Begum Sen Dogan

Dr. Begum Sen Dogan

ODTÜ MEMS Merkezi, Ankara, Turkey (Türkiye)
orcid

Research Focus & Metrics

Academic Career Length

11Years (2016-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

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13 July 2023 in Sensors and Actuators Reports
Verified
Journal Article
Open access
Begum Sen DoganBegum Sen Dogan
Begum Sen Dogan
EYEnder Yildirim
Ender Yildirim
SSSebnem Sahin
Sebnem Sahin
EOEbru Ozgur
Ebru Ozgur
OZOzge Zorlu
Ozge Zorlu
HKHaluk Kulah
Haluk Kulah

19 October 2023 in Biosensors
Verified
Journal Article
Open access
PDF file
Begum Sen DoganBegum Sen Dogan
Begum Sen Dogan
MDMehmet Alper Demir
Mehmet Alper Demir
BSBuket Sahin
Buket Sahin
EYEnder Yildirim
Ender Yildirim
GKGizem Karayalcin
Gizem Karayalcin
HKHaluk Külah
Haluk Külah
The isolation of circulating tumor cells (CTCs) from peripheral blood with high efficiency remains a challenge hindering the utilization of CTC enrichment methods in clinical practice. Here, we propose a microfluidic channel design for the size-based hydrodynamic enrichment of CTCs from blood in an epitope-independent and high-throughput manner. The microfluidic channel comprises a spiral-shaped part followed by a widening part, incorporating successive streamlined pillars, that improves the enrichment efficiency. The design was tested against two benchmark designs, a spiral microfluidic channel and a spiral microfluidic channel followed by a widening channel without the hydrofoils, by processing 5 mL of healthy blood samples spiked with 100 MCF-7 cells. The results proved that the design with hydrofoil-shaped pillars perform significantly better in terms of recovery (recovery rate of 67.9% compared to 23.6% in spiral and 56.7% in spiral with widening section), at a cost of slightly lower white blood cell (WBC) depletion (depletion rate of 94.2% compared to 98.6% in spiral and 94.2% in spiral with widening section), at 1500 µL/min flow rate. For analytical validation, the design was further tested with A549, SKOV-3, and BT-474 cell lines, yielding recovery rates of 62.3 ± 8.4%, 71.0 ± 6.5%, and 82.9 ± 9.9%, respectively. The results are consistent with the size and deformability variation in the respective cell lines, where the increasing size and decreasing deformability affect the recovery rate in a positive manner. The analysis before and after the microfluidic chip process showed that the process does not affect cell viability.

21 July 2020 in Micromachines
Verified
Journal Article
Open access
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Begum Sen DoganBegum Sen Dogan
Begum Sen Dogan
MOMeltem Okan
Meltem Okan
NANilüfer Afşar-Erkal
Nilüfer Afşar-Erkal
EÖEbru Özgür
Ebru Özgür
ÖZÖZGE ZORLU
ÖZGE ZORLU
HKHaluk Külah
Haluk Külah
Microbial Fuel Cells (MFCs) are biological fuel cells based on the oxidation of fuels by electrogenic bacteria to generate an electric current in electrochemical cells. There are several methods that can be employed to improve their performance. In this study, the effects of gold surface modification with different thiol molecules were investigated for their implementation as anode electrodes in micro-scale MFCs (µMFCs). Several double-chamber µMFCs with 10.4 µL anode and cathode chambers were fabricated using silicon-microelectromechanical systems (MEMS) fabrication technology. µMFC systems assembled with modified gold anodes were operated under anaerobic conditions with the continuous feeding of anolyte and catholyte to compare the effect of different thiol molecules on the biofilm formation of Shewanella oneidensis MR-1. Performances were evaluated using polarization curves, Electrochemical Impedance Spectroscopy (EIS), and Scanning Electron Microcopy (SEM). The results showed that µMFCs modified with thiol self-assembled monolayers (SAMs) (cysteamine and 11-MUA) resulted in more than a 50% reduction in start-up times due to better bacterial attachment on the anode surface. Both 11-MUA and cysteamine modifications resulted in dense biofilms, as observed in SEM images. The power output was found to be similar in cysteamine-modified and bare gold µMFCs. The power and current densities obtained in this study were comparable to those reported in similar studies in the literature.

23 October 2024 in PLOS ONE
Verified
Journal Article
Open access
PDF file
MKMeltem Kilercik
Meltem Kilercik
EÖEbru Özgür
Ebru Özgür
ŞŞŞebnem Şahin
Şebnem Şahin
Begum Sen DoganBegum Sen Dogan
Begum Sen Dogan
EMEge Mutlu
Ege Mutlu
HKHaluk Külah
Haluk Külah
Prostate cancer (PCa) is the second most common cancer among men and the fifth leading cause of cancer death. Circulating tumor cell (CTC) enumeration and characterisation in PCa has been shown to provide valuable information on prognosis of disease, therapy management and detection of resistance. Here, Cellsway’s microfluidic platform for high-throughput enrichment of intact CTC populations was used to isolate CTCs from the blood of 20 localised PCa patients and 10 healthy donor samples to evaluate the clinical performance of the technology. To enumerate and characterise CTCs, a multi-parameter flow cytometry analysis was performed on the enriched CTC suspension using CTC-specific biomarkers. CTCs were detected in 17 of 20 patient samples, which corresponds to 85% CTC positivity. The median CTC count per 7.5 ml blood was 2 (1–9). In 80% of patients (n = 16), the number of CTCs ranged from 1 to 5, and in 5% of patients (n = 1) the number of CTCs was above 5. No CTCs were observed in the blood samples of 10 healthy volunteers, demonstrating the high specificity and low risk of false positives of the technology.

2 January 2026 in Biosensors
Verified
Journal Article
Open access
PDF file
EÖEbru Özgür
Ebru Özgür
AÇAyça Çırçır
Ayça Çırçır
Begum Sen DoganBegum Sen Dogan
Begum Sen Dogan
ŞŞŞebnem Şahin
Şebnem Şahin
GKGizem Karayalcin
Gizem Karayalcin
SKSaadettin Kılıçkap
Saadettin Kılıçkap
Lung cancer is the leading cause of cancer-related mortality worldwide, with non-small-cell lung cancer (NSCLC) accounting for the majority of cases. Standard tissue biopsies are invasive and unsuitable for repeated monitoring. Liquid biopsy technologies, particularly circulating tumor cell (CTC) analysis, offer a minimally invasive alternative for real-time disease tracking. To address the need for efficient and reproducible CTC isolation, we developed the Cellsway microfluidic CTC enrichment and identification platform, which employs inertial hydrodynamics in a spiral-shaped microfluidic channel comprising hydrofoil-shaped pillars to enable high-throughput, label-free enrichment of CTCs while preserving cell integrity, followed by an optimized CTC identification assay. Analytical performance assessed through spiking experiments using NSCLC cell lines demonstrated recovery rates of 91.9% for H1975 cells and 78.3% for A549 cells. Clinical validation was performed on blood samples from 51 stage IV NSCLC patients. A 7.5 mL volume of peripheral blood was processed with the SwayBox platform, and enriched CTCs were identified through an optimized multiplex immunofluorescence protocol. CTCs were detected in 47% of NSCLC patients, with counts ranging from 0 to 72 cells per 7.5 mL of blood. At a cutoff of 1 CTC per 7.5 mL, the assay achieved a specificity of 95%. Patient-derived CTCs exhibited smaller mean diameters compared to cultured NSCLC cell lines, yet were effectively enriched through hydro-dynamic tuning. These findings demonstrate that the Cellsway platform enables efficient and re-producible CTC isolation with high specificity, supporting its potential utility for clinical monitoring and precision oncology in NSCLC.

1 November 2016 in Journal of Physics: Conference Series
Verified
Conference Paper
Open access
PDF file
Begum Sen DoganBegum Sen Dogan
Begum Sen Dogan
NENilüfer Afşar Erkal
Nilüfer Afşar Erkal
EÖEbru Özgür
Ebru Özgür
ÖZÖZGE ZORLU
ÖZGE ZORLU
HKHaluk Külah
Haluk Külah
This paper reports the design, fabrication, and testing of a microliter scale Microbial Fuel Cell (μMFC) based on silicon MEMS fabrication technology. μMFC systems are operated under different loads or open circuit to compare the effect of different acclimatization conditions on start-up time. Shewanella oneidensis MR-1 is preferred to be the biocatalyst. The internal resistance is calculated as 20 kΩ under these conditions. Acclimatization of μMFC under a finite load resulted in shorter start-up time (30 hours) when compared to the open load case. Power and current densities normalized to anode area are 2 μW/cm2 and 12 μA/cm2 respectively. When the load resistance value is closer to the internal resistance of the μMFC, higher power and current densities are achieved as expected, and it resulted in a shorter start-up time. Further studies focusing on the different acclimatization techniques for μMFC could pave the way to use μMFCs as fast and efficient portable power sources.