Integrated Biomedical Sensing and Imaging Laboratory

Publications

Complete publication list available on Google Scholar

  1. M Althumayri, A.Tarman, H. Ceylan Koydemir, “Bioinspired skin model for in vitro evaluation of bloodstream infections”, Nature: Scientific Reports (Under review)
  2. S. Mallawarachchi†, R.E. Cebecioglu†, M. Althumayri†, L. Beker, S.Fernando, H. Ceylan Koydemir, “Systematic design and evaluation of aptamers for specific detection of VEGF and PLGF biomarkers of preeclampsia”, BMC Biotechnology (Under review)
  3. M. Althumayri, R. Das, R. Banavath, L. Beker, A. Achim, H. Ceylan Koydemir, “Recent advances in transparent electrodes and their use in multimodal applications”,  Advanced Science, 2024, https://onlinelibrary.wiley.com/doi/10.1002/advs.202405099. 
  4. C. Isil, H. Ceylan Koydemir, M. Eryilmaz, K. de Haan, N. Pillar, K. Mentesoglu, A. F. Unal, Y. Rivenson, S. Chandrasekaran, O. B Garner, A. Ozcan, “Virtual Gram staining of label-free bacteria using darkfield microscopy and deep learning”, arXiv, 2024, https://doi.org/10.48550/arXiv.2407.12337.
  5. J. Korgaonkar, A. Tarman, H. Ceylan Koydemir*, S. Chukkapalli*, “Periodontal disease and emerging point-of-care technologies for its diagnosis”,  Lab Chip, 2024, https://doi.org/10.1039/D4LC00295D (featured in the back cover of the journal) (published in the theme of  Lab on a Chip Emerging Investigators)
  6. W. Xu , A. Y. Atik, L. Beker, H. Ceylan Koydemir, “Digital monitoring of the microchannel filling flow dynamics using a non-contactless smartphone-based nano-liter precision flow velocity meter”, Biosensors and Bioelectronics, 2024, https://doi.org/10.1016/j.bios.2024.116130.
  7. H. Ceylan Koydemir and A. Ozcan, “Low-cost and portable systems for biomedical imaging and sensing”. Current Opinion in Biomedical Engineering, 2024. https://doi.org/10.1016/j.cobme.2024.100527. 
  8. T. Yang, N. Anantrasirichai, O. Karakuş, M. Allinovi, H. Ceylan Koydemir, A. Achim, “DUBLINE: A Deep Unfolding Network for B-line Detection in Lung Ultrasound Images”, arXiv, 2023, https://arxiv.org/pdf/2311.06672.
  9. W. Xu, E. Venkat and H. Ceylan Koydemir, “Optical Point of Care Devices for Diagnosis of Urinary Tract Infections”. Current Opinion in Biomedical Engineering, 2023. https://doi.org/10.1016/j.cobme.2023.100513.V. Shah, X. Yang, A. Arnheim, S. Udani, D. Tseng, Y. Luo, M. Ouyang, G. Destgeer, O. Garner, H. Ceylan Koydemir, A. Ozcan, D. Di Carlo, “Amphiphilic Particle-Stabilized Nanoliter Droplet Reactors with a Multimodal Portable Reader for Distributive Biomarker Quantification”, 2023, ACS Nano, https://doi.org/10.1021/acsnano.3c04994.
  10. W. Xu , M. Althumayri, A. Mohammad, H. Ceylan Koydemir, “Foldable Low-Cost Point-of-Care Device for Testing Blood Coagulation Using Smartphones”, Biosensors and Bioelectronics, 2023, https://doi.org/10.1016/j.bios.2023.115755.
  11. V. Shah, X. Yang, A. Arnheim, S. Udani, D. Tseng, Y. Luo, M. Ouyang, G. Destgeer, O. Garner, H. Ceylan Koydemir, A. Ozcan, D. Di Carlo, “Amphiphilic particle-stabilized nanoliter droplet reactors with a multi-modal portable reader for distributive biomarker quantification”, bioRxiv, https://doi.org/10.1101/2023.04.24.538181, 2023. 
  12. E. Istif, H. Mirzajani, F. Mirlou, E. Y. Ozuaciksoz, H. Ceylan Koydemir, I. Yilgor, E. Yilgor, L. Beker, “Miniaturized wireless sensor enables real-time monitoring of food spoilage”, Nature Food, 2023, DOI: 10.1038/s43016-023-00750-9. 
  13. T. Liu, Y. Li, H. Ceylan Koydemir, Y. Zhang, E. Yang, M. Eryilmaz, H. Wang,  J. Li,B. Bai, G. Ma, A. Ozcan, “Rapid and stain-free quantification of viral plaque via lens-free holography and deep learning”, Nature Biomedical Engineering, 2023, https://doi.org/10.1038/s41551-023-01057-7.
  14. W. Xu and H. Ceylan Koydemir, “Non-invasive biomedical sensors for early detection and monitoring of bacterial biofilm growth at the point of care”, Lab on a Chip, 2022, https://doi.org/10.1039/D2LC00776B (featured on the journal’s back cover).
  15. Y. Li, T. Liu, H. Ceylan Koydemir, H. Wang, K. O’Riordan, B. Bai, Y. Haga, J. Kobashi, H. Tanaka, T. Tamaru, K. Yamaguchi, A. Ozcan, “Deep learning-enabled detection and classification of bacterial colonies using a thin-film resistor (TFT) image sensor”, ACS Photonics, 2022, https://doi.org/10.1021/acsphotonics.2c00572.
  16. T. Abbasiasl, F. Mirlou, E. Istif, H. Ceylan Koydemir, L. Beker, “A wearable paper-integrated microfluidic device for sequential analysis of sweat based on capillary action”, Sensors & Diagnostics, 2022, https://doi.org/10.1039/D2SD00032F.
  17. J. Leonard†, H. Ceylan Koydemir†, V. Koutnik, D. Tseng, A. Ozcan, S. Mohanty, “Smartphone-enabled rapid quantification of microplastics”, Journal of Hazardous Materials Letters, 2022, https://doi.org/10.1016/j.hazl.2022.100052.
  18. V. Koutnik, A. Borthakur, J. Leonard, S. Alkidim, H. Ceylan Koydemir, D. Tseng, A. Ozcan, S. Ravi, S. Mohanty, “Mobility of polypropylene microplastics in stormwater biofilters under freeze-thaw cycles”, Journal of Hazardous Materials Letters, 2022, https://doi.org/10.1016/j.hazl.2022.100048.
  19. V. Koutnik, J. Leonard, J. B. Glasman, H. Ceylan Koydemir, A. Novoselov, J. Brar, R. Bertel, D. Tseng, A. Ozcan, S. Ravi, S. Mohanty, “Microplastics in stormwater control measures: Where do they come from and where do they go?”, Water Research, 2022, https://doi.org/10.1016/j.watres.2021.118008.
  20. H. Ceylan Koydemir and A. Ozcan, “Smartphone-based sensors and imaging devices for global health”, Advanced Optical Technologies, 2021, https://doi.org/10.1515/aot-2021-0031.
  21. C. Isil†, K. de Haan†, Z. Gorocs†, H. Ceylan Koydemir†, S.Peterman, D. Baum, F. Song, T. Skandakumar, E. Gumustekin, A. Ozcan, “Phenotypic analysis of microalgae populations using a label-free imaging flow cytometer and deep learning”, ACS Photonics, 2021, https://doi.org/10.1021/acsphotonics.1c00220. 
  22. H. Ceylan Koydemir and A. Ray, “Mobile Diagnostic Devices for Digital Transformation in Personalized Healthcare”, Diagnostics, 2020, https://doi.org/10.3390/diagnostics10121008.
  23. Z. Gorocs, D. Baum, F. Song, K. de Haan, H. Ceylan Koydemir, Y. Qiu, Z. Cai, T. Skandakumar, S. Peterman, M. Tamamitsu, A. Ozcan, “Label-free detection of Giardia lamblia cysts using a deep learning-enabled portable imaging flow cytometer”, Lab on a Chip, 2020, https://doi.org/10.1039/D0LC00708K.
  24. K. de Haan†, H. Ceylan Koydemir†, Y. Rivenson, D. Tseng, E. A. Van Dyne, L. Bakic, D. Karinca, K. Liang, M. Ilango, E. Gumustekin, A. Ozcan, “Automated screening of sickle cells using a smartphone-based microscope and deep learning”, Nature: npj Digital Medicine, 2020, https://doi.org/10.1038/s41746-020-0282-y.
  25. H. Wang†, H. Ceylan Koydemir†, Y. Qiu†, B. Bai, Y. Zhang, Y. Jin, S. Tok, E.C. Yilmaz, E. Gumustekin, Y. Rivenson, A. Ozcan, “Early-detection and classification of live bacteria using time-lapse coherent imaging and deep learning”, Nature: Light Science and Applications, 2020, https://doi.org/10.1038/s41377-020-00358-9.
  26. F. Ghaderinezhad, H. Ceylan Koydemir, D. Tseng, D. Karinca, K. Liang, A. Ozcan, S. Tasoglu, “Sensing of electrolytes in urine using a miniaturized paper-based device”, Nature: Scientific Reports, 2020, https://doi.org/10.1038/s41598-020-70456-6.
  27. H. Ceylan Koydemir†, S. Rajpal†, E. Gumustekin, D. Karinca, K. Liang, Z. Gorocs, D. Tseng, A. Ozcan, “Smartphone-based turbidity reader”, Nature: Scientific Reports, 2019, DOI: 10.1038/s41598-019-56474-z.
  28. Y. Zhang , M. Ouyang , A. Ray, T. Liu, J. Kong, B. Bai, D. Kim, A. Guziak , Y. Luo , A. Feizi, K. Tsai, Z. Duan, X. Liu, D.H. Kim, C. Cheung, S. Yalcin, H. Ceylan Koydemir, O. Garner, D. Di Carlo, and A. Ozcan, “Computational cytometer based on magnetically-modulated coherent imaging and deep learning”, Nature: Light Science and Applications, 2019, DOI: 10.1038/s41377-019-0203-5.
  29. S. Tok, K. de Haan, D. Tseng, H. Ceylan Koydemir, A. Ozcan, “Early detection of E. coli and total coliform using an automated, colorimetric and fluorometric fiber optics-based device”, Lab on a Chip, 2019, DOI: 10.1039/C9LC00652D.
  30. T. Ghonge, H. Ceylan Koydemir, E. Valera, G. Berger, C. Garcia, N. Nawar, J. Tiao, G. Damhorst, A. Ganguli, U. Hassan, A. Ozcan, R. Bashir, “Smartphone-imaged, microfluidic technique for measuring CD64 expression from whole blood”, Analyst, 2019, DOI: 10.1039/C9AN00532C, (Selected as cover article of the journal).
  31. J. W. Snow, H. Ceylan Koydemir, D. K. Karinca, K. Liang, D. Tseng, A. Ozcan, “Rapid imaging, detection, and quantification of Nosema ceranae spores in honey bees using mobile phone based fluorescence microscopy”, Lab on a Chip, 2019, DOI:10.1039/C8LC01342J.
  32. H. Ceylan Koydemir, J.T. Coulibaly, D. Tseng, I. I. Bogoch, A. Ozcan, “Design and validation of a wide-field mobile-phone microscope for the label-free diagnosis of Schistosomiasis”, Travel Medicine and Infectious Disease, 2018, DOI: 10.1016/j.tmaid.2018.12.001.
  33. V. Müller, J. Sousa, H. Ceylan Koydemir, M. Veli, D. Tseng, L. Cerqueira, A. Ozcan, N. Azevedo, F. Westerlund, “Identification of pathogenic bacteria in complex samples using a smartphone based fluorescence microscope”, RSC Advances, 2018, DOI: 10.1039/C8RA06473C.
  34. Y. Zhang†, H. Ceylan Koydemir†, M. Schimogowa†, S. Yalcin, A. Guziak, T. Liu, I. Oguz, Y. Huang, B. Bai, Y. Luo, Y. Luo, Z. Wei, H. Wang, V. Bianco, B. Zhang, R. Nadkarni, K. Hill, and A. Ozcan, “Motility-based label-free detection of parasites in bodily fluids using holographic speckle analysis and deep learning”, Nature: Light Science and Applications, 2018, https://doi.org/10.1038/s41377-018-0110-1.
  35. Z. Gorocs, M. Tamamitsu, V. Bianco, P. Wolf, S. Roy, K. Shindo, K. Yanny, Y. Wu, H. Ceylan Koydemir, Y. Rivenson, and A. Ozcan, “A deep learning-enabled portable imaging flow cytometer for cost-effective, high-throughput and label-free analysis of natural water”, Nature: Light Science and Applications, 2018, DOI:10.1038/s41377-018-0067-0.
  36. Y. Wu, A. Calis, Y. Luo, C. Chen, M. Lutton, Y. Rivenson, X. Lin, H. Ceylan Koydemir, Y. Zhang, H. Wang, Z. Göröcs, and A. Ozcan, “Label-free bio-aerosol sensing using mobile microscopy and deep learning”, ACS Photonics, 2018, DOI: 10.1021/acsphotonics.8b01109.
  37. H. Ceylan Koydemir and A. Ozcan, “Smartphones Democratize Advanced Biomedical Instruments and Foster Innovation”, Clinical Pharmacology & Therapeutics, 2018, DOI: 10.1002/cpt.1081.
  38. Y. Rivenson†, H. Ceylan Koydemir†, H. Wang†, Z. Wei, Z. Ren, H. Günaydın, Y. Zhang, Z. Göröcs, K. Liang, D. Tseng, and A. Ozcan, “Deep learning enhanced mobile-phone microscopy”, ACS Photonics, 2018, DOI:10.1021/acsphotonics.8b00146.
  39. H. Ceylan Koydemir and A. Ozcan, “Wearable and implantable sensors for biomedical applications”, Annual Review of Analytical Chemistry, 2018, DOI: 10.1146/annurev-anchem-061417-125956.
  40. H. Ceylan Koydemir, S. Feng, K. Liang, R. Nadkarni, P. Benien, and A. Ozcan, “Comparison of supervised machine learning algorithms for waterborne pathogen detection using mobile-phone fluorescence microscopy,” Nanophotonics, 2017, DOI: nanoph-2017-0001.
  41. H. Ceylan Koydemir, A. Ozcan, “Mobile phones create new opportunities for microbiology related research and clinical applications”, Future Microbiology, 2017, DOI: 10.2217/fmb-2017-0046.
  42. I. I. Bogoch, H. Ceylan Koydemir, D. Tseng, R.K.D. Ephraim, E. Duah, J. Tee, J.R. Andrews, and A. Ozcan, “Evaluation of a mobile phone based microscope for screening of Schistosoma haematobium infection in rural Ghana”, The American Journal of Tropical Medicine and Hygiene, 2017, DOI: https://doi.org/10.4269/ajtmh.16-0912.
  43. Z. Göröcs, Y. Rivenson, H. Ceylan Koydemir, D. Tseng, T. L. Troy, V. Demas, and A. Ozcan, “Quantitative fluorescence sensing through highly autofluorescent, scattering, and absorbing media using mobile microscopy”, ACS Nano, 2016, DOI: 10.1021/acsnano.6b05129.
  44. B. Cortazar†, H. Ceylan Koydemir†, D. Tseng, S. Feng and A. Ozcan, “Quantification of plant chlorophyll content using Google Glass,” Lab on a Chip, 2015, DOI: 10.1039/c4lc01279h.
  45. H. Ceylan Koydemir, Z. Göröcs, D. Tseng, B. Cortazar, S. Feng, R.Y.L. Chan, J. Burbano, E. McLeod, and A. Ozcan, “Rapid imaging, detection and quantification of Giardia lamblia cysts using mobile-phone based fluorescent microscopy and machine learning,” Lab on a Chip, 2015, DOI: 10.1039/C4LC01358A, (Selected as a cover article of the journal, and it is a part of the themed collection: Lab on a Chip Recent HOT articles).
  46. H. Ceylan Koydemir, H. Külah, A. Alp, A. Uner, G. Hasçelik, C. Özgen, “A fully microfabricated electrochemical sensor and its implementation for detection of methicillin resistance in Staphylococcus aureus”, IEEE Sensors, 2014, DOI: 10.1109/JSEN.2014.2305152.
  47. H. Ceylan Koydemir, H. Külah, C. Özgen, “Solvent compatibility of parylene C film layer”, JMEMS, 2014, DOI: 10.1109/JMEMS.2013.2273032.
  48. H. Ceylan Koydemir, H. Külah, C. Özgen, A. Alp, G. Hasçelik, “MEMS biosensors for detection of methicillin resistant Staphylococcus aureus”, Biosensors and Bioelectronics, 2011, DOI: 10.1016/j.bios.2011.07.071, (In the list of most downloaded articles between October 2011 – February 2012).