Structural Modeling of the Patient-Specific Signaling Networks in Glioblastoma

Dıncer, Cansu
Tunçbağ, Nurcan


Structural mapping and network analysis of patient-specific mutations in glioblastoma
Kaya, Tuğba; Tunçbağ, Nurcan; Doğan, Tunca; Department of Bioinformatics (2018)
Cancer is one of the most common cause of death worldwide. It occurs as a result of a collection of somatic deviations from normal state. Therefore, many efforts have been invested to profile mutations in different types of tumors; such as, the Cancer Genome Atlas (TCGA) which deposits multiple omic data for more than 11,000 tumor samples. In this thesis, we present a pipeline which retrieves patient-specific mutation data in Glioblastoma from TCGA, maps these mutations on the protein structures in Protein ...
Structural modelling and functional analysis of the engineered small heat-shock protein, tpv-hsp14.3 from thermoplasma volcanium
Sheraj, Ilir; Kocabıyık, Semra; Department of Biology (2014)
In this study, a small heat shock protein tpv-Hsp14.3 from a thermoacidophilic Archaeon, Thermoplasma volcanium was studied. sHSPs are low molecular weight proteins involved in different stress responses to protect the cellular proteome and enhance survival of the host organism. For structure-function analysis of the protein, both experimental and computational tools were used. Sequence alignments with closely-related sHSPs showed high sequence conservation at the core α-Crystalline domain and a V/I/L-X-V/I...
Structural Analysis of Synchronization in Networks of Linear Oscillators
Tuna, Sezai Emre (2022-07-01)
In undirected networks of identical linear oscillators coupled through dissipative and restorative connectors (e.g., pendulums undergoing small vibrations connected via dampers and springs), the relation between asymptotic synchronization and coupling structure is studied. Conditions on the interconnection under which synchronization can be achieved for some selection of coupling strengths are established. How to strengthen those conditions so that synchronization is guaranteed for all admissible parameter ...
Structural Insights into Alternate Aggregated Prion Protein Forms
POLANO, maurizio; Bek, Alpan; BENETTİ, federico; lazzarino, marco; LEGNAME, giuseppe (Elsevier BV, 2009-11-13)
The conversion of the cellular form of the prion protein (PrPC) to an abnormal, alternatively folded isoform (PrPSc) is the central event in prion diseases or transmissible spongiform encephalopathies. Recent studies have demonstrated de novo generation of murine prions from recombinant prion protein (recPrP) after inoculation into transgenic and wild-type mice. These so-called synthetic prions lead to novel prion diseases with unique neuropathological and biochemical features. Moreover, the use of recPrP i...
Structural investigation of donor age effect on human bone marrow mesenchymal stem cells: FTIR spectroscopy and imaging
Aksoy, Ceren; AERTS KAYA, FATİMA SUSANNA F.; KUŞKONMAZ, BÜLENT BARIŞ; Uckan, Duygu; Severcan, Feride (2014-08-01)
Stem cell studies hold enormous potential for development of new therapies for tissue regeneration and repair. Bone marrow mesenchymal stem cells (BM-MSCs) can differentiate into a variety of nonhematopoietic tissues and contribute maintenance of healthy hematopoiesis by providing supportive cellular microenvironment into BM. Here, we investigated age-related differences in BM-MSCs by using attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy and FTIR imaging together with hierarch...
Citation Formats
C. Dıncer and N. Tunçbağ, “Structural Modeling of the Patient-Specific Signaling Networks in Glioblastoma,” 2017, Accessed: 00, 2021. [Online]. Available: