Honors & Awards


  • Size-based Isolation of EVs from iPSC-CM for Diagnosis of Cardiomyopathies, 2018 Seed Grant Competition: Postdocs at the Interface (August 2018- July 2019)

Professional Education


  • Doctor of Philosophy, Ege University (2015)
  • Master of Science, Ege University (2009)
  • Bachelor of Engineering, Ege University (2006)

Stanford Advisors


Lab Affiliations


All Publications


  • A Novel On-Chip Method for Differential Extraction of Sperm in Forensic Cases ADVANCED SCIENCE Inci, F., Ozen, M. O., Saylan, Y., Miansari, M., Cimen, D., Dhara, R., Chinnasamy, T., Yuksekkaya, M., Filippini, C., Kumar, D., Calamak, S., Yesil, Y., Durmus, N., Duncan, G., Klevan, L., Demirci, U. 2018; 5 (9): 1800121

    Abstract

    One out of every six American women has been the victim of a sexual assault in their lifetime. However, the DNA casework backlog continues to increase outpacing the nation's capacity since DNA evidence processing in sexual assault casework remains a bottleneck due to laborious and time-consuming differential extraction of victim's and perpetrator's cells. Additionally, a significant amount (60-90%) of male DNA evidence may be lost with existing procedures. Here, a microfluidic method is developed that selectively captures sperm using a unique oligosaccharide sequence (Sialyl-LewisX), a major carbohydrate ligand for sperm-egg binding. This method is validated with forensic mock samples dating back to 2003, resulting in 70-92% sperm capture efficiency and a 60-92% reduction in epithelial fraction. Captured sperm are then lysed on-chip and sperm DNA is isolated. This method reduces assay-time from 8 h to 80 min, providing an inexpensive alternative to current differential extraction techniques, accelerating identification of suspects and advancing public safety.

    View details for DOI 10.1002/advs.201800121

    View details for Web of Science ID 000444940600006

    View details for PubMedID 30250782

    View details for PubMedCentralID PMC6145299

  • Loss of Endothelial Derived WNT5A is Associated with Reduced Pericyte Recruitment and Small Vessel Loss in Pulmonary Arterial Hypertension. Circulation Yuan, K., Shamskhou, E. A., Orcholski, M. E., Nathan, A., Reddy, S., Honda, H., Mani, V., Zeng, Y., Ozen, M. O., Wang, L., Demirci, U., Tian, W., Nicolls, M. R., de Jesus Perez, V. A. 2018

    Abstract

    Pulmonary arterial hypertension (PAH) is a life-threatening disorder of the pulmonary circulation associated with loss and impaired regeneration of microvessels. Reduced pericyte coverage of pulmonary microvessels is a pathological feature of PAH and is partly due to the inability of pericytes to respond to signaling cues from neighboring pulmonary microvascular endothelial cells (PMVECs). We have shown that activation of the Wnt/PCP pathway is required for pericyte recruitment but whether production and release of specific Wnt ligands by PMVECs is responsible for Wnt/PCP activation in pericytes is unknown.Isolation of pericytes and PMVECs from healthy donor and PAH lungs was carried out using 3G5 or CD31 antibody conjugated magnetic beads. Wnt expression profile of PMVECs was documented via qPCR using a Wnt primer library. Exosome purification from PMVEC media was carried out using the ExoTIC device. Hemodynamic profile, right ventricular function and pulmonary vascular morphometry were obtained in a conditional endothelial specific Wnt5a knockout ( Wnt5aECKO) mouse model under normoxia, chronic hypoxia and hypoxia recovery.Quantification of Wnt ligand expression in healthy PMVECs co-cultured with pericytes demonstrated a 35-fold increase in Wnt5a, a known Wnt/PCP ligand. This Wnt5a spike was not seen in PAH PMVECs, which correlated with inability to recruit pericytes in matrigel co-culture assays. Exosomes purified from media demonstrated an increase in Wnt5a content when healthy PMVECs were co-cultured with pericytes, a finding that was not observed in exosomes of PAH PMVECs. Furthermore, the addition of either recombinant Wnt5a or purified healthy PMVEC exosomes increased pericyte recruitment to PAH PMVECs in co-culture studies. While no differences were noted in normoxia and chronic hypoxia, Wnt5aECKO mice demonstrated persistent pulmonary hypertension and right ventricular failure four weeks after recovery from chronic hypoxia, which correlated with significant reduction, muscularization and decreased pericyte coverage of microvessels.We identify Wnt5a as a key mediator for the establishment of pulmonary endothelial-pericyte interactions and its loss could contribute to PAH by reducing the viability of newly formed vessels. We speculate that therapies that mimic or restore Wnt5a production could help prevent loss of small vessels in PAH.

    View details for DOI 10.1161/CIRCULATIONAHA.118.037642

    View details for PubMedID 30586764

  • Investigation of in vitro digestibility of dietary microalga Chlorella vulgaris and cyanobacterium Spirulina platensis as a nutritional supplement 3 BIOTECH Kose, A., Ozen, M. O., Elibol, M., Oncel, S. S. 2017; 7: 170

    Abstract

    Microalgal proteins are promising sources for functional nutrition and a sustainable candidate for nutraceutical formulations. They also gain importance due to emerging focus on a healthy nutrition and increase in the number of chronic diseases. In this study, dried dietary species of microalga, Chlorella vulgaris, and cyanobacterium Spirulina platensis were hydrolyzed with pancreatin enzyme to obtain protein hydrolysates. The hydrolysis yield of biomass was 55.1 ± 0.1 and 64.8 ± 3.6% for C. vulgaris and S. platensis; respectively. Digestibility, as an indicator for dietary utilization, was also investigated. In vitro protein digestibility (IVPD) values depicted that cell wall structure due to the taxonomical differences affected both hydrolysis and digestibility yield of the crude biomass (p < 0.05). Epithelial cells (Vero) maintained their viability around 70%, even in relatively higher concentrations of hydrolysates in the culture. The protein hydrolysates showed no any antimicrobial activities. This study clearly shows that the conventional protein sources in nutraceutical formulations such as soy, whey, and fish proteins can be replaced by enzymatic hydrolysates of microalgae, which shows elevated digestibility values as a sustainable and reliable source.

    View details for DOI 10.1007/s13205-017-0832-4

    View details for Web of Science ID 000404651200012

    View details for PubMedID 28660455

    View details for PubMedCentralID PMC5489447

  • High-throughput Characterization of HIV-1 Reservoir Reactivation Using a Single-Cell-in-Droplet PCR Assay EBiomedicine Yucha, R. W., Hobbs, K. S., Hanhauser, E., Hogan, L. E., Nieves, W., Ozen, M. O., Inci, F., York, V., Gibson, E. A., Thanh, C., Shafiee, H., Assal, R., Kiselinova, M., Robles, Y. P., Bae, H., Leadabrand, K. S., Wang, S., Deeks, S. G., Kuritzkes, D. R., Demirci, U., Henrich, T. J. 2017
  • Monitoring Neutropenia for Cancer Patients at the Point of Care Small Methods Inan, H., et al 2017

    View details for DOI 10.1002/smtd.201700193

  • Biocompatible polymeric coatings do not inherently reduce the cytotoxicity of iron oxide nanoparticles TURKISH JOURNAL OF BIOLOGY Sendemir Urkmez, A., Bayir, E., Bilgi, E., Ozen, M. O. 2017; 41 (2): 322-332
  • Advances in biosensing strategies for HIV-1 detection, diagnosis, and therapeutic monitoring ADVANCED DRUG DELIVERY REVIEWS Lifson, M. A., Ozen, M. O., Inci, F., Wang, S., Inan, H., Baday, M., Henrich, T. J., Demirci, U. 2016; 103: 90-104

    Abstract

    HIV-1 is a major global epidemic that requires sophisticated clinical management. There have been remarkable efforts to develop new strategies for detecting and treating HIV-1, as it has been challenging to translate them into resource-limited settings. Significant research efforts have been recently devoted to developing point-of-care (POC) diagnostics that can monitor HIV-1 viral load with high sensitivity by leveraging micro- and nano-scale technologies. These POC devices can be applied to monitoring of antiretroviral therapy, during mother-to-child transmission, and identification of latent HIV-1 reservoirs. In this review, we discuss current challenges in HIV-1 diagnosis and therapy in resource-limited settings and present emerging technologies that aim to address these challenges using innovative solutions.

    View details for DOI 10.1016/j.addr.2016.05.018

    View details for Web of Science ID 000380083700007

    View details for PubMedID 27262924

    View details for PubMedCentralID PMC4943868

  • Engineering long shelf life multilayer biologically active surfaces on microfluidic devices for point of care applications SCIENTIFIC REPORTS Asghar, W., Yuksekkaya, M., Shafiee, H., Zhang, M., Ozen, M. O., Inci, F., Kocakulak, M., Demirci, U. 2016; 6

    Abstract

    Although materials and engineered surfaces are broadly utilized in creating assays and devices with wide applications in diagnostics, preservation of these immuno-functionalized surfaces on microfluidic devices remains a significant challenge to create reliable repeatable assays that would facilitate patient care in resource-constrained settings at the point-of-care (POC), where reliable electricity and refrigeration are lacking. To address this challenge, we present an innovative approach to stabilize surfaces on-chip with multiple layers of immunochemistry. The functionality of microfluidic devices using the presented method is evaluated at room temperature for up to 6-month shelf life. We integrated the preserved microfluidic devices with a lensless complementary metal oxide semiconductor (CMOS) imaging platform to count CD4(+) T cells from a drop of unprocessed whole blood targeting applications at the POC such as HIV management and monitoring. The developed immunochemistry stabilization method can potentially be applied broadly to other diagnostic immuno-assays such as viral load measurements, chemotherapy monitoring, and biomarker detection for cancer patients at the POC.

    View details for DOI 10.1038/srep21163

    View details for Web of Science ID 000370230000001

    View details for PubMedID 26883474

  • Supercritical fluid extraction of phycocyanin and investigation of cytotoxicity on human lung cancer cells JOURNAL OF SUPERCRITICAL FLUIDS Deniz, I., Ozen, M. O., Yesil-Celiktas, O. 2016; 108: 13-18
  • Screening of cytotoxic and antimicrobial activity potential of Anatolian Macrovipera lebetina obtusa (Ophidia: Viperidae) crude venom FRONTIERS IN LIFE SCIENCE Ozen, M. O., Igci, N., Yalcin, H. T., Gocmen, B., Nalbantsoy, A. 2015; 8 (4): 363-370
  • Multitarget, quantitative nanoplasmonic electrical field-enhanced resonating device (NE2RD) for diagnostics. Proceedings of the National Academy of Sciences of the United States of America Inci, F., Filippini, C., Baday, M., Ozen, M. O., Calamak, S., Durmus, N. G., Wang, S., Hanhauser, E., Hobbs, K. S., Juillard, F., Kuang, P. P., Vetter, M. L., Carocci, M., Yamamoto, H. S., Takagi, Y., Yildiz, U. H., Akin, D., Wesemann, D. R., Singhal, A., Yang, P. L., Nibert, M. L., Fichorova, R. N., Lau, D. T., Henrich, T. J., Kaye, K. M., Schachter, S. C., Kuritzkes, D. R., Steinmetz, L. M., Gambhir, S. S., Davis, R. W., Demirci, U. 2015; 112 (32): E4354-63

    Abstract

    Recent advances in biosensing technologies present great potential for medical diagnostics, thus improving clinical decisions. However, creating a label-free general sensing platform capable of detecting multiple biotargets in various clinical specimens over a wide dynamic range, without lengthy sample-processing steps, remains a considerable challenge. In practice, these barriers prevent broad applications in clinics and at patients' homes. Here, we demonstrate the nanoplasmonic electrical field-enhanced resonating device (NE(2)RD), which addresses all these impediments on a single platform. The NE(2)RD employs an immunodetection assay to capture biotargets, and precisely measures spectral color changes by their wavelength and extinction intensity shifts in nanoparticles without prior sample labeling or preprocessing. We present through multiple examples, a label-free, quantitative, portable, multitarget platform by rapidly detecting various protein biomarkers, drugs, protein allergens, bacteria, eukaryotic cells, and distinct viruses. The linear dynamic range of NE(2)RD is five orders of magnitude broader than ELISA, with a sensitivity down to 400 fg/mL This range and sensitivity are achieved by self-assembling gold nanoparticles to generate hot spots on a 3D-oriented substrate for ultrasensitive measurements. We demonstrate that this precise platform handles multiple clinical samples such as whole blood, serum, and saliva without sample preprocessing under diverse conditions of temperature, pH, and ionic strength. The NE(2)RD's broad dynamic range, detection limit, and portability integrated with a disposable fluidic chip have broad applications, potentially enabling the transition toward precision medicine at the point-of-care or primary care settings and at patients' homes.

    View details for DOI 10.1073/pnas.1510824112

    View details for PubMedID 26195743

    View details for PubMedCentralID PMC4538635

  • Effect of Ottoman Viper (Montivipera xanthina (Gray, 1849)) Venom on Various Cancer Cells and on Microorganisms CYTOTECHNOLOGY Yalcin, H. T., Ozen, M. O., Gocmen, B., Nalbantsoy, A. 2014; 66 (1): 87-94

    Abstract

    Cytotoxic and antimicrobial effects of Montivipera xanthina venom against LNCaP, MCF-7, HT-29, Saos-2, Hep3B, Vero cells and antimicrobial activity against selected bacterial and fungal species: Staphylococcus aureus ATCC 25923, Escherichia coli ATCC 25922, E. coli O157H7, Enterococcus faecalis 29212, Enterococcus faecium DSM 13590, Staphylococcus epidermidis ATCC 12228, S. typhimirium CCM 5445, Proteus vulgaris ATCC 6957 and Candida albicans ATCC 10239 were studied for evaluating the potential medical benefit of this snake venom. Cytotoxicity of venom was determined using MTT assay. Snake venom cytotoxicity was expressed as the venom dose that killed 50 % of the cells (IC50). The antimicrobial activity of venom was studied by minimal inhibitory concentration (MIC) and disc diffusion assay. MIC was determined using broth dilution method. The estimated IC50 values of venom varied from 3.8 to 12.7 or from 1.9 to 7.2 μg/ml after treatment with crude venom for 24 or 48 h for LNCaP, MCF-7, HT-29 and Saos-2 cells. There was no observable cytotoxic effect on Hep3B and Vero cells. Venom exhibited the most potent activity against C. albicans (MIC, 7.8 μg/ml and minimal fungicidal concentration, 62.5 μg/ml) and S. aureus (MIC, 31.25 μg/ml). This study is the first report showing the potential of M. xanthina venom as an alternative therapeutic approach due to its cytotoxic and antimicrobial effects.

    View details for DOI 10.1007/s10616-013-9540-z

    View details for Web of Science ID 000334174300009

    View details for PubMedID 23381026