Modeling the tumor specific structural networks by integrating alternative splicing events



Modeling the tumor specific network rewiring by integrating alternative splicing events with structural interactome
Demirel, Habibe Cans; Tunçbağ, Nurcan; Department of Biotechnology (2019)
Alternative splicing is a post-transcriptional regulation which is important for the diversity of the proteome and eventually the interactome. It enables the production of multiple proteins from a single gene with different structures. In a network point of view, these structural changes can introduce new interactions or cause the loss of the existing ones. The variations in this mechanism has been associated with various diseases including cancer. In this study, we reconstructed patient specific networks w...
Modeling and predicting binding affinity of phencyclidine-like compounds using machine learning methods
Erdas, Ozlem; Buyukbingol, Erdem; Alpaslan, Ferda Nur; Adejare, Adeboye (Wiley, 2010-01-01)
Machine learning methods have always been promising in the science and engineering fields, and the use of these methods in chemistry and drug design has advanced especially since the 1990s. In this study, molecular electrostatic potential (MEP) surfaces of phencyclidine-like (PCP-like) compounds are modeled and visualized in order to extract features that are useful in predicting binding affinities. In modeling, the Cartesian coordinates of MEP surface points are mapped onto a spherical self-organizing map ...
Modeling the combined effect of RNA-binding proteins and microRNAs in post-transcriptional regulation
HAFEZQORANİ, Saber; LAFZİ, Atefeh; de Bruin, Ruben G.; VAN ZONNEVELD, Anton Jan; van der Veer, Eric P.; Aydın Son, Yeşim; Kazan, Hilal (2016-05-19)
Recent studies show that RNA-binding proteins (RBPs) and microRNAs (miRNAs) function in coordination with each other to control post-transcriptional regulation (PTR). Despite this, the majority of research to date has focused on the regulatory effect of individual RBPs or miRNAs. Here, we mapped both RBP and miRNA binding sites on human 3'UTRs and utilized this collection to better understand PTR. We show that the transcripts that lack competition for HuR binding are destabilized more after HuR depletion. W...
Modeling the combined effect of RNA-binding proteins and micrornas in post-transcriptional regulation
HafezQorani, Saber; Aydın Son, Yeşim; Kazan, Hilal; Department of Medical Informatics (2015)
Post-transcriptional regulation (PTR) controls the gene expression between transcription and translation. Regulation at this level is carried out by the interactions of trans-acting RNA-binding proteins (RBPs) and microRNAs (miRNAs) with cis-regulatory elements in mRNA. Majority of previous work have focused on the effect of a single factor independent of other co-factors bound to the same mRNA. However, recent studies have shown that RBPs and miRNAs can act in cooperation or competition with each other. In...
Modeling Voxel Connectivity for Brain Decoding
Onal, Itir; Ozay, Mete; Yarman Vural, Fatoş Tunay (2015-06-12)
The massively dynamic nature of human brain cannot be represented by considering only a collection of voxel intensity values obtained from fMRI measurements. It has been observed that the degree of connectivity among voxels provide important information for modeling cognitive activities. Moreover, spatially close voxels act together to generate similar BOLD responses to the same stimuli. In this study, we propose a local mesh model, called Local Mesh Model with Temporal Measurements (LMM-TM), to first estim...
Citation Formats
H. C. Demirel and N. Tunçbağ, “Modeling the tumor specific structural networks by integrating alternative splicing events,” 2018, Accessed: 00, 2021. [Online]. Available: