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Publications in Peer-Reviewed Journals

“Verba volant scripta manent” Anonymous

The articles below are intended for viewing by Bilkent University/UNAM community or those, who otherwise have legitimate access to them. Click the PDF link/website link to view or download a PDF version of the publication.

* represents co-first authors, and the underline states co-corresponding authors.

80. Smart materials: rational design in biosystems via artificial intelligence

Sagdic, K., Eş, I., Sitti, M., and Inci, F.

Trends in Biotechnology, 2022

79. Bioinspired Material-Integrated Sensors for Improving Nanoplasmonic Characteristics

Inci, F.

Hacettepe Journal of Biology and Chemistry, 2022, 50, 2, 193-204

78. Benchmarking a Microfluidic-Based Filtration for Isolating Biological Particles

Inci, F.

Langmuir, 2022, 38, 5, 1897–1909

77. Advances in Biosensor Technologies for Acute Kidney Injury

Derin, E., and Inci, F.

ACS Sensors, 2022, 7, 2, 358–385

76. Unifying Efforts of Medicine, Chemistry and Engineering in Biosensing Technologies to Tackle the Challenges in COVID-19 Pandemic

Erdem, O., Eş, I., Saylan, Y. and Inci, F.

Analytical Chemistry, 2022

75. Smart Material-Integrated Systems for Isolation and Profiling of Rare Cancer Cells and Emboli

Sagdic, K., Inci. F.

Advanced Engineering Materials, 2021, 210085

74. Carbon-Based Nanomaterials and Sensing Tools for Wearable Health Monitoring Device

Erdem, O., Derin, E., Shirejini, S. Z, Sağdıç, K., Yılmaz, E. G., Yildiz, S., Akceoglu, G.A., Inci, F.

Advanced Materials Technologies, 2021, 202100572

73. The Yin and Yang of Exosome Isolation Methods: Conventional Practice, Microfluidics, and Commercial Kits
Shirejini, S.Z., Inci, F.
Biotechnology Advances, 2021; 107814

72. Recent Advances in Microneedle-Based Sensors for Sampling, Diagnosis and Monitoring of Chronic Diseases
Erdem, O, Es, I., Akceoglu, G.A., Saylan, Y., Inci, F.
Biosensors 2021, 11(9), 296

71. A Snapshot of Microfluidics in Point-of-Care Diagnostics: Multifaceted Integrity with Materials and Sensors
Akceoglu, G.A., Saylan, Y., and Inci, F.
Advanced Materials Technologies, 2021; 2100049

70. Smart Materials-integrated Sensor Technologies for COVID-19 Diagnosis
Erdem, O.*, Derin, E.*, Sağdıç, K., Yılmaz, E. G., Inci, F.
Emergent Materials, 2020; 4, 169–185

69. Bio-Inspired Magnetic Beads for Isolation of Sperm from Heterogenous Samples in Forensic Applications
Inci, F., Karaaslan, M.G., Gupta, R., Avadhani, A., Ogut, M.G., Atila, E.E., Duncan, G., Klevan, L., and Demirci, U.
FSI Genetics, 2021; 52, 102451

68. Entangled Nano-Plasmonic Cavities for Estimating Thickness of Surface Adsorbed Layers
Kojouri, A.M., Ozen, M.O., Shahabadi, M., Inci, F., Demirci, U.
ACS Nano, 2020

67. Enhancing the Nanoplasmonic Signal by a Nanoparticle Sandwiching Strategy to Detect Viruses
Inci, F., Karaaslan, M.G., Kojouri, A.M., Shah, P.A., Saylan, Y., Zeng, Y., Avadhani, A., Sinclair, R., Lau, D.T-Y, and Demirci, U.
Applied Materials Today, 2020; 20, 100709

66. A Confirmatory Test for Sperm in Sexual Assault Samples using a Microfluidic-Integrated Cell Phone Imaging System
Deshmukh, S.*, Inci, F.*, Karaaslan, M.G., Ogut, M.G., Klevan, L., Duncan, G., and Demirci, U.
FSI Genetics, 2020; 48, 102313

65. Advances in Biomimetic Systems for Molecular Recognition and Biosensing
Saylan, Y., Erdem, O., Inci, F., and Denizli, A.
Biomimetics, 2020; 5(2), 20.

64. Tunable Fano-resonant Metasurfaces on a Disposable Plastic-template for Multi-modal and Multiplex Biosensing
Ahmed, R.*, Ozen, M.O.*, Karaaslan, M.G., Prator, C.A., Thanh, C., Kumar, S., Torres, L., Iyer, N., Munter, S., Southern, S., Henrich, T.J., Inci, F., and Demirci, U.
Advanced Materials, 2020, 32 (19), 1907160

63. A Role for EGFR-Targeted Photoimmunotherapy Informed by Physical Stress
Nath, S., Pigula, M., Khan, A., Hanna, W., Ruhi, M. K., Dehkordy, F. M., Pushpavanam, K., Rege, K., Moore, K., Tsujita, Y., Conrad, C., Inci, F., Carmen, M. G., Franco, W., Celli, J. P., Demirci, U., Hasan, T., Huang, H-C., Rizvi, I
Journal of Clinical Medicine, 2020, 9(4), 924.

62. A disposable microfluidic-integrated hand-held plasmonic platform for protein detection
Inci, F.*, Saylan,Y.*, Kojouri, A.M., Ogut, M.G., Denizli, A., and Demirci, U.
Applied Materials Today 2020;100478

61. Real-time biosensing of proteins on a DVD nanoplasmonic grating
Ahmed, R.*, Ozen, M.O*, Inci, F.*, Karaaslan, M.G., Henrich, T.J., and Demirci, U.
Proceeding of SPIE, Plasmonics in Biology and Medicine XVI 2019; 108940N.

60. Plasmonic-based Platforms for Diagnosis of Infectious Diseases at the Point-of-Care
Lia, Z., Leusteana, L., Wua, D., Inci, F., Zheng, M., Demirci, U., Wang, S.
Biotechnology Advances 2019; 37 (8), 107440

59. A novel on-chip method for differential extraction of sperm in forensic cases
Inci, F., Ozen, M.O., Saylan, Y., Miansari, M., Cimen, D., Dhara, R., Chinnasamy, T., Yuksekkaya, M., Filippini, C., Kumar, D.K., Calamak, S., Yesil, Y., Durmus, N.G., Duncan, G., Klevan, L. and Demirci, U.
Advanced Science 2018; 5: 1800121

58. Handheld Volatilome Analyzer Based on Elastically Deformable Nanofibers
Yucel, M., Akin, O., Cayoren, M., Akduman, I., Palaniappan, A., Liedberg, B., Hizal, G., Inci, F. and Yildiz, U.H.
Analytical Chemistry 2018; 90 (8), 5122–5129

57. Guidance and Self-Sorting of Active Swimmers: 3D Periodic Arrays Increase Persistence Length of Human Sperm Selecting for the Fittest
Chinnasamy, T.*, Kingsley, J.L*, Inci, F.,Turek P.J., Rosen, M.P., Behr, B., Tüzel, E., Demirci, U.
Advanced Science 2017; 5(2):1700531

56. High-throughput Characterization of HIV-1 Reservoir Reactivation using a Novel Single-Cell-in-Droplet PCR Assay
Yucha, R., Hanhauser, E., Hobbs, K., Hogan, L., Inci, F., Shafiee, H., El Assal, R., Kiselinova, M., Bae, H., Leadabrand, K., Wang, S., Kuritzkes, D., Demirci, U., Henrich, T.
EBioMedicine 2017; 20:217-229

55. Isolation, detection, and quantification of cancer biomarkers in HPV-associated malignancies
Inan, H., Wang, S.,Inci, F., Baday, M., Zangar, R., Kesiraju, S., Anderson, K., Cunningham, B., Demirci, U.
Scientific Reports, 2017; 12;7(1):3322

54. An integrated double-filtration microfluidic device for isolation, enrichment and quantification of urinary extracellular vesicles for detection of bladder cancer
Liang, L.G., Kong, M.Q., Zhou, S., Sheng, Y.F., Wang, P., Yu, T., Gong, R.Z., Inci, F., Li, L.J., Demirci, U., and Wang, S.
Scientific Reports 2017; 7; 46224

53. Microchip-based ultrafast serodiagnostic assay for tuberculosis
Mani, V., Paleja, B., Larbi, K., Kumar, P., Tay, J., Siew, J.,Inci, F., Wang, S., Chee, C., Wang, Y., Demirci, U., Libero G., Singhal, A.
Scientific Reports 2016; 24; 6: 35845

52. Toxicology study of single-walled carbon nanotubes and reduced grapheme oxide in human sperm
Asghar, W., Shafiee, H., Velasco, V., Sah, V., Guo, S., El Assal, R., Inci, F.,Rajagopalan, A., Jahangir, M., Anchan, R., Mutter, G., Ozkan, M., Ozkan, C., Demirci, U.
Scientific Reports, 2016; 19; 6:30270

51. Engineering long shelf life multilayer biologically active surfaces on microfluidic devices for point of care applications
Asghar, W.*, Yuksekkaya, M.*, Shafiee, H., Zhang, M., Ozen, M.O., Inci, F., Kocakulak, M., Demirci, U.
Scientific Reports, 2016; 17;6:21163

50. Advances in addressing technical challenges of point-of-care diagnostics in resource-limited settings
Wang, S., Lifson, M., Inci, F.,Liang, L., Sheng, Y., Demirci, U
Expert Review of Molecular Diagnostics 2016; 16(4):449-59

49. Towards Artificial Tissue Models: Past, Present, and Future of 3-D Bioprinting
Yildiz, A., El Assal, R., Chen, P., Guven, S., Inci, F., Demirci, U.
Biofabrication 2016; 8(1):014103

48. Flexible substrate-based devices for point-of-care diagnostics
Wang, S., Chinnasamy, T., Lifson, M., Inci, F., Demirci, U
Trends in Biotechnology 2016; 34(11):909-921

47. Advances in biosensing strategies for HIV detection, diagnosis, and therapeutic monitoring
Lifson, M.A., Ozen, M., Inci F., Wang S., Inan H., Baday M., Henrich T.J., Demirci, U
Advanced Drug Delivery Reviews 2016; 1;103:90-104

46. Photonic crystals: emerging biosensors and their promise for point-of-care applications
Inan, H., Poyraz, M., Inci, F., Lifson, M.A., Baday M., Cunningham, B., Demirci, U
Chemical Society Reviews 2016; 46(2):366-388

45. Multitarget, quantitative nanoplasmonic electrical field-enhanced resonating device (NE2RD) for diagnostics
Inci, F., Fillippini, C., Baday, M., Ozen, M.O., Calamak, S., Durmus, N.G., Wang, S., Hanhauser, E., Hobbs, K., Juillard, F., Kuang, P., Vetter, M.L., Carocci, M., Tamamoto, H., Takagi, Y., Yildiz, U.H., Akin, D., Wesemann, D., Singhal, A., Yang, P., Nibert, M., Fichorova, R., Lau, D., Henrich, T., Kaye, K., Schachter, S., Kuritzkes, D., Steinmetz, L., Gambhir, S.S., Davis, R., Demirci, U.
Proceedings of the National Academy of Science (USA), 2015; 112(32) : E4354-63

44. Construction and Characterization of P-Glycoprotein Incorporated Tethered Lipid Bilayers
Inci, F., Celik, U., Turken, B., Ozer, O., and Kok, F.N.
Biochemistry and Biophysics Reports 2015; 2; 115-122

43. Portable Lensless Wide-field Microscopy Imaging Platform based on Digital Inline Holography and Multi-Frame Pixel Super-Resolution
Sobieranski, A.C., Inci, F., Tekin, H.C., Yuksekkaya, M., Comunello, E., Cobra, D., Wangenheim, A., Demirci, U.
Light: Science & Applications 2015; 4:e346

42. Portable microfluidic integrated plasmonic platform for pathogen detection
Tokel, O., Yildiz, U.H., Inci, F., Durmus, N.G., Ekiz, O.O., Turker, B., Cetin, C., Rao, S., Sridhar, K., Natarajan, N., Shafiee, H. Dana, Aykutlu, Demirci, U.
Scientific Reports 2015; 24; 5: 9152

41. Paper and flexible substrates as materials for biosensing platforms to detect multiple biotargets
Shafiee, H.*, Asghar, W.*, Inci, F.*, Yuksekkaya, M., Jahangir, M., Zhang, M., Durmus, NG., Gurkan, UA., Kuritzkes, D., Demirci. U.
Scientific Reports 2015; 6;5:8719

40. Recent advances in micro/nanotechnologies for global control of hepatitis B infection
Yildiz, U.H., Inci, F., Toy, M., Wang, S., Tekin, H.C., Javaid, A., Lau, D., Demirci, U.
Biotechnology Advances 2015; 33(1):178-90

39. Advances in nanotechnology and microfluidics for human papillomavirus diagnostics
Tasoglu, S., Tekin, H.C., Inci, F., Wang, S., Johanning, F.W., Johanning, G., Colevas, D., Demirci, U.
Proceedings of the IEEE 2015;103(2):161-178

38. Multiscale assembly for tissue engineering and regenerative medicine
Guven, S., Chen, P., Inci, F., Tasoglu, S., Erkmen, B., Demirci, U.
Biotechnology 2015; 33(5):269-79

37. Graphene–protein field effect biosensors: glucose sensing
Viswanathan, S., Narayanan, T., Aran, K., Fink, K., Paredes, J., Ajayan, P., Filipek, S., Miszta, P., Tekin, H.C., Inci, F., Demirci, U., Li, P., Bolotin, K., Liepmann, D., Renugopalakrishanan, V.
Materials Today 2015;18:9:513-22

36. Emerging technologies for point-of-care management of HIV infection
Shafiee, H., Wang, S., Inci, F., Toy, M., Henrich, T.J., Goroff, M., Reich, M.R., Kuritzkes, D.R., Demirci, U.
Annual Review of Medicine 2014; 66:387-405

35. Nanomechanical motion of Escherichia coli adhered to a surface
Lissandrello, C.*, Inci, F.*, Francom, M., Paul, M.R., Demirci, U., Ekinci, K.L.
Physics Letters 2014; 105, 113701

34. Nanostructured optical photonic crystal biosensor for HIV viral load measurement
Shafiee, H., Lidstone, E.A., Jahangir, M., Inci, F., Hanhauser, E., Henrich, T.J., Kuritzkes, D.R.,Cunningham, B.T., Demirci, U.
Scientific Reports 2014; 4: 4116

33. Portable Digital In-line Holography Platform for Sperm Cell Visualization and Quantification
Sobieranski, A.C., Inci, F., Tekin, H.C., Comunello, E., Wangenheim, A., and Demirci, U.
27th SIBGRAPI Conference on Graphics, Patterns and Images 2014

32.Advances in plasmonic technologies for point of care applications
Tokel, O., Inci, F., Demirci, U.
Chemical Reviews 2014; 114(11):5728-52

31.Emerging technologies for monitoring drug-resistant tuberculosis at the point-of-care
Manu, V.*, Wang, S.*, Inci, F.*, Singhal, A., Demirci, U.
Advanced Drug Delivery Reviews 2014; 30; 78:105-17

30. Nanoplasmonic quantitative detection of intact viruses from unprocessed whole blood
Inci, F., Tokel, O., Wang, S., Gurkan, U. A., Tasoglu, S., Kuritzkes, D., and Demirci, U.
ACS Nano 2013; 7 (6): 4733-4745

29. Nanoplasmonic Biosensing Platform for Multiple Pathogen Detection
Inci, F.*, Tokel, O.*, Wang, S., Gurkan, U.A., Kuritzkes, D.R., and Demirci, U.
Solid-State Sensors, Actuators and Microsystems (Transducers & Eurosensors XXVII) 2013

28. Acute On-Chip HIV Detection through label-free electrical sensing of viral nano-lysate on-chip
Shafiee, H., Jahangir. M., Inci. F., Wang. S., Willenbrecht, R., Giguel, F., Tsibris, A., Kuritzkes, D., Demirci, U.
Small 2013, 9 (115): 2553-2563

27. Acute HIV Detection by Viral Lysate Impedance Spectroscopy on a Microchip
Shafiee, H., Jahangir, M., Inci, F., Wang, S., Willenbrecht, R.B.M., Giguel, F.F., Kuritzkes, D.R., and Demirci, U.
IEEE – Solid-State Sensors, Actuators and Microsystems (Transducers & Eurosensors XXVII) 2013

26. Point-of-care assays for tuberculosis: role of nanotechnology/microfluidics
Wang, S., Inci, F., Libero, G., Singhal, A., Demirci, U.
Biotechnology Advances 2013, 31(4): 438-449

25. Release of magnetic nanoparticles from cell-encapsulating biodegradable Nanobiomaterials
Xu, F., Inci, F., Mullick, O., Gurkan, U. A., Sung, Y., Kavaz, D., Li, B., Denkbas, E. B., Demirci, U.
ACS Nano 2012; 6(8): 6640-6649

24. Portable microfluidic chip for detection of Escherichia coli in produce and blood
Wang, S.*, Inci, F.*, Chaunzwa, T. L., Ramanujam, A., Vasudevan, A., Subramanian, S., Ip, A. C. F., Sridharan, B., Gurkan, U.A., and Demirci, U.
International Journal of Nanomedicine 2012; 7: 1-10

23. Fructose-Enhanced Reduction of Bacterial Growth on Nanorough Surfaces
Durmus, N.G., Taylor, E.N., Inci, F., Kummer, K.M., Tarquinio, K.M., and Webster, T.J.
International Journal of Nanomedicine 2012; 7:537-45

22. Efficient on-chip isolation of HIV subtypes
Wang, S., Esfahani, M., Gurkan, U. A., Inci F., Kuritzkes, D. R, Demirci, U.
Lab Chip 2012; 12(8): 1508-15

21. Well-Defined Cholesterol Polymers with pH-Dependent Lipid Membrane Switching Activity
Sevimli, S., Inci, F., Zareie, H.M., and Bulmus, V.
Biomacromolecules 2012; 8;13(10):3064-75


20.Biomimetic Lipid Membranes: Fundamentals, Applications, and Commercialization
Kok, F.N., Yildiz, A.A., and Inci, F.
Springer Press 2019; 978-3-030-11595-1

19.Emerging Technologies for Point-of-Care Diagnostics
Inci, F., Wang, S., and Demirci, U.
World Scientific Publishing Company 2019 (in press)

18.Technology Innovation for Global Health Closing the Implementation Gap
Inci, F., Durmus, N.G., Blander, J., and Demirci, U.
World Scientific Publishing Company 2019 (in preparation)

Book Chapters

17. “Biomedical Applications: Liposomes and Supported Lipid Bilayers for Diagnostics, Theranostics, Imaging, Vaccine Formulation, and Tissue Engineering” in Biomimetic Lipid Membranes: Fundamentals, Applications, and Commercialization
Oncel, M.O.O., Garipcan, B., Inci, F.
Springer Press 2019; 978-3-030-11595-1

16. “Lipid Bilayers and Liposomes on Microfluidics Realm: Techniques and Applications” in Biomimetic Lipid Membranes: Fundamentals, Applications, and Commercialization
Inci, F.
Springer Press 2019; 978-3-030-11595-1

15. “Emerging Technologies for Point-of-Care Diagnostics” in Emerging Technologies for Point-of-Care Diagnostics (Edited by Fatih Inci, ShuQi Wang, and Utkan Demirci)
Inci, F., Demirci, U.
World Scientific Publishing Company 2019(in publication)

14. “Cell-Encapsulating Hydrogels for Biosensing” in Gel Handbook: Fundamentals, Properties and Applications Volume 3: Application of Hydrogels in Drug Delivery and Biosensing (Edited by Utkan Demirci and Ali Khademhosseini)
Chen, P., Wang, S.,Inci, F., Güven, S., Tasoglu, S., and Demirci, U.
World Scientific Press, 2016; 978-981-4656-10-8

13. “An integrated double-filtration device for detection of exosomes from urine for bladder cancer diagnosis” in Extracellular Vesicles: Methods and Protocols (Edited by Winston Patrick Kuo and Jia Shidong)
Liang, L., Sheng, Y., Zhao, S., Inci, F., Li, L.,Demirci, U., Wang, S.
Springer Press 2016; 978-1-4939-7253-1

12. “High sensitive biosensors for MicroRNA quantitation-A clinical perspective”, in Nanomaterials in Health Care (Edited by Venkatesan Renugopalakrishnan)
Ananta, J., Tekin, H.C., Inci, F., Massoud, T., Renugopalakrishanan, V., Viswanathan, S., Ajayan, P., Liepmann, D., Demirci, U., Paulmurugan, R.
Materials Research, Society and Cambridge University Press 2015 (in press)

11. “Applications of quantum dots for fluorescence imaging in biomedical research” in Microfluidic technologies for human health (Edited by Utkan Demirci, Ali Khademhosseini, Robert Langer, and Jeffrey Blander)
Wang, S. Q., Esfahani, M., Sarenac, D., Cheung, B., Vasudevan, Inci, F., and Demirci, U.
World Scientific Press 2012; 978-981-4405-51-5


10. Detection of Peritonitis in Patients on Peritoneal Dialysis at Home
Wang, S., Inci, F., and Demirci, U.
IEEE Pulse 2015(invited)

9. Assisted Reproductive Microchip Technologies to Improve Infertility
Wang, S., Inci, F., and Demirci, U.
IEEE Pulse 2015(invited)

8. Editorial of advanced health care technologies
Demirci U., Wang, S., and Inci, F.
Advanced Health Care Technologies, 2015:1 1-2


7. Entangled Nano-Plasmonic Cavities for Estimating Thickness of Surface Adsorbed Layers
U.S. Provisional Patent Application
U.S. Application Serial #: 62/980,595

Stanford Docket No.19-560
Date of Publication:  December 25, 2019

6. Imaging systems and methods of using the same
U.S. Publication #: US2016/019548
U.S. Provisional Patent Application #: 62/121,603
Client Ref.: BWH22764
Q&B File: 129319.00292
Date of File: February 25,2015
Date of Publication: September 1, 2016

5. Detection, capture and quantification of biological moieties from unprocessed bodily fluids using nanoplasmonic platform
U.S. Publication #: US20150160218
Date of File: July 3, 2013
Date of Publication: June 11, 2015.

4. Systems and methods for determining probative samples and isolation and quantitation of cells
U.S. Publication #: PCT/US15/53370
DXNO-001001WO 322658-2003
U.S. Provisional Patent Application #:62/058,072
Q&B File: 129319.00292
Date of Publication: September 30, 2015
Date of File: September 30, 2014

3. Quantitative nanoplasmonic platform for multiple targets
U.S. Provisional Patent Application
Stanford Docket No.15-315
Date of File: August 20, 2015

2. Methods for bacteria detection, monitoring of antibiotic agents, and energy harvesting using micromechanical devices
Invention #: BWH 22611 disclosed by Brigham and Women’s Hospital
Date of File: December 16, 2013

1. Controlled viable release of selectively captured label-free cells in microchannels
Invention #: BWH21303 disclosed by Brigham and Women’s Hospital
Date of File: April 10, 2012

Translated Products

CSI-Q ™ (Chip-Based Sperm Identification and Quantitation) Cartridges, 2017

NGDE ™ (Next-Generation Differential Extraction) System, 2017

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