Recent Advances in Analytical Chemistry

İlgü, Müslüm
Nilsen-hamilton, Marit
Aptamers are invitro selected oligonucleotides (DNA, RNA, oligos with modified nucleotides) that can have high affinity and specificity for a broad range of potential targets with high affinity and specificity. Here we focus on their applications as biosensors in the diagnostic field, although they can also be used as therapeutic agents. A small number of peptide aptamers have also been identified. In analytical settings, aptamers have the potential to extend the limit of current techniques as they offer many advantages over antibodies and can be used for real-time biomarker detection, cancer clinical testing, and detection of infectious microorganisms and viruses. Once optimized and validated, aptasensor technologies are expected to be highly beneficial to clinicians by providing a larger range and more rapid output of diagnostic readings than current technologies and support personalized medicine and faster implementation of optimal treatments.


Inference of Gene Regulatory Networks Via Multiple Data Sources and a Recommendation Method
Ozsoy, Makbule Gulcin; Polat, Faruk; Alhajj, Reda (2015-11-12)
Gene regulatory networks (GRNs) are composed of biological components, including genes, proteins and metabolites, and their interactions. In general, computational methods are used to infer the connections among these components. However, computational methods should take into account the general features of the GRNs, which are sparseness, scale-free topology, modularity and structure of the inferred networks. In this work, observing the common aspects between recommendation systems and GRNs, we decided to ...
Inference of large-scale networks via statistical approaches
Ayyıldız Demirci, Ezgi; Purutçuoğlu Gazi, Vilda; Department of Statistics (2019)
In system biology, the interactions between components such as genes, proteins, can be represented by a network. To understand the molecular mechanism of complex biological systems, construction of their networks plays a crucial role. However, estimation of these networks is a challenging problem because of their high dimensional and sparse structures. The Gaussian graphical model (GGM) is widely used approach to construct the undirected networks. GGM define the interactions between species by using the con...
Optimization of nucleic acid delivery via cationic polymers for genome engineering
Öktem, Ayşegül; Erson Bensan, Ayşe Elif; Department of Molecular Biology and Genetics (2019)
One of the most challenging aspects of genome engineering is the delivery of genome editing components such as plasmids, oligonucleotides, RNA and protein. In this work, in-house synthetized cationic polymer poly (2-hydroxypropylene imine) (pHP) was tested in order to achieve substantial delivery efficiency while preserving high culture viability. Applicability of this cationic polymer mediated nucleic acid delivery method for both plant and mammalian cells were demonstrated. Several parameters of plasmid a...
Design of a sequence based miRNA clustering method; analysis of fungal miRNAs and host organism target genes
Narcı, Kübra; Akkaya, Mahinur S.; Oğul, Hasan; Department of Bioinformatics (2014)
MicroRNAs are small non-coding RNA molecules which contain 21-25 nucleotides, and function in post transcriptional regulation by inhibiting the translation of mRNA targets. miRNAs typically affect gene regulation by forming composite feed forward circuits (cFFCs) which also comprise a transcription factor (TF) and a target gene. By analyzing these cFFCs, the contribution of miRNAs in altering TF networks can be revealed. These contributions could either be the de-escalation of the target gene repertoire or ...
Applications of terahertz spectroscopy in biosystems
Plusquellic, David F.; SİEGRİST, Karen; Heilweil, Edwin J.; Esentürk, Okan (Wiley, 2007-12-03)
Terahertz (THz) spectroscopic investigations of condensed-phase biological samples are reviewed ranging from the simple crystalline forms of amino acids, carbohydrates and polypeptides to the more complex aqueous forms of small proteins, DNA and RNA. Vibrationally resolved studies of crystalline samples have revealed the exquisite sensitivity of THz modes to crystalline order, temperature, conformational form, peptide sequence and local solvate environment and have given unprecedented measures of the bindin...
Citation Formats
M. İlgü and M. Nilsen-hamilton, Recent Advances in Analytical Chemistry. 2019.