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[PDF] Top 20 Transcription factor binding sites prediction based on modified nucleosomes.

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Transcription factor binding sites prediction based on modified nucleosomes.

Transcription factor binding sites prediction based on modified nucleosomes.

... for transcription factor binding site (TFBS) ...actual binding sites, they usually produce a large number of false positive (FP) predictions and so are impoverished sources of ...to ... See full document

10

A systems biology approach to transcription factor binding site prediction.

A systems biology approach to transcription factor binding site prediction.

... biding sites. On the other hand, using non-linear pattern-discovery-based conservation improved the performance considerably and use of both methods in combination provided the best ...only on ... See full document

10

Identifying functional transcription factor binding sites in yeast by considering their positional preference in the promoters.

Identifying functional transcription factor binding sites in yeast by considering their positional preference in the promoters.

... Although the quality of TFBS identification is improved with the approaches mentioned above, whether or not the computa- tionally predicted TFBSs are functional (i.e. biologically relevant) is still unknown. Therefore, ... See full document

7

A linear model for transcription factor binding affinity prediction in protein binding microarrays.

A linear model for transcription factor binding affinity prediction in protein binding microarrays.

... protein-DNA binding model using PBM data from the DREAM5 transcription factor/ DNA motif recognition ...murine transcription factors, each hybridized onto two different PBM platforms (HK and ... See full document

13

Interactions between the R2R3-MYB transcription factor, AtMYB61, and target DNA binding sites.

Interactions between the R2R3-MYB transcription factor, AtMYB61, and target DNA binding sites.

... Based on the model of AtMYB61, the molecular interactions shared between the binding sites of AtMYB61 to its targets supported in vitro binding data (Figure ...confirm binding ... See full document

11

DNA-MATRIX: a tool for constructing transcription factor binding sites Weight matrix

DNA-MATRIX: a tool for constructing transcription factor binding sites Weight matrix

... TF binding sites in DNA are very important for understanding the molecular mechanisms of gene ...the prediction of TF binding sites as in ...information on known TF ... See full document

3

High-precision, in vitro validation of the sequestration mechanism for generating ultrasensitive dose-response curves in regulatory networks.

High-precision, in vitro validation of the sequestration mechanism for generating ultrasensitive dose-response curves in regulatory networks.

... biotechnologies based on this effect [36], the hyperbolic –and thus not particularly sensitive– concentration/occupancy curves characteristic of single site binding limits their ...a ... See full document

8

Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression.

Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression.

... consequences on gene expression of TF binding ...genomic binding of A-P factors has changed extensively along the Drosophila tree with little effect on downstream gene ...BCD binding ... See full document

18

Probing the informational and regulatory plasticity of a transcription factor DNA-binding domain.

Probing the informational and regulatory plasticity of a transcription factor DNA-binding domain.

... MarA binding domain variants are shown in Table 1 and sequence logos generated from these variants are shown in Figure ...Each binding domain is referenced by residues 42, 45 and ...sequenced binding ... See full document

13

Prediction of nucleosome positioning based on transcription factor binding sites.

Prediction of nucleosome positioning based on transcription factor binding sites.

... of transcription factor binding sites (TFBSs) in 53,021 nucleosomal DNA sequences and 50,299 linker DNA ...overall prediction accuracy was ... See full document

7

Co-localization of the oncogenic transcription factor MYCN and the DNA methyl binding protein MeCP2 at genomic sites in neuroblastoma.

Co-localization of the oncogenic transcription factor MYCN and the DNA methyl binding protein MeCP2 at genomic sites in neuroblastoma.

... MeCP2 binding sites around the promoter region of JUNB which are similar to those previously described in SH- ...of transcription factor binding motifs at commonly bound MYCN/MeCP2 ... See full document

13

A structural-based strategy for recognition of transcription factor binding sites.

A structural-based strategy for recognition of transcription factor binding sites.

... the prediction of TFBS sites, we were motivated to explore other modifications that could improve the performance of vcFIRE in this ...three modified approaches was tested for DNA sequence decoy ... See full document

10

Differential Nucleosome Occupancies across Oct4-Sox2 Binding Sites in Murine Embryonic Stem Cells.

Differential Nucleosome Occupancies across Oct4-Sox2 Binding Sites in Murine Embryonic Stem Cells.

... was modified and de- veloped in our lab to enrich genomic pools of mononucleosomes ...possible binding sites of the transcription factor network of Oct4 and Sox2, which controls the ... See full document

18

Comprehensive human transcription factor binding site map for combinatory binding motifs discovery.

Comprehensive human transcription factor binding site map for combinatory binding motifs discovery.

... respective binding sites, we uncover the syntax of the crosstalk among them on the genomic scale, estimating the combinatorial binding patterns (CBPs) of the ...motifs’’ based on ... See full document

13

Nε-lysine acetylation of a bacterial transcription factor inhibits Its DNA-binding activity.

Nε-lysine acetylation of a bacterial transcription factor inhibits Its DNA-binding activity.

... We hypothesized that modifications or substitutions at Lys180 would have a negative effect on the DNA-binding activity of RcsB. To investigate this possibility, we performed electrophoretic mobility shift ... See full document

9

J. Braz. Chem. Soc.  vol.28 número3

J. Braz. Chem. Soc. vol.28 número3

... the binding mode of tiliroside to ...new binding site may contribute to the opening of new paths in the search for natural product inhibitors of this ... See full document

8

A simple ESR identification methodology for Electrolytic Capacitors conditon monitoring

A simple ESR identification methodology for Electrolytic Capacitors conditon monitoring

... importance as far as the end of life of electrolytic capacitors is concerned. Although an old-rule-of-thumb referred in a technical paper by Lauber (1985 cited Gasperi, 1996), has described that the end of life is when ... See full document

10

Genética molecular aplicada ao câncer cutâneo não melanoma.

Genética molecular aplicada ao câncer cutâneo não melanoma.

... Abstract: Non-melanoma skin cancers are the most common malignant neoplasms in humans. About 95% of all non-melanoma skin cancers are represented by basal cell carci- noma and squamous cell carcinoma. Their prevalences ... See full document

15

Prediction of P53 mutants (multiple sites) transcriptional activity based on structural (2D&3D) properties.

Prediction of P53 mutants (multiple sites) transcriptional activity based on structural (2D&3D) properties.

... in prediction compared to previous work. Our method placed emphasis on the 2D structure surface of the p53 mutants and the 3D structural changes of the tumor protein, that have been reported to be highly ... See full document

14

Determination of Nuclear Transcription Factor Activity Using a Modified Electrophoretic Mobility Shift Assay

Determination of Nuclear Transcription Factor Activity Using a Modified Electrophoretic Mobility Shift Assay

... the modified Bradford method, the yield of the nucleic protein was 50 to 60 µg/10 6 ...DNA-protein binding bands of various gray ...no binding bands. With the specific competition, the binding ... See full document

6

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