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Reconstruction of the Temporal Signaling Network in Salmonella Infected Human Cells
Date
2015-07-14
Author
Güngör, Budak
Eren Özsoy, Öykü
Aydın Son, Yeşim
Can, Tolga
Nurcan, Tunçbağ
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https://hdl.handle.net/11511/82708
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Budak, Güngör; Aydın Son, Yeşim; Tunçbağ, Nurcan; Department of Bioinformatics (2016)
Salmonella enterica is a bacterial pathogen whose mechanism of infection is usually through food sources. The pathogen proteins are translocated into the host cells to change the host signaling mechanisms either by activating or inhibiting the host proteins. In order to obtain a more complete view of the biological processes and the signaling networks and to reconstruct the temporal signaling network of the human host, we have used two network modeling approaches, the Prize-collecting Steiner Forest (PCSF) ...
Reconstruction of the temporal signaling network in Salmonella-infected human cells
Budak, Gungor; Ozsoy, Oyku Eren; Aydın Son, Yeşim; Can, Tolga; Tunçbağ, Nurcan (2015-07-20)
Salmonella enterica is a bacterial pathogen that usually infects its host through food sources. Translocation of the pathogen proteins into the host cells leads to changes in the signaling mechanism either by activating or inhibiting the host proteins. Given that the bacterial infection modifies the response network of the host, a more coherent view of the underlying biological processes and the signaling networks can be obtained by using a network modeling approach based on the reverse engineering principl...
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Cancer is a global health problem with high mortality and increasing prevalence. Mathematical modeling strategies have a great impact on the pharmaceutical industry through their cost and time-saving effects in drug discovery and development processes. Genome-scale metabolic models (GEMs) have been used to investigate complex disease mechanisms by integrating them with omics data [1]. Cancer has complex and dynamic biology including interactions between tumor cells and microenvironments. Each cell type has ...
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We report measurements of the temperature dependence of photoluminescence (PQ life-time and efficiency of Si nanocrystals (Si-Nc) embedded in silica matrix. We use a practical technique based on lock-in acquisition that allows us to simultaneously evaluate, at each emission-energy, intensity and decay-time of the detected signal. Samples are prepared by Silicon-ion implantation in a SiO2 layer followed by thermal annealing. The implantation dose of Si ions ranges between 2 x 10(16) cm(-2) and 2 x 10(17) cm(...
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SeaWiFS was collecting ocean color data since 1997. This means chlorophyll-a data for more than ten years. Since, SeaWiFS Chl-a data is validated for Black Sea this data set can be used for analysis. Nevertheless, the data is not gap free due to cloud effect. One of the main objectives of this work is to obtain a gap free, complete Chl-a data set for the Black Sea. For this purpose DINEOF method will be used. EOF analysis is a by-product of this method and the results are used to summarize some temporal and...
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B. Güngör, Ö. Eren Özsoy, Y. Aydın Son, T. Can, and T. Nurcan, “Reconstruction of the Temporal Signaling Network in Salmonella Infected Human Cells,” 2015, Accessed: 00, 2021. [Online]. Available: https://hdl.handle.net/11511/82708.