HENDEN, Şevki Onur
Characterizing the human genome's molecular functions and their variations across people is vital for understanding the cellular processes behind human genetic characteristics and diseases. With the advent of single-cell RNA sequencing (scRNA-seq), it is now possible to investigate gene expression in individual cells. Although a number of scRNA-seq bioinformatics tools are now available, many of them focus on overall gene expression levels and, as a result, often ignore heterogeneity caused by individual transcript expression. Differences in the relative abundance of expressed isoforms, such as those that occur between normal and diseased states, may have dramatic effects on phenotype or prognosis. This variation in expression may aid in the discovery of novel therapies as well as the better management of patients in certain situations. We propose a computational workflow for scRNA-seq data that identifies differential transcript usage from transcript abundances produced by widely used alignment tools such as Salmon. This approach enabled us to detect alterations in gene expression that were previously overlooked, in patients with breast cancer.


Monitoring of Tryptophan as a Biomarker for Cancerous Cells in Terahertz (THz) Sensing
Altan, Hakan; Gok, Seher; Ozyurt, Ipek; Severcan, Feride (2016-02-17)
Tryptophan is an extremely important amino acid for a variety of biological functions in living organisms. Changes in the concentration of this amino acid can point to identification of cancerous tissues or even confirm symptoms of depression in patients. Therefore it is extremely important to identify and quantify tryptophan concentrations in human blood as well as in in-vivo diagnostic studies. Here a reflection based terahertz pulsed spectroscopy system was used to study the interaction of THz pulses wit...
Identification and analysis of genomic regions with large between-population differentiation in humans
Myles, S.; Tang, K.; Somel, Mehmet; Green, R. E.; Kelso, J.; Stoneking, M. (Wiley, 2008-01-01)
The primary aim of genetic association and linkage studies is to identify genetic variants that contribute to phenotypic variation within human populations. Since the overwhelming majority of human genetic variation is found within populations, these methods are expected to be effective and can likely be extrapolated from one human population to another. However, they may lack power in detecting the genetic variants that contribute to phenotypes that differ greatly between human populations. Phenotypes that...
Discovering functional interaction patterns in protein-protein interaction networks
Turanalp, Mehmet E.; Can, Tolga (Springer Science and Business Media LLC, 2008-06-11)
Background: In recent years, a considerable amount of research effort has been directed to the analysis of biological networks with the availability of genome-scale networks of genes and/or proteins of an increasing number of organisms. A protein-protein interaction (PPI) network is a particular biological network which represents physical interactions between pairs of proteins of an organism. Major research on PPI networks has focused on understanding the topological organization of PPI networks, evolution...
Investigating the potential of bacillus calmette-guerin vaccine russia strain, cpg oligonucleotides and intravenous immunoglobulin to induce trained immunity in the context of antiviral immunity
Baydemir, İlayda; Gürsel, Mayda; Department of Molecular Biology and Genetics (2020-10-12)
Innate immune cells undergo metabolic and epigenetic reprogramming in response to specific stimuli, that enable a more robust immune response to secondary exposure to a wide variety of pathogens. This process of innate immune memory development has been termed as Trained Immunity (TI). BCG vaccine is one well-known inducer of innate immune memory. In vivo administration of CpG ODNs or Intravenous Immunoglobulin (IVIg) can also exert heterologous anti-microbial protective immunity. In this thesis, we sought ...
Ayaz, E. Serdar; Can, Tolga (2011-05-05)
RNAi system allows us to see the phenotypes when some genes are removed from living cells. By observing these phenotypes, we can build signaling pathways without dealing with the chemistry inside the cell. However it is costly in terms of time and space complexity. Furthermore, there are some interactions RNAi data cannot distinguish that results in many different signaling pathways all of which are consistent with the RNAi data. In this paper, we combine genetic algorithms with some greedy approaches to fi...
Citation Formats
Ş. O. HENDEN, “IDENTIFYING ISOFORM SWITCHES IN BREAST CANCER,” M.S. - Master of Science, Middle East Technical University, 2021.