleviate these issues. We present a novel statistical method that expands on an existing graphical haplotype reconstruction method (shapeIT) to incorporate phasing information from paired-end read data. The algorithm harnesses the haplotype graph information estimated by shapeIT from genotypes across the population and refines haplotype likelihoods for a given individual to be compatible with the sequencing data. Applying the method to HapMap individuals genotyped on the Affymetrix Axiom chip at 7,745,081 SNPs and on a trio sequenced by Complete Genomics, we found that the inclusion of paired end read data significantly improved phasing, with reductions in switch error on the order of 4-15% against shapeIT across all panels. As expected, the improvements were found to be most significant at sites harboring rare variants; furthermore, we found that longer read sizes and higher throughput translated to greater decreases in switching error, as did higher variance in the size of the insert separating the two reads--suggesting that multi-platform next generation sequencing may be exploited to yield particularly accurate haplotypes. Overall, the phasing improvements afforded by this new method highlight the power of integrating sequencing read information and population genotype data for reconstructing haplotypes in unrelated individuals.
Un debate filosófico en II Macabeos
Frenkel,Diana;
Circe de cl??sicos y modernos , 2007,
Abstract: this article focuses on the possible links between the discourse of the maccabeans′ mother and epicurus′ philosophy. in chap. 7 a mother and her seven sons die rather than eat forbidden food. the king himself -antiochus iv- tries to force the brothers to eat pork and the mother fanatically encourages them to die by expressing the belief in the resurrection and in the creation ex nihilo. antiochus iv was a follows of epicurean ideas and the author of ii macc. probably has to argue against him -a hateful personage- and the philosophical doctrine in this passage of the work.
Una visión del Egipto Ptolemaico según la Carta de Aristeas a Filócrates
Frenkel,Diana;
Circe de cl??sicos y modernos , 2006,
Abstract: the letter of aristeas tells about the greek translation on the torah made by seventy-two jewish scholars from jerusalem at the court of ptolemy philadelphus. the author uses regular forms and motives from the greek literature. the aim of this article is to show how the descriptions (ekphráseis) of ptolemy′s gifts and the eleazar′s priestly garments have the purpose to legitimize the life of the jewish community in egypt with a beneficent monarch who released the jews from slavery and initiated the torah translation into greek.
Hemidactylus frenatus (Squamata: Gekkonidae): call frequency, movement and condition of tail in Costa Rica
Frenkel,Caty;
Revista de Biología Tropical , 2006,
Abstract: call frequency and movements of the gecko hemidactylus frenatus were studied in punta morales, costa rica from april 1999 through may 2000. call activity of h. frenatus was positively related to air temperature at night and throughout the year. higher activity was at dusk, dawn, and during the hottest months. call frequency was related with gecko abundance per month, although not during the night. more males and females had a regenerated tail compared to juveniles, the last ones could have it complete or regenerated. females moved longer distances than males and juveniles. adults were found higher on walls. males and females were recaptured more times than juveniles, and the period of time between their recaptures was longer. members of this population do not seem to be as aggressive to other geckos as mentioned in the literature. rev. biol. trop. 54 (4): 1125-1130. epub 2006 dec. 15
Las políticas monetaria y fiscal en un régimen de tipo de cambio competitivo
Roberto Frenkel
Economia e Sociedade , 2008, DOI: 10.1590/s0104-06182008000400005
Abstract:
Hemidactylus frenatus (Squamata: Gekkonidae): call frequency, movement and condition of tail in Costa Rica
Caty Frenkel
Revista de Biología Tropical , 2006,
Abstract: Call frequency and movements of the gecko Hemidactylus frenatus were studied in Punta Morales, Costa Rica from April 1999 through May 2000. Call activity of H. frenatus was positively related to air temperature at night and throughout the year. Higher activity was at dusk, dawn, and during the hottest months. Call frequency was related with gecko abundance per month, although not during the night. More males and females had a regenerated tail compared to juveniles, the last ones could have it complete or regenerated. Females moved longer distances than males and juveniles. Adults were found higher on walls. Males and females were recaptured more times than juveniles, and the period of time between their recaptures was longer. Members of this population do not seem to be as aggressive to other geckos as mentioned in the literature. Rev. Biol. Trop. 54 (4): 1125-1130. Epub 2006 Dec. 15 Estudié la frecuencia de canto y el desplazamiento de la lagartija Hemidactylus frenatus en Punta Morales, CostaRica. La frecuencia de canto se corelaciona positivamente con la temperatura ambiental durante la noche y con la temperatura a lo largo del a o. La mayor actividad fue al anochecer, al amanecer y durante los meses más calurosos. La abundancia mensual de lagartijas se relacionó con la frecuencia de canto, no así la abundancia por noche. Las colas regeneradas son más frecuentes en hembras y machos que en las lagartijas jóvenes. Las hembras se desplazaron mayores distancias que machos y jóvenes. Los adultos se encontraban más alto en las paredes de los edificios. Los machos y hembras se recapturaron más veces que los jóvenes, y el tiempo entre recapturas fue mayor. Esta población no parece ser tan agresiva como se menciona en la literatura
Old and New Phases in Complex Liquids Phases nouvelles et phases anciennes dans les mélanges collo de-polymère
Frenkel D.
Oil & Gas Science and Technology , 2006, DOI: 10.2516/ogst:1996013
Abstract:
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